#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
A1CF	29974	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	52566613	52566613	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr10:52566613G>A	ENST00000373993.1	-	11	1705	c.1661C>T	c.(1660-1662)cCc>cTc	p.P554L	A1CF_ENST00000373997.3_Missense_Mutation_p.P546L|ASAH2B_ENST00000483649.1_Intron|A1CF_ENST00000374001.2_Missense_Mutation_p.P546L|A1CF_ENST00000373995.3_Missense_Mutation_p.P554L|A1CF_ENST00000395489.2_Missense_Mutation_p.P547L|A1CF_ENST00000282641.2_Missense_Mutation_p.P554L|A1CF_ENST00000395495.1_Missense_Mutation_p.P499L			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	554					cytidine to uridine editing (GO:0016554)|gene expression (GO:0010467)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|protein stabilization (GO:0050821)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.P546L(1)|p.P554L(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(4)|lung(14)|prostate(2)|skin(3)	29						TGCAGACACGGGTGCAGTTGC	0.473																																																	2	Substitution - Missense(2)	kidney(2)											120.0	107.0	112.0					10																	52566613		2203	4300	6503	SO:0001583	missense	29974			AF271790	CCDS7241.1, CCDS7242.1, CCDS7243.1, CCDS73133.1	10q21.1	2013-02-12			ENSG00000148584	ENSG00000148584		"""RNA binding motif (RRM) containing"""	24086	protein-coding gene	gene with protein product						11815617, 11072063	Standard	NM_014576		Approved	ACF, ASP, ACF64, ACF65, APOBEC1CF	uc001jjj.3	Q9NQ94	OTTHUMG00000018240	ENST00000373993.1:c.1661C>T	10.37:g.52566613G>A	ENSP00000363105:p.Pro554Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Missense_Mutation	SNP	ENST00000373993.1	37	CCDS7242.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.313437	0.81358	.	.	ENSG00000148584	ENST00000374001;ENST00000373993;ENST00000373997;ENST00000373995;ENST00000282641;ENST00000395495;ENST00000395488;ENST00000395489	T;T;T;T;T;T;T	0.11604	2.86;2.86;2.86;2.85;2.86;2.76;2.86	5.74	5.74	0.90152	.	1.504880	0.03648	N	0.240566	T	0.11324	0.0276	N	0.14661	0.345	0.30147	N	0.803419	B;B;B;B	0.23249	0.034;0.008;0.003;0.082	B;B;B;B	0.25140	0.036;0.011;0.009;0.058	T	0.33854	-0.9852	10	0.21540	T	0.41	-2.3948	17.4268	0.87528	0.0:0.0:1.0:0.0	.	547;554;546;554	F8W9F8;Q9NQ94;Q9NQ94-2;Q9NQ94-4	.;A1CF_HUMAN;.;.	L	546;554;546;554;554;499;529;547	ENSP00000363113:P546L;ENSP00000363105:P554L;ENSP00000363109:P546L;ENSP00000363107:P554L;ENSP00000282641:P554L;ENSP00000378873:P499L;ENSP00000378868:P547L	ENSP00000282641:P554L	P	-	2	0	A1CF	52236619	1.000000	0.71417	0.184000	0.23157	0.749000	0.42624	9.018000	0.93657	2.714000	0.92807	0.650000	0.86243	CCC		0.473	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2		NM_014576	
ACADVL	37	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	7125374	7125374	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:7125374C>T	ENST00000356839.5	+	8	905	c.726C>T	c.(724-726)acC>acT	p.T242T	DLG4_ENST00000399510.2_5'Flank|ACADVL_ENST00000543245.2_Silent_p.T265T|MIR324_ENST00000362183.1_RNA|ACADVL_ENST00000350303.5_Silent_p.T220T	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	242	Catalytic.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|energy derivation by oxidation of organic compounds (GO:0015980)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)	p.T242T(1)		breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(1)|ovary(4)|skin(1)	21						AATACTATACCCTCAATGGAA	0.592																																																	1	Substitution - coding silent(1)	kidney(1)											106.0	107.0	107.0					17																	7125374		2203	4300	6503	SO:0001819	synonymous_variant	37			BC012912	CCDS11090.1, CCDS42249.1, CCDS58509.1	17p13.1	2010-04-30	2010-04-30		ENSG00000072778	ENSG00000072778			92	protein-coding gene	gene with protein product		609575	"""acyl-Coenzyme A dehydrogenase, very long chain"""			8921384	Standard	NM_000018		Approved	VLCAD, LCACD, ACAD6	uc002gev.4	P49748	OTTHUMG00000102157	ENST00000356839.5:c.726C>T	17.37:g.7125374C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DEB6|F5H2A9|O76056|Q8WUL0	Silent	SNP	ENST00000356839.5	37	CCDS11090.1																																																																																				0.592	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5		NM_000018	
ANKMY1	51281	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	241496637	241496637	+	5'UTR	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:241496637G>A	ENST00000391987.1	-	0	215				ANKMY1_ENST00000361678.4_Missense_Mutation_p.S39F|ANKMY1_ENST00000401804.1_Missense_Mutation_p.S39F|ANKMY1_ENST00000406958.1_Missense_Mutation_p.S39F|ANKMY1_ENST00000373320.4_5'UTR|ANKMY1_ENST00000272972.3_Intron|ANKMY1_ENST00000373318.2_Missense_Mutation_p.S39F|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000403283.1_Missense_Mutation_p.S118F|ANKMY1_ENST00000462004.1_Intron|ANKMY1_ENST00000405523.3_Missense_Mutation_p.S39F|ANKMY1_ENST00000405002.1_Intron|DUSP28_ENST00000343217.2_5'Flank	NM_001282771.1	NP_001269700.1	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1								metal ion binding (GO:0046872)	p.S39F(1)		central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	30		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;1.03e-30)|all cancers(36;4.78e-28)|OV - Ovarian serous cystadenocarcinoma(60;1.45e-14)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;7.8e-06)|Lung(119;0.00271)|LUSC - Lung squamous cell carcinoma(224;0.01)|Colorectal(34;0.0101)|COAD - Colon adenocarcinoma(134;0.0476)		GTTCTTCAGGGACCCCGGCTC	0.677											OREG0015353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											45.0	53.0	50.0					2																	241496637		2203	4299	6502	SO:0001623	5_prime_UTR_variant	51281			AB034636	CCDS2535.1, CCDS2536.1, CCDS63184.1, CCDS63185.1, CCDS74681.1	2q37.3	2013-01-10			ENSG00000144504	ENSG00000144504		"""Zinc fingers, MYND-type"", ""Ankyrin repeat domain containing"""	20987	protein-coding gene	gene with protein product							Standard	XM_005247020		Approved	FLJ20499, ZMYND13	uc002vyz.1	Q9P2S6	OTTHUMG00000133355	ENST00000391987.1:c.-152C>T	2.37:g.241496637G>A		Somatic	2427	WXS	Illumina HiSeq	Phase_I	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000391987.1	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	G	10.26	1.302465	0.23736	.	.	ENSG00000144504	ENST00000373318;ENST00000406958;ENST00000361678;ENST00000403283;ENST00000401804;ENST00000405523;ENST00000411765	T;T;T;T;T;T	0.56776	2.84;3.53;2.16;2.4;0.44;2.14	2.48	-2.51	0.06365	.	.	.	.	.	T	0.23410	0.0566	N	0.08118	0	0.09310	N	0.999999	B;B;B	0.27791	0.119;0.119;0.189	B;B;B	0.23852	0.022;0.013;0.049	T	0.12656	-1.0539	9	0.49607	T	0.09	.	0.1302	0.00073	0.2761:0.1797:0.2797:0.2644	.	39;39;39	Q6GPI0;B5MBY4;Q9P2S6-2	.;.;.	F	39;39;39;118;39;39;39	ENSP00000362415:S39F;ENSP00000384555:S39F;ENSP00000355097:S39F;ENSP00000383968:S118F;ENSP00000385887:S39F;ENSP00000385635:S39F	ENSP00000355097:S39F	S	-	2	0	ANKMY1	241145310	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.873000	0.04214	-0.666000	0.05310	0.313000	0.20887	TCC		0.677	ANKMY1-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			NM_017844	
ATF7IP2	80063	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	10524764	10524764	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr16:10524764T>G	ENST00000396560.2	+	3	514	c.287T>G	c.(286-288)aTa>aGa	p.I96R	ATF7IP2_ENST00000324570.5_Missense_Mutation_p.I96R|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.I96R|ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.I96R	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	96					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.I96R(1)		large_intestine(3)	3						CAGAATTGCATAAAACCAGTA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											41.0	45.0	43.0					16																	10524764		2196	4299	6495	SO:0001583	missense	80063			AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.287T>G	16.37:g.10524764T>G	ENSP00000379808:p.Ile96Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	T	14.82	2.650853	0.47362	.	.	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.15	2.69	0.31865	.	1.040080	0.07640	N	0.930121	T	0.47801	0.1465	L	0.36672	1.1	0.09310	N	1	D;D	0.64830	0.994;0.962	P;P	0.62740	0.906;0.778	T	0.38950	-0.9637	10	0.62326	D	0.03	-3.8879	4.0965	0.09993	0.1806:0.099:0.0:0.7204	.	96;96	Q5U623-2;Q5U623	.;MCAF2_HUMAN	R	96	ENSP00000379807:I96R;ENSP00000379808:I96R;ENSP00000440791:I96R;ENSP00000348799:I96R;ENSP00000322811:I96R	ENSP00000322811:I96R	I	+	2	0	ATF7IP2	10432265	0.000000	0.05858	0.054000	0.19295	0.775000	0.43874	0.058000	0.14301	1.948000	0.56530	0.260000	0.18958	ATA		0.353	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1		NM_024997	
ATP10A	57194	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	25959134	25959134	+	Nonsense_Mutation	SNP	C	C	T	rs372456477		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr15:25959134C>T	ENST00000356865.6	-	10	2142	c.2031G>A	c.(2029-2031)tgG>tgA	p.W677*		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	677					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.W677*(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GCTCCGAGGCCCAGTTGTCCG	0.682																																																	1	Substitution - Nonsense(1)	kidney(1)						C	stop/TRP	0,4406		0,0,2203	25.0	27.0	27.0		2031	1.8	0.1	15		27	1,8597		0,1,4298	no	stop-gained	ATP10A	NM_024490.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		677/1500	25959134	1,13003	2203	4299	6502	SO:0001587	stop_gained	57194			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.2031G>A	15.37:g.25959134C>T	ENSP00000349325:p.Trp677*	Somatic		WXS	Illumina HiSeq	Phase_I	Q4G0S9|Q969I4	Nonsense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.281090	0.80692	0.0	1.16E-4	ENSG00000206190	ENST00000356865	.	.	.	3.77	1.82	0.25136	.	0.932679	0.09297	N	0.821422	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	-9.2291	8.7695	0.34724	0.0:0.7634:0.1514:0.0852	.	.	.	.	X	677	.	ENSP00000349325:W677X	W	-	3	0	ATP10A	23510227	0.000000	0.05858	0.091000	0.20842	0.003000	0.03518	0.425000	0.21346	0.373000	0.24621	-0.258000	0.10820	TGG		0.682	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1		NM_024490	
PCNXL4	64430	broad.mit.edu;ucsc.edu	37	14	60600702	60600703	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:60600702_60600703delGA	ENST00000406854.1	+	11	3836_3837	c.3282_3283delGA	c.(3280-3285)gggagafs	p.R1095fs	PCNXL4_ENST00000404681.2_Frame_Shift_Del_p.R1095fs|PCNXL4_ENST00000317623.4_Frame_Shift_Del_p.R861fs|PCNXL4_ENST00000406949.1_Intron|PCNXL4_ENST00000535349.1_3'UTR			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1095						integral component of membrane (GO:0016021)											TTTACACTGGGAGAGTGCTTAG	0.356																																																	0																																										SO:0001589	frameshift_variant	0			AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.3282_3283delGA	14.37:g.60600704_60600705delGA	ENSP00000384801:p.Arg1095fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8MXM2|Q9BQG8|Q9H9F2	Frame_Shift_Del	DEL	ENST00000406854.1	37																																																																																					0.356	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1		NM_022495	
C16orf78	123970	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	49407979	49407979	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr16:49407979G>A	ENST00000299191.3	+	1	246	c.129G>A	c.(127-129)ggG>ggA	p.G43G		NM_144602.2	NP_653203.1	Q8WTQ4	CP078_HUMAN	chromosome 16 open reading frame 78	43						nucleus (GO:0005634)		p.G43G(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|upper_aerodigestive_tract(1)	22						GGAGGCAGGGGAAGAAGAAAC	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											78.0	74.0	75.0					16																	49407979		2199	4300	6499	SO:0001819	synonymous_variant	123970			BC021181	CCDS10738.1	16q12.1	2008-02-05			ENSG00000166152	ENSG00000166152			28479	protein-coding gene	gene with protein product						12477932	Standard	NM_144602		Approved	MGC33367	uc002efr.3	Q8WTQ4	OTTHUMG00000133149	ENST00000299191.3:c.129G>A	16.37:g.49407979G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000299191.3	37	CCDS10738.1																																																																																				0.498	C16orf78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256846.1		NM_144602	
AAR2	25980	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	34828159	34828159	+	Silent	SNP	G	G	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr20:34828159G>C	ENST00000373932.3	+	2	715	c.369G>C	c.(367-369)ggG>ggC	p.G123G	AAR2_ENST00000320849.4_Silent_p.G123G|AAR2_ENST00000397286.3_Silent_p.G123G	NM_015511.3	NP_056326.2	Q9Y312	AAR2_HUMAN	AAR2 splicing factor homolog (S. cerevisiae)	123								p.G123G(1)									AGTTCCTGGGGCCTTACCCAT	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											96.0	96.0	96.0					20																	34828159		2203	4300	6503	SO:0001819	synonymous_variant	0				CCDS13273.1	20q11.23	2012-07-20	2012-07-20	2012-07-20	ENSG00000131043	ENSG00000131043			15886	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 4"""	C20orf4			Standard	NM_015511		Approved	bA234K24.2	uc002xfc.3	Q9Y312	OTTHUMG00000032380	ENST00000373932.3:c.369G>C	20.37:g.34828159G>C		Somatic		WXS	Illumina HiSeq	Phase_I	E1P5S7|Q9H4F9|Q9P1P3|Q9UFK9	Silent	SNP	ENST00000373932.3	37	CCDS13273.1																																																																																				0.582	AAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079001.2		NM_015511	
CA4	762	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	58234007	58234007	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:58234007C>T	ENST00000300900.4	+	3	298	c.199C>T	c.(199-201)Ctg>Ttg	p.L67L		NM_000717.3	NP_000708.1	P22748	CAH4_HUMAN	carbonic anhydrase IV	67					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|organ development (GO:0048513)|response to drug (GO:0042493)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|secretory granule membrane (GO:0030667)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.L67L(1)		kidney(1)|large_intestine(2)|lung(5)|ovary(1)	9	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.83e-12)|all cancers(12;6.83e-11)		Acetazolamide(DB00819)|Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Brinzolamide(DB01194)|Chlorothiazide(DB00880)|Cyclothiazide(DB00606)|Diclofenamide(DB01144)|Dorzolamide(DB00869)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Methazolamide(DB00703)|Methyclothiazide(DB00232)|Topiramate(DB00273)|Trichlormethiazide(DB01021)|Zonisamide(DB00909)	GGACAAAAAACTGGGACGCTT	0.567																																																	1	Substitution - coding silent(1)	kidney(1)											111.0	98.0	102.0					17																	58234007		2203	4300	6503	SO:0001819	synonymous_variant	762			L10955	CCDS11624.1	17q23.1	2012-08-21			ENSG00000167434	ENSG00000167434	4.2.1.1	"""Carbonic anhydrases"""	1375	protein-coding gene	gene with protein product		114760	"""retinitis pigmentosa 17 (autosomal dominant)"""	RP17		8325641	Standard	NM_000717		Approved	CAIV, Car4	uc002iym.4	P22748		ENST00000300900.4:c.199C>T	17.37:g.58234007C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DQA4|Q6FHI7	Silent	SNP	ENST00000300900.4	37	CCDS11624.1																																																																																				0.567	CA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449189.1		NM_000717	
CCDC155	147872	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	49897747	49897747	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr19:49897747C>T	ENST00000447857.3	+	3	263	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	20						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.R20W(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						CCTCCGGGAGCGGCCTGAGGA	0.607																																																	1	Substitution - Missense(1)	kidney(1)											70.0	74.0	73.0					19																	49897747		2085	4227	6312	SO:0001583	missense	147872				CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.58C>T	19.37:g.49897747C>T	ENSP00000404220:p.Arg20Trp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96MC3	Missense_Mutation	SNP	ENST00000447857.3	37	CCDS46140.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614557	0.28712	.	.	ENSG00000161609	ENST00000447857	T	0.32023	1.47	4.96	3.91	0.45181	.	0.284575	0.25944	N	0.027293	T	0.19565	0.0470	N	0.22421	0.69	0.21355	N	0.999717	B	0.02656	0.0	B	0.04013	0.001	T	0.11060	-1.0603	10	0.62326	D	0.03	-20.0934	8.5843	0.33649	0.0:0.895:0.0:0.105	.	20	Q8N6L0	CC155_HUMAN	W	20	ENSP00000404220:R20W	ENSP00000404220:R20W	R	+	1	2	CCDC155	54589559	0.874000	0.30092	0.976000	0.42696	0.052000	0.14988	1.451000	0.35145	2.465000	0.83290	0.462000	0.41574	CGG		0.607	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2		NM_144688	
CCDC53	51019	hgsc.bcm.edu;ucsc.edu	37	12	102433684	102433684	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:102433684delC	ENST00000240079.6	-	5	558	c.397delG	c.(397-399)gatfs	p.D133fs	CCDC53_ENST00000545679.1_Frame_Shift_Del_p.D132fs|CCDC53_ENST00000539515.1_5'UTR	NM_016053.2	NP_057137.1	Q9Y3C0	CCD53_HUMAN	coiled-coil domain containing 53	133						actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|WASH complex (GO:0071203)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						TATCTTGGATCCTTGGCTACA	0.398																																																	0													231.0	217.0	222.0					12																	102433684		1869	4120	5989	SO:0001589	frameshift_variant	51019			AF151874	CCDS44959.1, CCDS73512.1	12q23.3	2014-05-09			ENSG00000120860	ENSG00000120860			24256	protein-coding gene	gene with protein product						10810093, 20498093	Standard	XM_005268939		Approved	CGI-116	uc010svw.2	Q9Y3C0	OTTHUMG00000168187	ENST00000240079.6:c.397delG	12.37:g.102433684delC	ENSP00000240079:p.Asp133fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RC74|Q53FF0|Q6IAI4|Q96QK0	Frame_Shift_Del	DEL	ENST00000240079.6	37	CCDS44959.1																																																																																				0.398	CCDC53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398685.1		NM_016053	
CNTRL	11064	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	123900914	123900914	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr9:123900914A>T	ENST00000373855.1	+	16	2554	c.2294A>T	c.(2293-2295)gAg>gTg	p.E765V	CNTRL_ENST00000373850.1_Missense_Mutation_p.E213V|CNTRL_ENST00000373847.1_Missense_Mutation_p.E213V|CNTRL_ENST00000238341.5_Missense_Mutation_p.E765V			Q7Z7A1	CNTRL_HUMAN	centriolin	765					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)		p.E765V(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						GAAGAAAAGGAGCAAGAGAAC	0.418																																																	1	Substitution - Missense(1)	kidney(1)											101.0	103.0	103.0					9																	123900914		2203	4300	6503	SO:0001583	missense	0			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.2294A>T	9.37:g.123900914A>T	ENSP00000362962:p.Glu765Val	Somatic		WXS	Illumina HiSeq	Phase_I	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.668035	0.67814	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000373851;ENST00000373850;ENST00000373847	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	5.76	5.76	0.90799	.	.	.	.	.	T	0.40398	0.1115	L	0.27053	0.805	0.29549	N	0.851486	P;P;P	0.43477	0.808;0.773;0.664	B;B;B	0.41894	0.261;0.369;0.203	T	0.37842	-0.9688	9	0.40728	T	0.16	.	15.544	0.76081	1.0:0.0:0.0:0.0	.	765;765;765	B2RP65;F5GZN0;Q7Z7A1	.;.;CNTRL_HUMAN	V	765;765;765;247;213;213	ENSP00000362962:E765V;ENSP00000238341:E765V;ENSP00000362956:E213V;ENSP00000362953:E213V	ENSP00000238341:E765V	E	+	2	0	CNTRL	122940735	1.000000	0.71417	0.786000	0.31890	0.969000	0.65631	6.898000	0.75676	2.324000	0.78689	0.533000	0.62120	GAG		0.418	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1		NM_007018	
CLASP1	23332	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	122168512	122168512	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:122168512G>A	ENST00000263710.4	-	24	2743	c.2354C>T	c.(2353-2355)cCt>cTt	p.P785L	CLASP1_ENST00000541859.1_Missense_Mutation_p.P518L|CLASP1_ENST00000397587.3_Missense_Mutation_p.P757L|CLASP1_ENST00000409078.3_Missense_Mutation_p.P749L|CLASP1_ENST00000455322.2_Missense_Mutation_p.P749L|CLASP1_ENST00000541377.1_Missense_Mutation_p.P756L|CLASP1_ENST00000545861.1_Missense_Mutation_p.P525L	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	785	Interaction with microtubules, MAPRE1 and MAPRE3.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)	p.P785L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					CACAGAACCAGGTATTCTTCC	0.408																																																	1	Substitution - Missense(1)	kidney(1)											96.0	88.0	91.0					2																	122168512		1896	4127	6023	SO:0001583	missense	23332			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.2354C>T	2.37:g.122168512G>A	ENSP00000263710:p.Pro785Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	G	22.8	4.341585	0.81911	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861;ENST00000463621	T;T;T;T;T;T	0.49139	2.19;2.11;2.15;2.0;0.79;2.14	5.67	5.67	0.87782	Armadillo-type fold (1);	0.149785	0.64402	D	0.000007	T	0.43456	0.1248	L	0.58101	1.795	0.80722	D	1	P;P;P;P	0.44195	0.501;0.828;0.704;0.611	B;B;B;B	0.33620	0.058;0.167;0.053;0.118	T	0.45249	-0.9274	10	0.38643	T	0.18	-9.0619	17.9504	0.89051	0.0:0.0:1.0:0.0	.	749;757;756;785	E7EUA5;F5GWS0;B7ZLX3;Q7Z460	.;.;.;CLAP1_HUMAN	L	785;749;757;756;518;749;525;90	ENSP00000263710:P785L;ENSP00000389372:P749L;ENSP00000380717:P757L;ENSP00000441625:P756L;ENSP00000441770:P518L;ENSP00000386442:P749L	ENSP00000263710:P785L	P	-	2	0	CLASP1	121884982	1.000000	0.71417	0.934000	0.37439	0.996000	0.88848	9.302000	0.96175	2.680000	0.91292	0.563000	0.77884	CCT		0.408	CLASP1-201	KNOWN	basic	protein_coding	protein_coding			NM_015282	
