#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
ALG6	29929	hgsc.bcm.edu;ucsc.edu	37	1	63902501	63902506	+	In_Frame_Del	DEL	TCTCAG	TCTCAG	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	TCTCAG	TCTCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:63902501_63902506delTCTCAG	ENST00000371108.4	+	15	1639_1644	c.1334_1339delTCTCAG	c.(1333-1341)atctcagtc>atc	p.SV446del	ALG6_ENST00000494765.1_3'UTR|ALG6_ENST00000263440.4_In_Frame_Del_p.SV448del	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	446					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosyltransferase activity (GO:0046527)			endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CAGTTTCTTATCTCAGTCATCACTAT	0.369																																																	0																																										SO:0001651	inframe_deletion	29929			AF063604	CCDS30735.1	1p31.3	2013-03-01	2013-03-01		ENSG00000088035	ENSG00000088035	2.4.1.267		23157	protein-coding gene	gene with protein product	"""dolichyl-P-Glc:Man(9)GlcNAc(2)-PP-dolichol alpha- 1->3-glucosyltransferase"""	604566	"""asparagine-linked glycosylation 6 homolog (yeast, alpha-1,3-glucosyltransferase)"", ""asparagine-linked glycosylation 6, alpha-1,3-glucosyltransferase homolog (S. cerevisiae)"""			10359825, 11875054	Standard	NM_013339		Approved		uc021oof.1	Q9Y672	OTTHUMG00000009140	ENST00000371108.4:c.1334_1339delTCTCAG	1.37:g.63902501_63902506delTCTCAG	ENSP00000360149:p.Ser446_Val447del	Somatic		WXS	Illumina HiSeq	Phase_I	B3KMU2|Q5SXR9|Q9H3I0	In_Frame_Del	DEL	ENST00000371108.4	37	CCDS30735.1																																																																																				0.369	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2		NM_013339	
ANKMY1	51281	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	241465702	241465702	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:241465702A>G	ENST00000272972.3	-	5	1061	c.847T>C	c.(847-849)Ttt>Ctt	p.F283L	ANKMY1_ENST00000403283.1_Intron|ANKMY1_ENST00000391987.1_Missense_Mutation_p.F283L|ANKMY1_ENST00000373320.4_Intron|ANKMY1_ENST00000406958.1_Intron|ANKMY1_ENST00000361678.4_Intron|ANKMY1_ENST00000462004.1_5'UTR|ANKMY1_ENST00000373318.2_Intron|ANKMY1_ENST00000536462.1_Intron|ANKMY1_ENST00000405002.1_Intron|ANKMY1_ENST00000401804.1_Missense_Mutation_p.F372L|ANKMY1_ENST00000405523.3_Intron	NM_016552.2	NP_057636.2	Q9P2S6	ANKY1_HUMAN	ankyrin repeat and MYND domain containing 1	283							metal ion binding (GO:0046872)			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)		GCACTAGCAAAGTTGTCCTTC	0.562																																																	0													167.0	147.0	154.0					2																	241465702		2203	4300	6503	SO:0001583	missense	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	ENST00000272972.3:c.847T>C	2.37:g.241465702A>G	ENSP00000272972:p.Phe283Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B2RB78|Q4ZFV3|Q8IYX5|Q8NDK5|Q9H0V8|Q9NX10	Missense_Mutation	SNP	ENST00000272972.3	37	CCDS2536.1	.	.	.	.	.	.	.	.	.	.	A	1.353	-0.590995	0.03799	.	.	ENSG00000144504	ENST00000272972;ENST00000391987;ENST00000401804	T;T;T	0.33216	1.42;1.42;1.42	4.11	-0.32	0.12721	Ankyrin repeat-containing domain (4);	0.501265	0.17058	N	0.188657	T	0.07503	0.0189	N	0.01109	-1.01	0.09310	N	0.999999	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.30327	-0.9982	10	0.21014	T	0.42	-8.5545	3.3393	0.07113	0.4881:0.0:0.3242:0.1877	.	283;283	Q4ZFV3;Q9P2S6	.;ANKY1_HUMAN	L	283;283;372	ENSP00000272972:F283L;ENSP00000375847:F283L;ENSP00000385887:F372L	ENSP00000272972:F283L	F	-	1	0	ANKMY1	241114375	0.034000	0.19679	0.001000	0.08648	0.034000	0.12701	0.810000	0.27183	-0.038000	0.13624	0.482000	0.46254	TTT		0.562	ANKMY1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257187.2		NM_017844	
ARID1A	8289	broad.mit.edu;hgsc.bcm.edu	37	1	27097703	27097703	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:27097703C>T	ENST00000324856.7	+	12	3663	c.3292C>T	c.(3292-3294)Cag>Tag	p.Q1098*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q715*|ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q1098*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1098	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GCAGTATATCCAGTGTCTCTA	0.483			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	0													91.0	82.0	85.0					1																	27097703		2203	4300	6503	SO:0001587	stop_gained	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3292C>T	1.37:g.27097703C>T	ENSP00000320485:p.Gln1098*	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	43	9.856913	0.99281	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	.	.	.	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-6.1526	19.4303	0.94760	0.0:1.0:0.0:0.0	.	.	.	.	X	1098;1098;715	.	ENSP00000320485:Q1098X	Q	+	1	0	ARID1A	26970290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.590000	0.82653	2.830000	0.97506	0.655000	0.94253	CAG		0.483	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2		NM_139135	
ARID1B	57492	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	157522543	157522543	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:157522543delG	ENST00000350026.5	+	17	4777	c.4776delG	c.(4774-4776)gagfs	p.E1592fs	ARID1B_ENST00000275248.4_Frame_Shift_Del_p.E1587fs|ARID1B_ENST00000367148.1_Frame_Shift_Del_p.E1645fs|ARID1B_ENST00000346085.5_Frame_Shift_Del_p.E1605fs	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1592	Pro-rich.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TCAGAAGGGAGATCACCTTTC	0.512																																																	0													119.0	114.0	116.0					6																	157522543		2203	4296	6499	SO:0001589	frameshift_variant	57492			AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.4776delG	6.37:g.157522543delG	ENSP00000055163:p.Glu1592fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Frame_Shift_Del	DEL	ENST00000350026.5	37	CCDS5251.2																																																																																				0.512	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1		NM_020732	
B3GNT5	84002	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	182987783	182987783	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:182987783A>G	ENST00000326505.3	+	2	727	c.197A>G	c.(196-198)cAc>cGc	p.H66R	B3GNT5_ENST00000465010.1_Missense_Mutation_p.H66R|B3GNT5_ENST00000460419.1_Missense_Mutation_p.H66R|MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|MCF2L2_ENST00000473233.1_Intron	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	66					cellular protein metabolic process (GO:0044267)|central nervous system development (GO:0007417)|glycolipid biosynthetic process (GO:0009247)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	beta-galactosyl-N-acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase activity (GO:0008457)|galactosyltransferase activity (GO:0008378)|lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase activity (GO:0047256)|lipopolysaccharide N-acetylglucosaminyltransferase activity (GO:0008917)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(143;8.52e-13)|Ovarian(172;0.0355)		all cancers(12;4.52e-44)|Epithelial(37;8.82e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			TCTCTTAAGCACACCTCAGCG	0.408																																																	0													114.0	111.0	112.0					3																	182987783		2203	4300	6503	SO:0001583	missense	84002			AB045278	CCDS3244.1	3q28	2013-02-21			ENSG00000176597	ENSG00000176597	2.4.1.206	"""Beta 3-glycosyltransferases"""	15684	protein-coding gene	gene with protein product	"""lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase"""	615333				11283017	Standard	XM_005247824		Approved	B3GN-T5, beta3Gn-T5	uc003flk.3	Q9BYG0	OTTHUMG00000158436	ENST00000326505.3:c.197A>G	3.37:g.182987783A>G	ENSP00000316173:p.His66Arg	Somatic		WXS	Illumina HiSeq	Phase_I	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	37	CCDS3244.1	.	.	.	.	.	.	.	.	.	.	A	1.352	-0.591047	0.03799	.	.	ENSG00000176597	ENST00000326505;ENST00000460419;ENST00000464923;ENST00000465010	T;T;T	0.37584	1.19;1.19;1.19	5.92	-5.48	0.02592	.	1.356310	0.05326	N	0.527425	T	0.23133	0.0559	N	0.17674	0.51	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31081	-0.9956	10	0.15499	T	0.54	.	15.4861	0.75569	0.8287:0.0:0.1713:0.0	.	66	Q9BYG0	B3GN5_HUMAN	R	66	ENSP00000316173:H66R;ENSP00000420778:H66R;ENSP00000417868:H66R	ENSP00000316173:H66R	H	+	2	0	B3GNT5	184470477	0.389000	0.25205	0.007000	0.13788	0.552000	0.35366	0.488000	0.22371	-0.881000	0.03992	0.533000	0.62120	CAC		0.408	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1		NM_032047	
BACE2	25825	hgsc.bcm.edu	37	21	42598262	42598262	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr21:42598262A>T	ENST00000330333.6	+	2	845	c.382A>T	c.(382-384)Acg>Tcg	p.T128S	BACE2_ENST00000347667.5_Missense_Mutation_p.T128S|BACE2_ENST00000328735.6_Missense_Mutation_p.T128S	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2	128					membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				CTACATAGACACGTACTTTGA	0.488																																																	0													103.0	96.0	98.0					21																	42598262		2203	4300	6503	SO:0001583	missense	25825			AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.382A>T	21.37:g.42598262A>T	ENSP00000332979:p.Thr128Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.977605	0.00452	.	.	ENSG00000182240	ENST00000330333;ENST00000347667;ENST00000328735;ENST00000544566	T;T;T	0.40476	1.03;1.03;1.03	4.74	-6.91	0.01649	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.636280	0.16669	N	0.204425	T	0.12305	0.0299	N	0.03948	-0.315	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.29119	-1.0022	10	0.08381	T	0.77	.	7.7726	0.29017	0.639:0.0:0.1175:0.2435	.	128;128;128	Q9Y5Z0-3;Q9Y5Z0-2;Q9Y5Z0	.;.;BACE2_HUMAN	S	128;128;128;33	ENSP00000332979:T128S;ENSP00000327528:T128S;ENSP00000333854:T128S	ENSP00000333854:T128S	T	+	1	0	BACE2	41520132	0.103000	0.21917	0.023000	0.16930	0.034000	0.12701	0.177000	0.16801	-1.645000	0.01515	-0.464000	0.05259	ACG		0.488	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			
BACH2	60468	hgsc.bcm.edu	37	6	90660846	90660856	+	Frame_Shift_Del	DEL	CGGCCCCAGCT	CGGCCCCAGCT	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	CGGCCCCAGCT	CGGCCCCAGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:90660846_90660856delCGGCCCCAGCT	ENST00000257749.4	-	7	1676_1686	c.969_979delAGCTGGGGCCG	c.(967-981)ccagctggggccgccfs	p.AGAA324fs	BACH2_ENST00000537989.1_Frame_Shift_Del_p.AGAA324fs|BACH2_ENST00000343122.3_Frame_Shift_Del_p.AGAA324fs|RP3-512E2.2_ENST00000413986.1_RNA|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	324						cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	45		all_cancers(76;7.37e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.0063)		BRCA - Breast invasive adenocarcinoma(108;0.0799)		TCCAGGCAGGCGGCCCCAGCTGGGGCCGTGG	0.64																																																	0																																										SO:0001589	frameshift_variant	60468			AL121787	CCDS5026.1	6q15	2013-01-10			ENSG00000112182	ENSG00000112182		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	14078	protein-coding gene	gene with protein product		605394				10949928, 12829606	Standard	NM_001170794		Approved	BTBD25	uc003pnw.3	Q9BYV9	OTTHUMG00000015216	ENST00000257749.4:c.969_979delAGCTGGGGCCG	6.37:g.90660846_90660856delCGGCCCCAGCT	ENSP00000257749:p.Ala324fs	Somatic		WXS	Illumina HiSeq	Phase_I	E1P518|Q59H70|Q5T793|Q9NTS5	Frame_Shift_Del	DEL	ENST00000257749.4	37	CCDS5026.1																																																																																				0.640	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2		NM_021813	
SSUH2	51066	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	8673776	8673776	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:8673776C>A	ENST00000317371.4	-	12	1518	c.293G>T	c.(292-294)aGt>aTt	p.S98I	SSUH2_ENST00000341795.3_Missense_Mutation_p.S98I|SSUH2_ENST00000415132.1_Missense_Mutation_p.S98I|SSUH2_ENST00000544814.1_Missense_Mutation_p.S120I			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	98						cytoplasm (GO:0005737)											CCTGGATTCACTAAAGGTCTC	0.423																																																	0													96.0	92.0	93.0					3																	8673776		2203	4300	6503	SO:0001583	missense	0			AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.293G>T	3.37:g.8673776C>A	ENSP00000324551:p.Ser98Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.914881	0.52546	.	.	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814;ENST00000427408	T;T;T;T;T	0.46819	0.98;0.98;0.98;1.0;0.86	5.17	4.29	0.51040	.	0.248953	0.44285	D	0.000471	T	0.35158	0.0922	L	0.48642	1.525	0.34993	D	0.755243	B;P	0.45474	0.156;0.859	B;B	0.37304	0.106;0.246	T	0.48703	-0.9012	10	0.33141	T	0.24	-26.282	8.6627	0.34101	0.0:0.8985:0.0:0.1015	.	120;98	F5H2S5;Q9Y2M2	.;CC032_HUMAN	I	98;98;98;120;120	ENSP00000339150:S98I;ENSP00000324551:S98I;ENSP00000410757:S98I;ENSP00000439378:S120I;ENSP00000401289:S120I	ENSP00000324551:S98I	S	-	2	0	C3orf32	8648776	0.881000	0.30235	0.961000	0.40146	0.964000	0.63967	1.321000	0.33678	2.414000	0.81942	0.467000	0.42956	AGT		0.423	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1		NM_015931	
CADM1	23705	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	115102194	115102194	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:115102194C>T	ENST00000452722.3	-	4	461	c.441G>A	c.(439-441)ctG>ctA	p.L147L	CADM1_ENST00000537140.1_5'UTR|CADM1_ENST00000542447.2_Silent_p.L147L|CADM1_ENST00000536727.1_Silent_p.L147L|CADM1_ENST00000537058.1_Silent_p.L147L|CADM1_ENST00000331581.6_Silent_p.L147L	NM_014333.3	NP_055148.3			cell adhesion molecule 1											cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(9)|ovary(2)|skin(1)	32	all_hematologic(175;0.0628)	all_cancers(61;2.98e-14)|all_epithelial(67;2.64e-08)|all_hematologic(158;0.000154)|Melanoma(852;0.000952)|Acute lymphoblastic leukemia(157;0.00101)|Breast(348;0.0102)|Medulloblastoma(222;0.0429)|Prostate(24;0.145)|all_neural(223;0.237)		BRCA - Breast invasive adenocarcinoma(274;5.01e-06)|Epithelial(105;0.000305)|all cancers(92;0.00303)		TATCGATCATCAGATTACGTG	0.418																																																	0													186.0	156.0	166.0					11																	115102194		2201	4296	6497	SO:0001819	synonymous_variant	23705			AB017563	CCDS8373.1, CCDS53711.1, CCDS73397.1, CCDS73398.1, CCDS73399.1	11q23.2	2013-01-29	2007-02-07	2007-02-07	ENSG00000182985	ENSG00000182985		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5951	protein-coding gene	gene with protein product	"""nectin-like 2"""	605686	"""tumor suppressor in lung cancer 1"", ""immunoglobulin superfamily, member 4"""	TSLC1, IGSF4		10610705	Standard	NM_014333		Approved	NECL2, ST17, BL2, SYNCAM, IGSF4A, Necl-2, SYNCAM1, RA175	uc001ppi.4	Q9BY67	OTTHUMG00000168202	ENST00000452722.3:c.441G>A	11.37:g.115102194C>T		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000452722.3	37	CCDS8373.1	.	.	.	.	.	.	.	.	.	.	C	9.520	1.107919	0.20714	.	.	ENSG00000182985	ENST00000545380	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	T	0.64271	0.2583	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63171	-0.6697	4	.	.	.	.	12.3955	0.55382	0.0:0.8659:0.0:0.1341	.	.	.	.	N	146	.	.	D	-	1	0	CADM1	114607404	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.886000	0.28241	1.616000	0.50265	0.655000	0.94253	GAT		0.418	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2		NM_014333	
CARS2	79587	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	111335435	111335435	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr13:111335435delT	ENST00000257347.4	-	6	681	c.618delA	c.(616-618)aaafs	p.K206fs	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	206					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.163)		L-Cysteine(DB00151)	CGCCGACCAATTTGCCATACT	0.522																																																	0													123.0	121.0	121.0					13																	111335435		2203	4300	6503	SO:0001589	frameshift_variant	79587			BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	25695	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 2, mitochondrial (putative)"""	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.618delA	13.37:g.111335435delT	ENSP00000257347:p.Lys206fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NI84|Q96IV4	Frame_Shift_Del	DEL	ENST00000257347.4	37	CCDS9514.1																																																																																				0.522	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3		NM_024537	
