#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABTB1	80325	broad.mit.edu;hgsc.bcm.edu	37	3	127399686	127399686	+	3'UTR	SNP	T	T	C			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr3:127399686T>C	ENST00000232744.8	+	0	1891				ABTB1_ENST00000393363.3_3'UTR|ABTB1_ENST00000468137.1_3'UTR|ABTB1_ENST00000453791.2_3'UTR					ankyrin repeat and BTB (POZ) domain containing 1											central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	10						TTCTCTAAGCTGGTGTTCCCA	0.567																																																	0													12.0	12.0	12.0					3																	127399686		876	1991	2867	SO:0001624	3_prime_UTR_variant	80325			AB053324	CCDS3045.1, CCDS46901.1	3q21	2013-01-10			ENSG00000114626	ENSG00000114626		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	18275	protein-coding gene	gene with protein product		608308				10891360, 11494141	Standard	NM_172027		Approved	BPOZ, EF1ABP, Btb3, BTBD21	uc003ejt.3	Q969K4	OTTHUMG00000159636	ENST00000232744.8:c.*368T>C	3.37:g.127399686T>C		Somatic		WXS	Illumina HiSeq	Phase_I		RNA	SNP	ENST00000232744.8	37	CCDS3045.1																																																																																				0.567	ABTB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356595.1		NM_172027	
ARG2	384	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	68086727	68086727	+	Silent	SNP	C	C	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr14:68086727C>G	ENST00000261783.3	+	1	213	c.33C>G	c.(31-33)ctC>ctG	p.L11L	Y_RNA_ENST00000364659.1_RNA|ARG2_ENST00000556491.1_3'UTR	NM_001172.3	NP_001163.1	P78540	ARGI2_HUMAN	arginase 2	11					arginine metabolic process (GO:0006525)|cellular nitrogen compound metabolic process (GO:0034641)|nitric oxide biosynthetic process (GO:0006809)|small molecule metabolic process (GO:0044281)|striated muscle contraction (GO:0006941)|urea cycle (GO:0000050)|ureteric bud development (GO:0001657)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	arginase activity (GO:0004053)|metal ion binding (GO:0046872)	p.L11L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|ovary(1)|prostate(1)	11				all cancers(60;0.000582)|OV - Ovarian serous cystadenocarcinoma(108;0.00392)|BRCA - Breast invasive adenocarcinoma(234;0.00928)	L-Arginine(DB00125)|L-Ornithine(DB00129)	CGCGTCTCCTCCAGACGCGAG	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											28.0	29.0	29.0					14																	68086727		2200	4295	6495	SO:0001819	synonymous_variant	384			D86724	CCDS9785.1	14q24.1	2013-05-01	2013-05-01			ENSG00000081181			664	protein-coding gene	gene with protein product		107830	"""arginase, type II"""			8954792, 8898077	Standard	NM_001172		Approved		uc001xjs.3	P78540		ENST00000261783.3:c.33C>G	14.37:g.68086727C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2R690|Q6FHY8	Silent	SNP	ENST00000261783.3	37	CCDS9785.1																																																																																				0.617	ARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415190.2		NM_001172	
ATXN1	6310	broad.mit.edu;ucsc.edu	37	6	16327452	16327452	+	Missense_Mutation	SNP	G	G	C			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr6:16327452G>C	ENST00000244769.4	-	8	2026	c.1090C>G	c.(1090-1092)Cac>Gac	p.H364D	ATXN1_ENST00000436367.1_Missense_Mutation_p.H364D	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	364					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GGGCTCGGGTGGACCACCACG	0.687																																																	0													81.0	91.0	88.0					6																	16327452		2203	4300	6503	SO:0001583	missense	6310			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1090C>G	6.37:g.16327452G>C	ENSP00000244769:p.His364Asp	Somatic		WXS	Illumina GAIIx	Phase_I	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	G	17.71	3.457063	0.63401	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	D;D	0.82711	-1.64;-1.64	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	D	0.84147	0.5408	L	0.34521	1.04	0.43965	D	0.996643	D	0.63880	0.993	D	0.72338	0.977	D	0.86398	0.1740	10	0.59425	D	0.04	-21.9414	17.7777	0.88514	0.0:0.0:1.0:0.0	.	364	P54253	ATX1_HUMAN	D	364	ENSP00000244769:H364D;ENSP00000416360:H364D	ENSP00000244769:H364D	H	-	1	0	ATXN1	16435431	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	7.347000	0.79356	2.184000	0.69523	0.561000	0.74099	CAC		0.687	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3		NM_000332	
B3GNT7	93010	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	232263303	232263303	+	Missense_Mutation	SNP	G	G	C			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:232263303G>C	ENST00000287590.5	+	2	1134	c.873G>C	c.(871-873)aaG>aaC	p.K291N		NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	291					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.K291N(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		TGTACGGCAAGGCCAGCTATC	0.647																																																	1	Substitution - Missense(1)	kidney(1)											26.0	32.0	30.0					2																	232263303		1973	4134	6107	SO:0001583	missense	93010			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"""Beta 3-glycosyltransferases"""	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.873G>C	2.37:g.232263303G>C	ENSP00000287590:p.Lys291Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	G	12.15	1.851606	0.32699	.	.	ENSG00000156966	ENST00000287590	T	0.42131	0.98	5.05	5.05	0.67936	.	0.194734	0.53938	D	0.000054	T	0.46444	0.1393	L	0.40543	1.245	0.58432	D	0.999997	D	0.57571	0.98	P	0.62813	0.907	T	0.32771	-0.9894	10	0.22109	T	0.4	.	7.397	0.26942	0.1874:0.0:0.8126:0.0	.	291	Q8NFL0	B3GN7_HUMAN	N	291	ENSP00000287590:K291N	ENSP00000287590:K291N	K	+	3	2	B3GNT7	231971547	0.998000	0.40836	0.830000	0.32933	0.177000	0.22998	2.541000	0.45735	2.355000	0.79922	0.561000	0.74099	AAG		0.647	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1		NM_145236	
BTBD11	121551	hgsc.bcm.edu;ucsc.edu	37	12	107713815	107713815	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr12:107713815delG	ENST00000280758.5	+	1	1626	c.1098delG	c.(1096-1098)cagfs	p.Q366fs	BTBD11_ENST00000420571.2_Frame_Shift_Del_p.Q366fs|BTBD11_ENST00000490090.2_Frame_Shift_Del_p.Q366fs	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	366						integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						GTCTCCTGCAGCCCTACCAGC	0.617																																																	0													30.0	34.0	33.0					12																	107713815		1984	3967	5951	SO:0001589	frameshift_variant	121551			AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.1098delG	12.37:g.107713815delG	ENSP00000280758:p.Gln366fs	Somatic		WXS	Illumina HiSeq	Phase_I	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Frame_Shift_Del	DEL	ENST00000280758.5	37	CCDS31893.1																																																																																				0.617	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1		NM_152322	