CLCN2	1181	broad.mit.edu;ucsc.edu	37	3	184070571	184070571	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:184070571A>G	ENST00000265593.4	-	19	2342	c.2171T>C	c.(2170-2172)cTc>cCc	p.L724P	CLCN2_ENST00000457512.1_Missense_Mutation_p.L724P|CLCN2_ENST00000434054.2_Missense_Mutation_p.L680P|CLCN2_ENST00000423355.2_3'UTR|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000344937.7_Missense_Mutation_p.L707P|CLCN2_ENST00000475279.1_5'Flank	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	724					cell differentiation involved in salivary gland development (GO:0060689)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|retina development in camera-type eye (GO:0060041)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|voltage-gated chloride channel activity (GO:0005247)	p.L724P(1)		breast(2)|central_nervous_system(4)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	27	all_cancers(143;6.66e-11)|Ovarian(172;0.0339)		Epithelial(37;2.22e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Lubiprostone(DB01046)	GAGGCTCCGGAGGGCGATGCC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											30.0	30.0	30.0					3																	184070571		2202	4299	6501	SO:0001583	missense	1181			S77770	CCDS3263.1, CCDS54690.1, CCDS54691.1, CCDS54692.1	3q27.1	2013-09-19	2012-02-23		ENSG00000114859	ENSG00000114859		"""Ion channels / Chloride channels : Voltage-sensitive"""	2020	protein-coding gene	gene with protein product		600570	"""chloride channel 2"""			7795595	Standard	NM_004366		Approved	CLC2, EJM6, ClC-2	uc003foi.4	P51788	OTTHUMG00000156747	ENST00000265593.4:c.2171T>C	3.37:g.184070571A>G	ENSP00000265593:p.Leu724Pro	Somatic		WXS	Illumina GAIIx	Phase_I	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	37	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	a	14.39	2.522614	0.44866	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.85773	-1.98;-1.93;-2.03;-1.98	5.4	5.4	0.78164	.	0.485814	0.22598	N	0.057983	D	0.87188	0.6115	M	0.62723	1.935	0.80722	D	1	P;P;P;P;P	0.40553	0.721;0.721;0.676;0.721;0.548	P;P;P;P;B	0.49421	0.486;0.486;0.61;0.486;0.406	D	0.85312	0.1079	10	0.31617	T	0.26	-28.0872	13.001	0.58676	1.0:0.0:0.0:0.0	.	680;724;707;724;680	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	P	724;707;680;724	ENSP00000265593:L724P;ENSP00000345056:L707P;ENSP00000400425:L680P;ENSP00000391928:L724P	ENSP00000265593:L724P	L	-	2	0	CLCN2	185553265	1.000000	0.71417	0.998000	0.56505	0.403000	0.30841	6.806000	0.75195	2.052000	0.61016	0.374000	0.22700	CTC		0.602	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			
CNGA1	1259	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	47944154	47944154	+	Missense_Mutation	SNP	T	T	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr4:47944154T>A	ENST00000514170.1	-	9	780	c.461A>T	c.(460-462)gAa>gTa	p.E154V	CNGA1_ENST00000402813.3_Missense_Mutation_p.E223V|CNGA1_ENST00000544810.1_Missense_Mutation_p.E154V|CNGA1_ENST00000358519.4_Missense_Mutation_p.E154V|CNGA1_ENST00000420489.2_Missense_Mutation_p.E154V			P29973	CNGA1_HUMAN	cyclic nucleotide gated channel alpha 1	154					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.E154V(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|urinary_tract(1)	28						AACCACAACTTCTTTCTTCTC	0.383																																																	1	Substitution - Missense(1)	kidney(1)											101.0	95.0	97.0					4																	47944154		1836	4093	5929	SO:0001583	missense	1259			M84741	CCDS43226.1, CCDS47050.1	4p12	2013-02-14				ENSG00000198515		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2148	protein-coding gene	gene with protein product		123825		CNCG1, CNCG		7683629, 16382102	Standard	NM_000087		Approved	RCNC1, RCNCa, CNG1, RP49	uc003gxu.3	P29973		ENST00000514170.1:c.461A>T	4.37:g.47944154T>A	ENSP00000426862:p.Glu154Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7K6|J3KPZ2|Q16279|Q16485|Q4W5E3	Missense_Mutation	SNP	ENST00000514170.1	37	CCDS43226.1	.	.	.	.	.	.	.	.	.	.	T	17.75	3.466123	0.63625	.	.	ENSG00000198515	ENST00000402813;ENST00000514170;ENST00000544810;ENST00000358519;ENST00000420489	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.78	5.78	0.91487	.	0.153488	0.56097	D	0.000023	T	0.50633	0.1627	M	0.79011	2.435	0.53005	D	0.999966	D;D	0.71674	0.998;0.981	P;P	0.56343	0.796;0.69	T	0.49485	-0.8935	10	0.30854	T	0.27	.	16.1084	0.81241	0.0:0.0:0.0:1.0	.	154;154	Q4W5E3;P29973	.;CNGA1_HUMAN	V	223;154;154;154;154	ENSP00000384264:E223V;ENSP00000426862:E154V;ENSP00000443401:E154V;ENSP00000351320:E154V;ENSP00000389881:E154V	ENSP00000351320:E154V	E	-	2	0	CNGA1	47638911	1.000000	0.71417	0.998000	0.56505	0.127000	0.20565	5.903000	0.69877	2.207000	0.71202	0.460000	0.39030	GAA		0.383	CNGA1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372070.2		NM_000087	
COPA	1314	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	160310032	160310032	+	Silent	SNP	C	C	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:160310032C>A	ENST00000241704.7	-	2	322	c.93G>T	c.(91-93)ggG>ggT	p.G31G	COPA_ENST00000368069.3_Silent_p.G31G	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	31					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)	p.G31G(2)		central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ACTGGATGACCCCATTATGTA	0.398																																																	2	Substitution - coding silent(2)	kidney(2)											79.0	81.0	80.0					1																	160310032		2203	4300	6503	SO:0001819	synonymous_variant	1314			U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.93G>T	1.37:g.160310032C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T201|Q8IXZ9	Silent	SNP	ENST00000241704.7	37	CCDS1202.1																																																																																				0.398	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1		NM_004371	
CPSF3	51692	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	9580730	9580730	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:9580730G>A	ENST00000238112.3	+	8	1077	c.871G>A	c.(871-873)Gac>Aac	p.D291N	CPSF3_ENST00000460593.1_Missense_Mutation_p.D254N	NM_016207.3	NP_057291.1	Q9UKF6	CPSF3_HUMAN	cleavage and polyadenylation specific factor 3, 73kDa	291					gene expression (GO:0010467)|histone mRNA 3'-end processing (GO:0006398)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)|ribonucleoprotein complex (GO:0030529)	5'-3' exonuclease activity (GO:0008409)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)	p.D291N(1)		NS(1)|breast(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;2.39e-25)|all_epithelial(98;8.75e-19)|Lung NSC(108;2.38e-06)|Ovarian(717;0.0308)		all cancers(51;2.2e-40)|Epithelial(75;6.71e-35)|OV - Ovarian serous cystadenocarcinoma(76;4.35e-21)|STAD - Stomach adenocarcinoma(1183;0.00644)		TGCCATGAATGACAAAATCCG	0.388																																					Colon(194;1259 2048 3845 5218 19985)												1	Substitution - Missense(1)	kidney(1)											186.0	162.0	170.0					2																	9580730		2203	4300	6503	SO:0001583	missense	51692			AF171877	CCDS1664.1	2p25.1	2009-01-06	2002-08-29		ENSG00000119203	ENSG00000119203			2326	protein-coding gene	gene with protein product		606029	"""cleavage and polyadenylation specific factor 3, 73kD subunit"""			8929409	Standard	NM_016207		Approved	CPSF-73, CPSF73, YSH1	uc002qzo.2	Q9UKF6	OTTHUMG00000090415	ENST00000238112.3:c.871G>A	2.37:g.9580730G>A	ENSP00000238112:p.Asp291Asn	Somatic		WXS	Illumina HiSeq	Phase_I	O14769|Q53RS2|Q96F36	Missense_Mutation	SNP	ENST00000238112.3	37	CCDS1664.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472765	0.84640	.	.	ENSG00000119203	ENST00000238112;ENST00000540142;ENST00000427001;ENST00000460593	T;T	0.49139	0.79;0.79	5.36	5.36	0.76844	Beta-Casp domain (1);	0.000000	0.85682	D	0.000000	T	0.62490	0.2432	M	0.75447	2.3	0.80722	D	1	B;B	0.33212	0.402;0.075	B;P	0.44673	0.213;0.457	T	0.63829	-0.6548	10	0.56958	D	0.05	-27.3728	19.5055	0.95113	0.0:0.0:1.0:0.0	.	291;291	E7ER23;Q9UKF6	.;CPSF3_HUMAN	N	291;13;291;254	ENSP00000238112:D291N;ENSP00000418957:D254N	ENSP00000238112:D291N	D	+	1	0	CPSF3	9498181	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	9.747000	0.98863	2.672000	0.90937	0.551000	0.68910	GAC		0.388	CPSF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206843.1		NM_016207	
CUL7	9820	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	43020004	43020004	+	Missense_Mutation	SNP	A	A	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr6:43020004A>C	ENST00000265348.3	-	2	608	c.523T>G	c.(523-525)Tat>Gat	p.Y175D	CUL7_ENST00000535468.1_Missense_Mutation_p.Y227D			Q14999	CUL7_HUMAN	cullin 7	175					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)		p.Y175D(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CGAATCTGATAATCAGGACTA	0.572																																																	1	Substitution - Missense(1)	kidney(1)											70.0	64.0	66.0					6																	43020004		2203	4300	6503	SO:0001583	missense	9820			BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.523T>G	6.37:g.43020004A>C	ENSP00000265348:p.Tyr175Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.088524	0.55968	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.63417	0.04;-0.04	5.6	3.17	0.36434	Armadillo-like helical (1);	0.469770	0.23560	N	0.046864	T	0.26919	0.0659	N	0.08118	0	0.80722	D	1	B;D	0.56035	0.1;0.974	B;P	0.49752	0.026;0.621	T	0.37957	-0.9683	10	0.62326	D	0.03	-14.822	0.6426	0.00813	0.3552:0.1487:0.1191:0.3769	.	227;175	F5H0L1;Q14999	.;CUL7_HUMAN	D	175;227	ENSP00000265348:Y175D;ENSP00000438788:Y227D	ENSP00000265348:Y175D	Y	-	1	0	CUL7	43127982	0.808000	0.29022	0.993000	0.49108	0.996000	0.88848	1.092000	0.30927	0.902000	0.36520	0.459000	0.35465	TAT		0.572	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1		NM_014780	
CYP2D6	1565	hgsc.bcm.edu	37	22	42524795	42524795	+	Silent	SNP	A	A	G	rs28371713	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr22:42524795A>G	ENST00000360608.5	-	4	771	c.657T>C	c.(655-657)ttT>ttC	p.F219F	NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000439129.1_RNA|CYP2D6_ENST00000389970.3_Silent_p.F219F|CYP2D6_ENST00000359033.4_Silent_p.F168F	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	219					alkaloid catabolic process (GO:0009822)|alkaloid metabolic process (GO:0009820)|coumarin metabolic process (GO:0009804)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|heterocycle metabolic process (GO:0046483)|isoquinoline alkaloid metabolic process (GO:0033076)|monoterpenoid metabolic process (GO:0016098)|negative regulation of binding (GO:0051100)|negative regulation of cellular organofluorine metabolic process (GO:0090350)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(4)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21					Abiraterone(DB05812)|Acebutolol(DB01193)|Acetaminophen(DB00316)|Ajmaline(DB01426)|Almotriptan(DB00918)|Alogliptin(DB06203)|Alprenolol(DB00866)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amoxapine(DB00543)|Amphetamine(DB00182)|Amprenavir(DB00701)|Amsacrine(DB00276)|Antipyrine(DB01435)|Aprindine(DB01429)|Arformoterol(DB01274)|Aripiprazole(DB01238)|Artemether(DB06697)|Asenapine(DB06216)|Astemizole(DB00637)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzatropine(DB00245)|Benzyl alcohol(DB06770)|Bepridil(DB01244)|Betaxolol(DB00195)|Bicalutamide(DB01128)|Biperiden(DB00810)|Bisoprolol(DB00612)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Buspirone(DB00490)|Caffeine(DB00201)|Captopril(DB01197)|Carbinoxamine(DB00748)|Carteolol(DB00521)|Carvedilol(DB01136)|Celecoxib(DB00482)|Cephalexin(DB00567)|Cevimeline(DB00185)|Chlordiazepoxide(DB00475)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cholecalciferol(DB00169)|Ciclesonide(DB01410)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Cisapride(DB00604)|Citalopram(DB00215)|Clemastine(DB00283)|Clevidipine(DB04920)|Clomipramine(DB01242)|Clonidine(DB00575)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Codeine(DB00318)|Cyclobenzaprine(DB00924)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Darifenacin(DB00496)|Debrisoquin(DB04840)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Dihydrocodeine(DB01551)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dolasetron(DB00757)|Domperidone(DB01184)|Donepezil(DB00843)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronedarone(DB04855)|Duloxetine(DB00476)|Efavirenz(DB00625)|Eletriptan(DB00216)|Encainide(DB01228)|Enzalutamide(DB08899)|Epinastine(DB00751)|Erlotinib(DB00530)|Escitalopram(DB01175)|Ethylmorphine(DB01466)|Etoricoxib(DB01628)|Felodipine(DB01023)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fingolimod(DB08868)|Flecainide(DB01195)|Flunarizine(DB04841)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Galantamine(DB00674)|Gefitinib(DB00317)|Glutethimide(DB01437)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Halothane(DB01159)|Histamine Phosphate(DB00667)|Hydrocodone(DB00956)|Hydromorphone(DB00327)|Hydroxychloroquine(DB01611)|Hydroxyurea(DB01005)|Hydroxyzine(DB00557)|Idarubicin(DB01177)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Ipratropium bromide(DB00332)|Irbesartan(DB01029)|Isoniazid(DB00951)|Itraconazole(DB01167)|Ketoconazole(DB01026)|L-DOPA(DB01235)|Labetalol(DB00598)|Lansoprazole(DB00448)|Lercanidipine(DB00528)|Levomilnacipran(DB08918)|Lidocaine(DB00281)|Lisuride(DB00589)|Lomustine(DB01206)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Lovastatin(DB00227)|Lumefantrine(DB06708)|Maprotiline(DB00934)|Mefloquine(DB00358)|Mepyramine(DB06691)|Mequitazine(DB01071)|Mesoridazine(DB00933)|Methadone(DB00333)|Methamphetamine(DB01577)|Methazolamide(DB00703)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxyflurane(DB01028)|Methylnaltrexone(DB06800)|Methylphenidate(DB00422)|Methyprylon(DB01107)|Metoclopramide(DB01233)|Metoprolol(DB00264)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Midodrine(DB00211)|Mifepristone(DB00834)|Minaprine(DB00805)|Mirabegron(DB08893)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Morphine(DB00295)|Nateglinide(DB00731)|Nebivolol(DB04861)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niacin(DB00627)|Nicardipine(DB00622)|Nicergoline(DB00699)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nitrofural(DB00336)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxamniquine(DB01096)|Oxprenolol(DB01580)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Oxymorphone(DB01192)|Paliperidone(DB01267)|Palonosetron(DB00377)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Pergolide(DB01186)|Perhexiline(DB01074)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenformin(DB00914)|Phentermine(DB00191)|Pimozide(DB01100)|Pindolol(DB00960)|Pioglitazone(DB01132)|Piperazine(DB00592)|Pipotiazine(DB01621)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Primaquine(DB01087)|Procainamide(DB01035)|Prochlorperazine(DB00433)|Progesterone(DB00396)|Proguanil(DB01131)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Pyrimethamine(DB00205)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ranitidine(DB00863)|Ranolazine(DB00243)|Reboxetine(DB00234)|Remoxipride(DB00409)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivastigmine(DB00989)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertindole(DB06144)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tamsulosin(DB00706)|Tapentadol(DB06204)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Terbinafine(DB00857)|Tetrabenazine(DB04844)|Theophylline(DB00277)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Timolol(DB00373)|Tiotropium(DB01409)|Tipranavir(DB00932)|Tolterodine(DB01036)|Trabectedin(DB05109)|Tramadol(DB00193)|Tranylcypromine(DB00752)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Trospium(DB00209)|Vemurafenib(DB08881)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vilazodone(DB06684)|Vinblastine(DB00570)|Vinorelbine(DB00361)|Yohimbine(DB01392)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CCTCGCGCAGAAAGCCCGACT	0.667																																																	0													34.0	28.0	30.0					22																	42524795		2199	4299	6498	SO:0001819	synonymous_variant	1565			M20403	CCDS33657.1, CCDS46721.1	22q13.1	2014-09-17	2003-01-14		ENSG00000100197	ENSG00000100197		"""Cytochrome P450s"""	2625	protein-coding gene	gene with protein product		124030	"""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolizing), polypeptide 6"", ""cytochrome P450, family 2, subfamily D, polypeptide 7 pseudogene 2"", ""cytochrome P450, subfamily II (debrisoquine, sparteine, etc., -metabolising), polypeptide 7 pseudogene 2"", ""cytochrome P450, family 2, subfamily D, polypeptide 8 pseudogene 2"", ""cytochrome P450, subfamily IID (debrisoquine, sparteine, etc., -metabolising), polypeptide 8 pseudogene 2"""	CYP2DL1, CYP2D7P2, CYP2D7BP, CYP2D8P2, CYP2D7AP		8449513	Standard	NM_000106		Approved	CPD6, P450-DB1, CYP2D, P450C2D	uc003bce.3	P10635	OTTHUMG00000150918	ENST00000360608.5:c.657T>C	22.37:g.42524795A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Silent	SNP	ENST00000360608.5	37	CCDS46721.1																																																																																				0.667	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			
DDX53	168400	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	23019821	23019821	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:23019821C>T	ENST00000327968.5	+	1	1735	c.1647C>T	c.(1645-1647)gaC>gaT	p.D549D	RP11-40F8.2_ENST00000455399.1_lincRNA	NM_182699.3	NP_874358.2	Q86TM3	DDX53_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 53	549	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|RNA binding (GO:0003723)	p.D549D(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	35						GGAATATTGACGTATATGTAC	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											121.0	112.0	115.0					X																	23019821		2203	4300	6503	SO:0001819	synonymous_variant	168400			AY039237	CCDS35214.1	Xp22.13	2009-03-25			ENSG00000184735	ENSG00000184735		"""DEAD-boxes"""	20083	protein-coding gene	gene with protein product	"""cancer associated gene"", ""cancer/testis antigen 26"""						Standard	NM_182699		Approved	CAGE, CT26	uc004daj.3	Q86TM3	OTTHUMG00000021248	ENST00000327968.5:c.1647C>T	X.37:g.23019821C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q0D2N2|Q6NVV4	Silent	SNP	ENST00000327968.5	37	CCDS35214.1																																																																																				0.388	DDX53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056043.1		NM_182699	
DCAF12L1	139170	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	125686496	125686496	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:125686496G>A	ENST00000371126.1	-	1	338	c.96C>T	c.(94-96)gaC>gaT	p.D32D		NM_178470.4	NP_848565.2	Q5VU92	DC121_HUMAN	DDB1 and CUL4 associated factor 12-like 1	32								p.D32D(1)		breast(1)|central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(39)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68						GCCCCTCACCGTCCGCTGCCG	0.697																																																	1	Substitution - coding silent(1)	kidney(1)											17.0	22.0	20.0					X																	125686496		2017	3976	5993	SO:0001819	synonymous_variant	139170			BC035674	CCDS14610.1	Xq25	2013-01-09	2009-07-17	2009-07-17	ENSG00000198889	ENSG00000198889		"""WD repeat domain containing"""	29395	protein-coding gene	gene with protein product			"""WD repeat domain 40B"""	WDR40B		12477932	Standard	NM_178470		Approved	KIAA1892L	uc004eul.3	Q5VU92	OTTHUMG00000022353	ENST00000371126.1:c.96C>T	X.37:g.125686496G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IYK3	Silent	SNP	ENST00000371126.1	37	CCDS14610.1																																																																																				0.697	DCAF12L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058186.1		NM_178470	
DENND5B	160518	hgsc.bcm.edu;ucsc.edu	37	12	31540603	31540603	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:31540603delA	ENST00000389082.5	-	21	4023	c.3759delT	c.(3757-3759)attfs	p.I1253fs	DENND5B_ENST00000536562.1_Frame_Shift_Del_p.I1288fs|DENND5B_ENST00000306833.6_Frame_Shift_Del_p.I1288fs	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	1253	RUN 2. {ECO:0000255|PROSITE- ProRule:PRU00178}.				positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TGGTCTGCAGAATTCGGATAA	0.483																																																	0													108.0	101.0	103.0					12																	31540603		1982	4150	6132	SO:0001589	frameshift_variant	160518			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.3759delT	12.37:g.31540603delA	ENSP00000373734:p.Ile1253fs	Somatic		WXS	Illumina HiSeq	Phase_I	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Frame_Shift_Del	DEL	ENST00000389082.5	37	CCDS44857.1																																																																																				0.483	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1		NM_144973	