PSORS1C1	170679	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	31084879	31084879	+	Intron	SNP	C	C	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:31084879C>G	ENST00000259881.9	+	1	61				CDSN_ENST00000376288.2_Silent_p.G171G|PSORS1C1_ENST00000467107.1_3'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						CAGAGCCATTCCCTACTTGGA	0.547																																																	0													57.0	61.0	60.0					6																	31084879		2203	4300	6503	SO:0001627	intron_variant	1041			AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2211C>G	6.37:g.31084879C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Silent	SNP	ENST00000259881.9	37	CCDS34390.1																																																																																				0.547	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3		NM_014068	
CES2	8824	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	66976070	66976070	+	Silent	SNP	C	C	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr16:66976070C>G	ENST00000317091.4	+	9	2376	c.1392C>G	c.(1390-1392)ccC>ccG	p.P464P	RP11-361L15.4_ENST00000566869.1_RNA|CES2_ENST00000417689.1_Silent_p.P464P	NM_003869.5	NP_003860.2	O00748	EST2_HUMAN	carboxylesterase 2	400					catabolic process (GO:0009056)	endoplasmic reticulum (GO:0005783)	carboxylic ester hydrolase activity (GO:0052689)|methylumbelliferyl-acetate deacetylase activity (GO:0047374)			breast(1)|kidney(1)|large_intestine(2)|liver(2)|lung(4)|prostate(1)|urinary_tract(1)	12		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0663)|Epithelial(162;0.166)	Dabigatran etexilate(DB06695)|Irinotecan(DB00762)|Mycophenolate mofetil(DB00688)|Prasugrel(DB06209)	ATGGGGATCCCCAGACCCTCC	0.527																																					Ovarian(70;1230 1691 37888 38351)												0													129.0	103.0	112.0					16																	66976070		2200	4300	6500	SO:0001819	synonymous_variant	8824			BC032095	CCDS10825.1, CCDS45507.1	16q22.1	2010-10-12	2010-10-12		ENSG00000172831	ENSG00000172831		"""Carboxylesterases"""	1864	protein-coding gene	gene with protein product		605278	"""carboxylesterase 2 (intestine, liver)"""			9169443, 9144407, 20931200	Standard	NM_198061		Approved	CE-2, iCE, CES2A1	uc002eqr.3	O00748	OTTHUMG00000137517	ENST00000317091.4:c.1392C>G	16.37:g.66976070C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K367|Q16859|Q5MAB8|Q7Z366|Q8IUP4|Q8TCP8	Silent	SNP	ENST00000317091.4	37	CCDS10825.1																																																																																				0.527	CES2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268838.2		NM_003869	
COL12A1	1303	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	75827250	75827250	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:75827250A>T	ENST00000322507.8	-	47	7676	c.7367T>A	c.(7366-7368)tTt>tAt	p.F2456Y	COL12A1_ENST00000483888.2_Missense_Mutation_p.F2456Y|COL12A1_ENST00000345356.6_Missense_Mutation_p.F1292Y|COL12A1_ENST00000416123.2_Missense_Mutation_p.F2456Y	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2456	Nonhelical region (NC3).|VWFA 4. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ACCAACTACAAAGACACTGAA	0.393																																																	0													100.0	99.0	99.0					6																	75827250		1985	4166	6151	SO:0001583	missense	1303			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.7367T>A	6.37:g.75827250A>T	ENSP00000325146:p.Phe2456Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.922469	0.92319	.	.	ENSG00000111799	ENST00000322507;ENST00000425443;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888;ENST00000493109	D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	5.91	5.91	0.95273	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.88340	0.6410	L	0.49571	1.57	0.52099	D	0.999949	D;D	0.76494	0.999;0.999	D;D	0.91635	0.998;0.999	D	0.88575	0.3132	10	0.48119	T	0.1	.	16.3453	0.83126	1.0:0.0:0.0:0.0	.	1292;2456	Q99715-2;Q99715	.;COCA1_HUMAN	Y	2456;94;2456;1292;2456;2456;10	ENSP00000325146:F2456Y;ENSP00000399812:F94Y;ENSP00000305147:F1292Y;ENSP00000412864:F2456Y;ENSP00000421216:F2456Y;ENSP00000423423:F10Y	ENSP00000325146:F2456Y	F	-	2	0	COL12A1	75883970	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.339000	0.96797	2.261000	0.74972	0.533000	0.62120	TTT		0.393	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3		NM_004370	
COL15A1	1306	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	101765861	101765861	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:101765861G>A	ENST00000375001.3	+	8	1615	c.1192G>A	c.(1192-1194)Gtc>Atc	p.V398I		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	398	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				AGAGGAAGGGGTCACTCCAGT	0.607																																																	0													51.0	54.0	53.0					9																	101765861		2203	4300	6503	SO:0001583	missense	1306			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1192G>A	9.37:g.101765861G>A	ENSP00000364140:p.Val398Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369280	0.24771	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.89746	-2.56	3.77	-1.69	0.08186	.	1.815940	0.03549	N	0.225118	T	0.79695	0.4490	L	0.32530	0.975	0.09310	N	1	B	0.20887	0.049	B	0.15052	0.012	T	0.59974	-0.7353	10	0.23302	T	0.38	0.0033	1.2009	0.01884	0.206:0.3288:0.2974:0.1679	.	398	P39059	COFA1_HUMAN	I	398;368	ENSP00000364140:V398I	ENSP00000364140:V398I	V	+	1	0	COL15A1	100805682	0.000000	0.05858	0.000000	0.03702	0.570000	0.35934	-0.477000	0.06583	-0.348000	0.08286	0.561000	0.74099	GTC		0.607	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3		NM_001855	
CTAGE1	64693	hgsc.bcm.edu;ucsc.edu	37	18	19996490	19996491	+	5'Flank	INS	-	-	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr18:19996490_19996491insT	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Frame_Shift_Ins_p.A429fs			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					TTATCATGTGCTTTTTTCTCAT	0.351																																																	0																																										SO:0001631	upstream_gene_variant	64693			AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996496_19996496dupT	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	B0YIZ3	Frame_Shift_Ins	INS	ENST00000525417.1	37																																																																																					0.351	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1		NM_022663, NM_172241	
DCAKD	79877	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	43112204	43112204	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:43112204A>G	ENST00000452796.2	-	1	305	c.50T>C	c.(49-51)gTg>gCg	p.V17A	DCAKD_ENST00000342350.5_Missense_Mutation_p.V17A|DCAKD_ENST00000588499.1_Missense_Mutation_p.V17A|DCAKD_ENST00000588295.1_5'UTR|DCAKD_ENST00000310604.4_Missense_Mutation_p.V17A			Q8WVC6	DCAKD_HUMAN	dephospho-CoA kinase domain containing	17	DPCK.				coenzyme A biosynthetic process (GO:0015937)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)			cervix(1)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)	6		Prostate(33;0.155)				CACCTGGATCACTGAGCTCTT	0.617																																																	0													84.0	67.0	73.0					17																	43112204		2203	4300	6503	SO:0001583	missense	79877			BC006546	CCDS11493.1	17q21.31	2005-12-20				ENSG00000172992			26238	protein-coding gene	gene with protein product							Standard	XM_005257688		Approved	FLJ22955	uc010daa.1	Q8WVC6		ENST00000452796.2:c.50T>C	17.37:g.43112204A>G	ENSP00000413483:p.Val17Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3Z0|D3DX60|D3DX62|Q9BR71|Q9H5W1	Missense_Mutation	SNP	ENST00000452796.2	37	CCDS11493.1	.	.	.	.	.	.	.	.	.	.	A	29.7	5.026011	0.93518	.	.	ENSG00000172992	ENST00000342350;ENST00000452796;ENST00000310604	T;T;T	0.52295	0.79;0.79;0.67	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	T	0.64461	0.2600	M	0.78285	2.405	0.80722	D	1	D;P	0.55385	0.971;0.937	P;P	0.57548	0.7;0.823	T	0.67872	-0.5558	10	0.51188	T	0.08	0.5415	14.1135	0.65137	1.0:0.0:0.0:0.0	.	17;17	Q8WVC6-2;Q8WVC6	.;DCAKD_HUMAN	A	17	ENSP00000341504:V17A;ENSP00000413483:V17A;ENSP00000308515:V17A	ENSP00000308515:V17A	V	-	2	0	DCAKD	40467730	1.000000	0.71417	0.767000	0.31495	0.994000	0.84299	8.762000	0.91711	2.070000	0.61991	0.459000	0.35465	GTG		0.617	DCAKD-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449066.1		NM_024819	
DLGAP3	58512	hgsc.bcm.edu;ucsc.edu	37	1	35365794	35365799	+	In_Frame_Del	DEL	GCTGCC	GCTGCC	-	rs140339373		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	GCTGCC	GCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:35365794_35365799delGCTGCC	ENST00000373347.1	-	4	1451_1456	c.1183_1188delGGCAGC	c.(1183-1188)ggcagcdel	p.GS395del	DLGAP3_ENST00000235180.4_In_Frame_Del_p.GS395del			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	395					cell-cell signaling (GO:0007267)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)	beta-amyloid binding (GO:0001540)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(23)|ovary(4)|prostate(3)|skin(3)|urinary_tract(1)	46		Myeloproliferative disorder(586;0.0393)				CTTTGATGTAGCTGCCGCTCCGCATC	0.641																																																	0																																										SO:0001651	inframe_deletion	58512			AF131778	CCDS30670.1	1p35.3-p34.1	2008-02-05			ENSG00000116544	ENSG00000116544			30368	protein-coding gene	gene with protein product		611413				8619474, 9110174	Standard	NM_001080418		Approved	SAPAP3, DAP3	uc001byc.3	O95886	OTTHUMG00000004049	ENST00000373347.1:c.1183_1188delGGCAGC	1.37:g.35365794_35365799delGCTGCC	ENSP00000362444:p.Gly395_Ser396del	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TDD5|Q9H3X7	In_Frame_Del	DEL	ENST00000373347.1	37	CCDS30670.1																																																																																				0.641	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1		NM_021234	
DNAH5	1767	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	13865955	13865955	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr5:13865955C>A	ENST00000265104.4	-	27	4281	c.4177G>T	c.(4177-4179)Ggc>Tgc	p.G1393C	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1393	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					GCTGGCAGGCCAAAAAGCTCC	0.333									Kartagener syndrome																																								0													54.0	59.0	58.0					5																	13865955		2202	4298	6500	SO:0001583	missense	1767	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.4177G>T	5.37:g.13865955C>A	ENSP00000265104:p.Gly1393Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502809	0.85176	.	.	ENSG00000039139	ENST00000265104	T	0.26957	1.7	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.61148	0.2324	M	0.90650	3.135	0.80722	D	1	D	0.58970	0.984	D	0.67382	0.951	T	0.65957	-0.6042	10	0.66056	D	0.02	.	20.5605	0.99326	0.0:1.0:0.0:0.0	.	1393	Q8TE73	DYH5_HUMAN	C	1393	ENSP00000265104:G1393C	ENSP00000265104:G1393C	G	-	1	0	DNAH5	13918955	1.000000	0.71417	0.999000	0.59377	0.769000	0.43574	7.811000	0.86092	2.868000	0.98415	0.637000	0.83480	GGC		0.333	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2		NM_001369	
DYNC1H1	1778	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	102516411	102516411	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr14:102516411T>G	ENST00000360184.4	+	77	13852	c.13688T>G	c.(13687-13689)tTg>tGg	p.L4563W	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4563					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						CTCACAGGTTTGAAACTTCAA	0.587																																																	0													73.0	69.0	70.0					14																	102516411		2203	4300	6503	SO:0001583	missense	1778			AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.13688T>G	14.37:g.102516411T>G	ENSP00000348965:p.Leu4563Trp	Somatic		WXS	Illumina HiSeq	Phase_I	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.574890	0.86542	.	.	ENSG00000197102	ENST00000360184	T	0.15372	2.43	5.42	5.42	0.78866	Dynein heavy chain (1);	0.000000	0.64402	D	0.000003	T	0.51295	0.1666	M	0.91090	3.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63422	-0.6641	10	0.87932	D	0	.	15.4559	0.75314	0.0:0.0:0.0:1.0	.	4563	Q14204	DYHC1_HUMAN	W	4563	ENSP00000348965:L4563W	ENSP00000348965:L4563W	L	+	2	0	DYNC1H1	101586164	1.000000	0.71417	0.875000	0.34327	0.779000	0.44077	7.817000	0.86213	2.063000	0.61619	0.402000	0.26972	TTG		0.587	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1		NM_001376	
DYSF	8291	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	71909676	71909676	+	Missense_Mutation	SNP	T	T	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:71909676T>A	ENST00000258104.3	+	54	6350	c.6073T>A	c.(6073-6075)Ttc>Atc	p.F2025I	DYSF_ENST00000409744.1_Missense_Mutation_p.F2033I|DYSF_ENST00000409582.3_Missense_Mutation_p.F2063I|DYSF_ENST00000410020.3_Missense_Mutation_p.F2064I|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000394120.2_Missense_Mutation_p.F2026I|DYSF_ENST00000409366.1_Missense_Mutation_p.F2047I|DYSF_ENST00000409651.1_Missense_Mutation_p.F2057I|DYSF_ENST00000429174.2_Missense_Mutation_p.F2046I|DYSF_ENST00000410041.1_Missense_Mutation_p.F2043I|DYSF_ENST00000413539.2_Missense_Mutation_p.F2056I|DYSF_ENST00000409762.1_Missense_Mutation_p.F2042I	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	2025					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CGACACCTCCTTCCTGTGGTT	0.547																																																	0													161.0	129.0	140.0					2																	71909676		2203	4300	6503	SO:0001583	missense	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.6073T>A	2.37:g.71909676T>A	ENSP00000258104:p.Phe2025Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	31	5.087711	0.94100	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0;-2.0;-2.0;-2.0;-2.0;-2.0;-2.0;-2.0	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.93213	0.7838	M	0.90309	3.105	0.58432	D	0.999997	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.997;1.0;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999;1.0;1.0;1.0;0.99;0.999;0.97;0.998;0.999;0.999;0.997	D	0.94368	0.7593	10	0.87932	D	0	-25.343	13.1302	0.59377	0.0:0.0:0.0:1.0	.	789;2057;2064;2047;2012;2043;2033;2042;2032;2056;2063;2046;2011;2026;2025	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	I	2056;2042;2063;2046;2025;2057;2026;2033;2047;2064;2043	ENSP00000407046:F2056I;ENSP00000387137:F2042I;ENSP00000386547:F2063I;ENSP00000398305:F2046I;ENSP00000258104:F2025I;ENSP00000386683:F2057I;ENSP00000377678:F2026I;ENSP00000386285:F2033I;ENSP00000386512:F2047I;ENSP00000386881:F2064I;ENSP00000386617:F2043I	ENSP00000258104:F2025I	F	+	1	0	DYSF	71763184	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.971000	0.88012	2.034000	0.60081	0.533000	0.62120	TTC		0.547	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3		NM_003494	
EHHADH	1962	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	184922240	184922240	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:184922240C>T	ENST00000231887.3	-	6	949	c.874G>A	c.(874-876)Gca>Aca	p.A292T	EHHADH_ENST00000456310.1_Missense_Mutation_p.A196T	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	292	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CGCGCTGATGCTGTTTTCCAC	0.483																																																	0													112.0	107.0	109.0					3																	184922240		2203	4300	6503	SO:0001583	missense	1962			L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.874G>A	3.37:g.184922240C>T	ENSP00000231887:p.Ala292Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702534	0.30232	.	.	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.75704	-0.55;-0.96	5.53	3.49	0.39957	.	0.426413	0.27096	N	0.020959	T	0.71022	0.3291	L	0.58101	1.795	0.31197	N	0.700232	B	0.34241	0.444	B	0.39706	0.307	T	0.67894	-0.5552	10	0.12766	T	0.61	-12.9716	13.908	0.63848	0.3154:0.6846:0.0:0.0	.	292	Q08426	ECHP_HUMAN	T	292;292;196	ENSP00000231887:A292T;ENSP00000387746:A196T	ENSP00000231887:A292T	A	-	1	0	EHHADH	186404934	0.005000	0.15991	0.987000	0.45799	0.715000	0.41141	0.193000	0.17116	1.273000	0.44346	0.650000	0.86243	GCA		0.483	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			
ERBB4	2066	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	212530141	212530141	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:212530141C>A	ENST00000342788.4	-	15	2088	c.1778G>T	c.(1777-1779)tGt>tTt	p.C593F	ERBB4_ENST00000436443.1_Missense_Mutation_p.C593F|ERBB4_ENST00000402597.1_Missense_Mutation_p.C593F	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	593	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	GCCATCTGGACATTTTTCCAC	0.428										TSP Lung(8;0.080)																																							0													129.0	117.0	121.0					2																	212530141		2203	4300	6503	SO:0001583	missense	2066			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1778G>T	2.37:g.212530141C>A	ENSP00000342235:p.Cys593Phe	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.0|24.0	4.486145|4.486145	0.84854|0.84854	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.66460|.	-0.21;-0.21;-0.21|.	5.26|5.26	5.26|5.26	0.73747|0.73747	Growth factor, receptor (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.90665|0.90665	0.7072|0.7072	H|H	0.97983|0.97983	4.12|4.12	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	0.998;1.0;1.0;0.998;0.996|.	D;D;D;D;D|.	0.91635|.	0.976;0.999;0.994;0.981;0.957|.	D|D	0.93918|0.93918	0.7203|0.7203	9|5	.|.	.|.	.|.	.|.	19.2295|19.2295	0.93833|0.93833	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	593;593;452;593;593|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	F|F	593|593	ENSP00000342235:C593F;ENSP00000403204:C593F;ENSP00000385565:C593F|.	.|.	C|V	-|-	2|1	0|0	ERBB4|ERBB4	212238386|212238386	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.770000|7.770000	0.85390|0.85390	2.632000|2.632000	0.89209|0.89209	0.655000|0.655000	0.94253|0.94253	TGT|GTC		0.428	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1		NM_001042599	