C19orf33	64073	hgsc.bcm.edu	37	19	38795587	38795587	+	Missense_Mutation	SNP	A	A	G	rs76762399		TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr19:38795587A>G	ENST00000301246.5	+	4	405	c.304A>G	c.(304-306)Aag>Gag	p.K102E	C19orf33_ENST00000588605.1_3'UTR	NM_033520.1	NP_277055.1	Q9GZP8	IMUP_HUMAN	chromosome 19 open reading frame 33	102						nucleus (GO:0005634)						all_cancers(60;1.07e-06)		Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			gggcaagaagaaggagGCTCC	0.602																																																	0													80.0	84.0	82.0					19																	38795587		2198	4298	6496	SO:0001583	missense	64073			AF213678	CCDS12511.1	19q13.2	2012-10-26			ENSG00000167644	ENSG00000167644			16668	protein-coding gene	gene with protein product	"""immortalization-upregulated protein"", ""HAI-2 related small protein"", ""hepatocyte growth factor activator inhibitor type 2-related small protein"""					11080599	Standard	NM_033520		Approved	IMUP-1, IMUP-2, H2RSP, IMUP	uc002ohu.1	Q9GZP8	OTTHUMG00000181894	ENST00000301246.5:c.304A>G	19.37:g.38795587A>G	ENSP00000301246:p.Lys102Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P6G2|Q96H58|Q9HCR4	Missense_Mutation	SNP	ENST00000301246.5	37	CCDS12511.1	.	.	.	.	.	.	.	.	.	.	A	10.57	1.386721	0.25031	.	.	ENSG00000167644	ENST00000301246	.	.	.	4.65	1.27	0.21489	.	0.631638	0.14080	N	0.342742	T	0.26991	0.0661	L	0.32530	0.975	0.22710	N	0.99883	P	0.35507	0.506	B	0.37780	0.258	T	0.17531	-1.0366	9	0.87932	D	0	-18.943	6.8244	0.23874	0.7117:0.0:0.2883:0.0	.	102	Q9GZP8	IMUP_HUMAN	E	102	.	ENSP00000301246:K102E	K	+	1	0	C19orf33	43487427	0.981000	0.34729	0.010000	0.14722	0.004000	0.04260	1.231000	0.32624	0.282000	0.22254	0.459000	0.35465	AAG		0.602	C19orf33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458168.1		NM_033520	
C22orf42	150297	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	32555106	32555106	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr22:32555106G>A	ENST00000382097.3	-	1	169	c.97C>T	c.(97-99)Cct>Tct	p.P33S	RP1-90G24.8_ENST00000426354.1_lincRNA	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	33								p.P33S(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						ACAGTCTCAGGAATCTCACAC	0.577																																																	1	Substitution - Missense(1)	kidney(1)											100.0	88.0	92.0					22																	32555106		2203	4300	6503	SO:0001583	missense	150297			BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.97C>T	22.37:g.32555106G>A	ENSP00000371529:p.Pro33Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A4QPH5	Missense_Mutation	SNP	ENST00000382097.3	37	CCDS33639.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.767642	0.00645	.	.	ENSG00000205856	ENST00000382097	T	0.24151	1.87	0.131	-0.261	0.12963	.	.	.	.	.	T	0.08537	0.0212	N	0.08118	0	0.09310	N	1	P	0.39424	0.673	B	0.34991	0.193	T	0.17501	-1.0367	8	0.17832	T	0.49	.	.	.	.	.	33	Q6IC83	CV042_HUMAN	S	33	ENSP00000371529:P33S	ENSP00000371529:P33S	P	-	1	0	C22orf42	30885106	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.433000	0.01021	-1.335000	0.02241	-1.316000	0.01300	CCT		0.577	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2		NM_001010859	
CDHR5	53841	hgsc.bcm.edu	37	11	617406	617407	+	In_Frame_Ins	INS	-	-	CGCCCT	rs146893811	byFrequency	TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr11:617406_617407insCGCCCT	ENST00000358353.3	-	16	2804_2805	c.2482_2483insAGGGCG	c.(2482-2484)gcg>gAGGGCGcg	p.827_828insEG	IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397574.2_5'Flank|CDHR5_ENST00000349570.7_In_Frame_Ins_p.633_634insEG|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000525445.1_5'Flank|IRF7_ENST00000397562.3_5'Flank|IRF7_ENST00000348655.6_5'Flank|CDHR5_ENST00000397542.2_In_Frame_Ins_p.827_828insEG|IRF7_ENST00000397566.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	827					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						ACCCCTCCCCGCGCCCTCGCCC	0.698														49	0.00978435	0.034	0.0043	5008	,	,		12225	0.001		0.0	False		,,,				2504	0.0																0									,,	117,4087		2,113,1987					,,	1.9	0.0		dbSNP_134	25	47,8153		0,47,4053	no	coding,coding,coding	CDHR5	NM_031264.3,NM_021924.4,NM_001171968.1	,,	2,160,6040	A1A1,A1R,RR		0.5732,2.7831,1.3222	,,	,,		164,12240				SO:0001652	inframe_insertion	53841			AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.2477_2482dupAGGGCG	11.37:g.617407_617412dupCGCCCT	ENSP00000351118:p.Glu826_Gly827dup	Somatic		WXS	Illumina HiSeq	Phase_I	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	In_Frame_Ins	INS	ENST00000358353.3	37	CCDS7707.1																																																																																				0.698	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2		NM_021924	
CIB4	130106	broad.mit.edu;hgsc.bcm.edu	37	2	26806745	26806745	+	Missense_Mutation	SNP	A	A	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:26806745A>G	ENST00000288861.4	-	5	403	c.350T>C	c.(349-351)aTt>aCt	p.I117T	CIB4_ENST00000405346.3_5'UTR	NM_001029881.1	NP_001025052.1	A0PJX0	CIB4_HUMAN	calcium and integrin binding family member 4	117	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.						calcium ion binding (GO:0005509)	p.I117T(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCCTCATCAATGAAGCCATT	0.532																																																	1	Substitution - Missense(1)	kidney(1)											96.0	89.0	91.0					2																	26806745		2203	4300	6503	SO:0001583	missense	130106				CCDS33160.1	2p23.3	2013-01-10			ENSG00000157884	ENSG00000157884		"""EF-hand domain containing"""	33703	protein-coding gene	gene with protein product		610646				15574431	Standard	NM_001029881		Approved		uc002rhm.3	A0PJX0	OTTHUMG00000151993	ENST00000288861.4:c.350T>C	2.37:g.26806745A>G	ENSP00000288861:p.Ile117Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RU18	Missense_Mutation	SNP	ENST00000288861.4	37	CCDS33160.1	.	.	.	.	.	.	.	.	.	.	A	16.77	3.216271	0.58452	.	.	ENSG00000157884	ENST00000288861;ENST00000403670;ENST00000405346	T	0.78126	-1.15	5.53	4.36	0.52297	EF-hand-like domain (1);	0.000000	0.64402	D	0.000019	D	0.90896	0.7139	H	0.97415	4	0.41118	D	0.985799	D	0.71674	0.998	D	0.74023	0.982	D	0.91239	0.5020	10	0.87932	D	0	.	8.7577	0.34656	0.8315:0.0:0.0:0.1685	.	117	A0PJX0	CIB4_HUMAN	T	117;72;119	ENSP00000288861:I117T	ENSP00000288861:I117T	I	-	2	0	CIB4	26660249	0.997000	0.39634	0.917000	0.36280	0.914000	0.54420	4.623000	0.61247	0.919000	0.36945	-0.333000	0.08304	ATT		0.532	CIB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324709.1			
CEP68	23177	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	65299148	65299148	+	Silent	SNP	T	T	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:65299148T>G	ENST00000377990.2	+	3	1121	c.918T>G	c.(916-918)acT>acG	p.T306T	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000546106.1_Silent_p.T306T|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000260569.4_Silent_p.T306T	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	306					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.T306T(1)		breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						TTGACTATACTTACCCACTGA	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											73.0	85.0	81.0					2																	65299148		2203	4300	6503	SO:0001819	synonymous_variant	23177			BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.918T>G	2.37:g.65299148T>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Silent	SNP	ENST00000377990.2	37	CCDS1880.2																																																																																				0.577	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2		NM_015147	