DHX37	57647	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	125438720	125438720	+	Missense_Mutation	SNP	T	T	C	rs199731932		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:125438720T>C	ENST00000308736.2	-	19	2589	c.2491A>G	c.(2491-2493)Agc>Ggc	p.S831G	DHX37_ENST00000544745.1_Missense_Mutation_p.S618G	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	831							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.S831G(1)		breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		GCCCGCTTGCTCTTCAGCCTG	0.662													T|||	1	0.000199681	0.0	0.0	5008	,	,		16419	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											32.0	36.0	35.0					12																	125438720		2203	4300	6503	SO:0001583	missense	57647			AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2491A>G	12.37:g.125438720T>C	ENSP00000311135:p.Ser831Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BUI7|Q9P211	Missense_Mutation	SNP	ENST00000308736.2	37	CCDS9261.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	T	5.089	0.202025	0.09652	.	.	ENSG00000150990	ENST00000308736;ENST00000544745	T;T	0.02737	4.18;4.18	5.33	1.31	0.21738	Helicase-associated domain (2);	0.527560	0.22692	N	0.056809	T	0.00967	0.0032	N	0.00666	-1.275	0.19945	N	0.999947	B	0.02656	0.0	B	0.04013	0.001	T	0.49031	-0.8981	10	0.18276	T	0.48	-25.4861	9.4325	0.38620	0.0:0.7106:0.0:0.2894	.	831	Q8IY37	DHX37_HUMAN	G	831;618	ENSP00000311135:S831G;ENSP00000439009:S618G	ENSP00000311135:S831G	S	-	1	0	DHX37	124004673	0.432000	0.25554	0.048000	0.18961	0.735000	0.41995	0.757000	0.26433	0.000000	0.14550	-0.640000	0.03970	AGC		0.662	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_032656	
DMXL1	1657	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	118560454	118560454	+	Silent	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr5:118560454T>C	ENST00000311085.8	+	37	8345	c.8265T>C	c.(8263-8265)acT>acC	p.T2755T	DMXL1_ENST00000505312.1_3'UTR|DMXL1_ENST00000539542.1_Silent_p.T2776T	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2755								p.T2755T(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CTCATCCAACTCTTCCTTACT	0.249																																																	1	Substitution - coding silent(1)	kidney(1)											59.0	63.0	62.0					5																	118560454		2176	4245	6421	SO:0001819	synonymous_variant	1657			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.8265T>C	5.37:g.118560454T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000311085.8	37	CCDS4125.1																																																																																				0.249	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1		NM_005509	
DNAH9	1770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	11701032	11701032	+	Missense_Mutation	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:11701032T>C	ENST00000262442.4	+	43	8410	c.8342T>C	c.(8341-8343)cTg>cCg	p.L2781P	DNAH9_ENST00000454412.2_Missense_Mutation_p.L2781P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2781					cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.L2781P(2)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACCCAGACTCTGGTGGAGGCC	0.498																																																	2	Substitution - Missense(2)	lung(1)|kidney(1)											179.0	139.0	152.0					17																	11701032		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.8342T>C	17.37:g.11701032T>C	ENSP00000262442:p.Leu2781Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	T	16.57	3.161137	0.57368	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.33654	1.44;1.4	5.68	5.68	0.88126	.	0.178045	0.38720	N	0.001593	T	0.68604	0.3019	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76898	-0.2789	10	0.87932	D	0	.	15.9259	0.79615	0.0:0.0:0.0:1.0	.	2781	Q9NYC9	DYH9_HUMAN	P	2781;2781;1363	ENSP00000262442:L2781P;ENSP00000414874:L2781P	ENSP00000262442:L2781P	L	+	2	0	DNAH9	11641757	1.000000	0.71417	0.999000	0.59377	0.209000	0.24338	7.988000	0.88194	2.158000	0.67659	0.528000	0.53228	CTG		0.498	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
DNAH9	1770	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	11835416	11835416	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:11835416G>A	ENST00000262442.4	+	64	12259	c.12191G>A	c.(12190-12192)aGa>aAa	p.R4064K	DNAH9_ENST00000608377.1_Missense_Mutation_p.R376K|DNAH9_ENST00000396001.2_3'UTR|DNAH9_ENST00000454412.2_Missense_Mutation_p.R3988K	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	4064	AAA 6. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.R4064K(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GTGGCAGAAAGACGAAAATTT	0.493																																																	1	Substitution - Missense(1)	kidney(1)											243.0	218.0	227.0					17																	11835416		2203	4300	6503	SO:0001583	missense	1770			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.12191G>A	17.37:g.11835416G>A	ENSP00000262442:p.Arg4064Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.295314	0.81025	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703;ENST00000396001	T;T;T	0.28666	1.6;1.6;1.6	5.09	5.09	0.68999	Dynein heavy chain (1);	0.061922	0.85682	D	0.000000	T	0.78168	0.4241	H	0.99946	5.015	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89531	0.3785	10	0.87932	D	0	.	18.6962	0.91601	0.0:0.0:1.0:0.0	.	4064	Q9NYC9	DYH9_HUMAN	K	4064;3988;2570;376	ENSP00000262442:R4064K;ENSP00000414874:R3988K;ENSP00000379323:R376K	ENSP00000262442:R4064K	R	+	2	0	DNAH9	11776141	1.000000	0.71417	0.987000	0.45799	0.105000	0.19272	9.601000	0.98297	2.633000	0.89246	0.655000	0.94253	AGA		0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2		NM_001372	
ECHS1	1892	broad.mit.edu;hgsc.bcm.edu	37	10	135184121	135184121	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr10:135184121C>T	ENST00000368547.3	-	2	584	c.229G>A	c.(229-231)Gag>Aag	p.E77K	MIR3944_ENST00000581277.1_RNA	NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	77					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)	p.E77K(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		GGGTCCTCCTCGAAGGTCTTC	0.617																																					GBM(132;1720 1771 5373 10277 21402)												1	Substitution - Missense(1)	kidney(1)											63.0	53.0	57.0					10																	135184121		2200	4299	6499	SO:0001583	missense	1892				CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"""enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"""			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.229G>A	10.37:g.135184121C>T	ENSP00000357535:p.Glu77Lys	Somatic		WXS	Illumina HiSeq	Phase_I	O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	37	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729409	0.48833	.	.	ENSG00000127884	ENST00000368547	T	0.68903	-0.36	5.76	1.45	0.22620	Crotonase, core (1);	0.189811	0.53938	D	0.000046	T	0.66665	0.2812	M	0.67397	2.05	0.36065	D	0.841749	P	0.39216	0.664	B	0.38500	0.275	T	0.77696	-0.2491	10	0.87932	D	0	.	18.0901	0.89472	0.0:0.5351:0.4649:0.0	.	77	P30084	ECHM_HUMAN	K	77	ENSP00000357535:E77K	ENSP00000357535:E77K	E	-	1	0	ECHS1	135034111	0.999000	0.42202	0.007000	0.13788	0.001000	0.01503	3.537000	0.53590	0.357000	0.24183	-0.780000	0.03373	GAG		0.617	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			
EHD1	10938	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64645859	64645859	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr11:64645859C>T	ENST00000320631.3	-	1	332	c.78G>A	c.(76-78)cgG>cgA	p.R26R	EHD1_ENST00000359393.2_Silent_p.R26R	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	26					blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)	p.R26R(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						CGTACAGCTGCCGCAGCCCCT	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											50.0	47.0	48.0					11																	64645859		2201	4296	6497	SO:0001819	synonymous_variant	10938			AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"""EF-hand domain containing"""	3242	protein-coding gene	gene with protein product	"""testilin"""	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.78G>A	11.37:g.64645859C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O14611|Q2M3Q4|Q9UNR3	Silent	SNP	ENST00000320631.3	37	CCDS8084.1																																																																																				0.647	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2		NM_006795	
EIF3B	8662	broad.mit.edu;ucsc.edu	37	7	2404084	2404084	+	Silent	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr7:2404084A>G	ENST00000360876.4	+	6	1133	c.1077A>G	c.(1075-1077)ctA>ctG	p.L359L	EIF3B_ENST00000397011.2_Silent_p.L359L	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B									p.L359L(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		GCATTGCTCTATGGGGGGGAG	0.478																																																	1	Substitution - coding silent(1)	kidney(1)											104.0	108.0	106.0					7																	2404084		2203	4300	6503	SO:0001819	synonymous_variant	8662			U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"""RNA binding motif (RRM) containing"""	3280	protein-coding gene	gene with protein product		603917	"""eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"""	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1077A>G	7.37:g.2404084A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000360876.4	37	CCDS5332.1																																																																																				0.478	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1			
EPB41L3	23136	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	5406847	5406847	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr18:5406847A>T	ENST00000341928.2	-	16	2618	c.2278T>A	c.(2278-2280)Tcc>Acc	p.S760T	EPB41L3_ENST00000542652.2_5'UTR|EPB41L3_ENST00000544123.1_Missense_Mutation_p.S591T|EPB41L3_ENST00000427684.2_Missense_Mutation_p.S32T|EPB41L3_ENST00000400111.3_Missense_Mutation_p.S579T|EPB41L3_ENST00000342933.3_Missense_Mutation_p.S760T|EPB41L3_ENST00000540638.2_Missense_Mutation_p.S579T|EPB41L3_ENST00000542146.1_Missense_Mutation_p.S32T	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	760	Spectrin--actin-binding. {ECO:0000255}.				apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.S760T(1)		breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GGGGAGGTGGAAAGCCTCTTC	0.522																																																	1	Substitution - Missense(1)	kidney(1)											172.0	138.0	149.0					18																	5406847		2203	4300	6503	SO:0001583	missense	23136			AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.2278T>A	18.37:g.5406847A>T	ENSP00000343158:p.Ser760Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166782	0.78339	.	.	ENSG00000082397	ENST00000341928;ENST00000540638;ENST00000544123;ENST00000545076;ENST00000427684;ENST00000542146;ENST00000342933;ENST00000400111	D;D;T;T;D;D	0.85484	-1.69;-1.99;-0.28;-0.2;-1.69;-1.91	5.78	5.78	0.91487	SAB (1);	0.098330	0.64402	D	0.000001	D	0.88392	0.6424	L	0.43152	1.355	0.80722	D	1	D;D;D;P;D;P;D;D	0.89917	0.982;0.994;0.993;0.793;0.992;0.801;0.996;1.0	D;D;D;P;D;B;D;D	0.87578	0.961;0.991;0.99;0.78;0.987;0.337;0.985;0.998	D	0.84579	0.0660	10	0.11182	T	0.66	.	16.1138	0.81283	1.0:0.0:0.0:0.0	.	591;32;32;152;470;579;760;32	F5GX05;E7EUF8;F5H7W5;B7Z8M8;A8K968;Q9Y2J2-2;Q9Y2J2;B3KT50	.;.;.;.;.;.;E41L3_HUMAN;.	T	760;470;591;470;32;32;760;579	ENSP00000343158:S760T;ENSP00000441174:S591T;ENSP00000392195:S32T;ENSP00000442233:S32T;ENSP00000341138:S760T;ENSP00000382981:S579T	ENSP00000343158:S760T	S	-	1	0	EPB41L3	5396847	1.000000	0.71417	0.983000	0.44433	0.640000	0.38277	8.962000	0.93254	2.220000	0.72140	0.533000	0.62120	TCC		0.522	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1		NM_012307	
ERCC5	2073	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	103528030	103528030	+	Missense_Mutation	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr13:103528030T>C	ENST00000355739.4	+	15	4761	c.3338T>C	c.(3337-3339)gTa>gCa	p.V1113A	ERCC5_ENST00000472247.1_3'UTR|ERCC5_ENST00000375954.1_Missense_Mutation_p.V346A	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	1113					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)	p.V1113A(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTAATGAATGTACAAAGGAGA	0.468			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																														yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	1	Substitution - Missense(1)	kidney(1)											46.0	47.0	47.0					13																	103528030		2203	4300	6503	SO:0001583	missense	2073	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.3338T>C	13.37:g.103528030T>C	ENSP00000347978:p.Val1113Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	T	5.826	0.336718	0.11013	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.06768	3.56;3.26	4.76	-2.3	0.06785	.	2.080600	0.01879	N	0.037730	T	0.06554	0.0168	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.38200	-0.9672	10	0.07482	T	0.82	1.398	7.9319	0.29907	0.0:0.4729:0.1609:0.3661	.	1113	P28715	ERCC5_HUMAN	A	1538;1113;945;346	ENSP00000347978:V1113A;ENSP00000365121:V346A	ENSP00000347978:V1113A	V	+	2	0	ERCC5	102326031	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.766000	0.04725	-0.361000	0.08125	-0.256000	0.11100	GTA		0.468	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			
ETAA1	54465	hgsc.bcm.edu;ucsc.edu	37	2	67637078	67637096	+	Frame_Shift_Del	DEL	GAAATTCAGAGAAAAAGAC	GAAATTCAGAGAAAAAGAC	-	rs561747318	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	GAAATTCAGAGAAAAAGAC	GAAATTCAGAGAAAAAGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:67637078_67637096delGAAATTCAGAGAAAAAGAC	ENST00000272342.5	+	6	2819_2837	c.2689_2707delGAAATTCAGAGAAAAAGAC	c.(2689-2709)gaaattcagagaaaaagacaafs	p.EIQRKRQ897fs		NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	897						cytoplasm (GO:0005737)		p.R902S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						TTCTCCTGAAGAAATTCAGAGAAAAAGACAAGAAGCACT	0.347																																																	1	Substitution - Missense(1)	ovary(1)																																								SO:0001589	frameshift_variant	54465			AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.2689_2707delGAAATTCAGAGAAAAAGAC	2.37:g.67637078_67637096delGAAATTCAGAGAAAAAGAC	ENSP00000272342:p.Glu897fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q05BT7|Q53SC4	Frame_Shift_Del	DEL	ENST00000272342.5	37	CCDS1882.1																																																																																				0.347	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1		NM_019002	
AMER1	139285	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	63412535	63412535	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:63412535G>A	ENST00000330258.3	-	2	904	c.632C>T	c.(631-633)gCc>gTc	p.A211V	AMER1_ENST00000403336.1_Missense_Mutation_p.A211V|AMER1_ENST00000374869.3_Missense_Mutation_p.A211V	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	211					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)|p.A211V(2)									CACCTGAGGGGCTGAGCTCAC	0.592																																																	69	Whole gene deletion(67)|Substitution - Missense(2)	kidney(67)|ovary(1)|large_intestine(1)											50.0	46.0	47.0					X																	63412535		2202	4297	6499	SO:0001583	missense	0			AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.632C>T	X.37:g.63412535G>A	ENSP00000329117:p.Ala211Val	Somatic		WXS	Illumina HiSeq	Phase_I	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	4.631	0.117340	0.08881	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.13778	2.56;2.56;2.56	5.13	0.0126	0.14092	.	1.321610	0.04815	N	0.435942	T	0.13200	0.0320	M	0.62723	1.935	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.38090	-0.9677	10	0.11794	T	0.64	0.0364	3.8736	0.09047	0.4257:0.0:0.2851:0.2892	.	211	Q5JTC6	F123B_HUMAN	V	211	ENSP00000364003:A211V;ENSP00000329117:A211V;ENSP00000384722:A211V	ENSP00000329117:A211V	A	-	2	0	FAM123B	63329260	0.000000	0.05858	0.000000	0.03702	0.157000	0.22087	-0.051000	0.11885	-0.265000	0.09352	0.600000	0.82982	GCC		0.592	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1		NM_152424	
GALNTL5	168391	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	151684336	151684336	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr7:151684336G>A	ENST00000392800.2	+	5	882	c.628G>A	c.(628-630)Gca>Aca	p.A210T	GALNTL5_ENST00000431418.2_Missense_Mutation_p.A210T	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	210	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.A210T(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		GCTGATTCGAGCAAGGCTGAT	0.453																																																	1	Substitution - Missense(1)	kidney(1)											83.0	83.0	83.0					7																	151684336		2203	4300	6503	SO:0001583	missense	168391			AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.628G>A	7.37:g.151684336G>A	ENSP00000376548:p.Ala210Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Missense_Mutation	SNP	ENST00000392800.2	37	CCDS5929.1	.	.	.	.	.	.	.	.	.	.	g	11.93	1.784998	0.31593	.	.	ENSG00000106648	ENST00000431418;ENST00000392800	T;T	0.72282	-0.64;-0.64	4.3	-1.53	0.08611	Glycosyl transferase, family 2 (1);	1.232870	0.06158	N	0.675494	T	0.75547	0.3864	M	0.86651	2.83	0.09310	N	1	B	0.34181	0.44	B	0.38378	0.272	T	0.67421	-0.5675	10	0.87932	D	0	.	9.3641	0.38215	0.0:0.1225:0.3112:0.5663	.	210	Q7Z4T8	GLTL5_HUMAN	T	210	ENSP00000392582:A210T;ENSP00000376548:A210T	ENSP00000376548:A210T	A	+	1	0	GALNTL5	151315269	0.884000	0.30299	0.000000	0.03702	0.147000	0.21601	1.098000	0.31000	-0.438000	0.07232	0.556000	0.70494	GCA		0.453	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1		NM_145292	
GATA2	2624	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	128204803	128204803	+	Missense_Mutation	SNP	T	T	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:128204803T>A	ENST00000341105.2	-	3	969	c.638A>T	c.(637-639)tAc>tTc	p.Y213F	GATA2_ENST00000487848.1_Missense_Mutation_p.Y213F|GATA2_ENST00000430265.2_Missense_Mutation_p.Y213F	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	213					blood coagulation (GO:0007596)|cell differentiation in hindbrain (GO:0021533)|cell fate determination (GO:0001709)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|definitive hemopoiesis (GO:0060216)|embryonic placenta development (GO:0001892)|eosinophil fate commitment (GO:0035854)|GABAergic neuron differentiation (GO:0097154)|homeostasis of number of cells within a tissue (GO:0048873)|inner ear morphogenesis (GO:0042472)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fat cell proliferation (GO:0070345)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|pituitary gland development (GO:0021983)|positive regulation of angiogenesis (GO:0045766)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of phagocytosis (GO:0050766)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of forebrain neuron differentiation (GO:2000977)|regulation of histone acetylation (GO:0035065)|semicircular canal development (GO:0060872)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|ventral spinal cord interneuron differentiation (GO:0021514)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	C2H2 zinc finger domain binding (GO:0070742)|chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.Y213F(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(58)|kidney(2)|large_intestine(3)|lung(9)|prostate(3)|skin(1)|urinary_tract(1)	79				GBM - Glioblastoma multiforme(114;0.173)		TGACACCTGGTACTTGACGCC	0.627			Mis		AML(CML blast transformation)																																			Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	1	Substitution - Missense(1)	kidney(1)											145.0	130.0	135.0					3																	128204803		2203	4300	6503	SO:0001583	missense	2624			AF169253	CCDS3049.1, CCDS46903.1	3q21	2014-09-17	2001-11-28		ENSG00000179348	ENSG00000179348		"""GATA zinc finger domain containing"""	4171	protein-coding gene	gene with protein product		137295	"""GATA-binding protein 2"""			1714909	Standard	NM_032638		Approved	NFE1B	uc003eko.2	P23769	OTTHUMG00000159689	ENST00000341105.2:c.638A>T	3.37:g.128204803T>A	ENSP00000345681:p.Tyr213Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.969502	0.92855	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97209	-4.28;-4.29;-4.28	4.01	4.01	0.46588	.	0.404519	0.25622	N	0.029410	D	0.97785	0.9273	M	0.69823	2.125	0.58432	D	0.999998	D;D	0.67145	0.996;0.996	D;P	0.73380	0.98;0.908	D	0.97472	1.0041	10	0.42905	T	0.14	-10.8058	12.743	0.57264	0.0:0.0:0.0:1.0	.	213;213	P23769-2;P23769	.;GATA2_HUMAN	F	213	ENSP00000345681:Y213F;ENSP00000400259:Y213F;ENSP00000417074:Y213F	ENSP00000345681:Y213F	Y	-	2	0	GATA2	129687493	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.664000	0.68045	1.676000	0.50930	0.397000	0.26171	TAC		0.627	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1		NM_032638	
GPR1	2825	hgsc.bcm.edu;ucsc.edu	37	2	207041953	207041953	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:207041953delT	ENST00000407325.2	-	3	381	c.19delA	c.(19-21)acafs	p.T7fs	GPR1_ENST00000437420.1_Frame_Shift_Del_p.T7fs	NM_001098199.1|NM_001261452.1|NM_001261453.1|NM_001261454.1|NM_001261455.1|NM_005279.3	NP_001091669.1|NP_001248381.1|NP_001248382.1|NP_001248383.1|NP_001248384.1|NP_005270.2	P46091	GPR1_HUMAN	G protein-coupled receptor 1	7					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(1)	18		Lung NSC(271;7.93e-06)|Renal(323;0.000147)|Hepatocellular(293;0.000888)		UCEC - Uterine corpus endometrioid carcinoma (47;0.000241)|Epithelial(149;1.91e-37)|STAD - Stomach adenocarcinoma(1183;0.00178)|Lung(261;0.111)|LUSC - Lung squamous cell carcinoma(261;0.184)		TCAAATAATGTTTCCTCCAAA	0.328																																																	0													48.0	54.0	52.0					2																	207041953		2202	4298	6500	SO:0001589	frameshift_variant	2825				CCDS2368.1	2q33.3	2014-01-30			ENSG00000183671	ENSG00000183671		"""GPCR / Class A : Orphans"""	4463	protein-coding gene	gene with protein product		600239				7851889	Standard	NM_005279		Approved		uc031rqv.1	P46091	OTTHUMG00000132894	ENST00000407325.2:c.19delA	2.37:g.207041953delT	ENSP00000384345:p.Thr7fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5JUU6|A8K4L1|Q53TR9|Q6NVX4	Frame_Shift_Del	DEL	ENST00000407325.2	37	CCDS2368.1																																																																																				0.328	GPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256394.2		NM_001098199	