FAM120B	84498	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	170627090	170627090	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:170627090C>T	ENST00000476287.1	+	2	720	c.612C>T	c.(610-612)gtC>gtT	p.V204V	FAM120B_ENST00000537664.1_Silent_p.V227V|FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000540480.1_Silent_p.V216V	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	204					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		TGGACACCGTCATGCTCTGCA	0.532																																																	0													74.0	77.0	76.0					6																	170627090		2203	4300	6503	SO:0001819	synonymous_variant	84498			AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"""PPARgamma constitutive coactivator 1"", ""constitutive coactivator of PPAR-gamma"""	612266	"""KIAA1838"""	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.612C>T	6.37:g.170627090C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																				0.532	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2		NM_032448	
ERICH6	131831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	150398270	150398270	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:150398270G>T	ENST00000295910.6	-	9	1148	c.1096C>A	c.(1096-1098)Cat>Aat	p.H366N	FAM194A_ENST00000491361.1_Missense_Mutation_p.H220N	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TCAGAGAAATGAGTCTGTTCC	0.383																																																	0													206.0	184.0	192.0					3																	150398270		2203	4300	6503	SO:0001583	missense	131831																														ENST00000295910.6:c.1096C>A	3.37:g.150398270G>T	ENSP00000295910:p.His366Asn	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.575892	0.00887	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.12361	2.89;2.69	3.8	1.4	0.22301	.	2.083720	0.02116	N	0.055204	T	0.05731	0.0150	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31024	-0.9958	10	0.23302	T	0.38	-0.0015	8.235	0.31620	0.0:0.0:0.4332:0.5668	.	366	Q7L0X2	F194A_HUMAN	N	366;220;324	ENSP00000295910:H366N;ENSP00000419366:H220N	ENSP00000295910:H366N	H	-	1	0	FAM194A	151880960	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.069000	0.11542	0.297000	0.22615	-0.457000	0.05445	CAT		0.383	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			
FBXO9	26268	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	52943655	52943655	+	Silent	SNP	T	T	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:52943655T>C	ENST00000244426.6	+	4	568	c.396T>C	c.(394-396)acT>acC	p.T132T	FBXO9_ENST00000370939.3_Silent_p.T88T|FBXO9_ENST00000323557.7_Silent_p.T122T	NM_012347.4	NP_036479.1	Q9UK97	FBX9_HUMAN	F-box protein 9	132					fat cell differentiation (GO:0045444)|innate immune response (GO:0045087)|protein ubiquitination (GO:0016567)|regulation of TOR signaling (GO:0032006)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			kidney(1)|large_intestine(4)|lung(1)|pancreas(2)|skin(1)	9	Lung NSC(77;0.103)					TCAAGATTACTTATACCCGGT	0.363																																																	0													125.0	117.0	119.0					6																	52943655		1868	4096	5964	SO:0001819	synonymous_variant	26268			AF155114	CCDS55022.1, CCDS55023.1, CCDS55024.1	6p12.3-p11.2	2004-06-15	2004-06-15		ENSG00000112146	ENSG00000112146		"""F-boxes /  ""other"""""	13588	protein-coding gene	gene with protein product		609091	"""F-box only protein 9"""			10531035, 10531037	Standard	NM_012347		Approved	FBX9, NY-REN-57	uc021zao.1	Q9UK97	OTTHUMG00000014869	ENST00000244426.6:c.396T>C	6.37:g.52943655T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A6NFW3|B3KMM6|O75986|Q59EH8|Q6PKH7|Q9NT57|Q9Y593	Silent	SNP	ENST00000244426.6	37	CCDS55023.1																																																																																				0.363	FBXO9-002	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040950.3			
FGFBP3	143282	broad.mit.edu;hgsc.bcm.edu	37	10	93668183	93668183	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr10:93668183C>T	ENST00000311575.5	-	2	707	c.544G>A	c.(544-546)Ggc>Agc	p.G182S	RP11-402D21.2_ENST00000610263.1_RNA	NM_152429.4	NP_689642.3	Q8TAT2	FGFP3_HUMAN	fibroblast growth factor binding protein 3	182					positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of vascular permeability (GO:0043117)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	fibroblast growth factor binding (GO:0017134)|heparin binding (GO:0008201)			large_intestine(1)|prostate(1)	2		Colorectal(252;0.162)				GCGGCTGGGCCGGACGCACGC	0.751																																																	0													25.0	27.0	26.0					10																	93668183		2197	4295	6492	SO:0001583	missense	143282			AK075410	CCDS7418.1	10q23.33	2006-12-14	2006-12-14	2006-12-14	ENSG00000174721	ENSG00000174721			23428	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 13"""	C10orf13			Standard	NM_152429		Approved	MGC39320	uc001khq.4	Q8TAT2	OTTHUMG00000018751	ENST00000311575.5:c.544G>A	10.37:g.93668183C>T	ENSP00000339067:p.Gly182Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RD68|Q8NBN0	Missense_Mutation	SNP	ENST00000311575.5	37	CCDS7418.1	.	.	.	.	.	.	.	.	.	.	C	8.938	0.965038	0.18583	.	.	ENSG00000174721	ENST00000311575	T	0.12361	2.69	3.18	1.22	0.21188	.	1.020890	0.07878	N	0.969108	T	0.10981	0.0268	L	0.53249	1.67	0.09310	N	1	B	0.28552	0.215	B	0.18561	0.022	T	0.39820	-0.9595	10	0.17832	T	0.49	.	3.6061	0.08043	0.0:0.5436:0.2118:0.2446	.	182	Q8TAT2	FGFP3_HUMAN	S	182	ENSP00000339067:G182S	ENSP00000339067:G182S	G	-	1	0	FGFBP3	93658163	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.257000	0.18369	0.174000	0.19809	0.305000	0.20034	GGC		0.751	FGFBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049379.1		NM_152429	
FGFR4	2264	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	176524604	176524604	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr5:176524604A>C	ENST00000292408.4	+	18	2581	c.2336A>C	c.(2335-2337)gAt>gCt	p.D779A	FGFR4_ENST00000292410.3_Missense_Mutation_p.D739A|FGFR4_ENST00000393648.2_Missense_Mutation_p.D711A|FGFR4_ENST00000502906.1_Missense_Mutation_p.D779A|FGFR4_ENST00000393637.1_Missense_Mutation_p.D739A	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	779					alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	TCCTCCAGCGATTCTGTCTTC	0.632										TSP Lung(9;0.080)																																							0													115.0	86.0	96.0					5																	176524604		2203	4300	6503	SO:0001583	missense	2264			AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.2336A>C	5.37:g.176524604A>C	ENSP00000292408:p.Asp779Ala	Somatic		WXS	Illumina HiSeq	Phase_I	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	A	15.30	2.791637	0.50102	.	.	ENSG00000160867	ENST00000292408;ENST00000393648;ENST00000502906;ENST00000292410;ENST00000393637;ENST00000377207	D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	D	0.90469	0.7015	M	0.64997	1.995	0.58432	D	0.999996	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.994	D	0.91429	0.5164	10	0.87932	D	0	.	13.1893	0.59700	1.0:0.0:0.0:0.0	.	711;739;779	B4DVP5;P22455-2;P22455	.;.;FGFR4_HUMAN	A	779;711;779;739;739;1007	ENSP00000292408:D779A;ENSP00000377259:D711A;ENSP00000424960:D779A;ENSP00000292410:D739A;ENSP00000377254:D739A	ENSP00000292408:D779A	D	+	2	0	FGFR4	176457210	1.000000	0.71417	0.947000	0.38551	0.307000	0.27823	9.097000	0.94193	1.952000	0.56665	0.379000	0.24179	GAT		0.632	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			
FRMPD1	22844	broad.mit.edu;ucsc.edu	37	9	37708465	37708465	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:37708465A>G	ENST00000539465.1	+	4	922	c.329A>G	c.(328-330)gAc>gGc	p.D110G	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.D110G			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	110	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CCTGCTGAAGACCTTTCCTGG	0.453																																																	0													127.0	116.0	119.0					9																	37708465		2203	4300	6503	SO:0001583	missense	22844			AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.329A>G	9.37:g.37708465A>G	ENSP00000444411:p.Asp110Gly	Somatic		WXS	Illumina GAIIx	Phase_I	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.646847	0.67358	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.31247	1.5;1.5	5.91	3.51	0.40186	PDZ/DHR/GLGF (4);	0.315671	0.37715	N	0.001980	T	0.29620	0.0739	L	0.31120	0.905	0.80722	D	1	P	0.45715	0.865	P	0.51974	0.686	T	0.04140	-1.0974	10	0.52906	T	0.07	-6.9476	5.6494	0.17608	0.7393:0.1698:0.0909:0.0	.	110	Q5SYB0	FRPD1_HUMAN	G	110	ENSP00000366995:D110G;ENSP00000444411:D110G	ENSP00000366995:D110G	D	+	2	0	FRMPD1	37698465	1.000000	0.71417	0.998000	0.56505	0.706000	0.40770	3.176000	0.50863	0.465000	0.27167	-0.321000	0.08615	GAC		0.453	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1		NM_014907	
GIMAP8	155038	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	150171609	150171609	+	Missense_Mutation	SNP	G	G	C	rs536291210	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:150171609G>C	ENST00000307271.3	+	4	1766	c.1192G>C	c.(1192-1194)Gcc>Ccc	p.A398P		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	398	AIG1-type G 2.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		CAGATATAGTGCCTTCAACTA	0.443																																																	0													126.0	134.0	132.0					7																	150171609		2203	4300	6503	SO:0001583	missense	155038			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1192G>C	7.37:g.150171609G>C	ENSP00000305107:p.Ala398Pro	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	G	13.99	2.402518	0.42613	.	.	ENSG00000171115	ENST00000307271	T	0.61742	0.08	4.47	-5.28	0.02755	AIG1 (1);	1.933280	0.02733	N	0.115303	T	0.61800	0.2376	M	0.88310	2.945	0.09310	N	1	P	0.35107	0.484	B	0.36244	0.22	T	0.58730	-0.7585	10	0.56958	D	0.05	.	6.8779	0.24156	0.5454:0.0:0.335:0.1196	.	398	Q8ND71	GIMA8_HUMAN	P	398	ENSP00000305107:A398P	ENSP00000305107:A398P	A	+	1	0	GIMAP8	149802542	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	0.535000	0.23114	-1.142000	0.02869	0.650000	0.86243	GCC		0.443	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1		NM_175571	
GJD2	57369	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	35045023	35045023	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr15:35045023C>T	ENST00000290374.4	-	2	1098	c.622G>A	c.(622-624)Gcc>Acc	p.A208T	RP11-814P5.1_ENST00000503496.1_RNA|RP11-814P5.1_ENST00000558707.1_RNA	NM_020660.2	NP_065711.1	Q9UKL4	CXD2_HUMAN	gap junction protein, delta 2, 36kDa	208					action potential (GO:0001508)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|urinary_tract(1)	19		all_lung(180;9.67e-07)		all cancers(64;2.75e-18)|GBM - Glioblastoma multiforme(113;1.9e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		ATTTCCAGGGCATTTCGGAAC	0.502																																																	0													91.0	90.0	90.0					15																	35045023		2201	4298	6499	SO:0001583	missense	57369			AB037509	CCDS10040.1	15q13.1	2008-02-04	2007-11-06	2007-11-06	ENSG00000159248	ENSG00000159248		"""Ion channels / Gap junction proteins (connexins)"""	19154	protein-coding gene	gene with protein product	"""connexin 36"""	607058	"""gap junction protein, alpha 9, 36kDa"""	GJA9		10462698	Standard	NM_020660		Approved	CX36	uc001zis.2	Q9UKL4	OTTHUMG00000129674	ENST00000290374.4:c.622G>A	15.37:g.35045023C>T	ENSP00000290374:p.Ala208Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M241|Q9P2R0	Missense_Mutation	SNP	ENST00000290374.4	37	CCDS10040.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.165323	0.57476	.	.	ENSG00000159248	ENST00000290374	D	0.98192	-4.78	5.86	5.86	0.93980	.	0.000000	0.64402	D	0.000003	D	0.96046	0.8712	L	0.34521	1.04	0.80722	D	1	P	0.44429	0.835	B	0.38500	0.275	D	0.95412	0.8499	10	0.37606	T	0.19	.	20.1864	0.98220	0.0:1.0:0.0:0.0	.	208	Q9UKL4	CXD2_HUMAN	T	208	ENSP00000290374:A208T	ENSP00000290374:A208T	A	-	1	0	GJD2	32832315	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.818000	0.86416	2.781000	0.95711	0.650000	0.86243	GCC		0.502	GJD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251875.2			
GNB1	2782	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	1721888	1721888	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:1721888T>G	ENST00000378609.4	-	9	976	c.645A>C	c.(643-645)gaA>gaC	p.E215D		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	215					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		GGCACATGCCTTCTCGCACAT	0.567																																																	0													122.0	99.0	107.0					1																	1721888		2203	4300	6503	SO:0001583	missense	2782			BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"""WD repeat domain containing"""	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.645A>C	1.37:g.1721888T>G	ENSP00000367872:p.Glu215Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B1AJZ7|P04697|P04901|Q1RMY8	Missense_Mutation	SNP	ENST00000378609.4	37	CCDS34.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.859|7.859	0.725653|0.725653	0.15439|0.15439	.|.	.|.	ENSG00000078369|ENSG00000078369	ENST00000378609;ENST00000455156;ENST00000378606|ENST00000424622	T|.	0.01265|.	5.08|.	5.43|5.43	4.3|4.3	0.51218|0.51218	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);|.	0.094537|.	0.64402|.	D|.	0.000001|.	T|T	0.41627|0.41627	0.1167|0.1167	N|N	0.20304|0.20304	0.555|0.555	0.58432|0.58432	D|D	0.999998|0.999998	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.17258|0.17258	-1.0375|-1.0375	10|5	0.26408|.	T|.	0.33|.	-12.7705|-12.7705	10.4324|10.4324	0.44415|0.44415	0.0:0.0763:0.0:0.9237|0.0:0.0763:0.0:0.9237	.|.	215|.	P62873|.	GBB1_HUMAN|.	D|T	215;115;215|73	ENSP00000367872:E215D|.	ENSP00000367869:E215D|.	E|K	-|-	3|2	2|0	GNB1|GNB1	1711748|1711748	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	1.687000|1.687000	0.37680|0.37680	0.902000|0.902000	0.36520|0.36520	0.533000|0.533000	0.62120|0.62120	GAA|AAG		0.567	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3		NM_002074	
HEPHL1	341208	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	93779079	93779079	+	Silent	SNP	A	A	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:93779079A>C	ENST00000315765.9	+	2	419	c.411A>C	c.(409-411)tcA>tcC	p.S137S		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	137	Plastocyanin-like 1.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				ACAAAGATTCAGAAGGTAAAT	0.378																																																	0													64.0	63.0	63.0					11																	93779079		1848	4098	5946	SO:0001819	synonymous_variant	341208			BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.411A>C	11.37:g.93779079A>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q3C1W7	Silent	SNP	ENST00000315765.9	37	CCDS44710.1																																																																																				0.378	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2		XM_291947	
HLF	3131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	53398085	53398085	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:53398085G>A	ENST00000226067.5	+	4	1206	c.733G>A	c.(733-735)Gcc>Acc	p.A245T	HLF_ENST00000430986.2_Missense_Mutation_p.A160T|HLF_ENST00000575345.1_Missense_Mutation_p.A160T|HLF_ENST00000575307.1_3'UTR|HLF_ENST00000573945.1_Missense_Mutation_p.A160T	NM_002126.4	NP_002117.1	Q16534	HLF_HUMAN	hepatic leukemia factor	245	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				multicellular organismal development (GO:0007275)|rhythmic process (GO:0048511)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|ovary(2)	3						CTCCCGCGACGCCCGGAGGCT	0.557			T	TCF3	ALL																																			Dom	yes		17	17q22	3131	hepatic leukemia factor		L	0													34.0	39.0	37.0					17																	53398085		2203	4299	6502	SO:0001583	missense	3131				CCDS11585.1	17q22	2011-05-19			ENSG00000108924	ENSG00000108924			4977	protein-coding gene	gene with protein product		142385				1386162	Standard	XM_005257269		Approved	MGC33822	uc002iug.1	Q16534		ENST00000226067.5:c.733G>A	17.37:g.53398085G>A	ENSP00000226067:p.Ala245Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1X8|Q6FHS9	Missense_Mutation	SNP	ENST00000226067.5	37	CCDS11585.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.714179	0.89112	.	.	ENSG00000108924	ENST00000226067;ENST00000430986	T;T	0.45276	0.9;0.9	5.64	5.64	0.86602	Basic-leucine zipper (bZIP) transcription factor (2);Basic leucine zipper (1);	0.000000	0.85682	D	0.000000	T	0.73329	0.3573	M	0.91459	3.21	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.79410	-0.1815	10	0.87932	D	0	.	18.6863	0.91565	0.0:0.0:1.0:0.0	.	193;245	B4DIQ5;Q16534	.;HLF_HUMAN	T	245;160	ENSP00000226067:A245T;ENSP00000402496:A160T	ENSP00000226067:A245T	A	+	1	0	HLF	50753084	1.000000	0.71417	0.988000	0.46212	0.156000	0.22039	9.469000	0.97679	2.659000	0.90383	0.563000	0.77884	GCC		0.557	HLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439185.1		NM_002126	