CORO1A	11151	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	30198495	30198495	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr16:30198495G>A	ENST00000219150.5	+	5	892	c.587G>A	c.(586-588)cGt>cAt	p.R196H	RP11-455F5.5_ENST00000566144.1_RNA|CORO1A_ENST00000570045.1_Missense_Mutation_p.R196H|RP11-455F5.5_ENST00000567153.1_RNA|CORO1A_ENST00000565497.1_Missense_Mutation_p.R196H|RP11-455F5.5_ENST00000568506.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	196					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|calcium ion transport (GO:0006816)|cell-substrate adhesion (GO:0031589)|cellular component movement (GO:0006928)|cellular response to interleukin-4 (GO:0071353)|homeostasis of number of cells within a tissue (GO:0048873)|innate immune response (GO:0045087)|leukocyte chemotaxis (GO:0030595)|negative regulation of actin nucleation (GO:0051126)|phagocytosis (GO:0006909)|phagolysosome assembly (GO:0001845)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of T cell proliferation (GO:0042102)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|T cell homeostasis (GO:0043029)|uropod organization (GO:0032796)	actin filament (GO:0005884)|cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|lamellipodium (GO:0030027)|membrane (GO:0016020)|phagocytic cup (GO:0001891)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|cytoskeletal protein binding (GO:0008092)|phosphatidylinositol 3-kinase binding (GO:0043548)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)	p.R196H(1)		central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	9						ACCTCCTGCCGTGACAAGCGC	0.587																																																	1	Substitution - Missense(1)	kidney(1)											73.0	68.0	70.0					16																	30198495		2197	4300	6497	SO:0001583	missense	11151			X89109	CCDS10673.1	16p11.2	2014-09-17	2001-11-28		ENSG00000102879	ENSG00000102879		"""Coronins"", ""WD repeat domain containing"""	2252	protein-coding gene	gene with protein product	"""Clabp TACO"""	605000	"""coronin, actin-binding protein, 1A"""			9778037	Standard	NM_007074		Approved	HCORO1, p57, coronin-1	uc002dww.3	P31146	OTTHUMG00000132148	ENST00000219150.5:c.587G>A	16.37:g.30198495G>A	ENSP00000219150:p.Arg196His	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBL1|Q2YD73	Missense_Mutation	SNP	ENST00000219150.5	37	CCDS10673.1	.	.	.	.	.	.	.	.	.	.	.	28.2	4.901437	0.92035	.	.	ENSG00000102879	ENST00000219150	T	0.63096	-0.02	4.92	4.92	0.64577	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.052405	0.64402	D	0.000001	T	0.68348	0.2991	N	0.25825	0.765	0.42748	D	0.993761	D;D	0.76494	0.999;0.967	D;P	0.67725	0.953;0.875	T	0.72792	-0.4186	10	0.72032	D	0.01	-12.1923	17.0358	0.86474	0.0:0.0:1.0:0.0	.	252;196	Q59G88;P31146	.;COR1A_HUMAN	H	196	ENSP00000219150:R196H	ENSP00000219150:R196H	R	+	2	0	CORO1A	30105996	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	4.858000	0.62947	2.576000	0.86940	0.561000	0.74099	CGT		0.587	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2		NM_007074	
TRIAP1	51499	hgsc.bcm.edu	37	12	120884306	120884307	+	5'Flank	INS	-	-	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr12:120884306_120884307insG	ENST00000546954.1	-	0	0				AL021546.6_ENST00000551806.1_Intron|GATC_ENST00000551765.1_Frame_Shift_Ins_p.LG8fs|TRIAP1_ENST00000302432.3_5'Flank	NM_016399.2	NP_057483.1	O43715	TRIA1_HUMAN	TP53 regulated inhibitor of apoptosis 1						cellular response to UV (GO:0034644)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|phospholipid transport (GO:0015914)|positive regulation of phospholipid transport (GO:2001140)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of membrane lipid distribution (GO:0097035)	mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	p53 binding (GO:0002039)					all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTGGTGTGGCTGGGCCTTCGGG	0.683																																																	0																																										SO:0001631	upstream_gene_variant	283459				CCDS9198.1	12q24.31	2012-10-15			ENSG00000170855	ENSG00000170855			26937	protein-coding gene	gene with protein product	"""p53-inducible cell-survival factor"", ""mitochondrial distribution and morphology 35 homolog (S. cerevisiae)"""	614943				11042152, 15735003	Standard	NM_016399		Approved	P53CSV, WF-1, HSPC132, p53CSV, MDM35	uc001tyg.3	O43715	OTTHUMG00000047787		12.37:g.120884309_120884309dupG	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	B2R4Z7|Q5RKS5|Q6LCA7	Frame_Shift_Ins	INS	ENST00000546954.1	37	CCDS9198.1																																																																																				0.683	TRIAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108980.3		NM_016399	
GLB1	2720	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	33038793	33038793	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr3:33038793G>A	ENST00000399402.3	-	16	1819	c.1688C>T	c.(1687-1689)cCa>cTa	p.P563L	GLB1_ENST00000307377.8_Missense_Mutation_p.P462L|GLB1_ENST00000445488.2_Missense_Mutation_p.P641L|GLB1_ENST00000307363.5_Missense_Mutation_p.P593L	NM_001079811.1	NP_001073279	P16278	BGAL_HUMAN	galactosidase, beta 1	593					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)	beta-galactosidase activity (GO:0004565)|galactoside binding (GO:0016936)	p.P593L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	21		Melanoma(143;0.104)				GCCCCGGGCTGGCCAATAGCG	0.587																																																	1	Substitution - Missense(1)	kidney(1)											40.0	41.0	41.0					3																	33038793		1906	4118	6024	SO:0001583	missense	2720			M22590	CCDS43061.1, CCDS43062.1, CCDS46785.1	3p22.3	2012-10-02			ENSG00000170266	ENSG00000170266	3.2.1.23		4298	protein-coding gene	gene with protein product		611458	"""elastin receptor 1, 67kDa"", ""elastin receptor 1 (67kD)"""	ELNR1		110522, 3143362	Standard	NM_000404		Approved	EBP	uc003cfi.1	P16278	OTTHUMG00000155781	ENST00000399402.3:c.1688C>T	3.37:g.33038793G>A	ENSP00000382333:p.Pro563Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B2R7H8|B7Z6B0|P16279	Missense_Mutation	SNP	ENST00000399402.3	37	CCDS43062.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693553	0.88735	.	.	ENSG00000170266	ENST00000399402;ENST00000307363;ENST00000445488;ENST00000307377	D;D;D;D	0.95788	-3.81;-3.81;-3.81;-3.81	5.31	4.43	0.53597	Galactose-binding domain-like (1);	0.102175	0.64402	D	0.000002	D	0.97324	0.9125	M	0.77103	2.36	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.87578	0.998;0.996;0.991;0.985	D	0.97620	1.0135	10	0.72032	D	0.01	-10.5365	13.2546	0.60070	0.0775:0.0:0.9225:0.0	.	593;462;593;641	Q53G40;E7EQ29;P16278;B7Z6Q5	.;.;BGAL_HUMAN;.	L	563;593;641;462	ENSP00000382333:P563L;ENSP00000306920:P593L;ENSP00000393377:P641L;ENSP00000305920:P462L	ENSP00000306920:P593L	P	-	2	0	GLB1	33013797	1.000000	0.71417	0.745000	0.31077	0.984000	0.73092	9.602000	0.98312	1.249000	0.43950	0.456000	0.33151	CCA		0.587	GLB1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341570.2		NM_000404	
GNMT	27232	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	42931107	42931107	+	Silent	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr6:42931107G>A	ENST00000372808.3	+	5	646	c.636G>A	c.(634-636)gtG>gtA	p.V212V		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	212					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)	p.V212V(1)		kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	TGCTGATAGTGAACAACAAGG	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											53.0	45.0	48.0					6																	42931107		2203	4300	6503	SO:0001819	synonymous_variant	27232			AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.636G>A	6.37:g.42931107G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T8W2|Q9NNZ1|Q9NS24	Silent	SNP	ENST00000372808.3	37	CCDS4876.1																																																																																				0.592	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1		NM_018960	