GPR149	344758	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	154146980	154146980	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:154146980G>T	ENST00000389740.2	-	1	524	c.425C>A	c.(424-426)aCa>aAa	p.T142K		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	142					antral ovarian follicle growth (GO:0001547)|estrous cycle phase (GO:0060206)|negative regulation of ovulation (GO:0060280)|preantral ovarian follicle growth (GO:0001546)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T142K(1)		autonomic_ganglia(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(22)|ovary(7)|prostate(1)|skin(1)|urinary_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TCTGGAGGCTGTCTGGCTCCC	0.597																																																	1	Substitution - Missense(1)	kidney(1)											31.0	34.0	33.0					3																	154146980		1997	4169	6166	SO:0001583	missense	344758			AY255534	CCDS43162.1	3q25.2	2012-08-21			ENSG00000174948	ENSG00000174948		"""GPCR / Class A : Orphans"""	23627	protein-coding gene	gene with protein product						12679517	Standard	NM_001038705		Approved	PGR10, IEDA	uc003faa.3	Q86SP6	OTTHUMG00000159131	ENST00000389740.2:c.425C>A	3.37:g.154146980G>T	ENSP00000374390:p.Thr142Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	G	0.265	-0.997034	0.02145	.	.	ENSG00000174948	ENST00000389740	T	0.26518	1.73	5.52	2.7	0.31948	GPCR, rhodopsin-like superfamily (1);	0.740368	0.13382	N	0.392028	T	0.10680	0.0261	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.18871	0.023	T	0.28004	-1.0057	10	0.25106	T	0.35	-0.7188	2.4962	0.04622	0.1819:0.2441:0.4605:0.1135	.	142	Q86SP6	GP149_HUMAN	K	142	ENSP00000374390:T142K	ENSP00000374390:T142K	T	-	2	0	GPR149	155629674	0.004000	0.15560	0.001000	0.08648	0.051000	0.14879	1.476000	0.35420	0.717000	0.32145	-0.777000	0.03380	ACA		0.597	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1		XM_293580	
GRIA1	2890	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	153149881	153149881	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr5:153149881A>T	ENST00000285900.5	+	13	2519	c.2176A>T	c.(2176-2178)Att>Ttt	p.I726F	GRIA1_ENST00000448073.4_Missense_Mutation_p.I736F|GRIA1_ENST00000340592.5_Missense_Mutation_p.I726F|GRIA1_ENST00000521843.2_Missense_Mutation_p.I657F|GRIA1_ENST00000518783.1_Missense_Mutation_p.I736F|GRIA1_ENST00000518142.1_Missense_Mutation_p.I646F	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	726					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|long-term memory (GO:0007616)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|axonal spine (GO:0044308)|cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|dendrite membrane (GO:0032590)|dendritic spine (GO:0043197)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|neuron spine (GO:0044309)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|PDZ domain binding (GO:0030165)	p.I726F(2)		NS(1)|breast(4)|endometrium(7)|kidney(3)|large_intestine(24)|liver(2)|lung(23)|ovary(4)|pancreas(1)|prostate(5)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	81		Medulloblastoma(196;0.0391)|all_neural(177;0.16)|all_hematologic(541;0.21)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Perampanel(DB08883)|Sevoflurane(DB01236)	GAATGAGTACATTGAGCAGCG	0.512																																																	2	Substitution - Missense(2)	kidney(2)											118.0	100.0	106.0					5																	153149881		2203	4300	6503	SO:0001583	missense	2890				CCDS4322.1, CCDS47318.1, CCDS58986.1, CCDS58987.1, CCDS58988.1, CCDS58989.1	5q33	2012-08-29			ENSG00000155511	ENSG00000155511		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4571	protein-coding gene	gene with protein product		138248		GLUR1		1652753, 1319477	Standard	NM_000827		Approved	GluA1, GLURA	uc011dcy.2	P42261	OTTHUMG00000130148	ENST00000285900.5:c.2176A>T	5.37:g.153149881A>T	ENSP00000285900:p.Ile726Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Missense_Mutation	SNP	ENST00000285900.5	37	CCDS4322.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.268951	0.80469	.	.	ENSG00000155511	ENST00000285900;ENST00000544403;ENST00000518142;ENST00000537037;ENST00000340592;ENST00000521843;ENST00000544794;ENST00000518783;ENST00000448073	T;T;T;T;T;T;T	0.38077	1.48;1.48;1.16;1.48;1.48;1.48;1.16	5.41	5.41	0.78517	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.51618	0.1685	L	0.41573	1.285	0.80722	D	1	D;D;P;D;P	0.89917	1.0;1.0;0.9;1.0;0.917	D;D;P;D;P	0.87578	0.998;0.998;0.499;0.997;0.783	T	0.54316	-0.8312	10	0.87932	D	0	.	14.6134	0.68531	1.0:0.0:0.0:0.0	.	736;736;646;726;726	E7ESV8;B7Z9G9;B7Z3F6;P42261-2;P42261	.;.;.;.;GRIA1_HUMAN	F	726;726;646;680;726;659;657;736;736	ENSP00000285900:I726F;ENSP00000427920:I646F;ENSP00000339343:I726F;ENSP00000427864:I659F;ENSP00000442108:I657F;ENSP00000428994:I736F;ENSP00000415569:I736F	ENSP00000285900:I726F	I	+	1	0	GRIA1	153130074	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.125000	0.94402	2.042000	0.60477	0.533000	0.62120	ATT		0.512	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			
GRIK2	2898	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	102503283	102503283	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr6:102503283A>G	ENST00000421544.1	+	15	2880	c.2390A>G	c.(2389-2391)aAa>aGa	p.K797R	GRIK2_ENST00000369137.3_Missense_Mutation_p.K721R|GRIK2_ENST00000318991.6_Missense_Mutation_p.K797R|GRIK2_ENST00000369138.1_Missense_Mutation_p.K797R|GRIK2_ENST00000413795.1_Missense_Mutation_p.K797R|GRIK2_ENST00000369134.4_Missense_Mutation_p.K748R	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	797					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.K797R(2)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	ATGAAGGAGAAATGGTGGAGG	0.483																																																	2	Substitution - Missense(2)	kidney(2)											99.0	101.0	100.0					6																	102503283		2203	4300	6503	SO:0001583	missense	2898				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.2390A>G	6.37:g.102503283A>G	ENSP00000397026:p.Lys797Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.195301	0.78902	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000369134;ENST00000540076	T;T;T;T;T;T	0.16597	2.33;2.33;2.33;2.33;2.33;2.33	5.68	5.68	0.88126	Ionotropic glutamate receptor (2);	0.046223	0.85682	N	0.000000	T	0.25901	0.0631	L	0.52126	1.63	0.51233	D	0.999916	D;D;D	0.62365	0.989;0.991;0.989	D;D;D	0.70016	0.944;0.967;0.944	T	0.00950	-1.1503	10	0.40728	T	0.16	.	15.9826	0.80125	1.0:0.0:0.0:0.0	.	797;797;797	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	R	797;797;797;721;797;748;572	ENSP00000397026:K797R;ENSP00000405596:K797R;ENSP00000358134:K797R;ENSP00000358133:K721R;ENSP00000313276:K797R;ENSP00000358130:K748R	ENSP00000313276:K797R	K	+	2	0	GRIK2	102609976	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.339000	0.96797	2.176000	0.68965	0.477000	0.44152	AAA		0.483	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			
GRIN3A	116443	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	104341505	104341505	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr9:104341505C>T	ENST00000361820.3	-	7	3504	c.2904G>A	c.(2902-2904)aaG>aaA	p.K968K		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	968	PPP2CB binding site. {ECO:0000250}.				calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)	p.K968K(1)		breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	AGTATTGCAGCTTGGATTTGT	0.483																																																	1	Substitution - coding silent(1)	kidney(1)											234.0	182.0	199.0					9																	104341505		2203	4300	6503	SO:0001819	synonymous_variant	116443				CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2904G>A	9.37:g.104341505C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																				0.483	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			
GSG2	83903	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	3629541	3629541	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:3629541A>G	ENST00000325418.4	+	1	2331	c.2312A>G	c.(2311-2313)aAg>aGg	p.K771R	ITGAE_ENST00000263087.4_Intron|ITGAE_ENST00000571185.1_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	771	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)	p.K771R(1)									AAGCAAATTAAGAGAAAAATC	0.408																																																	1	Substitution - Missense(1)	kidney(1)											49.0	49.0	49.0					17																	3629541		2203	4300	6503	SO:0001583	missense	83903			AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.2312A>G	17.37:g.3629541A>G	ENSP00000325290:p.Lys771Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	A	0.021	-1.426199	0.01117	.	.	ENSG00000177602	ENST00000325418	T	0.06608	3.28	5.51	-7.31	0.01441	Domain of unknown function DUF3635 (1);Protein kinase, catalytic domain (1);	0.538057	0.17538	N	0.170656	T	0.05640	0.0148	L	0.39020	1.185	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.08106	-1.0738	10	0.87932	D	0	-4.6545	16.9484	0.86236	0.5137:0.0:0.4863:0.0	.	771	Q8TF76	HASP_HUMAN	R	771	ENSP00000325290:K771R	ENSP00000325290:K771R	K	+	2	0	GSG2	3576290	0.012000	0.17670	0.000000	0.03702	0.002000	0.02628	-0.041000	0.12084	-2.035000	0.00923	-1.139000	0.01908	AAG		0.408	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1		NM_031965	
HCCS	3052	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	11139773	11139773	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:11139773G>A	ENST00000321143.4	+	7	852	c.650G>A	c.(649-651)cGt>cAt	p.R217H	HCCS_ENST00000380763.3_Missense_Mutation_p.R217H|ARHGAP6_ENST00000534860.1_Intron|HCCS_ENST00000380762.4_Missense_Mutation_p.R217H	NM_001122608.2|NM_001171991.2|NM_005333.4	NP_001116080.1|NP_001165462.1|NP_005324.3	P53701	CCHL_HUMAN	holocytochrome c synthase	217			R -> C (in MCOPS7). {ECO:0000269|PubMed:17033964}.		organ morphogenesis (GO:0009887)|oxidation-reduction process (GO:0055114)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	holocytochrome-c synthase activity (GO:0004408)|metal ion binding (GO:0046872)	p.R217H(1)		kidney(1)|large_intestine(3)|lung(3)	7						ATCATAAACCGTTGCGGGACA	0.428																																					Ovarian(86;1338 1347 1462 10340 37882)												1	Substitution - Missense(1)	kidney(1)											187.0	160.0	169.0					X																	11139773		2203	4300	6503	SO:0001583	missense	3052				CCDS14139.1	Xp22	2014-01-31	2010-05-11		ENSG00000004961	ENSG00000004961	4.4.1.17		4837	protein-coding gene	gene with protein product	"""cytochrome c heme-lyase"""	300056	"""holocytochrome c synthase (cytochrome c heme-lyase)"", ""microphthalamia with linear skin defects"""	MLS		8364577, 12444108	Standard	NM_001122608		Approved	CCHL	uc004cuj.3	P53701	OTTHUMG00000021128	ENST00000321143.4:c.650G>A	X.37:g.11139773G>A	ENSP00000326579:p.Arg217His	Somatic		WXS	Illumina HiSeq	Phase_I	B3KUS1|Q502X8	Missense_Mutation	SNP	ENST00000321143.4	37	CCDS14139.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.236027	0.79800	.	.	ENSG00000004961	ENST00000321143;ENST00000380763;ENST00000380762	D;D;D	0.92545	-3.06;-3.06;-3.06	6.05	3.26	0.37387	.	0.047606	0.85682	N	0.000000	D	0.96842	0.8969	H	0.97077	3.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94995	0.8138	10	0.87932	D	0	-7.5709	7.7372	0.28821	0.0786:0.0:0.6331:0.2883	.	217	P53701	CCHL_HUMAN	H	217	ENSP00000326579:R217H;ENSP00000370140:R217H;ENSP00000370139:R217H	ENSP00000326579:R217H	R	+	2	0	HCCS	11049694	1.000000	0.71417	0.454000	0.27019	0.984000	0.73092	9.239000	0.95389	0.247000	0.21414	0.594000	0.82650	CGT		0.428	HCCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055742.1			
HNF1B	6928	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	36091725	36091725	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:36091725G>C	ENST00000225893.4	-	4	1267	c.906C>G	c.(904-906)aaC>aaG	p.N302K	HNF1B_ENST00000427275.2_Missense_Mutation_p.N276K|HNF1B_ENST00000561193.1_Missense_Mutation_p.N276K|HNF1B_ENST00000560016.1_Missense_Mutation_p.N302K	NM_000458.2|NM_001165923.1	NP_000449.1|NP_001159395.1	P35680	HNF1B_HUMAN	HNF1 homeobox B	302					anterior/posterior pattern specification (GO:0009952)|branching morphogenesis of an epithelial tube (GO:0048754)|embryonic digestive tract morphogenesis (GO:0048557)|endocrine pancreas development (GO:0031018)|endodermal cell fate specification (GO:0001714)|epithelial cell proliferation (GO:0050673)|genitalia development (GO:0048806)|hepatoblast differentiation (GO:0061017)|hindbrain development (GO:0030902)|inner cell mass cell differentiation (GO:0001826)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|mesonephric duct formation (GO:0072181)|negative regulation of mesenchymal cell apoptotic process involved in mesonephric nephron morphogenesis (GO:0061296)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric nephron tubule development (GO:0039020)|pronephros development (GO:0048793)|regulation of branch elongation involved in ureteric bud branching (GO:0072095)|regulation of endodermal cell fate specification (GO:0042663)|regulation of pronephros size (GO:0035565)|regulation of Wnt signaling pathway (GO:0030111)|response to glucose (GO:0009749)|ureteric bud elongation (GO:0060677)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.N302K(2)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(3)|large_intestine(2)|liver(1)|lung(3)|ovary(3)|prostate(1)|skin(2)	28		Breast(25;0.00765)|Ovarian(249;0.15)	STAD - Stomach adenocarcinoma(1;0.0142)			CCTTCCTGCGGTTTGCAAACC	0.612																																					Colon(71;102 1179 9001 27917 43397)												2	Substitution - Missense(2)	kidney(2)											140.0	113.0	122.0					17																	36091725		2203	4300	6503	SO:0001583	missense	6928			BC017714	CCDS11324.1, CCDS58538.1	17q12	2014-05-06	2007-08-24	2007-08-24	ENSG00000108753	ENSG00000275410		"""Homeoboxes / HNF class"""	11630	protein-coding gene	gene with protein product		189907	"""transcription factor 2, hepatic; LF-B3; variant hepatic nuclear factor"""	TCF2		1677179, 10484768	Standard	NM_000458		Approved	LFB3, VHNF1, HNF1beta, MODY5	uc002hok.4	P35680	OTTHUMG00000188478	ENST00000225893.4:c.906C>G	17.37:g.36091725G>C	ENSP00000225893:p.Asn302Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B4DKM3|E0YMJ9	Missense_Mutation	SNP	ENST00000225893.4	37	CCDS11324.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366508	0.82463	.	.	ENSG00000108753	ENST00000225893;ENST00000427275;ENST00000544593;ENST00000539087	D;D	0.99329	-5.75;-5.75	5.32	5.32	0.75619	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.178173	0.64402	D	0.000011	D	0.99309	0.9758	M	0.80616	2.505	0.80722	D	1	D;D;P	0.59357	0.968;0.985;0.891	P;P;B	0.61658	0.791;0.892;0.412	D	0.99208	1.0875	10	0.87932	D	0	-0.2386	17.7156	0.88336	0.0:0.0:1.0:0.0	.	276;302;302	E0YMJ6;P35680-3;P35680	.;.;HNF1B_HUMAN	K	302;276;302;190	ENSP00000225893:N302K;ENSP00000412212:N276K	ENSP00000225893:N302K	N	-	3	2	HNF1B	33165838	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.334000	0.59291	2.775000	0.95449	0.655000	0.94253	AAC		0.612	HNF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256807.3		NM_000458	
IFT172	26160	hgsc.bcm.edu;ucsc.edu	37	2	27702943	27702946	+	Frame_Shift_Del	DEL	ATAA	ATAA	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	ATAA	ATAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:27702943_27702946delATAA	ENST00000260570.3	-	9	959_962	c.856_859delTTAT	c.(856-861)ttatacfs	p.LY286fs	IFT172_ENST00000416524.2_Frame_Shift_Del_p.LY265fs|IFT172_ENST00000359466.6_Frame_Shift_Del_p.LY286fs	NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	286					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)				central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					GTGATGGTGTATAAATTGGTAATC	0.475																																																	0																																										SO:0001589	frameshift_variant	26160			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.856_859delTTAT	2.37:g.27702943_27702946delATAA	ENSP00000260570:p.Leu286fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Frame_Shift_Del	DEL	ENST00000260570.3	37	CCDS1755.1																																																																																				0.475	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2		NM_015662	
ITGB4	3691	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73736440	73736440	+	Splice_Site	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:73736440G>A	ENST00000200181.3	+	21	2635	c.2448G>A	c.(2446-2448)gtG>gtA	p.V816V	ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Splice_Site_p.V816V|ITGB4_ENST00000339591.3_Splice_Site_p.V816V|ITGB4_ENST00000449880.2_Splice_Site_p.V816V|ITGB4_ENST00000579662.1_Splice_Site_p.V816V	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	816					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)	p.V816V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTTCCTTAGTGCCCTACGGGC	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											52.0	45.0	47.0					17																	73736440		2203	4300	6503	SO:0001630	splice_region_variant	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.2447-1G>A	17.37:g.73736440G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																				0.647	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			Silent
EPG5	57724	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	43492338	43492338	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr18:43492338G>A	ENST00000282041.5	-	22	3934	c.3900C>T	c.(3898-3900)gtC>gtT	p.V1300V	EPG5_ENST00000585906.1_5'UTR	NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	1300					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)			p.V1300V(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						CAGAAGGTGTGACCAGAGCCT	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											58.0	67.0	64.0					18																	43492338		1946	4125	6071	SO:0001819	synonymous_variant	0			AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.3900C>T	18.37:g.43492338G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																				0.547	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1		NM_020964	
LCMT2	9836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	43621597	43621597	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr15:43621597A>G	ENST00000305641.5	-	1	1206	c.1091T>C	c.(1090-1092)tTc>tCc	p.F364S	ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000422466.2_5'Flank|ADAL_ENST00000389651.4_5'Flank|LCMT2_ENST00000544735.1_5'UTR|LCMT2_ENST00000567039.1_3'UTR	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	364					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)	p.F364S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(1)|urinary_tract(1)	20		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.1e-07)	L-Leucine(DB00149)	TGGGCTCAAGAAGACAGAGGC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											47.0	46.0	46.0					15																	43621597		2201	4299	6500	SO:0001583	missense	9836			AF265443	CCDS10094.1	15q15.3	2007-01-26			ENSG00000168806	ENSG00000168806			17558	protein-coding gene	gene with protein product	"""tRNA-yW synthesizing protein 4"""	611246				9628581, 17150819	Standard	NM_014793		Approved	KIAA0547, MGC9534, TYW4, PPM2	uc001zrg.3	O60294	OTTHUMG00000130705	ENST00000305641.5:c.1091T>C	15.37:g.43621597A>G	ENSP00000307214:p.Phe364Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	37	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	A	4.396	0.073218	0.08485	.	.	ENSG00000168806	ENST00000305641	T	0.72282	-0.64	5.54	4.41	0.53225	.	0.575927	0.16314	N	0.219841	T	0.39306	0.1073	N	0.01874	-0.695	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.18555	-1.0333	10	0.10377	T	0.69	-20.4168	7.9913	0.30242	0.9101:0.0:0.0899:0.0	.	364	O60294	LCMT2_HUMAN	S	364	ENSP00000307214:F364S	ENSP00000307214:F364S	F	-	2	0	LCMT2	41408889	0.501000	0.26099	0.765000	0.31456	0.182000	0.23217	2.148000	0.42235	1.112000	0.41740	0.533000	0.62120	TTC		0.562	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1		NM_014793	
LILRB5	10990	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	54760026	54760026	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr19:54760026G>A	ENST00000316219.5	-	4	642	c.535C>T	c.(535-537)Ctg>Ttg	p.L179L	LILRB5_ENST00000345866.6_Intron|LILRB5_ENST00000449561.2_Silent_p.L179L|LILRB5_ENST00000450632.1_Silent_p.L170L	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	179	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.L179L(1)|p.L170L(1)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAGGGAACAGGGCCTGGGAT	0.552																																																	2	Substitution - coding silent(2)	kidney(2)											56.0	66.0	63.0					19																	54760026		2203	4300	6503	SO:0001819	synonymous_variant	10990			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.535C>T	19.37:g.54760026G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q8N760	Silent	SNP	ENST00000316219.5	37	CCDS12885.1																																																																																				0.552	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2			