IDS	3423	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	148586585	148586585	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chrX:148586585G>C	ENST00000340855.6	-	1	292	c.83C>G	c.(82-84)aCg>aGg	p.T28R	IDS_ENST00000370441.4_Missense_Mutation_p.T28R|IDS_ENST00000422081.2_Intron|IDS_ENST00000541269.1_Intron|IDS_ENST00000490775.1_5'Flank|IDS_ENST00000428056.2_Missense_Mutation_p.T28R|IDS_ENST00000370443.4_Missense_Mutation_p.T28R|IDS_ENST00000427113.2_Intron	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	28					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					GTTGGCCTGCGTTTCGGATCC	0.647																																																	0			GRCh37	CI962295	IDS	I							99.0	74.0	82.0					X																	148586585		2202	4300	6502	SO:0001583	missense	3423			M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.83C>G	X.37:g.148586585G>C	ENSP00000339801:p.Thr28Arg	Somatic		WXS	Illumina HiSeq	Phase_I	D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	ENST00000340855.6	37	CCDS14685.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.491886	0.26774	.	.	ENSG00000010404	ENST00000340855;ENST00000370441;ENST00000370443;ENST00000428056;ENST00000521702	D;D;D;D;D	0.99462	-5.62;-5.61;-5.6;-5.94;-4.91	3.33	0.457	0.16661	.	0.681480	0.12849	N	0.434066	D	0.95999	0.8697	N	0.14661	0.345	0.09310	N	1	P;B;B	0.35242	0.492;0.001;0.001	B;B;B	0.31442	0.13;0.001;0.001	D	0.94466	0.7680	10	0.59425	D	0.04	.	2.6087	0.04885	0.2701:0.0:0.5022:0.2277	.	28;28;28	O60597;P22304-2;P22304	.;.;IDS_HUMAN	R	28	ENSP00000339801:T28R;ENSP00000359470:T28R;ENSP00000359472:T28R;ENSP00000390241:T28R;ENSP00000429745:T28R	ENSP00000339801:T28R	T	-	2	0	IDS	148394489	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.488000	0.06497	-0.025000	0.13918	-0.269000	0.10298	ACG		0.647	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3			
IKZF1	10320	broad.mit.edu;hgsc.bcm.edu	37	7	50467916	50467916	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:50467916C>T	ENST00000331340.3	+	8	1306	c.1151C>T	c.(1150-1152)tCg>tTg	p.S384L	IKZF1_ENST00000357364.4_Missense_Mutation_p.S297L|IKZF1_ENST00000438033.1_Missense_Mutation_p.S297L|IKZF1_ENST00000439701.1_Missense_Mutation_p.S342L|IKZF1_ENST00000349824.4_Missense_Mutation_p.S241L|IKZF1_ENST00000343574.5_Missense_Mutation_p.S297L|IKZF1_ENST00000346667.4_Missense_Mutation_p.S154L|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000359197.5_Missense_Mutation_p.S342L	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	384					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(28)|p.S384*(1)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				TTGGTGCCCTCGGAGCGCGAG	0.667			"""D,T"""	BCL6	"""ALL, DLBCL"""																																			"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	29	Unknown(28)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(28)|lung(1)											16.0	21.0	19.0					7																	50467916		2068	4190	6258	SO:0001583	missense	10320			U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.1151C>T	7.37:g.50467916C>T	ENSP00000331614:p.Ser384Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	37		.	.	.	.	.	.	.	.	.	.	C	15.90	2.970725	0.53614	.	.	ENSG00000185811	ENST00000346667;ENST00000343574;ENST00000359197;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000438033;ENST00000439701	T;T;T;T;T;T;T;T	0.06849	4.63;3.25;3.31;4.36;3.42;3.32;3.25;3.31	5.65	5.65	0.86999	.	0.269693	0.43747	D	0.000533	T	0.17323	0.0416	.	.	.	0.80722	D	1	P;P;P;P;P	0.48589	0.833;0.912;0.903;0.903;0.743	P;B;P;P;B	0.46940	0.532;0.242;0.475;0.475;0.231	T	0.00133	-1.2010	9	0.62326	D	0.03	-18.7428	19.7107	0.96095	0.0:1.0:0.0:0.0	.	297;154;297;342;384	Q13422-2;Q13422-6;Q13422-3;Q13422-7;Q13422	.;.;.;.;IKZF1_HUMAN	L	154;297;342;241;297;384;297;342	ENSP00000340080:S154L;ENSP00000342750:S297L;ENSP00000352123:S342L;ENSP00000342485:S241L;ENSP00000349928:S297L;ENSP00000331614:S384L;ENSP00000396554:S297L;ENSP00000413025:S342L	ENSP00000331614:S384L	S	+	2	0	IKZF1	50435410	0.999000	0.42202	0.066000	0.19879	0.753000	0.42808	4.589000	0.61006	2.659000	0.90383	0.585000	0.79938	TCG		0.667	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1		NM_006060	
INCENP	3619	broad.mit.edu;ucsc.edu	37	11	61908398	61908398	+	Missense_Mutation	SNP	T	T	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:61908398T>C	ENST00000394818.3	+	10	1677	c.1475T>C	c.(1474-1476)cTc>cCc	p.L492P	INCENP_ENST00000278849.4_Missense_Mutation_p.L492P	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	492					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GTACGGCCCCTCCGGACCTTT	0.632																																																	0													73.0	75.0	74.0					11																	61908398		2202	4299	6501	SO:0001583	missense	3619			AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1475T>C	11.37:g.61908398T>C	ENSP00000378295:p.Leu492Pro	Somatic		WXS	Illumina GAIIx	Phase_I	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.546817	0.45383	.	.	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.17691	2.26;2.32	5.3	4.1	0.47936	.	0.157127	0.29884	N	0.010941	T	0.14399	0.0348	M	0.64997	1.995	0.52099	D	0.999945	B;B;B	0.32350	0.109;0.366;0.251	B;B;B	0.29077	0.068;0.098;0.045	T	0.06972	-1.0797	10	0.30854	T	0.27	.	4.1352	0.10167	0.1799:0.0935:0.0:0.7266	.	492;492;492	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	P	492	ENSP00000378295:L492P;ENSP00000278849:L492P	ENSP00000278849:L492P	L	+	2	0	INCENP	61664974	0.942000	0.31987	1.000000	0.80357	0.984000	0.73092	2.011000	0.40922	2.015000	0.59207	0.533000	0.62120	CTC		0.632	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2		NM_020238	
KALRN	8997	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	124211627	124211627	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:124211627T>G	ENST00000240874.3	+	32	4881	c.4724T>G	c.(4723-4725)aTt>aGt	p.I1575S	KALRN_ENST00000360013.3_Missense_Mutation_p.I1575S|KALRN_ENST00000460856.1_Missense_Mutation_p.I1566S	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1575	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						ATCAAGAACATTCGAGAAGTG	0.463																																																	0													119.0	123.0	122.0					3																	124211627		2203	4300	6503	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4724T>G	3.37:g.124211627T>G	ENSP00000240874:p.Ile1575Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.6|23.6	4.435561|4.435561	0.83885|0.83885	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000460856;ENST00000240874;ENST00000360013	.|T;T;T	.|0.19806	.|2.12;2.12;2.12	5.4|5.4	5.4|5.4	0.78164|0.78164	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.48822|0.48822	0.1521|0.1521	M|M	0.78916|0.78916	2.43|2.43	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.989;1.0	.|D;D;D	.|0.91635	.|0.999;0.992;0.999	T|T	0.52961|0.52961	-0.8505|-0.8505	5|10	.|0.87932	.|D	.|0	.|.	15.5807|15.5807	0.76432|0.76432	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|1566;1575;1575	.|C9IZQ6;O60229;O60229-2	.|.;KALRN_HUMAN;.	V|S	1544|1566;1575;1575	.|ENSP00000418611:I1566S;ENSP00000240874:I1575S;ENSP00000353109:I1575S	.|ENSP00000240874:I1575S	F|I	+|+	1|2	0|0	KALRN|KALRN	125694317|125694317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.863000|7.863000	0.87023|0.87023	2.266000|2.266000	0.75297|0.75297	0.533000|0.533000	0.62120|0.62120	TTC|ATT		0.463	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4		NM_003947	
AP5Z1	9907	broad.mit.edu;ucsc.edu	37	7	4830219	4830219	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:4830219C>T	ENST00000348624.4	+	15	2029	c.1935C>T	c.(1933-1935)agC>agT	p.S645S	MIR4656_ENST00000579503.1_RNA|AP5Z1_ENST00000490487.1_3'UTR	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	645					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCGTCACCAGCGTGGTAAGGC	0.677																																																	0													42.0	51.0	48.0					7																	4830219		2108	4231	6339	SO:0001819	synonymous_variant	0			AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1935C>T	7.37:g.4830219C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																				0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			
KIAA1161	57462	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	34371724	34371724	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:34371724C>T	ENST00000297625.7	-	2	1341	c.1116G>A	c.(1114-1116)gtG>gtA	p.V372V		NM_020702.3	NP_065753.2	Q6NSJ0	K1161_HUMAN	KIAA1161	406					carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		GCTCGCGCTCCACGCCCTCGC	0.677																																																	0													24.0	28.0	26.0					9																	34371724		2034	4157	6191	SO:0001819	synonymous_variant	57462			AB032987		9p11.2	2009-11-06			ENSG00000164976	ENSG00000164976			19918	protein-coding gene	gene with protein product						10574461	Standard	XM_006716808		Approved	NET37	uc003zue.4	Q6NSJ0	OTTHUMG00000019816	ENST00000297625.7:c.1116G>A	9.37:g.34371724C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T587|Q5T588|Q9ULQ9	Silent	SNP	ENST00000297625.7	37																																																																																					0.677	KIAA1161-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000052158.1		XM_351807	
KLF17	128209	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	44596402	44596402	+	Missense_Mutation	SNP	G	G	T	rs540269615		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:44596402G>T	ENST00000372299.3	+	3	1202	c.1144G>T	c.(1144-1146)Gac>Tac	p.D382Y		NM_173484.3	NP_775755.3	Q5JT82	KLF17_HUMAN	Kruppel-like factor 17	382					gamete generation (GO:0007276)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(1)|lung(6)|ovary(3)|prostate(1)|skin(2)|stomach(1)	18	Acute lymphoblastic leukemia(166;0.155)					TGGAGAGCAGGACAGTCCTCC	0.502																																																	0													101.0	78.0	86.0					1																	44596402		2203	4300	6503	SO:0001583	missense	128209			BC049844	CCDS508.1	1p34.1	2011-11-15	2006-02-17	2006-02-17	ENSG00000171872	ENSG00000171872		"""Zinc fingers, C2H2-type"", ""Kruppel-like transcription factors"""	18830	protein-coding gene	gene with protein product		609602	"""zinc finger protein 393"""	ZNF393		16460907	Standard	NM_173484		Approved	Zfp393, FLJ40160	uc001clp.3	Q5JT82	OTTHUMG00000009664	ENST00000372299.3:c.1144G>T	1.37:g.44596402G>T	ENSP00000361373:p.Asp382Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q86VQ7|Q8N805	Missense_Mutation	SNP	ENST00000372299.3	37	CCDS508.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.202456	0.38905	.	.	ENSG00000171872	ENST00000372299	T	0.10288	2.89	4.47	1.44	0.22558	.	1.085760	0.07262	N	0.867668	T	0.12987	0.0315	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	P	0.56865	0.808	T	0.38520	-0.9657	10	0.49607	T	0.09	.	7.7948	0.29141	0.0:0.3414:0.4822:0.1763	.	382	Q5JT82	KLF17_HUMAN	Y	382	ENSP00000361373:D382Y	ENSP00000361373:D382Y	D	+	1	0	KLF17	44368989	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	0.191000	0.17076	0.342000	0.23796	0.561000	0.74099	GAC		0.502	KLF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026646.1		NM_173484	
KRT1	3848	hgsc.bcm.edu	37	12	53069223	53069243	+	In_Frame_Del	DEL	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	-	rs77846840|rs540699806|rs11170232|rs370799361|rs267607656	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	ACCTCCGGAGCCGTAGCTGCT	ACCTCCGGAGCCGTAGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENST00000252244.3	-	9	1727_1747	c.1669_1689delAGCAGCTACGGCTCCGGAGGT	c.(1669-1689)agcagctacggctccggaggtdel	p.SSYGSGG557del		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	Gly/Ser-rich.|Tail.				complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)	p.S557_G563delSSYGSGG(3)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						catagctgccacctccggagccgtagctgctacctccggag	0.697														1779	0.355232	0.4372	0.3905	5008	,	,		11351	0.1349		0.3459	False		,,,				2504	0.456																3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)								1255,1949		405,445,752						0.8	0.1		dbSNP_130	5	2781,3759		866,1049,1355	no	coding	KRT1	NM_006121.3		1271,1494,2107	A1A1,A1R,RR		42.5229,39.1698,41.4204				4036,5708				SO:0001651	inframe_deletion	3848			X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1669_1689delAGCAGCTACGGCTCCGGAGGT	12.37:g.53069223_53069243delACCTCCGGAGCCGTAGCTGCT	ENSP00000252244:p.Ser557_Gly563del	Somatic		WXS	Illumina HiSeq	Phase_I	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	In_Frame_Del	DEL	ENST00000252244.3	37	CCDS8836.1																																																																																				0.697	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1		NM_006121	
LIPE	3991	broad.mit.edu;hgsc.bcm.edu	37	19	42912198	42912198	+	Missense_Mutation	SNP	C	C	T	rs376903518		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:42912198C>T	ENST00000244289.4	-	4	1862	c.1586G>A	c.(1585-1587)cGg>cAg	p.R529Q	LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000593491.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE_ENST00000602000.1_5'UTR	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	529					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CTGTGTGATCCGCTCAAACTC	0.602																																																	0								C	GLN/ARG	0,4406		0,0,2203	90.0	78.0	82.0		1586	3.6	1.0	19		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	LIPE	NM_005357.2	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	529/1077	42912198	1,13005	2203	4300	6503	SO:0001583	missense	3991			L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.1586G>A	19.37:g.42912198C>T	ENSP00000244289:p.Arg529Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.606004	0.87157	0.0	1.16E-4	ENSG00000079435	ENST00000244289	T	0.34072	1.38	3.6	3.6	0.41247	Hormone-sensitive lipase, N-terminal (1);	0.000000	0.64402	D	0.000004	T	0.55289	0.1911	M	0.61703	1.905	0.50313	D	0.999868	D;D	0.89917	1.0;0.999	D;D	0.80764	0.978;0.994	T	0.58014	-0.7711	10	0.48119	T	0.1	-12.6325	14.5259	0.67887	0.0:1.0:0.0:0.0	.	529;529	A8K8W7;Q05469	.;LIPS_HUMAN	Q	529	ENSP00000244289:R529Q	ENSP00000244289:R529Q	R	-	2	0	LIPE	47604038	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	4.633000	0.61318	2.036000	0.60181	0.561000	0.74099	CGG		0.602	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1		NM_005357	
LRP6	4040	broad.mit.edu;hgsc.bcm.edu	37	12	12278312	12278312	+	Missense_Mutation	SNP	C	C	T	rs367658176		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:12278312C>T	ENST00000261349.4	-	21	4443	c.4367G>A	c.(4366-4368)aGt>aAt	p.S1456N	LRP6_ENST00000540415.1_5'UTR|BCL2L14_ENST00000396369.1_Intron|LRP6_ENST00000543091.1_Missense_Mutation_p.S1411N	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1456					anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				GGGGGGTCCACTGCTTCCCCC	0.433																																																	0													111.0	92.0	99.0					12																	12278312		2203	4300	6503	SO:0001583	missense	4040			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.4367G>A	12.37:g.12278312C>T	ENSP00000261349:p.Ser1456Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.072612	0.76415	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.50001	0.76;0.76	6.03	5.13	0.70059	.	0.000000	0.64402	D	0.000001	T	0.59293	0.2183	L	0.45137	1.4	0.80722	D	1	D;P	0.61080	0.989;0.615	D;B	0.72982	0.979;0.347	T	0.49579	-0.8925	10	0.26408	T	0.33	.	15.7129	0.77644	0.0:0.9337:0.0:0.0663	.	1411;1456	F5H7J9;O75581	.;LRP6_HUMAN	N	1456;1411	ENSP00000261349:S1456N;ENSP00000442472:S1411N	ENSP00000261349:S1456N	S	-	2	0	LRP6	12169579	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.691000	0.68249	2.861000	0.98227	0.655000	0.94253	AGT		0.433	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			