GPR152	390212	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	67220120	67220120	+	Missense_Mutation	SNP	A	A	C	rs199732498		TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr11:67220120A>C	ENST00000312457.2	-	1	80	c.76T>G	c.(76-78)Tac>Gac	p.Y26D	CABP4_ENST00000325656.5_5'Flank|CABP4_ENST00000438189.2_Intron|CABP4_ENST00000542025.2_3'UTR	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	26						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CCTTGGGGGTAGGAGTCCTCA	0.652																																					Pancreas(102;800 1581 2723 7382 33622)												0													54.0	55.0	55.0					11																	67220120		2194	4283	6477	SO:0001583	missense	390212			AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"""GPCR / Class A : Orphans"""	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.76T>G	11.37:g.67220120A>C	ENSP00000310255:p.Tyr26Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	.	.	.	.	.	.	.	.	.	.	A	16.87	3.242417	0.58995	.	.	ENSG00000175514	ENST00000312457	T	0.16196	2.36	5.07	5.07	0.68467	.	0.219602	0.23123	N	0.051673	T	0.17280	0.0415	L	0.27053	0.805	0.80722	D	1	P	0.48162	0.906	P	0.47402	0.546	T	0.01715	-1.1289	10	0.40728	T	0.16	.	12.8053	0.57610	1.0:0.0:0.0:0.0	.	26	Q8TDT2	GP152_HUMAN	D	26	ENSP00000310255:Y26D	ENSP00000310255:Y26D	Y	-	1	0	GPR152	66976696	1.000000	0.71417	1.000000	0.80357	0.653000	0.38743	3.738000	0.55067	2.132000	0.65825	0.459000	0.35465	TAC		0.652	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			
HLA-B	3106	hgsc.bcm.edu	37	6	31324542	31324542	+	Missense_Mutation	SNP	T	T	C	rs1131201|rs281864604	byFrequency	TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr6:31324542T>C	ENST00000412585.2	-	2	294	c.266A>G	c.(265-267)cAg>cGg	p.Q89R		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	89	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CTTGTAGATCTGTGTGTTCCG	0.672									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	444	0.0886581	0.1225	0.049	5008	,	,		6988	0.0665		0.0527	False		,,,				2504	0.1309																0													64.0	63.0	64.0					6																	31324542		2115	4146	6261	SO:0001583	missense	3106	Familial Cancer Database	;Lichen Sclerosis, Familial	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.266A>G	6.37:g.31324542T>C	ENSP00000399168:p.Gln89Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	5.583	0.292411	0.10567	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00010	9.39;9.39	3.2	-2.25	0.06888	MHC class I, alpha chain, alpha1/alpha2 (4);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	2.810030	0.03023	N	0.151052	T	0.00012	0.0000	N	0.02412	-0.56	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.17979	0.01;0.02;0.005	T	0.09292	-1.0681	10	0.02654	T	1	.	5.3015	0.15780	0.0:0.2931:0.1602:0.5467	rs1131201;rs3190900	89;89;64	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	R	89;100	ENSP00000399168:Q89R;ENSP00000405931:Q100R	ENSP00000399168:Q89R	Q	-	2	0	HLA-B	31432521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.279000	0.01159	-0.829000	0.04268	-2.398000	0.00225	CAG		0.672	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4		NM_005514	
IGF2	3481	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	2154815	2154815	+	Silent	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr11:2154815G>A	ENST00000416167.2	-	3	1404	c.238C>T	c.(238-240)Ctg>Ttg	p.L80L	IGF2_ENST00000434045.2_Silent_p.L136L|IGF2_ENST00000381392.1_Silent_p.L83L|IGF2_ENST00000381406.4_Silent_p.L83L|IGF2_ENST00000300632.5_Silent_p.L80L|IGF2_ENST00000381389.1_Silent_p.L80L|MIR483_ENST00000385070.1_RNA|IGF2_ENST00000418738.2_Silent_p.L80L|IGF2_ENST00000381395.1_Silent_p.L80L			P01344	IGF2_HUMAN	insulin-like growth factor 2	80	A.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|exocrine pancreas development (GO:0031017)|female pregnancy (GO:0007565)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|organ morphogenesis (GO:0009887)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nicotine (GO:0035094)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|striated muscle cell differentiation (GO:0051146)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	growth factor activity (GO:0008083)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|protein serine/threonine kinase activator activity (GO:0043539)|receptor activator activity (GO:0030546)	p.L80L(1)|p.L136L(1)		central_nervous_system(1)|kidney(1)|lung(1)|pancreas(1)|skin(1)|urinary_tract(1)	6		all_epithelial(84;5.04e-06)|Breast(177;0.000777)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)|all_lung(207;0.24)	Colorectal(5;0.0179)|COAD - Colon adenocarcinoma(6;0.029)	BRCA - Breast invasive adenocarcinoma(625;1.09e-05)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		TACGTCTCCAGGAGGGCCAGG	0.657																																																	2	Substitution - coding silent(2)	kidney(2)											52.0	43.0	46.0					11																	2154815		2202	4299	6501	SO:0001819	synonymous_variant	3481			M29645, AK025719	CCDS7728.1, CCDS44517.1	11p15.5	2014-09-16	2014-09-16		ENSG00000167244	ENSG00000167244			5466	protein-coding gene	gene with protein product	"""somatomedin A"""	147470	"""chromosome 11 open reading frame 43"""	C11orf43		2450353, 3167054	Standard	NM_000612		Approved	FLJ44734, IGF-II	uc009ydf.3	P01344	OTTHUMG00000009395	ENST00000416167.2:c.238C>T	11.37:g.2154815G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KX48|B7WP08|C9JAF2|E3UN45|P78449|Q14299|Q1WM26|Q9UC68|Q9UC69	Silent	SNP	ENST00000416167.2	37	CCDS7728.1																																																																																				0.657	IGF2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026053.2		NM_000612	
KDM6A	7403	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	44949174	44949174	+	Splice_Site	DEL	A	A	-			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chrX:44949174delA	ENST00000377967.4	+	25	3776	c.3735delA	c.(3733-3735)aca>ac	p.T1245fs	KDM6A_ENST00000536777.1_Splice_Site_p.T1200fs|KDM6A_ENST00000382899.4_Splice_Site_p.T1252fs|KDM6A_ENST00000543216.1_Splice_Site_p.T1166fs	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1245	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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)		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						GTCCACTTACAGGTATTATAA	0.353			"""D, N, F, S"""		"""renal, oesophageal SCC, MM"""																																Colon(129;1273 1667 15230 27352 52914)			Rec	yes		X	Xp11.2	7403	"""lysine (K)-specific demethylase 6A, UTX"""		"""E, L"""	6	Whole gene deletion(6)	oesophagus(2)|breast(2)|pancreas(2)											87.0	74.0	79.0					X																	44949174		2203	4300	6503	SO:0001630	splice_region_variant	7403			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.3736+1A>-	X.37:g.44949174delA		Somatic		WXS	Illumina HiSeq	Phase_I	Q52LL9|Q5JVQ7	Frame_Shift_Del	DEL	ENST00000377967.4	37	CCDS14265.1																																																																																				0.353	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1		NM_021140	Frame_Shift_Del
KIAA1244	57221	hgsc.bcm.edu	37	6	138657590	138657591	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr6:138657590_138657591delCA	ENST00000251691.4	+	34	6667_6668	c.6501_6502delCA	c.(6499-6504)ggcaggfs	p.R2168fs		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AGTGGCTGGGCAGGGTGGGCCG	0.569																																																	0																																										SO:0001589	frameshift_variant	57221			AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.6501_6502delCA	6.37:g.138657590_138657591delCA	ENSP00000251691:p.Arg2168fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000251691.4	37	CCDS5189.2																																																																																				0.569	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4		NM_020340	