LOR	4014	hgsc.bcm.edu	37	1	153233488	153233489	+	In_Frame_Ins	INS	-	-	GGCGGT	rs150026164	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:153233488_153233489insGGCGGT	ENST00000368742.3	+	2	120_121	c.63_64insGGCGGT	c.(64-66)ggc>GGCGGTggc	p.22_22G>GGG		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	22					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G22S(1)		lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGACCTCTggcggcggtggcgg	0.673														971	0.19389	0.3812	0.1542	5008	,	,		8118	0.0685		0.2326	False		,,,				2504	0.0583																1	Substitution - Missense(1)	lung(1)								1372,2418		364,644,887						1.9	0.9		dbSNP_130	14	1619,5813		315,989,2412	no	coding	LOR	NM_000427.2		679,1633,3299	A1A1,A1R,RR		21.7842,36.2005,26.653				2991,8231				SO:0001652	inframe_insertion	4014			M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.70_75dupGGCGGT	1.37:g.153233489_153233494dupGGCGGT	ENSP00000357731:p.GlyGly28dup	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T869|Q5XKF8	In_Frame_Ins	INS	ENST00000368742.3	37	CCDS30870.1																																																																																				0.673	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039107.1		NM_000427	
LRCH3	84859	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	197557694	197557694	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:197557694A>G	ENST00000425562.2	+	7	941	c.941A>G	c.(940-942)aAt>aGt	p.N314S	LRCH3_ENST00000441090.2_Missense_Mutation_p.N188S|LRCH3_ENST00000438796.2_Missense_Mutation_p.N314S|LRCH3_ENST00000536618.1_5'UTR|AC055764.1_ENST00000454526.1_RNA|LRCH3_ENST00000334859.4_Missense_Mutation_p.N314S|LRCH3_ENST00000414675.2_Missense_Mutation_p.N314S			Q96II8	LRCH3_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 3	314						cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.N314S(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	all_cancers(143;1.15e-09)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;4.82e-24)|all cancers(36;3.61e-22)|OV - Ovarian serous cystadenocarcinoma(49;7.08e-19)|LUSC - Lung squamous cell carcinoma(58;6.94e-07)|Lung(62;9.92e-07)	GBM - Glioblastoma multiforme(93;0.119)		TCAGGCTTCAATAGTGTGGAC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											199.0	202.0	201.0					3																	197557694		2203	4300	6503	SO:0001583	missense	84859			AL137527	CCDS3330.1	3q29	2006-04-12			ENSG00000186001	ENSG00000186001			28637	protein-coding gene	gene with protein product						12477932	Standard	NM_032773		Approved	MGC4126	uc003fyj.1	Q96II8	OTTHUMG00000155378	ENST00000425562.2:c.941A>G	3.37:g.197557694A>G	ENSP00000393579:p.Asn314Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B4E0T7|Q96FP9|Q9NT52	Missense_Mutation	SNP	ENST00000425562.2	37		.	.	.	.	.	.	.	.	.	.	A	21.6	4.174298	0.78452	.	.	ENSG00000186001	ENST00000438796;ENST00000441090;ENST00000414675;ENST00000334859;ENST00000425562	T;T;T;T;T	0.28895	2.11;1.59;2.16;2.34;2.13	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.39200	0.1069	N	0.24115	0.695	0.80722	D	1	D;D;D;B	0.76494	0.999;0.999;0.999;0.357	D;D;D;B	0.79784	0.96;0.993;0.982;0.237	T	0.13176	-1.0519	10	0.24483	T	0.36	-15.9044	14.4981	0.67702	1.0:0.0:0.0:0.0	.	188;314;314;314	E9PD99;B4E0T7;Q96II8-2;Q96II8-3	.;.;.;.	S	314;188;314;314;314	ENSP00000399751:N314S;ENSP00000394609:N188S;ENSP00000394965:N314S;ENSP00000334375:N314S;ENSP00000393579:N314S	ENSP00000334375:N314S	N	+	2	0	LRCH3	199042091	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.727000	0.91480	1.905000	0.55150	0.374000	0.22700	AAT		0.393	LRCH3-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000339965.1		NM_032773	
MAN2A2	4122	broad.mit.edu;ucsc.edu	37	15	91449980	91449980	+	Silent	SNP	C	C	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr15:91449980C>A	ENST00000559717.1	+	7	1305	c.846C>A	c.(844-846)ccC>ccA	p.P282P	MAN2A2_ENST00000360468.3_Silent_p.P282P|MAN2A2_ENST00000431652.2_5'Flank			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	282					cellular protein metabolic process (GO:0044267)|mannose metabolic process (GO:0006013)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.P282P(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|lung(13)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GTGCAACCCCCCGCTCTGGCT	0.647																																																	1	Substitution - coding silent(1)	kidney(1)											37.0	37.0	37.0					15																	91449980		2198	4298	6496	SO:0001819	synonymous_variant	4122			L28821	CCDS32332.1	15q25	2011-06-30			ENSG00000196547	ENSG00000196547			6825	protein-coding gene	gene with protein product		600988				8524845	Standard	NM_006122		Approved	MANA2X, HsT19662	uc002bqc.3	P49641		ENST00000559717.1:c.846C>A	15.37:g.91449980C>A		Somatic		WXS	Illumina GAIIx	Phase_I	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																				0.647	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5		NM_006122	
MAP3K15	389840	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	19389075	19389075	+	Splice_Site	SNP	A	A	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:19389075A>C	ENST00000338883.4	-	24	3400		c.e24+1		MAP3K15_ENST00000469203.2_Splice_Site|MAP3K15_ENST00000518578.1_Splice_Site|MAP3K15_ENST00000359173.3_Splice_Site	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15								ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.?(2)		NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					GGGGGCGCTCACCTGGGATGA	0.488																																																	2	Unknown(2)	kidney(2)											66.0	63.0	64.0					X																	19389075		2203	4300	6503	SO:0001630	splice_region_variant	389840			AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3400+1T>G	X.37:g.19389075A>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Splice_Site	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	A	13.98	2.399528	0.42512	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	.	.	.	5.25	4.09	0.47781	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2991	0.43642	0.921:0.0:0.079:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MAP3K15	19298996	1.000000	0.71417	0.550000	0.28217	0.386000	0.30323	7.050000	0.76620	0.748000	0.32831	0.451000	0.29950	.		0.488	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_001001671	Intron
MC3R	4159	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	54824370	54824370	+	Silent	SNP	C	C	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr20:54824370C>A	ENST00000243911.2	+	1	583	c.471C>A	c.(469-471)acC>acA	p.T157T		NM_019888.3	NP_063941.3	P41968	MC3R_HUMAN	melanocortin 3 receptor	157					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|homoiothermy (GO:0042309)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP biosynthetic process (GO:0030819)|regulation of blood pressure (GO:0008217)|regulation of heart rate (GO:0002027)|sodium ion homeostasis (GO:0055078)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)	p.T194T(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(3)|skin(1)	26			Colorectal(105;0.202)			GCATCATGACCGTGAGGAAGG	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											207.0	187.0	194.0					20																	54824370		2203	4300	6503	SO:0001819	synonymous_variant	4159				CCDS13449.2	20q13.2-q13.3	2012-08-10			ENSG00000124089	ENSG00000124089		"""GPCR / Class A : Melanocortin receptors"""	6931	protein-coding gene	gene with protein product		155540				8463333	Standard	NM_019888		Approved	MC3	uc002xxb.2	P41968	OTTHUMG00000032785	ENST00000243911.2:c.471C>A	20.37:g.54824370C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q4KN27|Q9H517	Silent	SNP	ENST00000243911.2	37	CCDS13449.2																																																																																				0.582	MC3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079786.2			
MTOR	2475	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	11169375	11169375	+	Missense_Mutation	SNP	A	A	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:11169375A>C	ENST00000361445.4	-	56	7576	c.7500T>G	c.(7498-7500)atT>atG	p.I2500M	MTOR_ENST00000376838.1_Missense_Mutation_p.I705M	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	2500	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.I2500M(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CCCTGTTAATAATCTGGATAG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											177.0	156.0	163.0					1																	11169375		2203	4300	6503	SO:0001583	missense	2475			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.7500T>G	1.37:g.11169375A>C	ENSP00000354558:p.Ile2500Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.123062	0.77436	.	.	ENSG00000198793	ENST00000361445;ENST00000376838;ENST00000455339	T;T;T	0.29917	3.08;2.85;1.55	5.82	-2.33	0.06724	Phosphatidylinositol 3-/4-kinase, catalytic (1);	0.047538	0.85682	D	0.000000	T	0.48447	0.1500	M	0.87328	2.875	0.53005	D	0.999969	D	0.71674	0.998	D	0.66497	0.944	T	0.45948	-0.9226	10	0.87932	D	0	-10.0412	4.8813	0.13681	0.3927:0.0:0.3693:0.238	.	2500	P42345	MTOR_HUMAN	M	2500;705;156	ENSP00000354558:I2500M;ENSP00000366034:I705M;ENSP00000398745:I156M	ENSP00000354558:I2500M	I	-	3	3	MTOR	11091962	0.935000	0.31712	0.970000	0.41538	0.992000	0.81027	0.184000	0.16939	-0.709000	0.05008	0.482000	0.46254	ATT		0.408	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1		NM_004958	
MUC4	4585	broad.mit.edu;hgsc.bcm.edu	37	3	195538680	195538680	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:195538680C>T	ENST00000346145.4	-	1	48	c.9G>A	c.(7-9)ggG>ggA	p.G3G	MUC4_ENST00000475231.1_Silent_p.G3G|MUC4_ENST00000349607.4_Silent_p.G3G|MUC4_ENST00000478685.1_5'UTR|MUC4_ENST00000463781.3_Silent_p.G3G	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	3					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.G3G(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCCAGCGTGCCCCCTTCATGG	0.657																																																	3	Substitution - coding silent(3)	kidney(3)											65.0	62.0	63.0					3																	195538680		2203	4300	6503	SO:0001819	synonymous_variant	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.9G>A	3.37:g.195538680C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																				0.657	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1		NM_018406	
MUC5B	727897	hgsc.bcm.edu	37	11	1271392	1271392	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr11:1271392G>A	ENST00000529681.1	+	31	13340	c.13282G>A	c.(13282-13284)Gcc>Acc	p.A4428T	MUC5B_ENST00000447027.1_Missense_Mutation_p.A4431T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4428	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GACCACAACAGCCACTACGAC	0.657																																																	0													123.0	146.0	138.0					11																	1271392		2071	4199	6270	SO:0001583	missense	727897			U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.13282G>A	11.37:g.1271392G>A	ENSP00000436812:p.Ala4428Thr	Somatic		WXS	Illumina HiSeq	Phase_I	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	6.270	0.417995	0.11870	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.17054	2.3;2.49	2.21	-0.115	0.13560	.	.	.	.	.	T	0.15262	0.0368	L	0.57536	1.79	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.003	T	0.31806	-0.9930	9	0.87932	D	0	.	3.933	0.09293	0.1795:0.2529:0.5676:0.0	.	4901;4431	A7Y9J9;E9PBJ0	.;.	T	4428;4431;4372;4278;207	ENSP00000436812:A4428T;ENSP00000415793:A4431T	ENSP00000343037:A4372T	A	+	1	0	MUC5B	1227968	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.769000	0.01792	0.033000	0.15463	0.186000	0.17326	GCC		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2		XM_001126093	
NKRF	55922	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	118723545	118723545	+	Missense_Mutation	SNP	G	G	T	rs140452307	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:118723545G>T	ENST00000371527.1	-	2	2495	c.1843C>A	c.(1843-1845)Cgc>Agc	p.R615S	NKRF_ENST00000304449.5_Missense_Mutation_p.R615S|NKRF_ENST00000487600.1_Intron|NKRF_ENST00000542113.1_Missense_Mutation_p.R630S	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	615	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.			AR -> ES (in Ref. 1; CAB56459). {ECO:0000305}.	negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.R615S(1)|p.R630S(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						CTCTCGGAGCGGGCGTAGTTT	0.443																																																	2	Substitution - Missense(2)	kidney(2)											153.0	134.0	140.0					X																	118723545		2203	4300	6503	SO:0001583	missense	55922			AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"""G patch domain containing"""	19374	protein-coding gene	gene with protein product		300440	"""NF-kappaB repressing factor"""			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.1843C>A	X.37:g.118723545G>T	ENSP00000360582:p.Arg615Ser	Somatic		WXS	Illumina HiSeq	Phase_I	G3V1N1|Q4VC41|Q9UJ91	Missense_Mutation	SNP	ENST00000371527.1	37	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	G	1.135	-0.651183	0.03506	.	.	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	T;T;T	0.43688	0.95;0.95;0.94	5.77	5.77	0.91146	Single-stranded nucleic acid binding R3H (3);	0.507790	0.22516	N	0.059023	T	0.22282	0.0537	N	0.11201	0.11	0.34346	D	0.68934	B	0.02656	0.0	B	0.06405	0.002	T	0.16897	-1.0387	10	0.06236	T	0.91	-8.2935	13.4935	0.61411	0.0:0.152:0.848:0.0	.	615	O15226	NKRF_HUMAN	S	615;615;630	ENSP00000360582:R615S;ENSP00000304803:R615S;ENSP00000442308:R630S	ENSP00000304803:R615S	R	-	1	0	NKRF	118607573	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	2.671000	0.46842	2.424000	0.82194	0.600000	0.82982	CGC		0.443	NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1		NM_017544	
NOC4L	79050	broad.mit.edu;ucsc.edu	37	12	132636049	132636049	+	Missense_Mutation	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:132636049T>C	ENST00000330579.1	+	12	1135	c.1094T>C	c.(1093-1095)gTg>gCg	p.V365A	NOC4L_ENST00000538784.1_5'UTR|NOC4L_ENST00000535343.1_3'UTR	NM_024078.1	NP_076983.1	Q9BVI4	NOC4L_HUMAN	nucleolar complex associated 4 homolog (S. cerevisiae)	365					rRNA processing (GO:0006364)	integral component of membrane (GO:0016021)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.V365A(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|skin(2)	14	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.2e-08)|Epithelial(86;3.34e-07)|all cancers(50;1.97e-05)		GCCTACCTGGTGGCCGCCTTC	0.716																																																	1	Substitution - Missense(1)	kidney(1)											14.0	17.0	16.0					12																	132636049		2179	4277	6456	SO:0001583	missense	79050				CCDS9277.1	12q24.33	2011-08-12			ENSG00000184967	ENSG00000184967			28461	protein-coding gene	gene with protein product		612819				12446671	Standard	NM_024078		Approved	MGC3162, NET49, UTP19	uc001ujz.1	Q9BVI4	OTTHUMG00000168260	ENST00000330579.1:c.1094T>C	12.37:g.132636049T>C	ENSP00000328854:p.Val365Ala	Somatic		WXS	Illumina GAIIx	Phase_I	Q8N2S5|Q96I14	Missense_Mutation	SNP	ENST00000330579.1	37	CCDS9277.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.062131	0.55432	.	.	ENSG00000184967	ENST00000330579	T	0.64803	-0.12	5.18	5.18	0.71444	CCAAT-binding factor (1);	0.000000	0.85682	D	0.000000	T	0.50803	0.1637	L	0.38175	1.15	0.80722	D	1	P	0.44260	0.83	B	0.37888	0.26	T	0.51466	-0.8702	10	0.31617	T	0.26	-32.6755	14.6937	0.69103	0.0:0.0:0.0:1.0	.	365	Q9BVI4	NOC4L_HUMAN	A	365	ENSP00000328854:V365A	ENSP00000328854:V365A	V	+	2	0	NOC4L	131202002	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	4.483000	0.60264	1.951000	0.56629	0.459000	0.35465	GTG		0.716	NOC4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398999.1		NM_024078	
NOS3	4846	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	150697631	150697631	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr7:150697631C>T	ENST00000484524.1	+	9	1177	c.1177C>T	c.(1177-1179)Ctg>Ttg	p.L393L	NOS3_ENST00000467517.1_Silent_p.L393L|NOS3_ENST00000297494.3_Silent_p.L393L|NOS3_ENST00000461406.1_Silent_p.L187L	NM_001160111.1	NP_001153583.1	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.L393L(1)		NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CACCTCGTCCCTGTGGAAAGA	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											121.0	90.0	100.0					7																	150697631		2203	4300	6503	SO:0001819	synonymous_variant	4846				CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000484524.1:c.1177C>T	7.37:g.150697631C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q495E5	Silent	SNP	ENST00000484524.1	37	CCDS55182.1																																																																																				0.602	NOS3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351550.1		NM_000603	
NUPL1	9818	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	25899186	25899186	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr13:25899186T>G	ENST00000381736.3	+	10	1261	c.1011T>G	c.(1009-1011)caT>caG	p.H337Q	NUPL1_ENST00000381718.3_Missense_Mutation_p.H325Q|NUPL1_ENST00000463407.1_Missense_Mutation_p.H337Q|NUPL1_ENST00000466694.1_3'UTR	NM_001008564.1|NM_014089.3	NP_001008564.1|NP_054808.1	Q9BVL2	NUPL1_HUMAN	nucleoporin like 1	337	14 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	nucleocytoplasmic transporter activity (GO:0005487)	p.H337Q(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(7)|stomach(1)|urinary_tract(1)	16		Lung SC(185;0.0225)|Breast(139;0.0351)		all cancers(112;0.0092)|Epithelial(112;0.0477)|OV - Ovarian serous cystadenocarcinoma(117;0.165)|GBM - Glioblastoma multiforme(144;0.244)		GACTTCAACATGAATATGCAG	0.328																																					Pancreas(166;1040 2004 4560 4728 37041)|GBM(109;1045 1520 7614 9308 19618)												1	Substitution - Missense(1)	kidney(1)											75.0	77.0	77.0					13																	25899186		2203	4300	6503	SO:0001583	missense	9818			AB007870	CCDS9314.1, CCDS31949.1	13q12.12	2011-04-12			ENSG00000139496	ENSG00000139496			20261	protein-coding gene	gene with protein product		607615				9455477	Standard	NM_014089		Approved	KIAA0410	uc001uqi.3	Q9BVL2	OTTHUMG00000016608	ENST00000381736.3:c.1011T>G	13.37:g.25899186T>G	ENSP00000371155:p.His337Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A6NI12|B4DZJ1|O43160|Q5JRG2|Q5JRG5	Missense_Mutation	SNP	ENST00000381736.3	37	CCDS9314.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.505062	0.85282	.	.	ENSG00000139496	ENST00000381736;ENST00000381745;ENST00000313619;ENST00000463407;ENST00000381718;ENST00000381747;ENST00000394327	T;T;T;T;T	0.48522	1.4;1.42;1.42;1.41;0.81	5.42	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	M	0.69823	2.125	0.80722	D	1	P;D;D	0.60160	0.82;0.973;0.987	B;P;P	0.59889	0.446;0.668;0.865	T	0.61936	-0.6960	10	0.46703	T	0.11	-12.0255	10.7179	0.46023	0.0:0.0758:0.0:0.9242	.	325;337;337	A6NI12;Q9BVL2;Q9BVL2-2	.;NUPL1_HUMAN;.	Q	337;325;314;337;325;337;284	ENSP00000371155:H337Q;ENSP00000418555:H337Q;ENSP00000371137:H325Q;ENSP00000371166:H337Q;ENSP00000408147:H284Q	ENSP00000318459:H314Q	H	+	3	2	NUPL1	24797186	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	2.803000	0.47924	2.179000	0.69175	0.482000	0.46254	CAT		0.328	NUPL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044228.2			
TENM1	10178	hgsc.bcm.edu;ucsc.edu	37	X	123556363	123556363	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:123556363delG	ENST00000371130.3	-	23	4272	c.4209delC	c.(4207-4209)cccfs	p.P1403fs	TENM1_ENST00000422452.2_Frame_Shift_Del_p.P1410fs|STAG2_ENST00000469481.1_3'UTR	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1403					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GGCAGTGAATGGGGCGTCCTG	0.498																																																	0													118.0	97.0	104.0					X																	123556363		2203	4300	6503	SO:0001589	frameshift_variant	0			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.4209delC	X.37:g.123556363delG	ENSP00000360171:p.Pro1403fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RTR5|Q5JZ17	Frame_Shift_Del	DEL	ENST00000371130.3	37	CCDS14609.1																																																																																				0.498	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1		NM_014253	
OR1E1	8387	hgsc.bcm.edu	37	17	3301113	3301113	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:3301113delC	ENST00000322608.2	-	1	591	c.592delG	c.(592-594)gtgfs	p.V198fs		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	198					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|large_intestine(2)|lung(5)	10						ATAAATATCACCCATTCATTA	0.463																																																	0													55.0	53.0	54.0					17																	3301113		2203	4300	6503	SO:0001589	frameshift_variant	8387			U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.592delG	17.37:g.3301113delC	ENSP00000313384:p.Val198fs	Somatic		WXS	Illumina HiSeq	Phase_I	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Frame_Shift_Del	DEL	ENST00000322608.2	37	CCDS11024.1																																																																																				0.463	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1		NM_003553	
OR3A1	4994	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	3195481	3195481	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr17:3195481G>A	ENST00000323404.1	-	1	395	c.396C>T	c.(394-396)ccC>ccT	p.P132P	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	132					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P132P(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						TGTAGGTGAGGGGCCGGCAGA	0.592																																					GBM(20;287 516 18743 28660 36594)												1	Substitution - coding silent(1)	kidney(1)											102.0	98.0	99.0					17																	3195481		2203	4300	6503	SO:0001819	synonymous_variant	4994			X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.396C>T	17.37:g.3195481G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q4VB06|Q6IFM4	Silent	SNP	ENST00000323404.1	37	CCDS11023.1																																																																																				0.592	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2			