MCTP2	55784	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	95001402	95001402	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr15:95001402A>G	ENST00000357742.4	+	19	2287	c.2287A>G	c.(2287-2289)Atg>Gtg	p.M763V	MCTP2_ENST00000451018.3_Missense_Mutation_p.M708V	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	763					calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			AAGAATCTATATGGTACAGGA	0.318																																																	0													112.0	119.0	117.0					15																	95001402		2197	4298	6495	SO:0001583	missense	55784			AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.2287A>G	15.37:g.95001402A>G	ENSP00000350377:p.Met763Val	Somatic		WXS	Illumina HiSeq	Phase_I	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Missense_Mutation	SNP	ENST00000357742.4	37	CCDS32338.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.031019	0.54790	.	.	ENSG00000140563	ENST00000451018;ENST00000357742	T;T	0.66815	-0.23;-0.05	4.94	4.94	0.65067	Phosphoribosyltransferase C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.81064	0.4745	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	0.961;1.0	P;D	0.83275	0.794;0.996	T	0.81048	-0.1109	10	0.36615	T	0.2	.	14.931	0.70914	1.0:0.0:0.0:0.0	.	708;763	Q6DN12-2;Q6DN12	.;MCTP2_HUMAN	V	708;763	ENSP00000395109:M708V;ENSP00000350377:M763V	ENSP00000350377:M763V	M	+	1	0	MCTP2	92802406	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.863000	0.69568	1.976000	0.57569	0.454000	0.30748	ATG		0.318	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3		NM_018349	
MEGF8	1954	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	42848626	42848626	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:42848626C>A	ENST00000251268.6	+	11	1822	c.1822C>A	c.(1822-1824)Ctc>Atc	p.L608I	MEGF8_ENST00000334370.4_Missense_Mutation_p.L608I	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	608	PSI 1.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				CCTGGGCCGCCTCCTGGGTGA	0.672																																																	0													25.0	30.0	28.0					19																	42848626		2201	4296	6497	SO:0001583	missense	1954			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.1822C>A	19.37:g.42848626C>A	ENSP00000251268:p.Leu608Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	C	15.56	2.871153	0.51695	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.20738	2.05;2.05	4.85	4.85	0.62838	.	0.286088	0.27792	N	0.017830	T	0.14013	0.0339	N	0.14661	0.345	0.80722	D	1	P;P	0.46512	0.826;0.879	B;B	0.40825	0.341;0.222	T	0.08249	-1.0731	10	0.30078	T	0.28	.	15.4477	0.75243	0.0:1.0:0.0:0.0	.	608;608	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	I	608	ENSP00000334219:L608I;ENSP00000251268:L608I	ENSP00000251268:L608I	L	+	1	0	MEGF8	47540466	1.000000	0.71417	0.998000	0.56505	0.901000	0.52897	5.239000	0.65371	2.251000	0.74343	0.306000	0.20318	CTC		0.672	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1		NM_001410	
MGEA5	10724	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	103565869	103565869	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr10:103565869C>T	ENST00000361464.3	-	6	1079	c.684G>A	c.(682-684)gtG>gtA	p.V228V	MGEA5_ENST00000439817.1_Silent_p.V228V|MGEA5_ENST00000370094.3_Silent_p.V228V|MGEA5_ENST00000357797.5_Silent_p.V228V|MGEA5_ENST00000419011.2_3'UTR	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	228					aging (GO:0007568)|dATP metabolic process (GO:0046060)|glycoprotein catabolic process (GO:0006516)|N-acetylglucosamine metabolic process (GO:0006044)|necrotic cell death (GO:0070265)|negative regulation of cardiac muscle adaptation (GO:0010616)|negative regulation of protein glycosylation (GO:0060051)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cell killing (GO:0031343)|positive regulation of DNA metabolic process (GO:0051054)|positive regulation of glucose import (GO:0046326)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of proteolysis (GO:0045862)|protein targeting to membrane (GO:0006612)|response to steroid hormone (GO:0048545)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|hyalurononglucosaminidase activity (GO:0004415)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	23		Colorectal(252;0.207)		Epithelial(162;4.67e-09)|all cancers(201;2.54e-07)		GAGACTGAGACACATTTGGAT	0.353																																																	0													63.0	60.0	61.0					10																	103565869		2203	4300	6503	SO:0001819	synonymous_variant	10724			AF036144	CCDS7520.1, CCDS44471.1	10q24.1-q24.3	2008-08-01			ENSG00000198408	ENSG00000198408			7056	protein-coding gene	gene with protein product	"""nuclear cytoplasmic O-GlcNAcase and acetyltransferase"""	604039				9811929, 16356930	Standard	NM_012215		Approved	MEA5, NCOAT, OGA	uc001ktv.2	O60502	OTTHUMG00000018939	ENST00000361464.3:c.684G>A	10.37:g.103565869C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Silent	SNP	ENST00000361464.3	37	CCDS7520.1																																																																																				0.353	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1		NM_012215	
MLC1	23209	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	50518782	50518782	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr22:50518782G>T	ENST00000311597.5	-	4	918	c.312C>A	c.(310-312)aaC>aaA	p.N104K	MLC1_ENST00000395876.2_Missense_Mutation_p.N104K|MLC1_ENST00000535444.1_Missense_Mutation_p.N25K|MLC1_ENST00000450140.2_Intron|MLC1_ENST00000538737.1_Missense_Mutation_p.N104K|MLC1_ENST00000431262.2_Missense_Mutation_p.N74K	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	104					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CCACATTGGCGTTCCTCCTGG	0.587																																																	0													63.0	48.0	53.0					22																	50518782		2203	4300	6503	SO:0001583	missense	23209			D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.312C>A	22.37:g.50518782G>T	ENSP00000310375:p.Asn104Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	G	1.372	-0.585944	0.03827	.	.	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000431262;ENST00000535444;ENST00000442311	D;D;D;D;D;D	0.93426	-2.74;-2.74;-2.74;-2.75;-2.74;-3.22	5.34	-7.47	0.01365	.	0.241155	0.48286	N	0.000191	T	0.79545	0.4464	L	0.27053	0.805	0.09310	N	1	P;P;P	0.44690	0.785;0.673;0.841	B;B;B	0.41466	0.348;0.274;0.358	T	0.81420	-0.0941	10	0.08381	T	0.77	-36.7196	1.4848	0.02444	0.3915:0.0993:0.285:0.2242	.	104;74;104	F5H1B9;B7Z659;Q15049	.;.;MLC1_HUMAN	K	104;104;104;74;25;74	ENSP00000379216:N104K;ENSP00000310375:N104K;ENSP00000445805:N104K;ENSP00000415877:N74K;ENSP00000438910:N25K;ENSP00000401385:N74K	ENSP00000310375:N104K	N	-	3	2	MLC1	48860909	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.923000	0.04000	-1.344000	0.02216	-2.630000	0.00154	AAC		0.587	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2		NM_015166	
MLPH	79083	hgsc.bcm.edu	37	2	238455269	238455270	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:238455269_238455270insG	ENST00000264605.3	+	13	1854_1855	c.1560_1561insG	c.(1561-1563)gggfs	p.G521fs	MLPH_ENST00000338530.4_Frame_Shift_Ins_p.G493fs|MLPH_ENST00000445024.2_3'UTR|MLPH_ENST00000409373.1_Frame_Shift_Ins_p.G401fs|MLPH_ENST00000410032.1_Frame_Shift_Ins_p.G378fs	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	521					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		CTCGAGTGGCTGGGAAACTTGG	0.525																																																	0																																										SO:0001589	frameshift_variant	79083			AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.1563dupG	2.37:g.238455272_238455272dupG	ENSP00000264605:p.Gly521fs	Somatic		WXS	Illumina HiSeq	Phase_I	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Frame_Shift_Ins	INS	ENST00000264605.3	37	CCDS2518.1																																																																																				0.525	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2		NM_024101	
NAV3	89795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	78362323	78362323	+	Missense_Mutation	SNP	C	C	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:78362323C>G	ENST00000397909.2	+	5	685	c.512C>G	c.(511-513)gCc>gGc	p.A171G	NAV3_ENST00000536525.2_Missense_Mutation_p.A171G|NAV3_ENST00000228327.6_Missense_Mutation_p.A171G|NAV3_ENST00000266692.7_Missense_Mutation_p.A171G			Q8IVL0	NAV3_HUMAN	neuron navigator 3	171	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						AACTTAAAAGCCATTCTAGGG	0.333										HNSCC(70;0.22)																																							0													67.0	70.0	69.0					12																	78362323		1877	4099	5976	SO:0001583	missense	89795			AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.512C>G	12.37:g.78362323C>G	ENSP00000381007:p.Ala171Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.73|16.73	3.203831|3.203831	0.58234|0.58234	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692|ENST00000550503	D;D;D;D;D|.	0.95035|.	-3.59;-3.59;-3.59;-3.59;-3.59|.	5.73|5.73	5.73|5.73	0.89815|0.89815	Calponin homology domain (5);|.	0.000000|.	0.37906|.	U|.	0.001896|.	T|T	0.73289|0.73289	0.3568|0.3568	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	B;B|.	0.31174|.	0.004;0.311|.	B;B|.	0.40228|.	0.062;0.323|.	T|T	0.69091|0.69091	-0.5237|-0.5237	10|5	0.87932|.	D|.	0|.	-15.5348|-15.5348	19.9618|19.9618	0.97254|0.97254	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	171;171|.	Q8IVL0;Q8IVL0-2|.	NAV3_HUMAN;.|.	G|R	171|17	ENSP00000446628:A171G;ENSP00000446132:A171G;ENSP00000381007:A171G;ENSP00000228327:A171G;ENSP00000266692:A171G|.	ENSP00000228327:A171G|.	A|S	+|+	2|3	0|2	NAV3|NAV3	76886454|76886454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.594000|3.594000	0.54008|0.54008	2.719000|2.719000	0.93026|0.93026	0.632000|0.632000	0.83419|0.83419	GCC|AGC		0.333	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1		NM_001024383	
NHS	4810	broad.mit.edu;hgsc.bcm.edu	37	X	17742451	17742451	+	Missense_Mutation	SNP	T	T	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chrX:17742451T>C	ENST00000380060.3	+	5	1416	c.1078T>C	c.(1078-1080)Tgc>Cgc	p.C360R	NHS_ENST00000485305.1_3'UTR|NHS_ENST00000398097.3_Missense_Mutation_p.C204R	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	381					cell differentiation (GO:0030154)|lens development in camera-type eye (GO:0002088)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(5)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(1)|lung(26)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	71	Hepatocellular(33;0.183)					TAGTATACGCTGCTCTCTGGT	0.433																																																	0													136.0	115.0	122.0					X																	17742451		2203	4300	6503	SO:0001583	missense	4810				CCDS14181.1, CCDS48087.1	Xp22.3-p21.1	2014-06-18			ENSG00000188158	ENSG00000188158			7820	protein-coding gene	gene with protein product		300457					Standard	NM_001136024		Approved		uc004cxx.3	Q6T4R5	OTTHUMG00000022799	ENST00000380060.3:c.1078T>C	X.37:g.17742451T>C	ENSP00000369400:p.Cys360Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	T	14.80	2.644836	0.47258	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.39406	1.08;1.18	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.48390	0.1497	L	0.31664	0.95	0.80722	D	1	P;D;D;D	0.89917	0.927;1.0;1.0;1.0	P;D;D;D	0.91635	0.82;0.999;0.999;0.998	T	0.35773	-0.9775	10	0.07030	T	0.85	-16.2173	14.8956	0.70642	0.0:0.0:0.0:1.0	.	381;202;204;360	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	R	360;204;202	ENSP00000369400:C360R;ENSP00000381170:C204R	ENSP00000369397:C202R	C	+	1	0	NHS	17652372	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	6.180000	0.71981	1.968000	0.57251	0.486000	0.48141	TGC		0.433	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1		NM_198270	
NID2	22795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	52472479	52472479	+	Missense_Mutation	SNP	C	C	T	rs201207693		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr14:52472479C>T	ENST00000216286.5	-	21	4092	c.4093G>A	c.(4093-4095)Gca>Aca	p.A1365T	NID2_ENST00000541773.1_Missense_Mutation_p.A1264T	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1365					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GGGTAGACTGCAGTTATCCCG	0.418																																																	0								C	THR/ALA	0,4406		0,0,2203	130.0	115.0	120.0		4093	5.3	1.0	14		120	1,8599	1.2+/-3.3	0,1,4299	no	missense	NID2	NM_007361.3	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1365/1376	52472479	1,13005	2203	4300	6503	SO:0001583	missense	22795			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.4093G>A	14.37:g.52472479C>T	ENSP00000216286:p.Ala1365Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.639|9.639	1.138536|1.138536	0.21123|0.21123	0.0|0.0	1.16E-4|1.16E-4	ENSG00000087303|ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773|ENST00000556572	D;D|.	0.84146|.	-1.81;-1.68|.	6.17|6.17	5.26|5.26	0.73747|0.73747	Six-bladed beta-propeller, TolB-like (1);|.	0.288540|.	0.39020|.	N|.	0.001488|.	T|T	0.50752|0.50752	0.1634|0.1634	L|L	0.39633|0.39633	1.23|1.23	0.30834|0.30834	N|N	0.736449|0.736449	B;B;B|.	0.30686|.	0.026;0.29;0.001|.	B;B;B|.	0.33196|.	0.016;0.159;0.007|.	T|T	0.53373|0.53373	-0.8448|-0.8448	10|5	0.12430|.	T|.	0.62|.	.|.	17.4035|17.4035	0.87467|0.87467	0.0:0.8754:0.1246:0.0|0.0:0.8754:0.1246:0.0	.|.	959;1264;1365|.	E7EPP3;Q14112-2;Q14112|.	.;.;NID2_HUMAN|.	T|Y	1365;959;1264|633	ENSP00000216286:A1365T;ENSP00000443730:A1264T|.	ENSP00000216286:A1365T|.	A|C	-|-	1|2	0|0	NID2|NID2	51542229|51542229	0.985000|0.985000	0.35326|0.35326	0.974000|0.974000	0.42286|0.42286	0.975000|0.975000	0.68041|0.68041	1.840000|1.840000	0.39230|0.39230	1.565000|1.565000	0.49641|0.49641	0.655000|0.655000	0.94253|0.94253	GCA|TGC		0.418	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			
NOC3L	64318	hgsc.bcm.edu;ucsc.edu	37	10	96112093	96112093	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr10:96112093delA	ENST00000371361.3	-	8	1026	c.926delT	c.(925-927)ttgfs	p.L309fs	NOC3L_ENST00000543788.1_Frame_Shift_Del_p.L47fs|NOC3L_ENST00000463649.1_5'UTR|NOC3L_ENST00000371350.1_Frame_Shift_Del_p.L309fs	NM_022451.9	NP_071896.8	Q8WTT2	NOC3L_HUMAN	nucleolar complex associated 3 homolog (S. cerevisiae)	309					fat cell differentiation (GO:0045444)	nuclear speck (GO:0016607)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			endometrium(3)|large_intestine(17)|lung(5)|ovary(1)|skin(2)|stomach(1)	29		Colorectal(252;0.0897)				CAGATTTTCCAAATAAAACTT	0.328																																																	0													84.0	87.0	86.0					10																	96112093		2202	4299	6501	SO:0001589	frameshift_variant	64318			AL355341	CCDS7433.1	10q23.33	2004-04-20	2005-08-01	2005-08-01	ENSG00000173145	ENSG00000173145			24034	protein-coding gene	gene with protein product		610769	"""chromosome 10 open reading frame 117"""	C10orf117		15564382	Standard	NM_022451		Approved	AD24, FLJ12820, FAD24	uc001kjq.1	Q8WTT2	OTTHUMG00000018788	ENST00000371361.3:c.926delT	10.37:g.96112093delA	ENSP00000360412:p.Leu309fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q9H5M6|Q9H9D8	Frame_Shift_Del	DEL	ENST00000371361.3	37	CCDS7433.1																																																																																				0.328	NOC3L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049466.1		NM_022451	
NUDT19	390916	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	33183154	33183154	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:33183154C>A	ENST00000397061.3	+	1	288	c.288C>A	c.(286-288)ttC>ttA	p.F96L	CTD-2538C1.2_ENST00000592431.1_lincRNA	NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	96	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					CGGCGCCATTCAGCCGCACCG	0.726																																																	0													17.0	20.0	19.0					19																	33183154		2021	4135	6156	SO:0001583	missense	390916				CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965		"""Nudix motif containing"""	32036	protein-coding gene	gene with protein product							Standard	NM_001105570		Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.288C>A	19.37:g.33183154C>A	ENSP00000380251:p.Phe96Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000397061.3	37	CCDS42543.1	.	.	.	.	.	.	.	.	.	.	C	8.079	0.772012	0.16051	.	.	ENSG00000213965	ENST00000397061	T	0.39997	1.05	3.94	-4.76	0.03229	NUDIX hydrolase domain (2);NUDIX hydrolase domain-like (1);	0.669254	0.12501	U	0.463338	T	0.15132	0.0365	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19910	-1.0291	10	0.19590	T	0.45	-34.8731	4.0995	0.10007	0.1165:0.2539:0.4612:0.1683	.	96	A8MXV4	NUD19_HUMAN	L	96	ENSP00000380251:F96L	ENSP00000380251:F96L	F	+	3	2	NUDT19	37874994	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.134000	0.15932	-0.625000	0.05604	0.313000	0.20887	TTC		0.726	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000450338.3		XM_372723	