NRROS	375387	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	196388312	196388313	+	Missense_Mutation	DNP	GG	GG	AT			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr3:196388312_196388313GG>AT	ENST00000328557.4	+	3	2001_2002	c.1798_1799GG>AT	c.(1798-1800)GGg>ATg	p.G600M		NM_198565.1	NP_940967.1	Q86YC3	NRROS_HUMAN	negative regulator of reactive oxygen species	600					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G600V(2)|p.G600R(1)									TGACTGCTGTGGGGTGGATGGC	0.609																																																	3	Substitution - Missense(3)	lung(2)|kidney(1)																																								SO:0001583	missense	375387			AY358322	CCDS3319.1	3q29	2013-07-02	2013-07-02	2013-07-02	ENSG00000174004	ENSG00000174004			24613	protein-coding gene	gene with protein product		615322	"""leucine rich repeat containing 33"""	LRRC33		12975309	Standard	NM_198565		Approved	UNQ3030, ELLP3030, MGC50789, GARPL1	uc003fwv.3	Q86YC3	OTTHUMG00000155569	Exception_encountered	3.37:g.196388312_196388313delinsAT	ENSP00000328625:p.Gly600Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000328557.4	37	CCDS3319.1																																																																																				0.609	NRROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340676.1		NM_198565	
MEPCE	56257	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	100031142	100031142	+	Missense_Mutation	SNP	T	T	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr7:100031142T>A	ENST00000310512.2	+	4	2423	c.2035T>A	c.(2035-2037)Tac>Aac	p.Y679N	RP11-758P17.2_ENST00000492523.1_RNA|PPP1R35_ENST00000476185.1_5'Flank|MEPCE_ENST00000414441.1_Missense_Mutation_p.Y210N|RP11-758P17.3_ENST00000475250.1_RNA	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	679	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)	p.Y679N(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCGTCCTGTGTACCTGTTCCA	0.587																																																	1	Substitution - Missense(1)	kidney(1)											70.0	70.0	70.0					7																	100031142		2203	4300	6503	SO:0001583	missense	56257			AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"""bin3, bicoid-interacting 3, homolog (Drosophila)"""	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.2035T>A	7.37:g.100031142T>A	ENSP00000308546:p.Tyr679Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	37	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	T	18.89	3.719543	0.68844	.	.	ENSG00000146834	ENST00000414441;ENST00000425355;ENST00000310512	.	.	.	5.29	4.13	0.48395	Bin3-type S-adenosyl-L-methionine binding domain (1);Bicoid-interacting 3 (1);	0.158139	0.44097	D	0.000482	T	0.68751	0.3035	M	0.68317	2.08	0.45076	D	0.998099	D	0.89917	1.0	D	0.72338	0.977	T	0.66555	-0.5894	9	0.37606	T	0.19	-27.2854	7.628	0.28222	0.0:0.0943:0.0:0.9057	.	679	Q7L2J0	MEPCE_HUMAN	N	210;210;679	.	ENSP00000308546:Y679N	Y	+	1	0	MEPCE	99869078	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.413000	0.73308	1.028000	0.39785	0.379000	0.24179	TAC		0.587	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			
NFE2L2	4780	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	178098799	178098799	+	Missense_Mutation	SNP	T	T	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:178098799T>G	ENST00000397062.3	-	2	800	c.246A>C	c.(244-246)gaA>gaC	p.E82D	NFE2L2_ENST00000446151.2_Missense_Mutation_p.E66D|NFE2L2_ENST00000464747.1_Missense_Mutation_p.E66D|NFE2L2_ENST00000397063.4_Missense_Mutation_p.E66D|NFE2L2_ENST00000423513.1_Missense_Mutation_p.E66D	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2	82					cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E82D(8)|p.G81_F83delGEF(1)		central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			TTGGGAGAAATTCACCTGTCT	0.433			Mis		"""NSCLC, HNSCC"""					HNSCC(56;0.16)																														Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	9	Substitution - Missense(8)|Deletion - In frame(1)	endometrium(3)|liver(2)|upper_aerodigestive_tract(1)|cervix(1)|oesophagus(1)|kidney(1)											138.0	137.0	137.0					2																	178098799		1903	4104	6007	SO:0001583	missense	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"""basic leucine zipper proteins"""	7782	protein-coding gene	gene with protein product	"""NF-E2-related factor 2"""	600492	"""nuclear factor (erythroid-derived 2)-like 2"""			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.246A>C	2.37:g.178098799T>G	ENSP00000380252:p.Glu82Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Missense_Mutation	SNP	ENST00000397062.3	37	CCDS42782.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.706902	0.89018	.	.	ENSG00000116044	ENST00000397063;ENST00000397062;ENST00000446151;ENST00000448782;ENST00000421929;ENST00000423513	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.67;1.67;1.53	5.78	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.58395	0.2119	M	0.87180	2.865	0.54753	D	0.999981	D;D;D;D	0.89917	0.999;0.997;1.0;0.999	D;D;D;D	0.83275	0.991;0.978;0.996;0.991	T	0.64976	-0.6280	10	0.72032	D	0.01	.	11.2269	0.48888	0.0:0.0712:0.0:0.9288	.	66;66;66;82	E9PGJ7;B4DNB0;C9JFL6;Q16236	.;.;.;NF2L2_HUMAN	D	66;82;66;66;66;66	ENSP00000380253:E66D;ENSP00000380252:E82D;ENSP00000411575:E66D;ENSP00000400073:E66D;ENSP00000412191:E66D;ENSP00000410015:E66D	ENSP00000380252:E82D	E	-	3	2	NFE2L2	177807045	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.909000	0.39917	2.210000	0.71456	0.460000	0.39030	GAA		0.433	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4		NM_006164	
NFRKB	4798	hgsc.bcm.edu	37	11	129743673	129743674	+	Frame_Shift_Ins	INS	-	-	G	rs140340409		TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr11:129743673_129743674insG	ENST00000446488.3	-	21	2619_2620	c.2516_2517insC	c.(2515-2517)ccafs	p.P839fs	NFRKB_ENST00000304521.5_Frame_Shift_Ins_p.P839fs|NFRKB_ENST00000524794.1_Frame_Shift_Ins_p.P864fs|NFRKB_ENST00000524746.1_Frame_Shift_Ins_p.P839fs	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	839					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TGGCAGTGGCTGGAACCCGGAT	0.614																																																	0																																										SO:0001589	frameshift_variant	4798				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.2517dupC	11.37:g.129743675_129743675dupG	ENSP00000400476:p.Pro839fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q12869|Q15312|Q9H048	Frame_Shift_Ins	INS	ENST00000446488.3	37	CCDS44770.1																																																																																				0.614	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2		NM_006165	
ODF3L1	161753	hgsc.bcm.edu;ucsc.edu	37	15	76019407	76019407	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr15:76019407delC	ENST00000332145.2	+	4	574	c.351delC	c.(349-351)aacfs	p.N117fs	DNM1P35_ENST00000501931.1_RNA	NM_175881.3	NP_787077.1	Q8IXM7	OD3L1_HUMAN	outer dense fiber of sperm tails 3-like 1	117										kidney(1)|lung(1)	2						CAGGCCTGAACCCCACCCTCG	0.592																																																	0													102.0	117.0	112.0					15																	76019407		2195	4291	6486	SO:0001589	frameshift_variant	161753			BC039862	CCDS10285.1	15q23	2008-02-05			ENSG00000182950	ENSG00000182950			28735	protein-coding gene	gene with protein product							Standard	NM_175881		Approved	MGC48986	uc002bax.1	Q8IXM7	OTTHUMG00000142837	ENST00000332145.2:c.351delC	15.37:g.76019407delC	ENSP00000329584:p.Asn117fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000332145.2	37	CCDS10285.1																																																																																				0.592	ODF3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286473.1		NM_175881	