OR7A5	26659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	14938974	14938974	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr19:14938974A>G	ENST00000322301.3	-	2	167	c.80T>C	c.(79-81)cTc>cCc	p.L27P	OR7A5_ENST00000594432.1_Missense_Mutation_p.L27P|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	27					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L27P(1)		breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						CAGCCCAAAGAGGAAGGGTTG	0.478																																																	1	Substitution - Missense(1)	kidney(1)											60.0	56.0	58.0					19																	14938974		2203	4300	6503	SO:0001583	missense	26659			X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.80T>C	19.37:g.14938974A>G	ENSP00000316955:p.Leu27Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B2R682|Q6IFP1|Q96R96	Missense_Mutation	SNP	ENST00000322301.3	37	CCDS12318.1	.	.	.	.	.	.	.	.	.	.	a	13.49	2.253852	0.39896	.	.	ENSG00000188269	ENST00000322301	T	0.17691	2.26	3.13	3.13	0.36017	.	0.315632	0.17086	N	0.187566	T	0.39682	0.1087	M	0.92507	3.315	0.09310	N	0.999998	P	0.52577	0.954	P	0.52909	0.713	T	0.35525	-0.9785	10	0.87932	D	0	.	9.762	0.40537	1.0:0.0:0.0:0.0	.	27	Q15622	OR7A5_HUMAN	P	27	ENSP00000316955:L27P	ENSP00000316955:L27P	L	-	2	0	OR7A5	14799974	0.016000	0.18221	0.007000	0.13788	0.187000	0.23431	2.814000	0.48010	1.474000	0.48178	0.113000	0.15668	CTC		0.478	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1		NM_017506	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52588748	52588748	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:52588748delG	ENST00000296302.7	-	27	4602	c.4601delC	c.(4600-4602)ccafs	p.P1536fs	PBRM1_ENST00000409767.1_Intron|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.P1456fs|SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.P1481fs|PBRM1_ENST00000409114.3_Intron|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.P1429fs|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000337303.4_Intron|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.P1449fs			Q86U86	PB1_HUMAN	polybromo 1	1536	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		ACCCGGTGGTGGGATGCCCGG	0.567			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													40.0	39.0	39.0					3																	52588748		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4601delC	3.37:g.52588748delG	ENSP00000296302:p.Pro1536fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.567	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PDZD3	79849	broad.mit.edu;hgsc.bcm.edu	37	11	119059909	119059909	+	Missense_Mutation	SNP	G	G	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr11:119059909G>C	ENST00000531114.1	+	8	2230	c.1681G>C	c.(1681-1683)Gca>Cca	p.A561P	PDZD3_ENST00000322712.4_Missense_Mutation_p.A481P|PDZD3_ENST00000525131.1_Missense_Mutation_p.A482P|PDZD3_ENST00000355547.5_Missense_Mutation_p.A495P|PDZD3_ENST00000392817.2_Missense_Mutation_p.A561P			Q86UT5	NHRF4_HUMAN	PDZ domain containing 3	561					cGMP-mediated signaling (GO:0019934)|ion transport (GO:0006811)|negative regulation of cGMP biosynthetic process (GO:0030827)|negative regulation of guanylate cyclase activity (GO:0031283)|receptor guanylyl cyclase signaling pathway (GO:0007168)|response to toxic substance (GO:0009636)|water transport (GO:0006833)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytosol (GO:0005829)|subapical complex (GO:0035003)	guanylate cyclase inhibitor activity (GO:0030251)|ion channel inhibitor activity (GO:0008200)|protein C-terminus binding (GO:0008022)	p.A481P(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	14	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.52e-05)		CCCTGGGGCTGCAGAGGTGAG	0.612																																																	1	Substitution - Missense(1)	kidney(1)											13.0	15.0	14.0					11																	119059909		2199	4294	6493	SO:0001583	missense	79849			AK091966	CCDS8417.1, CCDS53719.1	11q23.3	2008-02-05	2006-01-24	2006-01-24	ENSG00000172367	ENSG00000172367			19891	protein-coding gene	gene with protein product		607146	"""PDZ domain containing 2"""	PDZK2		11950846	Standard	NM_024791		Approved	FLJ22756, IKEPP	uc001pvz.3	Q86UT5	OTTHUMG00000166224	ENST00000531114.1:c.1681G>C	11.37:g.119059909G>C	ENSP00000431164:p.Ala561Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N6R4|Q8NAW7|Q8NEX7|Q9H5Z3	Missense_Mutation	SNP	ENST00000531114.1	37		.	.	.	.	.	.	.	.	.	.	G	12.16	1.854917	0.32791	.	.	ENSG00000172367	ENST00000525131;ENST00000531114;ENST00000355547;ENST00000322712;ENST00000454065;ENST00000392817	T;T;T;T;T	0.73152	1.61;1.48;1.61;-0.72;1.48	5.15	2.18	0.27775	.	2.040040	0.02514	N	0.091815	T	0.55337	0.1914	N	0.14661	0.345	0.09310	N	1	P;P;P;B	0.35745	0.518;0.518;0.51;0.165	B;B;B;B	0.34931	0.133;0.133;0.192;0.094	T	0.51725	-0.8669	10	0.51188	T	0.08	1.696	5.9452	0.19215	0.1703:0.2928:0.5369:0.0	.	482;561;495;481	E9PPZ1;Q86UT5;Q86UT5-2;B0YJ61	.;NHRF4_HUMAN;.;.	P	482;561;495;481;495;561	ENSP00000434559:A482P;ENSP00000431164:A561P;ENSP00000347742:A495P;ENSP00000327107:A481P;ENSP00000376564:A561P	ENSP00000327107:A481P	A	+	1	0	PDZD3	118565119	0.000000	0.05858	0.003000	0.11579	0.242000	0.25591	0.159000	0.16442	0.546000	0.28920	0.561000	0.74099	GCA		0.612	PDZD3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000388471.1		NM_024791	
PLXND1	23129	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	129286540	129286540	+	Splice_Site	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:129286540C>T	ENST00000324093.4	-	21	4152		c.e21+1		PLXND1_ENST00000393239.1_Splice_Site	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1						angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.?(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						CCGCCCACTACCTTTGCGGAT	0.612																																					Ovarian(97;366 1484 3738 22084 39045)												1	Unknown(1)	kidney(1)											68.0	63.0	65.0					3																	129286540		2203	4300	6503	SO:0001630	splice_region_variant	23129			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.3973+1G>A	3.37:g.129286540C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Splice_Site	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.741635	0.69304	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2562	0.66053	0.0:0.9263:0.0:0.0737	.	.	.	.	.	-1	.	.	.	-	.	.	PLXND1	130769230	1.000000	0.71417	0.997000	0.53966	0.685000	0.39939	3.403000	0.52615	2.490000	0.84030	0.655000	0.94253	.		0.612	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4		NM_015103	Intron
PPFIBP1	8496	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	27824429	27824429	+	Silent	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:27824429T>C	ENST00000318304.8	+	14	1546	c.1263T>C	c.(1261-1263)acT>acC	p.T421T	PPFIBP1_ENST00000542629.1_Silent_p.T390T|PPFIBP1_ENST00000228425.6_Silent_p.T404T|PPFIBP1_ENST00000537927.1_Silent_p.T268T	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	421					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)		p.T421T(1)|p.T404T(1)	PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					GCATGGAAACTTCTGAAAAAT	0.323																																																	2	Substitution - coding silent(2)	kidney(2)											81.0	80.0	80.0					12																	27824429		2203	4299	6502	SO:0001819	synonymous_variant	8496			AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1263T>C	12.37:g.27824429T>C		Somatic		WXS	Illumina HiSeq	Phase_I	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																				0.323	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1		NM_003622	
PTAR1	375743	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	72338543	72338543	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr9:72338543G>A	ENST00000340434.4	-	6	649	c.646C>T	c.(646-648)Ctt>Ttt	p.L216F	PTAR1_ENST00000377200.5_Missense_Mutation_p.L137F	NM_001099666.1	NP_001093136.1	Q7Z6K3	PTAR1_HUMAN	protein prenyltransferase alpha subunit repeat containing 1	216					protein prenylation (GO:0018342)		protein prenyltransferase activity (GO:0008318)	p.L216F(2)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)	5						TCATCAAGAAGAATCTTTTAA	0.358																																																	2	Substitution - Missense(2)	kidney(2)											61.0	59.0	60.0					9																	72338543		1819	4088	5907	SO:0001583	missense	375743			BC053622	CCDS47978.1	9q21.13	2008-10-01			ENSG00000188647	ENSG00000188647		"""Prenyltransferase alpha subunit repeat containing"""	30449	protein-coding gene	gene with protein product						12477932	Standard	NM_001099666		Approved		uc004ahj.4	Q7Z6K3	OTTHUMG00000019982	ENST00000340434.4:c.646C>T	9.37:g.72338543G>A	ENSP00000344299:p.Leu216Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T7V5|Q5T7V6	Missense_Mutation	SNP	ENST00000340434.4	37	CCDS47978.1	.	.	.	.	.	.	.	.	.	.	G	13.98	2.397880	0.42512	.	.	ENSG00000188647	ENST00000377200;ENST00000340434	T;T	0.49720	0.77;0.77	5.69	5.69	0.88448	Protein prenyltransferase (1);	0.116735	0.64402	D	0.000010	T	0.44912	0.1316	L	0.53780	1.695	0.80722	D	1	B	0.28552	0.215	B	0.21917	0.037	T	0.33085	-0.9882	10	0.15952	T	0.53	.	20.181	0.98201	0.0:0.0:1.0:0.0	.	216	Q7Z6K3	PTAR1_HUMAN	F	137;216	ENSP00000366405:L137F;ENSP00000344299:L216F	ENSP00000344299:L216F	L	-	1	0	PTAR1	71528363	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.303000	0.72794	2.840000	0.97914	0.655000	0.94253	CTT		0.358	PTAR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052582.4		NM_001099666	
RBM45	129831	hgsc.bcm.edu	37	2	178977303	178977304	+	Frame_Shift_Ins	INS	-	-	G	rs146365140		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:178977303_178977304insG	ENST00000286070.5	+	1	122_123	c.30_31insG	c.(31-33)gggfs	p.G11fs		NM_152945.2	NP_694453.2	Q8IUH3	RBM45_HUMAN	RNA binding motif protein 45	11					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.00854)|Epithelial(96;0.00957)|all cancers(119;0.037)			CTGCGAGCGGCGGGGGCTTCCG	0.644											OREG0015102	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					0																																										SO:0001589	frameshift_variant	129831			AF526533	CCDS33335.1	2q31.2	2013-02-12			ENSG00000155636	ENSG00000155636		"""RNA binding motif (RRM) containing"""	24468	protein-coding gene	gene with protein product	"""developmentally regulated RNA binding protein 1"""	608888				12220514	Standard	XM_005246287		Approved	DRB1, FLJ44612	uc002ulv.3	Q8IUH3	OTTHUMG00000154202	ENST00000286070.5:c.35dupG	2.37:g.178977308_178977308dupG	ENSP00000286070:p.Gly11fs	Somatic	1950	WXS	Illumina HiSeq	Phase_I	Q6NYL0|Q8NFC9	Frame_Shift_Ins	INS	ENST00000286070.5	37	CCDS33335.1																																																																																				0.644	RBM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334375.2		NM_152945	
RDH11	51109	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	68151823	68151823	+	Missense_Mutation	SNP	A	A	G	rs182091562		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:68151823A>G	ENST00000381346.4	-	6	873	c.763T>C	c.(763-765)Ttt>Ctt	p.F255L	RP11-1012A1.4_ENST00000554493.1_5'UTR|RDH11_ENST00000428130.2_Missense_Mutation_p.F185L|RP11-1012A1.4_ENST00000553306.1_Silent_p.P85P|RDH11_ENST00000553384.1_Missense_Mutation_p.F242L	NM_001252650.1|NM_016026.3	NP_001239579.1|NP_057110.3	Q8TC12	RDH11_HUMAN	retinol dehydrogenase 11 (all-trans/9-cis/11-cis)	255					adaptation of rhodopsin mediated signaling (GO:0016062)|phototransduction, visible light (GO:0007603)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|photoreceptor inner segment (GO:0001917)	NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)	p.F255L(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)	12				all cancers(60;0.00047)|OV - Ovarian serous cystadenocarcinoma(108;0.00206)|BRCA - Breast invasive adenocarcinoma(234;0.00924)	Vitamin A(DB00162)	TTGATGAAAAAGGAGAAAAGC	0.488																																																	1	Substitution - Missense(1)	kidney(1)											101.0	88.0	92.0					14																	68151823		2203	4300	6503	SO:0001583	missense	51109			AF151840	CCDS32104.1, CCDS58326.1	14q24.1	2013-10-15	2006-05-09		ENSG00000072042	ENSG00000072042	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	17964	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 1"", ""androgen-regulated short-chain dehydrogenase/reductase 1"""	607849	"""retinol dehydrogenase 11 (all-trans and 9-cis)"""			12226107, 8018917, 19027726	Standard	NM_016026		Approved	MDT1, SDR7C1, ARSDR1	uc001xjv.4	Q8TC12	OTTHUMG00000171196	ENST00000381346.4:c.763T>C	14.37:g.68151823A>G	ENSP00000370750:p.Phe255Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDK3|A8K062|B2RB26|B4DDW0|Q0QD40|Q6IAH5|Q9NRW0|Q9Y391	Missense_Mutation	SNP	ENST00000381346.4	37	CCDS32104.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	8.875	0.950152	0.18431	.	.	ENSG00000072042	ENST00000381346;ENST00000553384;ENST00000428130;ENST00000554035;ENST00000557273	D;D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41;-2.08	5.07	-0.318	0.12728	NAD(P)-binding domain (1);	1.101550	0.07016	N	0.826018	T	0.72771	0.3502	N	0.05050	-0.12	0.09310	N	1	B;B;B	0.12013	0.005;0.002;0.001	B;B;B	0.10450	0.002;0.005;0.001	T	0.58070	-0.7701	10	0.11485	T	0.65	.	5.4924	0.16783	0.5799:0.2733:0.1467:0.0	.	185;242;255	B4DDW0;Q8TC12-2;Q8TC12	.;.;RDH11_HUMAN	L	255;242;185;141;168	ENSP00000370750:F255L;ENSP00000452079:F242L;ENSP00000416395:F185L;ENSP00000450802:F141L;ENSP00000450651:F168L	ENSP00000370750:F255L	F	-	1	0	RDH11	67221576	0.122000	0.22280	0.240000	0.24138	0.956000	0.61745	0.818000	0.27295	-0.207000	0.10187	0.482000	0.46254	TTT		0.488	RDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412257.3			
RIMKLA	284716	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	42880337	42880337	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:42880337G>A	ENST00000431473.3	+	5	997	c.868G>A	c.(868-870)Gat>Aat	p.D290N		NM_173642.3	NP_775913.2	Q8IXN7	RIMKA_HUMAN	ribosomal modification protein rimK-like family member A	290	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)	p.D249N(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						ATGCAACTTAGATGTGGGTGG	0.502																																																	1	Substitution - Missense(1)	kidney(1)											247.0	223.0	231.0					1																	42880337		2203	4300	6503	SO:0001583	missense	284716			BC039737	CCDS466.2	1p34.2	2011-09-21	2008-10-13	2008-10-13	ENSG00000177181	ENSG00000177181	6.3.2.N6		28725	protein-coding gene	gene with protein product	"""N-acetylaspartylglutamate synthetase II"""		"""family with sequence similarity 80, member A"""	FAM80A		20657015, 21454531	Standard	NM_173642		Approved	MGC47816, RP11-157D18.1, NAAGS-II	uc001chi.2	Q8IXN7	OTTHUMG00000007335	ENST00000431473.3:c.868G>A	1.37:g.42880337G>A	ENSP00000414330:p.Asp290Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VUS5	Missense_Mutation	SNP	ENST00000431473.3	37	CCDS466.2	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971126	0.74246	.	.	ENSG00000177181	ENST00000431473	.	.	.	5.23	5.23	0.72850	ATP-grasp fold (1);ATP-grasp fold, RimK-type (1);	0.000000	0.85682	D	0.000000	T	0.64114	0.2569	L	0.42686	1.345	0.80722	D	1	P	0.51449	0.945	P	0.55545	0.778	T	0.62709	-0.6797	9	0.40728	T	0.16	-29.6406	16.306	0.82848	0.0:0.0:1.0:0.0	.	290	Q8IXN7	RIMKA_HUMAN	N	290	.	ENSP00000414330:D290N	D	+	1	0	RIMKLA	42652924	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.297000	0.96120	2.447000	0.82792	0.561000	0.74099	GAT		0.502	RIMKLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019174.3		NM_173642	
RPN2	6185	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	35842239	35842239	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr20:35842239G>T	ENST00000237530.6	+	9	1374	c.1063G>T	c.(1063-1065)Gac>Tac	p.D355Y	RPN2_ENST00000373622.5_Missense_Mutation_p.D323Y	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	355					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)	p.D355Y(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				AGTTGAAGGTGACAACCGGTA	0.373																																																	1	Substitution - Missense(1)	kidney(1)											148.0	135.0	139.0					20																	35842239		2203	4300	6503	SO:0001583	missense	6185			Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"""oligosaccharyltransferase complex subunit (non-catalytic)"""	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1063G>T	20.37:g.35842239G>T	ENSP00000237530:p.Asp355Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	ENST00000237530.6	37	CCDS13291.1	.	.	.	.	.	.	.	.	.	.	G	19.76	3.887715	0.72410	.	.	ENSG00000118705	ENST00000237530;ENST00000373622	T;T	0.51574	0.7;0.7	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.67363	0.2885	M	0.65498	2.005	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;0.999;1.0;0.998	T	0.69506	-0.5127	10	0.72032	D	0.01	-21.244	16.2425	0.82423	0.0:0.0:1.0:0.0	.	230;323;355;355	A6NKT1;Q5JYR6;P04844;B2RE46	.;.;RPN2_HUMAN;.	Y	355;323	ENSP00000237530:D355Y;ENSP00000362724:D323Y	ENSP00000237530:D355Y	D	+	1	0	RPN2	35275653	1.000000	0.71417	0.993000	0.49108	0.736000	0.42039	7.802000	0.85969	2.700000	0.92200	0.557000	0.71058	GAC		0.373	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079076.2		NM_002951	
SCN3A	6328	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	165952091	165952091	+	Missense_Mutation	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:165952091A>G	ENST00000360093.3	-	25	4852	c.4361T>C	c.(4360-4362)tTt>tCt	p.F1454S	SCN3A_ENST00000409101.3_Missense_Mutation_p.F1405S|SCN3A_ENST00000540861.1_5'Flank|SCN3A_ENST00000283254.7_Missense_Mutation_p.F1454S|SCN3A_ENST00000465043.1_5'Flank	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1454					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.F1405S(1)|p.F1454S(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GAATGACCCAAAGATGATAAA	0.284																																																	2	Substitution - Missense(2)	kidney(2)											82.0	79.0	80.0					2																	165952091		2203	4300	6503	SO:0001583	missense	6328			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.4361T>C	2.37:g.165952091A>G	ENSP00000353206:p.Phe1454Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	29.8	5.033972	0.93575	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101	D;D;D	0.98666	-5.06;-5.06;-5.06	5.25	5.25	0.73442	.	0.062442	0.64402	D	0.000009	D	0.99330	0.9765	M	0.93763	3.455	0.80722	D	1	D;D;B	0.69078	0.997;0.997;0.131	D;D;B	0.78314	0.991;0.991;0.32	D	0.98837	1.0753	10	0.87932	D	0	.	15.619	0.76790	1.0:0.0:0.0:0.0	.	1405;1405;1454	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	S	1454;1454;1405	ENSP00000353206:F1454S;ENSP00000283254:F1454S;ENSP00000386726:F1405S	ENSP00000283254:F1454S	F	-	2	0	SCN3A	165660337	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	9.087000	0.94110	2.333000	0.79357	0.482000	0.46254	TTT		0.284	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_006922	
SCG2	7857	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	224462769	224462769	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:224462769G>T	ENST00000305409.2	-	2	1464	c.1232C>A	c.(1231-1233)tCc>tAc	p.S411Y		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)	p.S411Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		GCCACTCTTGGAGAGCATCCT	0.507																																																	1	Substitution - Missense(1)	kidney(1)											74.0	70.0	71.0					2																	224462769		2203	4300	6503	SO:0001583	missense	7857			M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1232C>A	2.37:g.224462769G>T	ENSP00000304133:p.Ser411Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000305409.2	37	CCDS2457.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.849091	0.51270	.	.	ENSG00000171951	ENST00000305409;ENST00000450330	T	0.01821	4.62	5.86	5.86	0.93980	.	0.344763	0.28544	N	0.014976	T	0.03783	0.0107	L	0.60455	1.87	0.39392	D	0.966449	B	0.20459	0.045	B	0.27076	0.076	T	0.35748	-0.9776	10	0.72032	D	0.01	.	14.9736	0.71251	0.0:0.0:0.8574:0.1426	.	411	P13521	SCG2_HUMAN	Y	411;271	ENSP00000304133:S411Y	ENSP00000304133:S411Y	S	-	2	0	SCG2	224171013	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.779000	0.62375	2.781000	0.95711	0.650000	0.86243	TCC		0.507	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2		NM_003469	
SECISBP2L	9728	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	49293222	49293222	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr15:49293222G>T	ENST00000559471.1	-	15	2363	c.2100C>A	c.(2098-2100)ttC>ttA	p.F700L	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.F655L|SECISBP2L_ENST00000559122.1_5'UTR	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	700							poly(A) RNA binding (GO:0044822)	p.F655L(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TGCGTTCCTGGAAACTGACAA	0.373																																																	1	Substitution - Missense(1)	kidney(1)											99.0	88.0	92.0					15																	49293222		2197	4295	6492	SO:0001583	missense	9728			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593			28997	protein-coding gene	gene with protein product		615756					Standard	NM_001193489		Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2100C>A	15.37:g.49293222G>T	ENSP00000453854:p.Phe700Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.078801	0.76528	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.76839	-1.05	5.09	0.897	0.19258	.	0.000000	0.85682	D	0.000000	D	0.83585	0.5286	M	0.83118	2.625	0.48696	D	0.999699	D;D	0.67145	0.996;0.993	P;P	0.58266	0.836;0.826	T	0.81814	-0.0760	10	0.48119	T	0.1	.	9.2249	0.37400	0.3818:0.0:0.6182:0.0	.	700;655	Q93073;Q93073-2	SBP2L_HUMAN;.	L	655;700	ENSP00000261847:F655L	ENSP00000261847:F655L	F	-	3	2	SECISBP2L	47080514	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.758000	0.38410	0.227000	0.20999	0.563000	0.77884	TTC		0.373	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1		NM_014701	