OR51E1	143503	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	4674702	4674702	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:4674702T>G	ENST00000396952.5	+	2	1596	c.946T>G	c.(946-948)Tca>Gca	p.S316A	OR51E1_ENST00000530215.1_3'UTR	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	315						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|ovary(1)|pancreas(1)|skin(1)|stomach(2)	30		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;7.37e-14)|GBM - Glioblastoma multiforme(2;2.85e-05)|BRCA - Breast invasive adenocarcinoma(625;0.00222)|LUSC - Lung squamous cell carcinoma(625;0.19)		CACACACGCTTCAGAGCCCTA	0.428																																																	0													69.0	65.0	66.0					11																	4674702		2201	4298	6499	SO:0001583	missense	143503			AY775731	CCDS31358.2	11p15.4	2012-08-22	2004-11-03	2004-11-06	ENSG00000180785	ENSG00000180785		"""GPCR / Class A : Olfactory receptors"""	15194	protein-coding gene	gene with protein product		611267	"""olfactory receptor, family 51, subfamily E, member 1 pseudogene"""	OR51E1P, OR52A3P, GPR164			Standard	NM_152430		Approved	GPR136	uc001lzi.4	Q8TCB6	OTTHUMG00000157024	ENST00000396952.5:c.946T>G	11.37:g.4674702T>G	ENSP00000380155:p.Ser316Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	.	.	.	.	.	.	.	.	.	.	T	0.225	-1.025671	0.02045	.	.	ENSG00000180785	ENST00000396952	T	0.08102	3.13	4.77	3.61	0.41365	.	0.161380	0.29431	N	0.012165	T	0.04003	0.0112	N	0.08118	0	0.09310	N	0.999992	B	0.02656	0.0	B	0.04013	0.001	T	0.41215	-0.9521	10	0.27082	T	0.32	.	7.4792	0.27395	0.3487:0.0:0.0:0.6513	.	315	Q8TCB6	O51E1_HUMAN	A	316	ENSP00000380155:S316A	ENSP00000380155:S316A	S	+	1	0	OR51E1	4631278	0.007000	0.16637	0.012000	0.15200	0.007000	0.05969	0.121000	0.15667	0.926000	0.37118	0.533000	0.62120	TCA		0.428	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2		NM_152430	
OR2AG1	144125	broad.mit.edu;hgsc.bcm.edu	37	11	6806985	6806985	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:6806985C>T	ENST00000307401.4	+	1	738	c.717C>T	c.(715-717)gtC>gtT	p.V239V		NM_001004489.2	NP_001004489.1	Q9H205	O2AG1_HUMAN	olfactory receptor, family 2, subfamily AG, member 1	239						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.19e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		AAGCCCTTGTCACCTGCTCTT	0.493																																																	0													193.0	169.0	177.0					11																	6806985		2201	4296	6497	SO:0001819	synonymous_variant	144125			AB065823	CCDS31414.1	11p15.4	2012-08-09			ENSG00000170803	ENSG00000170803		"""GPCR / Class A : Olfactory receptors"""	15142	protein-coding gene	gene with protein product				OR2AG3			Standard	NM_001004489		Approved		uc001mer.2	Q9H205	OTTHUMG00000165735	ENST00000307401.4:c.717C>T	11.37:g.6806985C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B9EKV7|Q6IFG7|Q96R26	Silent	SNP	ENST00000307401.4	37	CCDS31414.1																																																																																				0.493	OR2AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385980.1		NM_001004489	
PCDHGA3	56112	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	140724196	140724196	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr5:140724196C>T	ENST00000253812.6	+	1	596	c.596C>T	c.(595-597)gCc>gTc	p.A199V	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018916.3|NM_032011.1	NP_061739.2|NP_114400.1	Q9Y5H0	PCDG3_HUMAN	protocadherin gamma subfamily A, 3	199	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A199V(1)		breast(1)	1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGAGCGGGCCCTGGACCGT	0.542																																																	1	Substitution - Missense(1)	endometrium(1)											55.0	58.0	57.0					5																	140724196		2117	4255	6372	SO:0001583	missense	56112			AF152510	CCDS47290.1, CCDS75329.1	5q31	2010-01-26			ENSG00000254245	ENSG00000254245		"""Cadherins / Protocadherins : Clustered"""	8701	other	protocadherin		606290				10380929	Standard	NM_032011		Approved	PCDH-GAMMA-A3		Q9Y5H0	OTTHUMG00000163680	ENST00000253812.6:c.596C>T	5.37:g.140724196C>T	ENSP00000253812:p.Ala199Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q9Y5D4	Missense_Mutation	SNP	ENST00000253812.6	37	CCDS47290.1	.	.	.	.	.	.	.	.	.	.	.	4.235	0.042492	0.08196	.	.	ENSG00000254245	ENST00000253812	T	0.20332	2.08	5.65	3.86	0.44501	Cadherin (3);Cadherin-like (1);	0.255401	0.19796	U	0.105879	T	0.19644	0.0472	L	0.60455	1.87	0.09310	N	1	B;B	0.25850	0.136;0.021	B;B	0.23852	0.049;0.033	T	0.12091	-1.0561	10	0.37606	T	0.19	.	7.7587	0.28940	0.1339:0.7231:0.0:0.143	.	199;199	Q9Y5H0-2;Q9Y5H0	.;PCDG3_HUMAN	V	199	ENSP00000253812:A199V	ENSP00000253812:A199V	A	+	2	0	PCDHGA3	140704380	0.001000	0.12720	0.079000	0.20413	0.035000	0.12851	1.502000	0.35704	1.533000	0.49186	-0.137000	0.14449	GCC		0.542	PCDHGA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377017.1		NM_018916	
CFAP221	200373	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	120388454	120388454	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:120388454G>T	ENST00000413369.3	+	19	2038	c.1951G>T	c.(1951-1953)Gat>Tat	p.D651Y	PCDP1_ENST00000602047.1_Missense_Mutation_p.D365Y	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					CATGTCTCTAGATTATGATCC	0.443																																																	0													189.0	176.0	180.0					2																	120388454		2203	4300	6503	SO:0001583	missense	200373																														ENST00000413369.3:c.1951G>T	2.37:g.120388454G>T	ENSP00000393222:p.Asp651Tyr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000413369.3	37	CCDS33282.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.54|14.54	2.565389|2.565389	0.45694|0.45694	.|.	.|.	ENSG00000163075|ENSG00000163075	ENST00000295220;ENST00000413369|ENST00000443972;ENST00000413057	T|.	0.33438|.	1.41|.	5.06|5.06	2.14|2.14	0.27477|0.27477	.|.	1.000500|.	0.08068|.	N|.	0.999452|.	T|.	0.22742|.	0.0549|.	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999999|0.999999	D;P|.	0.54964|.	0.969;0.955|.	P;P|.	0.51135|.	0.66;0.543|.	T|.	0.20240|.	-1.0281|.	10|.	0.72032|.	D|.	0.01|.	-3.4422|-3.4422	4.724|4.724	0.12933|0.12933	0.1847:0.0:0.6445:0.1708|0.1847:0.0:0.6445:0.1708	.|.	495;651|.	Q4G0U5-3;Q4G0U5|.	.;PCDP1_HUMAN|.	Y|Y	365;651|209;198	ENSP00000393222:D651Y|.	ENSP00000295220:D365Y|.	D|X	+|+	1|3	0|2	AC069154.2|AC069154.2	120104924|120104924	0.552000|0.552000	0.26505|0.26505	0.011000|0.011000	0.14972|0.14972	0.131000|0.131000	0.20780|0.20780	0.957000|0.957000	0.29215|0.29215	0.718000|0.718000	0.32166|0.32166	0.563000|0.563000	0.77884|0.77884	GAT|TAG		0.443	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			
PFKP	5214	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	3151561	3151561	+	Silent	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr10:3151561A>G	ENST00000381125.4	+	10	1054	c.978A>G	c.(976-978)ggA>ggG	p.G326G	PFKP_ENST00000381075.2_Silent_p.G318G	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	326	N-terminal catalytic PFK domain 1.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		GCCGCATGGGAGTGGAGGCAG	0.637																																																	0													62.0	50.0	54.0					10																	3151561		2203	4299	6502	SO:0001819	synonymous_variant	5214			AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.978A>G	10.37:g.3151561A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1																																																																																				0.637	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1		NM_002627	
PGLYRP4	57115	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	153303264	153303264	+	Silent	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:153303264G>C	ENST00000359650.5	-	9	1165	c.1101C>G	c.(1099-1101)acC>acG	p.T367T	PGLYRP4_ENST00000368739.3_Silent_p.T363T|RNU6-160P_ENST00000384591.1_RNA	NM_020393.2	NP_065126.2	Q96LB8	PGRP4_HUMAN	peptidoglycan recognition protein 4	367					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	23	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			AATGAGGCCAGGTGCTGATGA	0.552																																																	0													122.0	113.0	116.0					1																	153303264		2203	4300	6503	SO:0001819	synonymous_variant	57115			AF242518	CCDS30871.1	1q21	2008-02-05			ENSG00000163218	ENSG00000163218			30015	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I beta precursor"""	608198				11461926	Standard	XR_241090		Approved	SBBI67, PGRPIB, PGLYRPIbeta, PGRP-Ibeta	uc001fbo.3	Q96LB8	OTTHUMG00000037057	ENST00000359650.5:c.1101C>G	1.37:g.153303264G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K838|Q3B822|Q3B823|Q5SY63|Q5SY64|Q9HD75	Silent	SNP	ENST00000359650.5	37	CCDS30871.1																																																																																				0.552	PGLYRP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089978.1		NM_020393	
PHKA2	5256	hgsc.bcm.edu;ucsc.edu	37	X	18961909	18961920	+	In_Frame_Del	DEL	AATTGCCTCAAG	AATTGCCTCAAG	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	AATTGCCTCAAG	AATTGCCTCAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chrX:18961909_18961920delAATTGCCTCAAG	ENST00000379942.4	-	7	1290_1301	c.625_636delCTTGAGGCAATT	c.(625-636)cttgaggcaattdel	p.LEAI209del		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	209					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CCAGTTCATCAATTGCCTCAAGAGCTGCCTAC	0.415																																																	0																																										SO:0001651	inframe_deletion	5256				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.625_636delCTTGAGGCAATT	X.37:g.18961909_18961920delAATTGCCTCAAG	ENSP00000369274:p.Leu209_Ile212del	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	In_Frame_Del	DEL	ENST00000379942.4	37	CCDS14190.1																																																																																				0.415	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1		NM_000292	
PLXND1	23129	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	129324804	129324804	+	Silent	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:129324804G>A	ENST00000324093.4	-	1	857	c.679C>T	c.(679-681)Ctg>Ttg	p.L227L	PLXND1_ENST00000393239.1_Silent_p.L227L	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	227	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		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						TGGTCCTCCAGGCTGCGGTTG	0.701																																					Ovarian(97;366 1484 3738 22084 39045)												0													25.0	27.0	26.0					3																	129324804		2201	4298	6499	SO:0001819	synonymous_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.679C>T	3.37:g.129324804G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Silent	SNP	ENST00000324093.4	37	CCDS33854.1																																																																																				0.701	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4		NM_015103	
PMS2	5395	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	6029494	6029494	+	Missense_Mutation	SNP	C	C	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:6029494C>G	ENST00000265849.7	-	10	1186	c.1081G>C	c.(1081-1083)Gga>Cga	p.G361R	PMS2_ENST00000469652.1_Intron|PMS2_ENST00000406569.3_Missense_Mutation_p.G361R|PMS2_ENST00000441476.2_Missense_Mutation_p.G255R|PMS2_ENST00000382321.4_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	361					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		TCAAACATTCCTATCAAAGAG	0.373			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																														yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	0													118.0	112.0	114.0					7																	6029494		2203	4300	6503	SO:0001583	missense	5395	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1081G>C	7.37:g.6029494C>G	ENSP00000265849:p.Gly361Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	.	.	.	.	.	.	.	.	.	.	c	17.99	3.522742	0.64747	.	.	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;T	0.80738	-1.41;-1.41;-1.41	5.73	4.85	0.62838	Ribosomal protein S5 domain 2-type fold (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.635714	0.16912	N	0.194450	T	0.80248	0.4588	N	0.25485	0.75	0.34739	D	0.730541	B;D;D	0.61080	0.197;0.989;0.966	B;B;P	0.58780	0.044;0.402;0.845	T	0.80752	-0.1242	10	0.21540	T	0.41	-1.9642	14.5361	0.67960	0.0:0.9301:0.0:0.0699	.	361;361;255	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	R	361;314;255;361	ENSP00000265849:G361R;ENSP00000392843:G255R;ENSP00000384308:G361R	ENSP00000265849:G361R	G	-	1	0	PMS2	5996020	0.374000	0.25081	0.986000	0.45419	0.995000	0.86356	1.783000	0.38664	1.440000	0.47531	0.650000	0.86243	GGA		0.373	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3		NM_000535	
POLE	5426	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	133226298	133226298	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:133226298delT	ENST00000320574.5	-	30	3803	c.3760delA	c.(3760-3762)atcfs	p.I1254fs	POLE_ENST00000535270.1_Frame_Shift_Del_p.I1227fs	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1254					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TGCCCCAAGATTTCCTGCCAG	0.627								DNA polymerases (catalytic subunits)																																									0													118.0	118.0	118.0					12																	133226298		2203	4300	6503	SO:0001589	frameshift_variant	5426				CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3760delA	12.37:g.133226298delT	ENSP00000322570:p.Ile1254fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q13533|Q86VH9	Frame_Shift_Del	DEL	ENST00000320574.5	37	CCDS9278.1																																																																																				0.627	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2		NM_006231	
POLR3B	55703	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	106772092	106772092	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:106772092G>C	ENST00000228347.4	+	8	766	c.544G>C	c.(544-546)Gag>Cag	p.E182Q	POLR3B_ENST00000539066.1_Missense_Mutation_p.E124Q	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	182					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)	p.E182*(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						TCTTATCCAAGAGCAGCTGTC	0.418																																																	1	Substitution - Nonsense(1)	large_intestine(1)											148.0	141.0	143.0					12																	106772092		2203	4300	6503	SO:0001583	missense	55703			AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.544G>C	12.37:g.106772092G>C	ENSP00000228347:p.Glu182Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	31	5.058319	0.93846	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.68025	-0.3;-0.3	5.73	5.73	0.89815	RNA polymerase, beta subunit, protrusion (1);	0.000000	0.85682	D	0.000000	D	0.89434	0.6714	H	0.97874	4.095	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	D	0.92866	0.6310	10	0.87932	D	0	-13.7127	19.49	0.95047	0.0:0.0:1.0:0.0	.	182	Q9NW08	RPC2_HUMAN	Q	182;182;124	ENSP00000228347:E182Q;ENSP00000445721:E124Q	ENSP00000228347:E182Q	E	+	1	0	POLR3B	105296222	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.703000	0.98714	2.704000	0.92352	0.650000	0.86243	GAG		0.418	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1		NM_018082	
PRR12	57479	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50098148	50098148	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:50098148C>A	ENST00000418929.2	+	4	568	c.556C>A	c.(556-558)Cat>Aat	p.H186N		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0	Pro-rich.						DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CCTGTCCCCTCATGACGTGCT	0.687																																																	0													25.0	28.0	27.0					19																	50098148		1960	4136	6096	SO:0001583	missense	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.556C>A	19.37:g.50098148C>A	ENSP00000394510:p.His186Asn	Somatic		WXS	Illumina HiSeq	Phase_I	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.886799	0.33348	.	.	ENSG00000126464	ENST00000418929	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	T	0.78717	0.4327	.	.	.	0.37107	D	0.900153	D	0.67145	0.996	D	0.76071	0.987	D	0.84652	0.0701	7	0.72032	D	0.01	.	15.4155	0.74962	0.0:1.0:0.0:0.0	.	186	Q9ULL5-3	.	N	186	.	ENSP00000394510:H186N	H	+	1	0	PRR12	54789960	1.000000	0.71417	0.999000	0.59377	0.790000	0.44656	5.447000	0.66606	2.252000	0.74401	0.563000	0.77884	CAT		0.687	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1		NM_020719	