POLR1A	25885	hgsc.bcm.edu	37	2	86272423	86272424	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:86272423_86272424insG	ENST00000263857.6	-	21	3324_3325	c.2946_2947insC	c.(2944-2949)accagcfs	p.S983fs	POLR1A_ENST00000409681.1_Frame_Shift_Ins_p.S983fs			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	983					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CCTGAGCGGCTGGTTTTCACAG	0.545																																																	0																																										SO:0001589	frameshift_variant	25885			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.2947dupC	2.37:g.86272425_86272425dupG	ENSP00000263857:p.Ser983fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Frame_Shift_Ins	INS	ENST00000263857.6	37	CCDS42706.1																																																																																				0.545	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2		NM_015425	
RPS20	6224	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	56986629	56986629	+	Silent	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr8:56986629G>A	ENST00000521262.1	-	2	346	c.93C>T	c.(91-93)tcC>tcT	p.S31S	CTA-397H3.3_ENST00000521403.1_RNA|RPS20_ENST00000523936.1_Silent_p.S31S|RPS20_ENST00000520490.1_5'UTR|RPS20_ENST00000519606.1_Silent_p.S31S|RPS20_ENST00000519807.1_Silent_p.S31S|SNORD54_ENST00000459159.1_RNA|RPS20_ENST00000009589.3_Silent_p.S31S|RPS20_ENST00000520627.1_Intron|RPS20_ENST00000518875.1_Silent_p.S31S|RPS20_ENST00000524349.1_5'UTR			P60866	RS20_HUMAN	ribosomal protein S20	31					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.S31S(2)					all_lung(136;0.0548)|Lung NSC(129;0.0718)|all_epithelial(80;0.155)	Epithelial(17;0.00117)|all cancers(17;0.00879)			CCTTTTCCAAGGATTTTACGT	0.488																																																	2	Substitution - coding silent(2)	kidney(2)											81.0	87.0	85.0					8																	56986629		2203	4300	6503	SO:0001819	synonymous_variant	6224			L06498	CCDS6163.1, CCDS55231.1	8q12.1	2011-04-05				ENSG00000008988		"""S ribosomal proteins"""	10405	protein-coding gene	gene with protein product		603682				9582194, 8479924	Standard	NM_001023		Approved	S20	uc003xsm.2	P60866		ENST00000521262.1:c.93C>T	8.37:g.56986629G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R4F4|B4DW28|P17075|Q5M8S9	Silent	SNP	ENST00000521262.1	37																																																																																					0.488	RPS20-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378166.1		NM_001023	
SEC31A	22872	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	83788377	83788377	+	Silent	SNP	A	A	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr4:83788377A>G	ENST00000395310.2	-	9	1157	c.975T>C	c.(973-975)gaT>gaC	p.D325D	SEC31A_ENST00000348405.4_Silent_p.D325D|SEC31A_ENST00000432794.1_Silent_p.D325D|SEC31A_ENST00000448323.1_Silent_p.D325D|SEC31A_ENST00000264405.5_Silent_p.D97D|SEC31A_ENST00000311785.7_Silent_p.D325D|SEC31A_ENST00000508502.1_Silent_p.D325D|SEC31A_ENST00000513858.1_Silent_p.D325D|SEC31A_ENST00000326950.5_Silent_p.D325D|SEC31A_ENST00000509142.1_Silent_p.D325D|SEC31A_ENST00000436790.2_5'UTR|SEC31A_ENST00000505984.1_Silent_p.D325D|SEC31A_ENST00000500777.2_Silent_p.D325D|SEC31A_ENST00000508479.1_Silent_p.D325D|SEC31A_ENST00000443462.2_Silent_p.D320D|SEC31A_ENST00000355196.2_Silent_p.D325D|SEC31A_ENST00000505472.1_Silent_p.D325D	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	325	Interaction with SEC13.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)	p.D325D(2)	SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				TGATACGCCCATCAAACGAAG	0.418																																																	2	Substitution - coding silent(2)	kidney(2)											130.0	115.0	120.0					4																	83788377		2203	4300	6503	SO:0001819	synonymous_variant	22872			AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.975T>C	4.37:g.83788377A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Silent	SNP	ENST00000395310.2	37	CCDS3596.1																																																																																				0.418	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1		NM_016211	
SIX3	6496	broad.mit.edu;hgsc.bcm.edu	37	2	45171737	45171737	+	Silent	SNP	C	C	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr2:45171737C>A	ENST00000260653.3	+	2	1179	c.837C>A	c.(835-837)ggC>ggA	p.G279G	SIX3-AS1_ENST00000419364.1_RNA	NM_005413.3	NP_005404.1	O95343	SIX3_HUMAN	SIX homeobox 3	279					brain development (GO:0007420)|circadian behavior (GO:0048512)|diencephalon development (GO:0021536)|eye development (GO:0001654)|forebrain anterior/posterior pattern specification (GO:0021797)|forebrain dorsal/ventral pattern formation (GO:0021798)|lens induction in camera-type eye (GO:0060235)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|protein import into nucleus (GO:0006606)|telencephalon development (GO:0021537)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|transcription corepressor binding (GO:0001222)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|skin(1)	11		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				GACCGAGCGGCATGCGCTCGC	0.756																																																	0													5.0	6.0	6.0					2																	45171737		1688	3619	5307	SO:0001819	synonymous_variant	6496			AF092047	CCDS1821.1	2p21	2011-06-20	2007-07-13		ENSG00000138083	ENSG00000138083		"""Homeoboxes / SINE class"""	10889	protein-coding gene	gene with protein product		603714	"""holoprosencephaly 2, alobar or semilobar"", ""sine oculis homeobox homolog 3 (Drosophila)"""	HPE2		9889003, 10369266	Standard	NM_005413		Approved		uc002run.2	O95343	OTTHUMG00000152424	ENST00000260653.3:c.837C>A	2.37:g.45171737C>A		Somatic		WXS	Illumina HiSeq	Phase_I	D6W5A5|Q53T42	Silent	SNP	ENST00000260653.3	37	CCDS1821.1																																																																																				0.756	SIX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326192.1		NM_005413	
SORBS2	8470	hgsc.bcm.edu;ucsc.edu	37	4	186545056	186545067	+	In_Frame_Del	DEL	CATGTCCCGGGG	CATGTCCCGGGG	-	rs532835164|rs141059121		TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	CATGTCCCGGGG	CATGTCCCGGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr4:186545056_186545067delCATGTCCCGGGG	ENST00000284776.7	-	13	2013_2024	c.1504_1515delCCCCGGGACATG	c.(1504-1515)ccccgggacatgdel	p.PRDM502del	SORBS2_ENST00000431808.1_In_Frame_Del_p.PRDM502del|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000418609.1_In_Frame_Del_p.PRDM406del|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000355634.5_In_Frame_Del_p.PRDM602del|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	502					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GTGTGGGCACCATGTCCCGGGGCACCTCCTCC	0.575																																					Esophageal Squamous(153;41 2433 9491 36028)												0																																										SO:0001651	inframe_deletion	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1504_1515delCCCCGGGACATG	4.37:g.186545056_186545067delCATGTCCCGGGG	ENSP00000284776:p.Pro502_Met505del	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	In_Frame_Del	DEL	ENST00000284776.7	37	CCDS3845.1																																																																																				0.575	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3		NM_003603	
SSTR4	6754	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	23016583	23016583	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr20:23016583G>A	ENST00000255008.3	+	1	527	c.463G>A	c.(463-465)Gcg>Acg	p.A155T	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	155					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					TCTGCGCGCGGCGACCTACCG	0.657																																					Esophageal Squamous(15;850 1104 16640)												0													48.0	52.0	50.0					20																	23016583		2200	4294	6494	SO:0001583	missense	6754				CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.463G>A	20.37:g.23016583G>A	ENSP00000255008:p.Ala155Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.558611	0.27827	.	.	ENSG00000132671	ENST00000255008	T	0.71934	-0.61	3.87	1.69	0.24217	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000009	T	0.58552	0.2130	L	0.41906	1.305	0.43187	D	0.995016	B	0.33379	0.41	B	0.37091	0.241	T	0.46665	-0.9175	10	0.30078	T	0.28	.	7.7421	0.28848	0.2367:0.0:0.7633:0.0	.	155	P31391	SSR4_HUMAN	T	155	ENSP00000255008:A155T	ENSP00000255008:A155T	A	+	1	0	SSTR4	22964583	0.995000	0.38212	0.013000	0.15412	0.023000	0.10783	2.270000	0.43355	0.227000	0.20999	0.655000	0.94253	GCG		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			