SETD2	29072	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	47162024	47162024	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:47162024G>A	ENST00000409792.3	-	3	4144	c.4102C>T	c.(4102-4104)Caa>Taa	p.Q1368*		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1368					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.Q865*(1)|p.Q1368*(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TCAGGTGCTTGCACTGACCCC	0.368			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	2	Substitution - Nonsense(2)	kidney(2)											69.0	71.0	70.0					3																	47162024		2203	4300	6503	SO:0001587	stop_gained	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4102C>T	3.37:g.47162024G>A	ENSP00000386759:p.Gln1368*	Somatic		WXS	Illumina HiSeq	Phase_I	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Nonsense_Mutation	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	40	7.979585	0.98594	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792;ENST00000412450	.	.	.	5.32	5.32	0.75619	.	0.000000	0.53938	D	0.000049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	19.1936	0.93677	0.0:0.0:1.0:0.0	.	.	.	.	X	1368;1368;1368;1324	.	ENSP00000386759:Q1368X	Q	-	1	0	SETD2	47137028	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.263000	0.95617	2.770000	0.95276	0.563000	0.77884	CAA		0.368	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	
SLC35B3	51000	broad.mit.edu;hgsc.bcm.edu	37	6	8422803	8422803	+	Silent	SNP	C	C	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr6:8422803C>G	ENST00000379660.4	-	5	923	c.474G>C	c.(472-474)ggG>ggC	p.G158G	SLC35B3_ENST00000339306.5_Silent_p.G158G	NM_001142540.1|NM_001142541.1|NM_015948.3	NP_001136012.1|NP_001136013.1|NP_057032.2	Q9H1N7	S35B3_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B3	158					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.G158G(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(1)|prostate(1)	15	Ovarian(93;0.0569)					TGTTTGATAACCCCATAGTAC	0.373																																					Melanoma(83;700 1353 9357 11478 30548)												1	Substitution - coding silent(1)	kidney(1)											118.0	112.0	114.0					6																	8422803		2203	4300	6503	SO:0001819	synonymous_variant	51000			AF132953	CCDS4508.1	6p24.3	2013-07-17	2013-07-17	2003-09-10	ENSG00000124786	ENSG00000124786		"""Solute carriers"""	21601	protein-coding gene	gene with protein product	"""3' phosphoadenosine 5' phosphosulfate transporter 2"""	610845	"""chromosome 6 open reading frame 196"", ""solute carrier family 35, member B3"""	C6orf196		10810093	Standard	XM_005249156		Approved	CGI-19, dJ453H5.1, PAPST2	uc010joe.3	Q9H1N7	OTTHUMG00000014224	ENST00000379660.4:c.474G>C	6.37:g.8422803C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A6NKX9|Q1XH11|Q6MZJ0|Q7Z662|Q9Y308	Silent	SNP	ENST00000379660.4	37	CCDS4508.1																																																																																				0.373	SLC35B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039802.1		NM_015948	
SLC7A14	57709	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	170198277	170198277	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:170198277G>A	ENST00000231706.5	-	7	2109	c.1794C>T	c.(1792-1794)atC>atT	p.I598I	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	598					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.I598I(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			CAACCAGAAGGATGGCCCACC	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											81.0	77.0	78.0					3																	170198277		2203	4300	6503	SO:0001819	synonymous_variant	57709			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.1794C>T	3.37:g.170198277G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																				0.537	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2		NM_020949	
ST7L	54879	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	113098583	113098583	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:113098583C>T	ENST00000358039.4	-	12	1607	c.1303G>A	c.(1303-1305)Gat>Aat	p.D435N	ST7L_ENST00000369668.2_Missense_Mutation_p.D435N|ST7L_ENST00000544629.1_Missense_Mutation_p.D370N|ST7L_ENST00000343210.7_Missense_Mutation_p.D435N|ST7L_ENST00000538187.1_Missense_Mutation_p.D379N|ST7L_ENST00000490067.1_Missense_Mutation_p.D418N|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000369666.1_Missense_Mutation_p.D418N|ST7L_ENST00000543570.1_Intron|ST7L_ENST00000360743.4_Missense_Mutation_p.D435N|ST7L_ENST00000369669.1_Missense_Mutation_p.D252N	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	435					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)		p.D435N(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTCACTATCACCCCGTTTC	0.368																																																	1	Substitution - Missense(1)	kidney(1)											118.0	108.0	112.0					1																	113098583		2203	4300	6503	SO:0001583	missense	54879			AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1303G>A	1.37:g.113098583C>T	ENSP00000350734:p.Asp435Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	C	35	5.436330	0.96168	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187	T;T;T;T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59;1.59;1.59;1.59	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.55625	0.1932	M	0.83223	2.63	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;0.999;1.0;1.0;1.0;1.0;1.0;1.0	T	0.61505	-0.7049	10	0.87932	D	0	-15.273	19.1881	0.93653	0.0:1.0:0.0:0.0	.	379;370;370;435;418;418;435;435	B7Z7D4;B7Z3J2;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;.;.;.;ST7L_HUMAN	N	435;435;216;370;252;418;435;435;418;379	ENSP00000350734:D435N;ENSP00000353972:D435N;ENSP00000445499:D370N;ENSP00000358683:D252N;ENSP00000417140:D418N;ENSP00000358682:D435N;ENSP00000345312:D435N;ENSP00000358680:D418N;ENSP00000444021:D379N	ENSP00000345312:D435N	D	-	1	0	ST7L	112900106	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	7.814000	0.86154	2.625000	0.88918	0.585000	0.79938	GAT		0.368	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			
STAB2	55576	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	104071251	104071251	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:104071251C>T	ENST00000388887.2	+	25	2871	c.2667C>T	c.(2665-2667)ggC>ggT	p.G889G		NM_017564.9	NP_060034.9			stabilin 2									p.G889G(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						TCAAAACTGGCACGGGCACCC	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											86.0	90.0	88.0					12																	104071251		2203	4300	6503	SO:0001819	synonymous_variant	55576			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2667C>T	12.37:g.104071251C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																				0.537	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			
SUPT7L	9913	broad.mit.edu;hgsc.bcm.edu	37	2	27876614	27876614	+	Splice_Site	SNP	C	C	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:27876614C>G	ENST00000337768.5	-	6	1552	c.983G>C	c.(982-984)aGt>aCt	p.S328T	SUPT7L_ENST00000406540.1_Splice_Site_p.S326T|SUPT7L_ENST00000464789.2_Splice_Site_p.S326T|SUPT7L_ENST00000405491.1_Splice_Site_p.S326T|SUPT7L_ENST00000404798.2_Splice_Site_p.S193T	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	328					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)	p.S328T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					TACCTCTGCACCTAGAAACAG	0.433																																																	1	Substitution - Missense(1)	kidney(1)											127.0	119.0	122.0					2																	27876614		1935	4148	6083	SO:0001630	splice_region_variant	9913			AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.983-1G>C	2.37:g.27876614C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4E3W3|Q6IB21|Q9H2T6	Missense_Mutation	SNP	ENST00000337768.5	37	CCDS42667.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.829457	0.50845	.	.	ENSG00000119760	ENST00000337768;ENST00000406540;ENST00000405491;ENST00000464789;ENST00000404798	.	.	.	5.96	5.96	0.96718	.	0.133387	0.64402	D	0.000002	T	0.42988	0.1227	N	0.08118	0	0.38683	D	0.952592	B;B;B	0.18310	0.016;0.027;0.016	B;B;B	0.21546	0.01;0.035;0.015	T	0.31336	-0.9947	9	0.33141	T	0.24	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	193;326;328	B4E3W3;O94864-2;O94864	.;.;ST65G_HUMAN	T	328;326;326;326;193	.	ENSP00000336750:S328T	S	-	2	0	SUPT7L	27730118	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.816000	0.55658	2.832000	0.97577	0.655000	0.94253	AGT		0.433	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1		NM_014860	Missense_Mutation
SYNC	81493	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	33149611	33149611	+	Splice_Site	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:33149611C>T	ENST00000409190.3	-	4	1896	c.1438G>A	c.(1438-1440)Ggg>Agg	p.G480R	SYNC_ENST00000373484.3_Intron|RBBP4_ENST00000373493.5_3'UTR	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	480	Tail.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)	p.G480R(1)|p.G149R(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						CAAAGATCACCTTGAGACTGT	0.478																																																	2	Substitution - Missense(2)	kidney(2)											298.0	298.0	298.0					1																	33149611		2203	4300	6503	SO:0001630	splice_region_variant	81493			AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.1438+1G>A	1.37:g.33149611C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	.	.	.	.	.	.	.	.	.	.	C	22.5	4.294391	0.81025	.	.	ENSG00000162520	ENST00000409190	D	0.97811	-4.55	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000009	D	0.97315	0.9122	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96416	0.9308	9	.	.	.	-23.267	15.7376	0.77859	0.0:1.0:0.0:0.0	.	480	Q9H7C4	SYNCI_HUMAN	R	480	ENSP00000386439:G480R	.	G	-	1	0	SYNC	32922198	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	2.231000	0.43009	2.873000	0.98535	0.561000	0.74099	GGG		0.478	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3		NM_030786	Missense_Mutation
TRIM33	51592	hgsc.bcm.edu;ucsc.edu	37	1	114948266	114948267	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:114948266_114948267insT	ENST00000358465.2	-	15	2616_2617	c.2533_2534insA	c.(2533-2535)atgfs	p.M845fs	TRIM33_ENST00000369543.2_Frame_Shift_Ins_p.M845fs|TRIM33_ENST00000476908.1_5'UTR|TRIM33_ENST00000450349.2_Frame_Shift_Ins_p.M477fs	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	845					gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GCTTTCATTCATATCTGCAGGT	0.48			T	RET	papillary thyroid																																			Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	0																																										SO:0001589	frameshift_variant	51592			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"", ""RING-type (C3HC4) zinc fingers"""	16290	protein-coding gene	gene with protein product	"""transcriptional intermediary factor 1 gamma"", ""ret-fused gene 7"""	605769	"""tripartite motif-containing 33"""			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.2534dupA	1.37:g.114948267_114948267dupT	ENSP00000351250:p.Met845fs	Somatic		WXS	Illumina HiSeq	Phase_I	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Frame_Shift_Ins	INS	ENST00000358465.2	37	CCDS872.1																																																																																				0.480	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1		NM_015906	
TRIP11	9321	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	92499570	92499570	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:92499570T>G	ENST00000267622.4	-	2	540	c.167A>C	c.(166-168)gAa>gCa	p.E56A	TRIP11_ENST00000555105.1_5'UTR	NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	56					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.E56A(1)		breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GGCTTCAATTTCCTTTGTCCT	0.284			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)			Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	1	Substitution - Missense(1)	kidney(1)											61.0	65.0	64.0					14																	92499570		2203	4289	6492	SO:0001583	missense	9321			L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.167A>C	14.37:g.92499570T>G	ENSP00000267622:p.Glu56Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.308914	0.81247	.	.	ENSG00000100815	ENST00000267622	T	0.66815	-0.23	5.85	4.71	0.59529	.	0.309211	0.32328	N	0.006245	T	0.76162	0.3949	M	0.65498	2.005	0.42008	D	0.990925	D	0.58268	0.982	P	0.59487	0.858	T	0.78038	-0.2360	10	0.66056	D	0.02	.	11.7861	0.52043	0.0:0.0683:0.0:0.9317	.	56	Q15643	TRIPB_HUMAN	A	56	ENSP00000267622:E56A	ENSP00000267622:E56A	E	-	2	0	TRIP11	91569323	1.000000	0.71417	0.959000	0.39883	0.981000	0.71138	5.858000	0.69532	1.049000	0.40321	0.533000	0.62120	GAA		0.284	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			
TTC24	164118	broad.mit.edu;hgsc.bcm.edu	37	1	156553240	156553240	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:156553240C>T	ENST00000368237.3	+	4	1150	c.1150C>T	c.(1150-1152)Cag>Tag	p.Q384*	TTC24_ENST00000368236.3_Nonsense_Mutation_p.Q384*|TTC24_ENST00000478081.1_Intron			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	384								p.Q384*(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGCCCAGTGTCAGGTGAGACC	0.597											OREG0013875	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Nonsense(1)	kidney(1)											24.0	27.0	26.0					1																	156553240		2016	4170	6186	SO:0001587	stop_gained	164118				CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1150C>T	1.37:g.156553240C>T	ENSP00000357220:p.Gln384*	Somatic	1779	WXS	Illumina HiSeq	Phase_I	Q5T3H7	Nonsense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	.	.	.	.	.	.	.	.	.	.	C	37	6.164580	0.97338	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	.	.	.	5.24	5.24	0.73138	.	0.316812	0.23463	N	0.047911	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-14.1332	15.6823	0.77381	0.0:1.0:0.0:0.0	.	.	.	.	X	384	.	ENSP00000357219:Q384X	Q	+	1	0	TTC24	154819864	1.000000	0.71417	0.998000	0.56505	0.911000	0.54048	4.306000	0.59117	2.739000	0.93911	0.555000	0.69702	CAG		0.597	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1		XM_089384	
TTN	7273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	179416718	179416718	+	Missense_Mutation	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:179416718G>T	ENST00000591111.1	-	285	86210	c.85986C>A	c.(85984-85986)aaC>aaA	p.N28662K	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.N27735K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.N21238K|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.N30303K|TTN_ENST00000359218.5_Missense_Mutation_p.N21363K|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.N21430K|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000592689.1_RNA			Q8WZ42	TITIN_HUMAN	titin	28662	Fibronectin type-III 108. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.N21238K(1)|p.N21363K(1)|p.N27733K(1)|p.N27735K(1)|p.N21430K(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTCCGTATCTGTTTTCTGCTC	0.438																																																	5	Substitution - Missense(5)	kidney(5)											118.0	124.0	122.0					2																	179416718		2157	4259	6416	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.85986C>A	2.37:g.179416718G>T	ENSP00000465570:p.Asn28662Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	13.87	2.367088	0.41902	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60920	0.15;0.15;0.15;0.15	5.76	1.39	0.22231	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.84065	0.5390	H	0.99090	4.425	0.50813	D	0.999892	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	D	0.86877	0.2039	9	0.87932	D	0	.	11.4274	0.50018	0.2902:0.0:0.7098:0.0	.	21238;21363;21430;28662	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	27735;21238;21430;21363;21235	ENSP00000343764:N27735K;ENSP00000434586:N21238K;ENSP00000340554:N21430K;ENSP00000352154:N21363K	ENSP00000340554:N21430K	N	-	3	2	TTN	179124964	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	1.178000	0.31981	0.353000	0.24079	0.655000	0.94253	AAC		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
USP33	23032	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	78195568	78195568	+	Missense_Mutation	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:78195568T>C	ENST00000370793.1	-	10	1133	c.787A>G	c.(787-789)Aca>Gca	p.T263A	USP33_ENST00000357428.1_Missense_Mutation_p.T263A|USP33_ENST00000370792.3_Missense_Mutation_p.T263A|USP33_ENST00000370794.3_Missense_Mutation_p.T232A	NM_015017.4	NP_055832.3	Q8TEY7	UBP33_HUMAN	ubiquitin specific peptidase 33	263	USP.				axon guidance (GO:0007411)|cell migration (GO:0016477)|centrosome duplication (GO:0051298)|endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell body (GO:0044297)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|VCB complex (GO:0030891)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.T263A(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|prostate(2)|urinary_tract(1)	44						CCCCGAAATGTTGGATTTACA	0.308																																					Melanoma(152;72 1870 11110 26780 42647)												1	Substitution - Missense(1)	kidney(1)											85.0	92.0	90.0					1																	78195568		2203	4300	6503	SO:0001583	missense	23032			AF383173	CCDS678.1, CCDS679.1, CCDS680.1	1p31	2008-02-05	2005-08-08		ENSG00000077254	ENSG00000077254		"""Ubiquitin-specific peptidases"""	20059	protein-coding gene	gene with protein product		615146	"""ubiquitin specific protease 33"""			12838346	Standard	NM_015017		Approved	KIAA1097, VDU1	uc001dht.4	Q8TEY7	OTTHUMG00000009651	ENST00000370793.1:c.787A>G	1.37:g.78195568T>C	ENSP00000359829:p.Thr263Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TEY6|Q96AV6|Q9H9F0|Q9UPQ5	Missense_Mutation	SNP	ENST00000370793.1	37	CCDS678.1	.	.	.	.	.	.	.	.	.	.	T	15.00	2.702646	0.48307	.	.	ENSG00000077254	ENST00000370794;ENST00000370793;ENST00000357428;ENST00000370792	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.32	4.03	0.46877	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.087082	0.85682	D	0.000000	T	0.07098	0.0180	N	0.17594	0.5	0.33544	D	0.595191	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.002;0.002;0.004	T	0.18555	-1.0333	10	0.22706	T	0.39	.	8.6762	0.34181	0.0:0.1614:0.0:0.8386	.	263;232;263	Q8TEY7-3;Q8TEY7-2;Q8TEY7	.;.;UBP33_HUMAN	A	232;263;263;263	ENSP00000359830:T232A;ENSP00000359829:T263A;ENSP00000350009:T263A;ENSP00000359828:T263A	ENSP00000350009:T263A	T	-	1	0	USP33	77968156	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.568000	0.45965	2.152000	0.67230	0.528000	0.53228	ACA		0.308	USP33-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026923.2		NM_015017	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188245	10188245	+	Missense_Mutation	SNP	G	G	T	rs104893830		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:10188245G>T	ENST00000256474.2	+	2	1228	c.388G>T	c.(388-390)Gtt>Ttt	p.V130F	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	130	Involved in binding to CCT complex.		V -> L (in ECYT2 and VHLD; type I). {ECO:0000269|PubMed:12393546, ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.V130L(9)|p.V130>F(1)|p.V130F(1)|p.H125fs*27(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGGGCTTCTGGTTAACCAAAC	0.463		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	12	Substitution - Missense(10)|Deletion - Frameshift(1)|Complex - compound substitution(1)	kidney(12)	GRCh37	CM031394|CM961427	VHL	M	rs104893830						205.0	189.0	195.0					3																	10188245		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.388G>T	3.37:g.10188245G>T	ENSP00000256474:p.Val130Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.964999	0.74131	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99857	-7.22	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96551	0.9408	10	0.87932	D	0	-11.5971	16.3181	0.82935	0.0:0.0:1.0:0.0	.	130	P40337	VHL_HUMAN	F	130;48	ENSP00000256474:V130F	ENSP00000256474:V130F	V	+	1	0	VHL	10163245	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	7.274000	0.78538	2.530000	0.85305	0.563000	0.77884	GTT		0.463	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VPS37A	137492	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	17125809	17125809	+	Missense_Mutation	SNP	T	T	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr8:17125809T>G	ENST00000324849.4	+	3	917	c.243T>G	c.(241-243)agT>agG	p.S81R	VPS37A_ENST00000324815.3_Missense_Mutation_p.S81R|VPS37A_ENST00000521829.1_Missense_Mutation_p.S56R	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	81					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.S81R(1)		autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		CAGTGATCAGTGTTTATCCAC	0.348																																																	1	Substitution - Missense(1)	kidney(1)											124.0	118.0	120.0					8																	17125809		2203	4300	6503	SO:0001583	missense	137492				CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"""hepatocellular carcinoma related protein 1"""	609927	"""vacuolar protein sorting 37A (yeast)"", ""polyglutamine binding protein 2"""	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.243T>G	8.37:g.17125809T>G	ENSP00000318629:p.Ser81Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	37	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656854	0.67586	.	.	ENSG00000155975	ENST00000324849;ENST00000324815;ENST00000518038;ENST00000521829	T;T	0.56776	0.44;0.45	4.8	1.12	0.20585	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.55257	0.1909	L	0.43923	1.385	0.51767	D	0.999937	D;D	0.76494	0.999;0.999	D;D	0.80764	0.967;0.994	T	0.52786	-0.8529	10	0.09843	T	0.71	-13.3548	8.9154	0.35579	0.0:0.2254:0.0:0.7746	.	56;81	Q8NEZ2-2;Q8NEZ2	.;VP37A_HUMAN	R	81;81;92;56	ENSP00000318629:S81R;ENSP00000429680:S56R	ENSP00000318173:S81R	S	+	3	2	VPS37A	17170180	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.878000	0.48515	0.364000	0.24374	0.533000	0.62120	AGT		0.348	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2		NM_152415	