PTPN22	26191	broad.mit.edu;hgsc.bcm.edu	37	1	114394727	114394727	+	Splice_Site	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:114394727C>A	ENST00000359785.5	-	10	886		c.e10-1		PTPN22_ENST00000525799.1_Splice_Site|PTPN22_ENST00000528414.1_Intron|PTPN22_ENST00000460620.1_Intron|PTPN22_ENST00000420377.2_Splice_Site|PTPN22_ENST00000538253.1_Splice_Site	NM_001193431.1|NM_015967.5	NP_001180360.1|NP_057051	Q9Y2R2	PTN22_HUMAN	protein tyrosine phosphatase, non-receptor type 22 (lymphoid)						negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphoanandamide dephosphorylation (GO:0035644)|protein dephosphorylation (GO:0006470)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of innate immune response (GO:0045088)|regulation of natural killer cell proliferation (GO:0032817)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	kinase binding (GO:0019900)|protein tyrosine phosphatase activity (GO:0004725)|SH3 domain binding (GO:0017124)			NS(1)|breast(1)|kidney(3)|large_intestine(4)|lung(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Lung SC(450;0.184)	all_cancers(81;1.93e-08)|all_epithelial(167;4.37e-08)|all_lung(203;5.22e-06)|Lung NSC(69;8.94e-06)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGGAATTATCTATCAAATTA	0.348																																																	0													48.0	46.0	47.0					1																	114394727		2202	4300	6502	SO:0001630	splice_region_variant	26191			AF001846	CCDS863.1, CCDS864.1, CCDS864.2	1p13.2	2011-06-09	2005-02-02		ENSG00000134242	ENSG00000134242		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9652	protein-coding gene	gene with protein product		600716	"""protein tyrosine phosphatase, non-receptor type 8"""	PTPN8		10068674, 1373816	Standard	NM_015967		Approved	Lyp, Lyp1, Lyp2	uc001eds.3	Q9Y2R2	OTTHUMG00000011936	ENST00000359785.5:c.751-1G>T	1.37:g.114394727C>A		Somatic		WXS	Illumina HiSeq	Phase_I	A0N0K6|B1ALC8|D4NZ71|E9PLD8|E9PPI1|O95063|O95064|Q6IPX8|Q8WVM1	Splice_Site	SNP	ENST00000359785.5	37	CCDS863.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.782141	0.70222	.	.	ENSG00000134242	ENST00000359785;ENST00000538253;ENST00000420377;ENST00000525799;ENST00000354605	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6773	0.91532	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PTPN22	114196250	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	7.106000	0.77039	2.716000	0.92895	0.561000	0.74099	.		0.348	PTPN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033015.1		NM_015967	Intron
PRRC2C	23215	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	171509126	171509126	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:171509126G>A	ENST00000338920.4	+	16	2752	c.2515G>A	c.(2515-2517)Gac>Aac	p.D839N	PRRC2C_ENST00000426496.2_Missense_Mutation_p.D839N|PRRC2C_ENST00000367742.3_Missense_Mutation_p.D841N|PRRC2C_ENST00000392078.3_Missense_Mutation_p.D841N	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	839					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGCTGCGTTGGACCAGGAACA	0.383																																																	0													139.0	142.0	141.0					1																	171509126		2203	4300	6503	SO:0001583	missense	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.2515G>A	1.37:g.171509126G>A	ENSP00000343629:p.Asp839Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Missense_Mutation	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648073	0.47258	.	.	ENSG00000117523	ENST00000392078;ENST00000451306;ENST00000426496;ENST00000367742;ENST00000338920;ENST00000392080;ENST00000483654	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	5.85	5.85	0.93711	.	0.316812	0.22461	N	0.059755	T	0.04815	0.0130	L	0.27053	0.805	0.49915	D	0.999831	P	0.41848	0.763	B	0.39840	0.311	T	0.45498	-0.9257	10	0.42905	T	0.14	.	20.2313	0.98350	0.0:0.0:1.0:0.0	.	839	Q9Y520-4	.	N	841;840;839;841;839;596;598	ENSP00000375928:D841N;ENSP00000410219:D839N;ENSP00000356716:D841N;ENSP00000343629:D839N	ENSP00000343629:D839N	D	+	1	0	PRRC2C	169775750	1.000000	0.71417	0.038000	0.18304	0.604000	0.37047	8.381000	0.90152	2.784000	0.95788	0.580000	0.79431	GAC		0.383	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4		NM_015172	
PZP	5858	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	9305466	9305466	+	Missense_Mutation	SNP	C	C	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:9305466C>G	ENST00000261336.2	-	31	4103	c.4075G>C	c.(4075-4077)Gat>Cat	p.D1359H	PZP_ENST00000381997.2_Missense_Mutation_p.D1145H	NM_002864.2	NP_002855.2	P20742	PZP_HUMAN	pregnancy-zone protein	1359					female pregnancy (GO:0007565)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D1359N(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(21)|lung(46)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)	102						TTGTGTCCATCGCAAGTTTGG	0.433																																					Melanoma(125;1402 1695 4685 34487 38571)												1	Substitution - Missense(1)	upper_aerodigestive_tract(1)											140.0	128.0	132.0					12																	9305466		2203	4300	6503	SO:0001583	missense	5858			X54380, M24416, X51541	CCDS8600.1	12p13-p12.2	2008-02-01			ENSG00000126838	ENSG00000126838			9750	protein-coding gene	gene with protein product		176420					Standard	NM_002864		Approved	CPAMD6	uc001qvl.3	P20742	OTTHUMG00000154915	ENST00000261336.2:c.4075G>C	12.37:g.9305466C>G	ENSP00000261336:p.Asp1359His	Somatic		WXS	Illumina HiSeq	Phase_I	A6ND27|Q15273|Q2NKL2|Q7M4N7	Missense_Mutation	SNP	ENST00000261336.2	37	CCDS8600.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800257	0.31869	.	.	ENSG00000126838	ENST00000261336;ENST00000381997	T;T	0.32272	1.46;1.46	3.79	1.31	0.21738	Alpha-macroglobulin, receptor-binding (2);	0.349456	0.20529	U	0.090551	T	0.48909	0.1526	M	0.86178	2.8	0.25303	N	0.989268	D;D	0.65815	0.985;0.995	P;P	0.59761	0.8;0.863	T	0.38824	-0.9643	10	0.72032	D	0.01	.	6.5741	0.22555	0.0:0.5731:0.0:0.4269	.	1145;1359	P20742-2;P20742	.;PZP_HUMAN	H	1359;1145	ENSP00000261336:D1359H;ENSP00000371427:D1145H	ENSP00000261336:D1359H	D	-	1	0	PZP	9196733	0.002000	0.14202	0.729000	0.30791	0.894000	0.52154	0.010000	0.13242	0.131000	0.18576	0.563000	0.77884	GAT		0.433	PZP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337624.1		NM_002864	
RAET1G	353091	hgsc.bcm.edu	37	6	150240945	150240945	+	Silent	SNP	G	G	A	rs189388116	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:150240945G>A	ENST00000367360.2	-	2	160	c.93C>T	c.(91-93)caC>caT	p.H31H	RAET1E-AS1_ENST00000446954.2_RNA|RAET1E-AS1_ENST00000605899.1_RNA|RP11-244K5.8_ENST00000606915.1_RNA|RAET1G_ENST00000479265.1_Silent_p.H31H	NM_001001788.2	NP_001001788.2			retinoic acid early transcript 1G											NS(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(4)|urinary_tract(1)	13		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.73e-12)		AGCAAAGAGAGTGAGGGTCTG	0.532													g|||	46	0.0091853	0.034	0.0014	5008	,	,		21939	0.0		0.0	False		,,,				2504	0.0																0								G		113,4293	85.3+/-124.0	2,109,2092	63.0	67.0	66.0		93	-0.2	0.0	6		66	0,8594		0,0,4297	no	coding-synonymous	RAET1G	NM_001001788.2		2,109,6389	AA,AG,GG		0.0,2.5647,0.8692		31/335	150240945	113,12887	2203	4297	6500	SO:0001819	synonymous_variant	353091			AY172579	CCDS43514.1	6q24.1-25.1	2009-04-29	2004-11-22		ENSG00000203722	ENSG00000203722			16795	protein-coding gene	gene with protein product		609244	"""retinoic acid early transcript 1G pseudogene"""			11827464, 15240696	Standard	NM_001001788		Approved	ULBP5	uc010kii.1	Q6H3X3	OTTHUMG00000015802	ENST00000367360.2:c.93C>T	6.37:g.150240945G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000367360.2	37	CCDS43514.1																																																																																				0.532	RAET1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042668.2			
RALBP1	10928	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	9516929	9516929	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr18:9516929delG	ENST00000019317.4	+	3	554	c.331delG	c.(331-333)gttfs	p.V111fs	RP11-61L19.3_ENST00000609094.1_RNA|RALBP1_ENST00000383432.3_Frame_Shift_Del_p.V111fs|RNU2-27P_ENST00000516185.1_RNA			Q15311	RBP1_HUMAN	ralA binding protein 1	111					ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GGGAATCCATGTTTTCAAGAA	0.383																																																	0													51.0	53.0	52.0					18																	9516929		2203	4300	6503	SO:0001589	frameshift_variant	10928			L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.331delG	18.37:g.9516929delG	ENSP00000019317:p.Val111fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DUI0	Frame_Shift_Del	DEL	ENST00000019317.4	37	CCDS11845.1																																																																																				0.383	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1		NM_006788	
RGS3	5998	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	116356377	116356377	+	Intron	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:116356377G>C	ENST00000374140.2	+	23	3289				RGS3_ENST00000374134.3_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.E60Q|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000343817.5_Intron|RGS3_ENST00000462143.1_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						CCTCCTGTCTGAGTCCCAGCC	0.622																																																	0													71.0	80.0	77.0					9																	116356377		2203	4298	6501	SO:0001627	intron_variant	5998			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-333G>C	9.37:g.116356377G>C		Somatic		WXS	Illumina HiSeq	Phase_I	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.872060	0.51695	.	.	ENSG00000138835	ENST00000462403	T	0.61158	0.13	5.42	4.52	0.55395	.	.	.	.	.	T	0.34106	0.0886	N	0.08118	0	0.80722	D	1	B	0.30482	0.281	B	0.24701	0.055	T	0.27739	-1.0065	9	0.87932	D	0	.	8.2015	0.31428	0.0854:0.1569:0.7577:0.0	.	60	Q5VZ06	.	Q	60	ENSP00000436168:E60Q	ENSP00000436168:E60Q	E	+	1	0	RGS3	115396198	0.991000	0.36638	1.000000	0.80357	0.785000	0.44390	2.087000	0.41653	1.263000	0.44181	0.650000	0.86243	GAG		0.622	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3		NM_017790	
RNASEH2A	10535	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	12921170	12921170	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:12921170G>C	ENST00000221486.4	+	6	683	c.589G>C	c.(589-591)Gag>Cag	p.E197Q		NM_006397.2	NP_006388.2	O75792	RNH2A_HUMAN	ribonuclease H2, subunit A	197					DNA replication (GO:0006260)|mismatch repair (GO:0006298)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	nucleus (GO:0005634)|ribonuclease H2 complex (GO:0032299)	metal ion binding (GO:0046872)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|skin(1)|urinary_tract(1)	14						GCAGTTCGTGGAGAAACTGCA	0.567																																																	0													111.0	101.0	104.0					19																	12921170		2203	4300	6503	SO:0001583	missense	10535			Z97029	CCDS12282.1	19p13.13	2014-09-17	2006-08-17			ENSG00000104889	3.1.26.-		18518	protein-coding gene	gene with protein product		606034	"""ribonuclease H2, large subunit"", ""Aicardi-Goutieres syndrome 4"""			9789007, 16845400	Standard	NM_006397		Approved	RNASEHI, RNHIA, RNHL, AGS4	uc002mvg.1	O75792		ENST00000221486.4:c.589G>C	19.37:g.12921170G>C	ENSP00000221486:p.Glu197Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCY1|Q96F11	Missense_Mutation	SNP	ENST00000221486.4	37	CCDS12282.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594412	0.66219	.	.	ENSG00000104889	ENST00000221486	D	0.85861	-2.04	5.57	5.57	0.84162	Ribonuclease HII/HIII domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	D	0.91415	0.7291	M	0.61703	1.905	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.91725	0.5392	10	0.66056	D	0.02	-15.0013	18.3103	0.90197	0.0:0.0:1.0:0.0	.	197	O75792	RNH2A_HUMAN	Q	197	ENSP00000221486:E197Q	ENSP00000221486:E197Q	E	+	1	0	RNASEH2A	12782170	1.000000	0.71417	0.534000	0.28014	0.019000	0.09904	8.686000	0.91250	2.623000	0.88846	0.561000	0.74099	GAG		0.567	RNASEH2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451507.1		NM_006397	
SAP130	79595	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	128757928	128757929	+	Missense_Mutation	DNP	GA	GA	AG			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:128757928_128757929GA>AG	ENST00000259235.3	-	8	1176_1177	c.1047_1048TC>CT	c.(1045-1050)tcTCac>tcCTac	p.H350Y	SAP130_ENST00000259234.6_Missense_Mutation_p.H324Y|SAP130_ENST00000357702.5_Missense_Mutation_p.H350Y	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	350					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			NS(4)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	45	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0771)		AATGCAGGGTGAGATGGTAGTG	0.475																																																	0																																										SO:0001583	missense	79595			BC017453	CCDS2153.1, CCDS54397.1	2q14.3	2008-02-05	2006-02-02		ENSG00000136715	ENSG00000136715			29813	protein-coding gene	gene with protein product		609697	"""sin3A-associated protein, 130kDa"""			11230166, 12724404	Standard	NM_001145928		Approved	FLJ12761	uc010fmd.2	Q9H0E3	OTTHUMG00000131571	ENST00000259235.3:c.1047_1048delinsAG	2.37:g.128757928_128757929delinsAG	ENSP00000259235:p.His350Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation|Silent	SNP	ENST00000259235.3	37	CCDS2153.1																																																																																				0.475	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3		NM_024545	
SARDH	1757	broad.mit.edu;ucsc.edu	37	9	136578237	136578237	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:136578237G>A	ENST00000371872.4	-	9	1417	c.1160C>T	c.(1159-1161)aCg>aTg	p.T387M	SARDH_ENST00000439388.1_Missense_Mutation_p.T387M|SARDH_ENST00000422262.2_Missense_Mutation_p.T219M	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	387					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		GTGGTCGGGCGTGAAGGATTC	0.602																																																	0													40.0	42.0	41.0					9																	136578237		2202	4300	6502	SO:0001583	missense	1757				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1160C>T	9.37:g.136578237G>A	ENSP00000360938:p.Thr387Met	Somatic		WXS	Illumina GAIIx	Phase_I	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.900652	0.72754	.	.	ENSG00000123453	ENST00000371872;ENST00000439388;ENST00000422262;ENST00000427237;ENST00000539227;ENST00000535281	T;T;T	0.55588	0.51;0.51;0.51	4.09	4.09	0.47781	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	T	0.81688	0.4875	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89048	0.3453	10	0.87932	D	0	-15.6329	16.6835	0.85299	0.0:0.0:1.0:0.0	.	387	Q9UL12	SARDH_HUMAN	M	387;387;219;387;387;387	ENSP00000360938:T387M;ENSP00000403084:T387M;ENSP00000415537:T219M	ENSP00000360938:T387M	T	-	2	0	SARDH	135568058	1.000000	0.71417	0.895000	0.35142	0.803000	0.45373	9.370000	0.97159	1.991000	0.58162	0.484000	0.47621	ACG		0.602	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			
SLC17A6	57084	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	22364829	22364829	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:22364829A>C	ENST00000263160.3	+	3	813	c.376A>C	c.(376-378)Atg>Ctg	p.M126L		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	126					ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|synaptic vesicle membrane (GO:0030672)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(28)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)	50						AACCGTGGGGATGATCCACGG	0.532																																																	0													96.0	104.0	101.0					11																	22364829		2203	4300	6503	SO:0001583	missense	57084			AB032435	CCDS7856.1	11p14.3	2013-07-18	2013-07-18		ENSG00000091664	ENSG00000091664		"""Solute carriers"""	16703	protein-coding gene	gene with protein product	"""vesicular glutamate transporter 2"", ""differentiation-associated Na-dependent inorganic phosphate cotransporter"""	607563	"""solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 6"""			11306821	Standard	NM_020346		Approved	DNPI, VGLUT2	uc001mqk.3	Q9P2U8	OTTHUMG00000166063	ENST00000263160.3:c.376A>C	11.37:g.22364829A>C	ENSP00000263160:p.Met126Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKS2	Missense_Mutation	SNP	ENST00000263160.3	37	CCDS7856.1	.	.	.	.	.	.	.	.	.	.	A	6.138	0.393638	0.11638	.	.	ENSG00000091664	ENST00000263160;ENST00000546171	T	0.49720	0.77	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.164801	0.64402	D	0.000005	T	0.20455	0.0492	N	0.02169	-0.655	0.47476	D	0.999439	B	0.02656	0.0	B	0.06405	0.002	T	0.22906	-1.0203	10	0.02654	T	1	.	15.4324	0.75112	1.0:0.0:0.0:0.0	.	126	Q9P2U8	VGLU2_HUMAN	L	126;14	ENSP00000263160:M126L	ENSP00000263160:M126L	M	+	1	0	SLC17A6	22321405	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.132000	0.50523	2.036000	0.60181	0.533000	0.62120	ATG		0.532	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1		NM_020346	