HIRIP3	8479	hgsc.bcm.edu	37	16	30002435	30002436	+	IGR	INS	-	-	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr16:30002435_30002436insG	ENST00000279392.3	-	0	3385				TAOK2_ENST00000279394.3_Frame_Shift_Ins_p.A900fs	NM_003609.4	NP_003600.2	Q9BW71	HIRP3_HUMAN	HIRA interacting protein 3						chromatin assembly or disassembly (GO:0006333)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(9)	17						CTTGAGCGGCAGGCCCGTGAGA	0.649																																																	0																																										SO:0001628	intergenic_variant	9344			AJ223351	CCDS10664.1, CCDS58449.1	16p12.1	2008-02-05	2001-11-29		ENSG00000149929	ENSG00000149929			4917	protein-coding gene	gene with protein product		603365	"""HIRA-interacting protein 3"""			9710638	Standard	NM_003609		Approved		uc002dve.3	Q9BW71	OTTHUMG00000132118		16.37:g.30002437_30002437dupG		Somatic		WXS	Illumina HiSeq	Phase_I	H3BSR3|O75707|O75708	Frame_Shift_Ins	INS	ENST00000279392.3	37	CCDS10664.1																																																																																				0.649	HIRIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255160.2		NM_003609	
TMC8	147138	hgsc.bcm.edu	37	17	76127732	76127732	+	Silent	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr17:76127732G>A	ENST00000318430.5	+	2	437	c.63G>A	c.(61-63)ctG>ctA	p.L21L	TMC6_ENST00000590602.1_5'Flank|TMC6_ENST00000322914.3_Intron|TMC6_ENST00000322933.4_5'Flank|TMC8_ENST00000589691.1_Intron|TMC6_ENST00000589553.1_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	21					ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			CGGAGGAGCTGTGGGAGGCAG	0.736																																																	0													7.0	9.0	9.0					17																	76127732		2111	4161	6272	SO:0001819	synonymous_variant	147138			AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.63G>A	17.37:g.76127732G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																				0.736	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			
TNFRSF4	7293	broad.mit.edu;hgsc.bcm.edu	37	1	1149473	1149473	+	Missense_Mutation	SNP	G	G	T			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr1:1149473G>T	ENST00000379236.3	-	1	39	c.35C>A	c.(34-36)cCg>cAg	p.P12Q	TNFRSF4_ENST00000453580.1_5'Flank	NM_003327.3	NP_003318.1	P43489	TNR4_HUMAN	tumor necrosis factor receptor superfamily, member 4	12					cellular defense response (GO:0006968)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of immunoglobulin secretion (GO:0051024)|regulation of apoptotic process (GO:0042981)|regulation of protein kinase activity (GO:0045859)|T cell proliferation (GO:0042098)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			large_intestine(1)|lung(2)|urinary_tract(1)	4	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGCCGCACACGGCCCGCGGCC	0.687																																																	0													11.0	14.0	13.0					1																	1149473		2166	4257	6423	SO:0001583	missense	7293			X75962	CCDS11.1	1p36	2008-02-05			ENSG00000186827	ENSG00000186827		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11918	protein-coding gene	gene with protein product		600315		TXGP1L		7510240, 2828930	Standard	NM_003327		Approved	ACT35, OX40, CD134	uc001ade.3	P43489	OTTHUMG00000001415	ENST00000379236.3:c.35C>A	1.37:g.1149473G>T	ENSP00000368538:p.Pro12Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q13663|Q2M312|Q5T7M0	Missense_Mutation	SNP	ENST00000379236.3	37	CCDS11.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899231	0.33535	.	.	ENSG00000186827	ENST00000379236	T	0.61158	0.13	2.69	2.69	0.31865	.	0.917030	0.09077	N	0.851928	T	0.68897	0.3051	L	0.50333	1.59	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.54043	-0.8352	10	0.56958	D	0.05	-10.5799	8.9169	0.35587	0.0:0.0:1.0:0.0	.	12	P43489	TNR4_HUMAN	Q	12	ENSP00000368538:P12Q	ENSP00000368538:P12Q	P	-	2	0	TNFRSF4	1139336	0.001000	0.12720	0.008000	0.14137	0.011000	0.07611	0.272000	0.18644	1.532000	0.49169	0.491000	0.48974	CCG		0.687	TNFRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004086.1			
YME1L1	10730	hgsc.bcm.edu	37	10	27436462	27436463	+	Frame_Shift_Del	DEL	GC	GC	-	rs74970402|rs200312868|rs398102294	byFrequency	TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr10:27436462_27436463delGC	ENST00000326799.3	-	3	451_452	c.303_304delGC	c.(301-306)tggcacfs	p.WH101fs	YME1L1_ENST00000375972.3_Intron|YME1L1_ENST00000477432.1_Frame_Shift_Del_p.WH101fs|YME1L1_ENST00000376016.3_Intron	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	101					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						GGACGGAtgtgccagttatcgg	0.441														533	0.10643	0.3888	0.0274	5008	,	,		20833	0.0		0.0	False		,,,				2504	0.0																0									,	1408,2856		237,934,961					,	1.1	0.0		dbSNP_131	197	44,8210		0,44,4083	yes	frameshift,intron	YME1L1	NM_139312.1,NM_014263.2	,	237,978,5044	A1A1,A1R,RR		0.5331,33.0206,11.5993	,	,		1452,11066				SO:0001589	frameshift_variant	10730			AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.303_304delGC	10.37:g.27436462_27436463delGC	ENSP00000318480:p.Trp101fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Frame_Shift_Del	DEL	ENST00000326799.3	37	CCDS7152.1																																																																																				0.441	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1		NM_139312	
ZDHHC16	84287	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	99211881	99211881	+	Missense_Mutation	SNP	C	C	T			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr10:99211881C>T	ENST00000370854.3	+	3	467	c.278C>T	c.(277-279)tCc>tTc	p.S93F	ZDHHC16_ENST00000353979.3_Missense_Mutation_p.S93F|ZDHHC16_ENST00000352634.4_Missense_Mutation_p.S93F|ZDHHC16_ENST00000393760.1_Missense_Mutation_p.S93F|ZDHHC16_ENST00000495735.1_3'UTR|ZDHHC16_ENST00000345745.5_Intron|ZDHHC16_ENST00000370842.2_Missense_Mutation_p.S93F|ZDHHC16_ENST00000370846.4_Missense_Mutation_p.S93F	NM_032327.2	NP_115703.2	Q969W1	ZDH16_HUMAN	zinc finger, DHHC-type containing 16	93					apoptotic process (GO:0006915)|protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.S93F(1)		kidney(4)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	14		Colorectal(252;0.0846)		Epithelial(162;5.81e-10)|all cancers(201;4.19e-08)		CTGACAGGCTCCATTGTAGCT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											166.0	116.0	133.0					10																	99211881		2203	4300	6503	SO:0001583	missense	84287			AF258563	CCDS7460.1, CCDS7461.1, CCDS7462.1, CCDS7463.1, CCDS73176.1	10q24.1	2008-05-02			ENSG00000171307	ENSG00000171307		"""Zinc fingers, DHHC-type"""	20714	protein-coding gene	gene with protein product						12021275	Standard	NM_198043		Approved	APH2	uc001knk.3	Q969W1	OTTHUMG00000018847	ENST00000370854.3:c.278C>T	10.37:g.99211881C>T	ENSP00000359891:p.Ser93Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D3DR52|D3DR53|D3DR54|Q5JTG7|Q5JTH0|Q8N4Z6|Q8WY84|Q9BSV3	Missense_Mutation	SNP	ENST00000370854.3	37	CCDS7460.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.74|17.74	3.464558|3.464558	0.63513|0.63513	.|.	.|.	ENSG00000171307|ENSG00000171307	ENST00000420089;ENST00000417044|ENST00000370854;ENST00000393760;ENST00000414567;ENST00000370846;ENST00000352634;ENST00000353979;ENST00000370842	.|T;T;T;T;T;T;T	.|0.35789	.|1.29;1.29;1.29;1.29;1.29;1.29;1.29	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.58566|0.58566	0.2131|0.2131	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	.|D;D;D;P;P;P	.|0.89917	.|1.0;1.0;0.998;0.811;0.778;0.671	.|D;D;D;P;B;B	.|0.91635	.|0.999;0.993;0.991;0.693;0.398;0.224	T|T	0.51748|0.51748	-0.8666|-0.8666	5|10	.|0.10902	.|T	.|0.67	-27.601|-27.601	19.4725|19.4725	0.94969|0.94969	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|93;93;68;93;93;93	.|B4DNL2;B1AMU0;B1AMU1;Q969W1-3;Q969W1-2;Q969W1	.|.;.;.;.;.;ZDH16_HUMAN	S|F	69;35|93	.|ENSP00000359891:S93F;ENSP00000377357:S93F;ENSP00000400719:S93F;ENSP00000359883:S93F;ENSP00000345383:S93F;ENSP00000323360:S93F;ENSP00000359879:S93F	.|ENSP00000345383:S93F	P|S	+|+	1|2	0|0	ZDHHC16|ZDHHC16	99201871|99201871	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	5.943000|5.943000	0.70211|0.70211	2.611000|2.611000	0.88343|0.88343	0.561000|0.561000	0.74099|0.74099	CCA|TCC		0.547	ZDHHC16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049658.2		NM_032327	