WBSCR17	64409	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	71177037	71177038	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr7:71177037_71177038GC>AT	ENST00000333538.5	+	11	2337_2338	c.1703_1704GC>AT	c.(1702-1704)tGC>tAT	p.C568Y	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	568	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.C568C(1)|p.C568>?(1)|p.C568Y(1)		NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				ACGGGACGCTGCCTGGAGGTGG	0.569																																																	3	Substitution - Missense(1)|Complex(1)|Substitution - coding silent(1)	kidney(3)																																								SO:0001583	missense	64409			AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	Exception_encountered	7.37:g.71177037_71177038delinsAT	ENSP00000329654:p.Cys568Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NFV9|Q9NTA8	Missense_Mutation|Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																				0.569	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1		NM_022479	
WWC3	55841	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	10085338	10085338	+	Silent	SNP	C	C	T	rs148094144		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chrX:10085338C>T	ENST00000380861.4	+	11	1630	c.1239C>T	c.(1237-1239)ttC>ttT	p.F413F	WWC3_ENST00000454666.1_Silent_p.F413F	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	413	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)	p.F413F(1)		NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						TTCTACGCTTCGACCTCATTC	0.662																																																	1	Substitution - coding silent(1)	kidney(1)						C		1,3834		0,1,1631,571	75.0	72.0	73.0		1239	-7.1	0.4	X	dbSNP_134	73	0,6728		0,0,2428,1872	no	coding-synonymous	WWC3	NM_015691.3		0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095		413/1093	10085338	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	55841			AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1239C>T	X.37:g.10085338C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																				0.662	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1		NM_015691	
XDH	7498	broad.mit.edu;ucsc.edu	37	2	31598321	31598321	+	Silent	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:31598321G>A	ENST00000379416.3	-	15	1575	c.1527C>T	c.(1525-1527)tgC>tgT	p.C509C		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	509					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)	p.C509C(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GGGTGAGGGTGCACCGGAAGT	0.612																																					Colon(66;682 1445 30109 40147)												1	Substitution - coding silent(1)	kidney(1)											95.0	90.0	91.0					2																	31598321		2203	4300	6503	SO:0001819	synonymous_variant	7498			D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1527C>T	2.37:g.31598321G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																				0.612	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1		NM_000379	
YLPM1	56252	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	75248501	75248501	+	Silent	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:75248501A>T	ENST00000552421.1	+	4	1879	c.1755A>T	c.(1753-1755)gcA>gcT	p.A585A	YLPM1_ENST00000238571.3_Intron|YLPM1_ENST00000325680.7_Silent_p.A585A			P49750	YLPM1_HUMAN	YLP motif containing 1	0					regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.A585A(1)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		TCTCTTCTGCAGGGCCACCAC	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											136.0	141.0	139.0					14																	75248501		2019	4158	6177	SO:0001819	synonymous_variant	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.1755A>T	14.37:g.75248501A>T		Somatic		WXS	Illumina HiSeq	Phase_I	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000552421.1	37																																																																																					0.597	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1		NM_019589	
ZNF107	51427	broad.mit.edu;hgsc.bcm.edu	37	7	64167976	64167976	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr7:64167976delA	ENST00000395391.1	+	4	2669	c.1294delA	c.(1294-1296)aaafs	p.K432fs	ZNF107_ENST00000344930.3_Frame_Shift_Del_p.K432fs|ZNF107_ENST00000423627.1_Frame_Shift_Del_p.K432fs			Q9UII5	ZN107_HUMAN	zinc finger protein 107	432					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				TAGACATAAGAAAATTCATAC	0.348																																																	0													32.0	36.0	35.0					7																	64167976		2193	4296	6489	SO:0001589	frameshift_variant	51427			AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.1294delA	7.37:g.64167976delA	ENSP00000378789:p.Lys432fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000395391.1	37	CCDS5527.1																																																																																				0.348	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1		NM_016220	
ZNF354B	117608	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	178293302	178293302	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr5:178293302C>T	ENST00000322434.3	+	3	317	c.91C>T	c.(91-93)Ctg>Ttg	p.L31L		NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.L31L(1)		breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTGGAGAAAGCTGGCTCCTTC	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											153.0	144.0	147.0					5																	178293302		2203	4300	6503	SO:0001819	synonymous_variant	117608			AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.91C>T	5.37:g.178293302C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																				0.507	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1		NM_058230	
ZNF419	79744	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	58005254	58005254	+	Missense_Mutation	SNP	G	G	A			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr19:58005254G>A	ENST00000221735.7	+	5	1515	c.1329G>A	c.(1327-1329)atG>atA	p.M443I	ZNF419_ENST00000354197.4_Intron|ZNF419_ENST00000347466.6_Missense_Mutation_p.M411I|ZNF419_ENST00000426954.2_Missense_Mutation_p.M431I|AC003005.4_ENST00000601674.1_Intron|ZNF419_ENST00000442920.2_Missense_Mutation_p.M430I|ZNF419_ENST00000424930.2_Missense_Mutation_p.M444I|ZNF419_ENST00000415379.2_Missense_Mutation_p.M397I			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	443					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.M411I(1)|p.M418I(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CAACCCTCATGCAACATCGAA	0.423																																																	2	Substitution - Missense(2)	kidney(2)											115.0	121.0	119.0					19																	58005254		2203	4300	6503	SO:0001583	missense	79744			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.1329G>A	19.37:g.58005254G>A	ENSP00000221735:p.Met443Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Missense_Mutation	SNP	ENST00000221735.7	37	CCDS54326.1	.	.	.	.	.	.	.	.	.	.	G	0.608	-0.826113	0.02734	.	.	ENSG00000105136	ENST00000284020;ENST00000424930;ENST00000426954;ENST00000442920;ENST00000517598;ENST00000347466;ENST00000415379;ENST00000221735	T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23	2.11	-0.544	0.11847	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04861	0.0131	N	0.02192	-0.645	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.001;0.0;0.001	B;B;B;B;B;B;B	0.06405	0.001;0.001;0.002;0.002;0.0;0.001;0.0	T	0.42982	-0.9419	9	0.08381	T	0.77	.	5.1677	0.15094	0.1727:0.0:0.53:0.2973	.	397;397;430;431;444;411;443	E9PFX9;B4DXU7;E9PCP4;E9PET3;E9PED0;Q96HQ0-2;Q96HQ0	.;.;.;.;.;.;ZN419_HUMAN	I	418;444;431;430;444;411;397;443	ENSP00000388864:M444I;ENSP00000390916:M431I;ENSP00000414709:M430I;ENSP00000299860:M411I;ENSP00000392129:M397I;ENSP00000221735:M443I	ENSP00000221735:M443I	M	+	3	0	ZNF419	62697066	0.000000	0.05858	0.000000	0.03702	0.748000	0.42578	-4.664000	0.00201	-0.385000	0.07833	0.205000	0.17691	ATG		0.423	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1		NM_024691	
ACIN1	22985	broad.mit.edu	37	14	23549554	23549554	+	Silent	SNP	G	G	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:23549554G>T	ENST00000262710.1	-	6	1491	c.1164C>A	c.(1162-1164)tcC>tcA	p.S388S	ACIN1_ENST00000457657.1_Silent_p.S348S|ACIN1_ENST00000605057.1_Silent_p.S330S|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000555053.1_Silent_p.S388S	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	388	Glu-rich.				apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S388S(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		GTCGAGGAGGGGAAGGAGACT	0.473																																																	1	Substitution - coding silent(1)	kidney(1)											68.0	68.0	68.0					14																	23549554		2203	4300	6503	SO:0001819	synonymous_variant	22985			AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.1164C>A	14.37:g.23549554G>T		Somatic		WXS	Illumina GAIIx	Phase_I	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Silent	SNP	ENST00000262710.1	37	CCDS9587.1																																																																																				0.473	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3		NM_014977	
PHF7	51533	broad.mit.edu	37	3	52443747	52443747	+	5'Flank	SNP	A	A	G			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr3:52443747A>G	ENST00000327906.3	+	0	0				BAP1_ENST00000460680.1_Missense_Mutation_p.L17P|BAP1_ENST00000296288.5_Missense_Mutation_p.L17P|PHF7_ENST00000347025.2_5'Flank	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.L17P(1)|p.?(1)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		TTCCACGAGCAGGGTGAAGAG	0.697																																																	2	Substitution - Missense(1)|Unknown(1)	eye(1)|kidney(1)											32.0	39.0	36.0					3																	52443747		2203	4299	6502	SO:0001631	upstream_gene_variant	8314			AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"""Zinc fingers, PHD-type"""	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52443747A>G	Exception_encountered	Somatic		WXS	Illumina GAIIx	Phase_I	K4DI82	Missense_Mutation	SNP	ENST00000327906.3	37	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.608218	0.87258	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	T;T	0.54279	0.58;0.58	4.5	4.5	0.54988	Peptidase C12, ubiquitin carboxyl-terminal hydrolase 1 (4);	0.000000	0.85682	D	0.000000	T	0.73418	0.3584	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77278	-0.2647	10	0.52906	T	0.07	-1.916	14.118	0.65167	1.0:0.0:0.0:0.0	.	17	Q92560	BAP1_HUMAN	P	17	ENSP00000417132:L17P;ENSP00000296288:L17P	ENSP00000296288:L17P	L	-	2	0	BAP1	52418787	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.781000	0.91805	1.809000	0.52856	0.533000	0.62120	CTG		0.697	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1		NM_016483	
EP400	57634	broad.mit.edu	37	12	132547093	132547093	+	Silent	SNP	A	A	G	rs10902490|rs528214697	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr12:132547093A>G	ENST00000333577.4	+	48	8398	c.8289A>G	c.(8287-8289)caA>caG	p.Q2763Q	EP400_ENST00000389561.2_Silent_p.Q2727Q|EP400_ENST00000330386.6_Silent_p.Q2646Q|EP400_ENST00000332482.4_Silent_p.Q2690Q|EP400_ENST00000389562.2_Silent_p.Q2726Q			Q96L91	EP400_HUMAN	E1A binding protein p400	2763	Interaction with ZNF42. {ECO:0000250}.|Poly-Gln.				chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.Q2726Q(9)		NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		agcagcaacaacagcagcagc	0.567																																																	9	Substitution - coding silent(9)	lung(3)|kidney(2)|endometrium(2)|central_nervous_system(2)											25.0	29.0	28.0					12																	132547093		2173	4217	6390	SO:0001819	synonymous_variant	57634			U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.8289A>G	12.37:g.132547093A>G		Somatic		WXS	Illumina GAIIx	Phase_I	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																					0.567	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			NM_015409	
IFT140	9742	broad.mit.edu	37	16	1570643	1570643	+	Missense_Mutation	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr16:1570643A>T	ENST00000426508.2	-	27	3983	c.3620T>A	c.(3619-3621)cTg>cAg	p.L1207Q	IFT140_ENST00000361339.5_Missense_Mutation_p.L401Q	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	1207					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)		p.L1207Q(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CTTGGTGGCCAGGTGGTAGCT	0.672																																																	1	Substitution - Missense(1)	kidney(1)											39.0	34.0	36.0					16																	1570643		2196	4299	6495	SO:0001583	missense	9742			AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.3620T>A	16.37:g.1570643A>T	ENSP00000406012:p.Leu1207Gln	Somatic		WXS	Illumina GAIIx	Phase_I	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.253793	0.80135	.	.	ENSG00000187535	ENST00000397417;ENST00000361339;ENST00000426508	T;T	0.49720	0.77;0.77	5.78	5.78	0.91487	.	0.168249	0.40640	N	0.001043	T	0.70159	0.3192	M	0.80028	2.48	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.79784	0.973;0.993	T	0.70769	-0.4782	10	0.39692	T	0.17	.	16.3979	0.83621	1.0:0.0:0.0:0.0	.	1207;894	Q96RY7;B4DR58	IF140_HUMAN;.	Q	1207;401;1207	ENSP00000354895:L401Q;ENSP00000406012:L1207Q	ENSP00000354895:L401Q	L	-	2	0	IFT140	1510644	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	9.210000	0.95106	2.333000	0.79357	0.533000	0.62120	CTG		0.672	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2		NM_014714	
Unknown	0	broad.mit.edu	37	13	19409453	19409453	+	IGR	SNP	T	T	C	rs138555198	byFrequency	TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr13:19409453T>C								LINC00418 (115584 upstream) : RP11-38M15.11 (24513 downstream)																							TCAACATGTATCCAGAACCAA	0.279													.|||	386	0.0770767	0.2005	0.0576	5008	,	,		17750	0.0		0.0706	False		,,,				2504	0.0102																0																																										SO:0001628	intergenic_variant	0																															13.37:g.19409453T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.279									
Unknown	0	broad.mit.edu	37	9	66500808	66500808	+	IGR	SNP	T	T	G	rs62562158		TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr9:66500808T>G								RP11-262H14.1 (31498 upstream) : RP11-262H14.7 (16397 downstream)																							CCACCTACGGTCGGTTGTGTG	0.632																																																	0																																										SO:0001628	intergenic_variant	0																															9.37:g.66500808T>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.632									
Unknown	0	broad.mit.edu	37	1	121298440	121298440	+	IGR	SNP	T	T	C			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr1:121298440T>C								RP11-344P13.6 (37813 upstream) : RP11-344P13.1 (17303 downstream)																							AGTGAACAACTTGAGAATAAT	0.373																																																	0																																										SO:0001628	intergenic_variant	0																															1.37:g.121298440T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.373									
NLRP7	199713	broad.mit.edu	37	19	55451068	55451068	+	Silent	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr19:55451068C>T	ENST00000590030.1	-	3	1159	c.1119G>A	c.(1117-1119)ctG>ctA	p.L373L	NLRP7_ENST00000448121.2_Silent_p.L373L|NLRP7_ENST00000328092.5_Silent_p.L373L|NLRP7_ENST00000340844.2_Silent_p.L373L|NLRP7_ENST00000588756.1_Silent_p.L373L|NLRP7_ENST00000592784.1_Silent_p.L373L|NLRP7_ENST00000446217.1_Silent_p.L401L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	373	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)	p.L373L(2)		autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TCTGCAGCTTCAGAGTCGTGC	0.662																																																	2	Substitution - coding silent(2)	kidney(2)											30.0	32.0	31.0					19																	55451068		2198	4299	6497	SO:0001819	synonymous_variant	199713			AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1119G>A	19.37:g.55451068C>T		Somatic		WXS	Illumina GAIIx	Phase_I	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																				0.662	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1		NM_139176	
RARS	5917	broad.mit.edu	37	5	167927655	167927655	+	Silent	SNP	A	A	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr5:167927655A>T	ENST00000231572.3	+	8	936	c.882A>T	c.(880-882)gtA>gtT	p.V294V	RARS_ENST00000538719.1_Silent_p.V88V|RARS_ENST00000520421.1_3'UTR	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	294					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.V294V(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		ATCAGTGTGTAGTTCTGCTCC	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											75.0	81.0	79.0					5																	167927655		2203	4300	6503	SO:0001819	synonymous_variant	5917			BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.882A>T	5.37:g.167927655A>T		Somatic		WXS	Illumina GAIIx	Phase_I	B2RBS9|Q53GY4|Q9BWA1	Silent	SNP	ENST00000231572.3	37	CCDS4367.1																																																																																				0.388	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2		NM_002887	
SPTB	6710	broad.mit.edu	37	14	65241143	65241143	+	Missense_Mutation	SNP	C	C	T			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr14:65241143C>T	ENST00000389721.5	-	23	4977	c.4945G>A	c.(4945-4947)Ggc>Agc	p.G1649S	SPTB_ENST00000556626.1_Missense_Mutation_p.G1649S|SPTB_ENST00000542895.1_Missense_Mutation_p.G1649S|SPTB_ENST00000389720.3_Missense_Mutation_p.G1649S|SPTB_ENST00000389722.3_Missense_Mutation_p.G1649S	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1649					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)	p.G1649S(1)		breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		GACAGCAGGCCCTGGGCCCGG	0.667																																																	1	Substitution - Missense(1)	kidney(1)											10.0	12.0	11.0					14																	65241143		2178	4275	6453	SO:0001583	missense	6710				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.4945G>A	14.37:g.65241143C>T	ENSP00000374371:p.Gly1649Ser	Somatic		WXS	Illumina GAIIx	Phase_I	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	9.297	1.052116	0.19827	.	.	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000335612;ENST00000553938;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	5.39	-6.0	0.02206	.	0.625698	0.17626	N	0.167542	T	0.11495	0.0280	N	0.01656	-0.775	0.24470	N	0.994392	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.12156	0.007;0.001;0.001	T	0.30679	-0.9970	10	0.09084	T	0.74	.	3.187	0.06604	0.1055:0.3364:0.1073:0.4507	.	433;1649;1653	E7EV95;P11277;Q59FP5	.;SPTB1_HUMAN;.	S	1653;1649;433;314;1649;1649;1649;1649	ENSP00000374372:G1649S;ENSP00000451324:G314S;ENSP00000451752:G1649S;ENSP00000374371:G1649S;ENSP00000443882:G1649S;ENSP00000374370:G1649S	ENSP00000334218:G433S	G	-	1	0	SPTB	64310896	0.000000	0.05858	0.953000	0.39169	0.431000	0.31685	-0.424000	0.07025	-0.978000	0.03533	0.542000	0.68232	GGC		0.667	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			
NPIPA8	101059953	broad.mit.edu	37	16	18441114	18441116	+	Splice_Site	DEL	CAC	CAC	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr16:18441114_18441116delCAC	ENST00000339303.5	-	1	15		c.e1+1					P0DM63	NPIA8_HUMAN	nuclear pore complex interacting protein family, member A8																		CGGCCATACTCACCACTGGGACT	0.709																																																	0																																										SO:0001630	splice_region_variant	0				CCDS61865.1	16p12.3	2013-06-11			ENSG00000214940	ENSG00000214940			41983	protein-coding gene	gene with protein product	"""morpheus gene family member 9"""					11586358	Standard	NM_001282511		Approved	LCR16a9		P0DM63	OTTHUMG00000166284	ENST00000339303.5:c.4043+1GTG>-	16.37:g.18441117_18441119delCAC		Somatic		WXS	Illumina GAIIx	Phase_I		Splice_Site	DEL	ENST00000339303.5	37																																																																																					0.709	NPIPA8-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				Intron
IGKV2-26	28922	broad.mit.edu	37	2	89495754	89495754	+	IGR	DEL	A	A	-			TCGA-CW-5580-01A-01D-1669-08	TCGA-CW-5580-11A-02D-1669-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6e4ed3ae-aa80-453a-95be-0af96a7bc4e3	54af26e6-d457-44ae-b574-4e74df45fd7c	g.chr2:89495754delA								IGKV2-24 (19110 upstream) : IGKV1-27 (17153 downstream)																							AAACCAATACAAATAGGTGTA	0.532																																																	0																																										SO:0001628	intergenic_variant	0																															2.37:g.89495754delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.532									