HSPG2	3339	broad.mit.edu	37	1	22166039	22166039	+	Missense_Mutation	SNP	G	G	C			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr1:22166039G>C	ENST00000374695.3	-	73	9793	c.9714C>G	c.(9712-9714)agC>agG	p.S3238R		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	3238	Ig-like C2-type 18.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGGGCGCGGGGCTGCCTGTGG	0.647																																																	0													39.0	38.0	38.0					1																	22166039		2203	4300	6503	SO:0001583	missense	3339			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.9714C>G	1.37:g.22166039G>C	ENSP00000363827:p.Ser3238Arg	Somatic		WXS	Illumina GAIIx	Phase_I	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	G	3.643	-0.073131	0.07228	.	.	ENSG00000142798	ENST00000374695	T	0.67523	-0.27	5.5	4.59	0.56863	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.150229	0.30979	N	0.008500	T	0.51261	0.1664	N	0.21142	0.635	0.32402	N	0.551841	B;P	0.39044	0.002;0.656	B;B	0.37198	0.014;0.243	T	0.58487	-0.7628	10	0.21014	T	0.42	.	14.4737	0.67533	0.0:0.2793:0.7207:0.0	.	1178;3238	Q59EG0;P98160	.;PGBM_HUMAN	R	3238	ENSP00000363827:S3238R	ENSP00000363827:S3238R	S	-	3	2	HSPG2	22038626	0.987000	0.35691	1.000000	0.80357	0.129000	0.20672	0.413000	0.21148	1.330000	0.45394	-0.257000	0.10917	AGC		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1		NM_005529	
OGFR	11054	broad.mit.edu	37	20	61442846	61442846	+	Silent	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr20:61442846G>A	ENST00000290291.6	+	6	523	c.498G>A	c.(496-498)cgG>cgA	p.R166R	OGFR_ENST00000370461.1_Silent_p.R114R	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	166					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					TCCAGGAGCGGCTTGTCCGGG	0.632																																																	0													19.0	22.0	21.0					20																	61442846		2194	4294	6488	SO:0001819	synonymous_variant	11054			AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.498G>A	20.37:g.61442846G>A		Somatic		WXS	Illumina GAIIx	Phase_I	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Silent	SNP	ENST00000290291.6	37	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	G	0.826	-0.746779	0.03065	.	.	ENSG00000060491	ENST00000370469	.	.	.	4.56	-0.48	0.12085	.	.	.	.	.	T	0.58878	0.2153	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59177	-0.7503	5	0.87932	D	0	-32.982	5.7837	0.18320	0.2883:0.0:0.575:0.1366	.	.	.	.	D	22	.	ENSP00000359500:G22D	G	+	2	0	OGFR	60913291	0.755000	0.28372	0.080000	0.20451	0.014000	0.08584	-0.051000	0.11885	0.097000	0.17492	-0.254000	0.11334	GGC		0.632	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			
TBX10	347853	broad.mit.edu	37	11	67401787	67401787	+	Missense_Mutation	SNP	T	T	G			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr11:67401787T>G	ENST00000335385.3	-	4	509	c.422A>C	c.(421-423)gAc>gCc	p.D141A		NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	141					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						TGTGGCTGGGTCTGCCTTGCC	0.642																																																	0													53.0	49.0	51.0					11																	67401787		2199	4293	6492	SO:0001583	missense	347853			AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.422A>C	11.37:g.67401787T>G	ENSP00000335191:p.Asp141Ala	Somatic		WXS	Illumina GAIIx	Phase_I	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.054807	0.75960	.	.	ENSG00000167800	ENST00000335385	D	0.89617	-2.54	3.56	3.56	0.40772	p53-like transcription factor, DNA-binding (1);	0.000000	0.64402	D	0.000004	D	0.93284	0.7860	M	0.93978	3.48	0.58432	D	0.999998	D	0.57571	0.98	P	0.51833	0.681	D	0.94209	0.7457	10	0.87932	D	0	.	11.2552	0.49050	0.0:0.0:0.0:1.0	.	141	O75333	TBX10_HUMAN	A	141	ENSP00000335191:D141A	ENSP00000335191:D141A	D	-	2	0	TBX10	67158363	1.000000	0.71417	0.997000	0.53966	0.794000	0.44872	5.993000	0.70616	1.501000	0.48654	0.254000	0.18369	GAC		0.642	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1		NM_005995	
TSPAN19	144448	broad.mit.edu	37	12	85423547	85423547	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr12:85423547delC	ENST00000532498.2	-	3	169	c.89delG	c.(88-90)ggafs	p.G30fs	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	30						integral component of membrane (GO:0016021)				ovary(1)	1						TGCACCAAATCCCATGAATAA	0.259																																																	0													31.0	29.0	29.0					12																	85423547		1725	3953	5678	SO:0001589	frameshift_variant	144448				CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"""Tetraspanins"""	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.89delG	12.37:g.85423547delC	ENSP00000433816:p.Gly30fs	Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Del	DEL	ENST00000532498.2	37	CCDS44949.1																																																																																				0.259	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2		NM_001100917	
DNM1P47	100216544	broad.mit.edu	37	15	102312241	102312241	+	RNA	DEL	A	A	-	rs59860046|rs371768420	byFrequency	TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr15:102312241delA	ENST00000561463.1	+	0	13609				RN7SL209P_ENST00000488309.2_RNA					DNM1 pseudogene 47																		AGTGGCCGGGAAATTTGCTGT	0.592													|||unknown(NO_COVERAGE)	1711	0.341653	0.5144	0.3516	5008	,	,		9688	0.0565		0.5089	False		,,,				2504	0.2229																0																																												0			AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102312241delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000561463.1	37																																																																																					0.592	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1		NG_009149	
MIR4477B	100616194	broad.mit.edu	37	9	68413573	68413573	+	RNA	SNP	G	G	A			TCGA-B2-4098-01A-01D-1458-08	TCGA-B2-4098-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	76faa3c6-4474-433c-89e3-e78b68573ac5	db55656f-778d-4864-8679-61caa7e12c02	g.chr9:68413573G>A	ENST00000581659.1	+	0	0					NR_039688.1|NR_039689.1				microRNA 4477b																		CAGTGGCGCCGGATCTAGGAA	0.597																																																	0																																												0					9	2011-09-12						"""ncRNAs / Micro RNAs"""	41898	non-coding RNA	RNA, micro							Standard	NR_039689		Approved	hsa-mir-4477b					9.37:g.68413573G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000581659.1	37																																																																																					0.597	MIR4477B-201	KNOWN	basic	miRNA	miRNA			NR_039689	