SNX11	29916	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	46198653	46198653	+	Missense_Mutation	SNP	A	A	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:46198653A>C	ENST00000393405.2	+	8	950	c.596A>C	c.(595-597)gAa>gCa	p.E199A	SNX11_ENST00000582104.1_Missense_Mutation_p.E191A|SNX11_ENST00000580219.1_Missense_Mutation_p.E191A|SNX11_ENST00000452859.2_Missense_Mutation_p.E55A|SNX11_ENST00000439357.2_Missense_Mutation_p.E138A|SNX11_ENST00000359238.2_Missense_Mutation_p.E199A	NM_152244.1	NP_689450.1	Q9Y5W9	SNX11_HUMAN	sorting nexin 11	199					intracellular protein transport (GO:0006886)|vesicle organization (GO:0016050)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol phosphate binding (GO:1901981)			breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	14						CCTCCCAGTGAAGAAAAGGAC	0.507																																																	0													138.0	134.0	136.0					17																	46198653		2203	4300	6503	SO:0001583	missense	29916			AF121861	CCDS11526.1	17q21.32	2011-05-03			ENSG00000002919	ENSG00000002919		"""Sorting nexins"""	14975	protein-coding gene	gene with protein product		614906					Standard	NM_013323		Approved		uc002ing.1	Q9Y5W9		ENST00000393405.2:c.596A>C	17.37:g.46198653A>C	ENSP00000377059:p.Glu199Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRL6|B4DPY5|D3DTV0|Q53YC0|Q9H885	Missense_Mutation	SNP	ENST00000393405.2	37	CCDS11526.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.558725	0.45590	.	.	ENSG00000002919	ENST00000452859;ENST00000393405;ENST00000439357;ENST00000359238	T;T	0.66638	-0.22;-0.22	6.16	5.07	0.68467	.	0.124188	0.52532	D	0.000063	T	0.59676	0.2211	L	0.50333	1.59	0.41362	D	0.987434	B;B;B	0.17667	0.023;0.023;0.013	B;B;B	0.12156	0.007;0.007;0.005	T	0.56601	-0.7952	10	0.49607	T	0.09	-11.6932	10.4097	0.44285	0.8359:0.1641:0.0:0.0	.	138;191;199	B4DKH7;B4DPY5;Q9Y5W9	.;.;SNX11_HUMAN	A	55;199;138;199	ENSP00000377059:E199A;ENSP00000352175:E199A	ENSP00000352175:E199A	E	+	2	0	SNX11	43553652	1.000000	0.71417	0.997000	0.53966	0.630000	0.37929	2.756000	0.47549	1.117000	0.41842	0.528000	0.53228	GAA		0.507	SNX11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443423.1			
SORBS3	10174	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	22414254	22414254	+	Missense_Mutation	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr8:22414254G>C	ENST00000240123.7	+	4	630	c.247G>C	c.(247-249)Ggc>Cgc	p.G83R	SORBS3_ENST00000523402.1_Missense_Mutation_p.G83R	NM_005775.4	NP_005766.3	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3	83					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)	18		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		GACCTGGCCAGGCCCTGGGAG	0.602																																																	0													81.0	66.0	71.0					8																	22414254		2203	4300	6503	SO:0001583	missense	10174				CCDS6031.1	8p21.3	2008-02-05			ENSG00000120896	ENSG00000120896			30907	protein-coding gene	gene with protein product		610795				9885244, 12510380	Standard	NM_001018003		Approved	SCAM-1, SH3D4, vinexin	uc003xbv.3	O60504	OTTHUMG00000131728	ENST00000240123.7:c.247G>C	8.37:g.22414254G>C	ENSP00000240123:p.Gly83Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q5BJE4|Q6NX54|Q96FY4|Q9UQE4	Missense_Mutation	SNP	ENST00000240123.7	37	CCDS6031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.25|18.25	3.583574|3.583574	0.65992|0.65992	.|.	.|.	ENSG00000120896|ENSG00000120896	ENST00000240123;ENST00000523402|ENST00000520563;ENST00000524057	T|.	0.06933|.	3.24|.	4.92|4.92	4.04|4.04	0.47022|0.47022	.|.	0.550815|.	0.15015|.	N|.	0.285355|.	T|T	0.41903|0.41903	0.1179|0.1179	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.38195|.	0.622|.	B|.	0.43658|.	0.426|.	T|T	0.17930|0.17930	-1.0353|-1.0353	10|5	0.72032|.	D|.	0.01|.	-11.2865|-11.2865	9.2562|9.2562	0.37584|0.37584	0.1003:0.0:0.8997:0.0|0.1003:0.0:0.8997:0.0	.|.	83|.	O60504|.	VINEX_HUMAN|.	R|T	83|37;19	ENSP00000240123:G83R|.	ENSP00000240123:G83R|.	G|R	+|+	1|2	0|0	SORBS3|SORBS3	22470199|22470199	0.165000|0.165000	0.22948|0.22948	0.999000|0.999000	0.59377|0.59377	0.934000|0.934000	0.57294|0.57294	2.011000|2.011000	0.40922|0.40922	1.043000|1.043000	0.40175|0.40175	-0.140000|-0.140000	0.14226|0.14226	GGC|AGG		0.602	SORBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254647.3		NM_005775	
SOS1	6654	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	39281850	39281850	+	Missense_Mutation	SNP	T	T	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:39281850T>G	ENST00000426016.1	-	6	711	c.625A>C	c.(625-627)Atg>Ctg	p.M209L	SOS1_ENST00000428721.2_Missense_Mutation_p.M152L|SOS1_ENST00000402219.2_Missense_Mutation_p.M209L|SOS1_ENST00000395038.2_Missense_Mutation_p.M209L			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	209	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				ATTTCTGCCATAAATGCTTTT	0.308									Noonan syndrome																																								0													82.0	92.0	89.0					2																	39281850		2203	4293	6496	SO:0001583	missense	6654	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.625A>C	2.37:g.39281850T>G	ENSP00000387784:p.Met209Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.364897	0.41902	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000395038;ENST00000263879;ENST00000428721	D;D;D;D	0.91011	-2.77;-2.77;-2.77;-2.77	5.88	5.88	0.94601	Dbl homology (DH) domain (4);	0.000000	0.85682	D	0.000000	T	0.81541	0.4844	N	0.08118	0	0.58432	D	0.999995	B	0.09022	0.002	B	0.14578	0.011	T	0.76299	-0.3010	10	0.22109	T	0.4	.	16.2792	0.82664	0.0:0.0:0.0:1.0	.	209	Q07889	SOS1_HUMAN	L	209;209;209;209;152	ENSP00000387784:M209L;ENSP00000384675:M209L;ENSP00000378479:M209L;ENSP00000399992:M152L	ENSP00000263879:M209L	M	-	1	0	SOS1	39135354	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.431000	0.80335	2.243000	0.73865	0.533000	0.62120	ATG		0.308	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3		NM_005633	
SPINT1	6692	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	41136788	41136788	+	Silent	SNP	C	C	T	rs557336289		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr15:41136788C>T	ENST00000344051.4	+	2	270	c.36C>T	c.(34-36)ctC>ctT	p.L12L	SPINT1_ENST00000431806.1_Silent_p.L12L|RP11-532F12.5_ENST00000568419.1_RNA|RP11-532F12.5_ENST00000565315.1_RNA|SPINT1_ENST00000562057.1_Silent_p.L12L|RP11-532F12.5_ENST00000564302.1_RNA|RP11-532F12.5_ENST00000568525.1_RNA			O43278	SPIT1_HUMAN	serine peptidase inhibitor, Kunitz type 1	12					branching involved in labyrinthine layer morphogenesis (GO:0060670)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|placenta blood vessel development (GO:0060674)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	16		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		gcgcccgcctcgccccggccg	0.766													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11949	0.0		0.0	False		,,,				2504	0.0																0													10.0	12.0	12.0					15																	41136788		1883	3690	5573	SO:0001819	synonymous_variant	6692				CCDS10067.1, CCDS45231.1	15q13.3	2008-02-05	2005-08-17		ENSG00000166145	ENSG00000166145			11246	protein-coding gene	gene with protein product		605123	"""serine protease inhibitor, Kunitz type 1"""				Standard	XM_006720657		Approved	HAI, MANSC2	uc001zna.3	O43278	OTTHUMG00000130068	ENST00000344051.4:c.36C>T	15.37:g.41136788C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z7D2	Silent	SNP	ENST00000344051.4	37	CCDS10067.1																																																																																				0.766	SPINT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252359.2		NM_003710	
SRBD1	55133	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	45832575	45832575	+	Silent	SNP	T	T	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:45832575T>A	ENST00000263736.4	-	2	68	c.6A>T	c.(4-6)tcA>tcT	p.S2S		NM_018079.4	NP_060549.4	Q8N5C6	SRBD1_HUMAN	S1 RNA binding domain 1	2					nucleobase-containing compound metabolic process (GO:0006139)		hydrolase activity, acting on ester bonds (GO:0016788)|RNA binding (GO:0003723)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(13)|large_intestine(8)|lung(15)|skin(2)|stomach(1)|urinary_tract(1)	49		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	LUSC - Lung squamous cell carcinoma(58;0.0917)|Lung(47;0.154)			TTGGCAATGATGACATCTAGA	0.343																																																	0													154.0	152.0	153.0					2																	45832575		2203	4300	6503	SO:0001819	synonymous_variant	55133			AK056536	CCDS1823.1	2p21	2008-02-05			ENSG00000068784	ENSG00000068784			25521	protein-coding gene	gene with protein product						12477932	Standard	NM_018079		Approved	FLJ10379	uc002rus.3	Q8N5C6	OTTHUMG00000128814	ENST00000263736.4:c.6A>T	2.37:g.45832575T>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q53T56|Q96TA4|Q9NW11	Silent	SNP	ENST00000263736.4	37	CCDS1823.1																																																																																				0.343	SRBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250747.3		NM_018079	
ST8SIA1	6489	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	22354654	22354654	+	Missense_Mutation	SNP	A	A	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:22354654A>T	ENST00000396037.4	-	5	1384	c.903T>A	c.(901-903)aaT>aaA	p.N301K	ST8SIA1_ENST00000539510.1_Missense_Mutation_p.N158K	NM_003034.3	NP_003025.1	Q92185	SIA8A_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 1	301					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|glycosphingolipid biosynthetic process (GO:0006688)|positive regulation of cell proliferation (GO:0008284)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity (GO:0003828)|sialyltransferase activity (GO:0008373)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25						GCTCATGCATATTCACAGAGA	0.527																																																	0													72.0	72.0	72.0					12																	22354654		2203	4300	6503	SO:0001583	missense	6489			L32867	CCDS8697.1	12p12.1-p11.2	2013-03-01	2003-01-14	2005-02-07	ENSG00000111728	ENSG00000111728	2.4.99.8	"""Sialyltransferases"""	10869	protein-coding gene	gene with protein product	"""ST8Sia I"""	601123	"""sialyltransferase 8 (alpha-N-acetylneuraminate: alpha-2,8-sialytransferase, GD3 synthase) A"""	SIAT8, SIAT8A		7901202	Standard	NM_003034		Approved		uc001rfo.4	Q92185	OTTHUMG00000169098	ENST00000396037.4:c.903T>A	12.37:g.22354654A>T	ENSP00000379353:p.Asn301Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4H6|Q17RL0|Q6PZN5|Q93064	Missense_Mutation	SNP	ENST00000396037.4	37	CCDS8697.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.426985	0.62733	.	.	ENSG00000111728	ENST00000396037;ENST00000539510	T	0.21734	1.99	5.73	-1.21	0.09524	.	0.230654	0.50627	D	0.000107	T	0.18002	0.0432	L	0.46157	1.445	0.37686	D	0.923674	B;B	0.29301	0.241;0.016	B;B	0.27500	0.08;0.027	T	0.20940	-1.0260	10	0.72032	D	0.01	-10.0115	13.475	0.61303	0.21:0.0:0.79:0.0	.	158;301	G3V1U7;Q92185	.;SIA8A_HUMAN	K	301;158	ENSP00000379353:N301K	ENSP00000379353:N301K	N	-	3	2	ST8SIA1	22245921	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	0.722000	0.25925	-0.041000	0.13558	0.533000	0.62120	AAT		0.527	ST8SIA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402245.2		NM_003034	
STAG3	10734	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	99801730	99801731	+	Silent	DNP	GC	GC	AT			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:99801730_99801731GC>AT	ENST00000426455.1	+	26	3194_3195	c.2787_2788GC>AT	c.(2785-2790)ctGCtg>ctATtg	p.929_930LL>LL	STAG3_ENST00000440830.1_3'UTR|GATS_ENST00000436886.2_Intron|GATS_ENST00000543273.1_RNA|STAG3_ENST00000317296.5_Silent_p.929_930LL>LL|STAG3_ENST00000394018.2_Silent_p.871_872LL>LL	NM_001282716.1	NP_001269645.1	Q9UJ98	STAG3_HUMAN	stromal antigen 3	929					chromosome segregation (GO:0007059)|synaptonemal complex assembly (GO:0007130)	chromosome, centromeric region (GO:0000775)|extracellular space (GO:0005615)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)|nucleolus (GO:0005730)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)|transverse filament (GO:0000802)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(11)|lung(30)|ovary(5)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	66	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAATCCTGCTGCTGAGCCTCAA	0.5																																																	0																																										SO:0001819	synonymous_variant	10734			AJ007798	CCDS34703.1, CCDS64730.1, CCDS75642.1	7q22	2008-02-01			ENSG00000066923	ENSG00000066923			11356	protein-coding gene	gene with protein product		608489				10698974	Standard	XM_005250116		Approved		uc003utx.1	Q9UJ98	OTTHUMG00000155183	Exception_encountered	7.37:g.99801730_99801731delinsAT		Somatic		WXS	Illumina HiSeq	Phase_I	A6H8Z1|B4DZ10|D6W5U8|H7BYK9|Q8NDP3	Silent	SNP	ENST00000426455.1	37	CCDS34703.1																																																																																				0.500	STAG3-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338734.2		NM_012447	
SYNJ2	8871	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	158464376	158464376	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:158464376C>A	ENST00000355585.4	+	5	815	c.740C>A	c.(739-741)tCt>tAt	p.S247Y	SYNJ2_ENST00000367121.3_Missense_Mutation_p.S247Y|SYNJ2_ENST00000449859.2_Missense_Mutation_p.S196Y|SYNJ2_ENST00000367122.2_Missense_Mutation_p.S247Y	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	247	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	nucleotide binding (GO:0000166)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|RNA binding (GO:0003723)			biliary_tract(1)|endometrium(9)|kidney(3)|large_intestine(11)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	46				OV - Ovarian serous cystadenocarcinoma(65;4.42e-18)|BRCA - Breast invasive adenocarcinoma(81;4.23e-05)		GGAGTGTCATCTTTTGTCCAG	0.493																																																	0													147.0	125.0	132.0					6																	158464376		2203	4300	6503	SO:0001583	missense	8871			AB002346	CCDS5254.1	6q25.3	2008-05-15			ENSG00000078269	ENSG00000078269			11504	protein-coding gene	gene with protein product		609410					Standard	NM_003898		Approved	INPP5H	uc003qqx.2	O15056	OTTHUMG00000015904	ENST00000355585.4:c.740C>A	6.37:g.158464376C>A	ENSP00000347792:p.Ser247Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.829122	0.90955	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000449859	T;T;T;T	0.74421	-0.84;-0.84;-0.84;-0.84	5.47	5.47	0.80525	Synaptojanin, N-terminal (2);	0.000000	0.53938	D	0.000051	D	0.91054	0.7185	H	0.99336	4.52	0.51767	D	0.999935	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.999;0.998	D	0.91939	0.5561	10	0.87932	D	0	.	18.2975	0.90151	0.0:1.0:0.0:0.0	.	196;247;247;247	B4DJU8;E7ER60;O15056;O15056-3	.;.;SYNJ2_HUMAN;.	Y	247;247;247;196	ENSP00000356089:S247Y;ENSP00000356088:S247Y;ENSP00000347792:S247Y;ENSP00000388371:S196Y	ENSP00000347792:S247Y	S	+	2	0	SYNJ2	158384364	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	7.458000	0.80787	-0.442000	0.07190	0.533000	0.62120	TCT		0.493	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			
TAGAP	117289	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	159457430	159457430	+	Frame_Shift_Del	DEL	C	C	-	rs116639718	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr6:159457430delC	ENST00000367066.3	-	10	1956	c.1625delG	c.(1624-1626)ggtfs	p.G542fs	TAGAP_ENST00000326965.6_Frame_Shift_Del_p.G364fs|RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000607796.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	542					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|autonomic_ganglia(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(2)|skin(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.16e-16)|BRCA - Breast invasive adenocarcinoma(81;5.87e-06)		CTTTCTGACACCCCTCGGGAC	0.567																																																	0													53.0	58.0	56.0					6																	159457430		2203	4300	6503	SO:0001589	frameshift_variant	117289			AF385429	CCDS5261.1, CCDS5262.1, CCDS5263.1	6q25.3	2011-09-07	2008-03-25		ENSG00000164691	ENSG00000164691		"""Rho GTPase activating proteins"""	15669	protein-coding gene	gene with protein product		609667	"""T-cell activation GTPase activating protein"""			16375659, 18311140, 18356936	Standard	NM_152133		Approved	FLJ32631, IDDM21, ARHGAP47	uc003qrz.3	Q8N103	OTTHUMG00000015923	ENST00000367066.3:c.1625delG	6.37:g.159457430delC	ENSP00000356033:p.Gly542fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Frame_Shift_Del	DEL	ENST00000367066.3	37	CCDS5261.1																																																																																				0.567	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1		NM_054114	
TGM5	9333	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	43552757	43552757	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr15:43552757C>A	ENST00000220420.5	-	2	38	c.31G>T	c.(31-33)Gac>Tac	p.D11Y	TGM5_ENST00000349114.4_Missense_Mutation_p.D11Y	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	11					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	CTCTGGAGGTCTGTGAGGGCC	0.562																																																	0													92.0	96.0	95.0					15																	43552757		2202	4299	6501	SO:0001583	missense	9333			AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.31G>T	15.37:g.43552757C>A	ENSP00000220420:p.Asp11Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.533749	0.64972	.	.	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	D;D	0.90261	-2.64;-2.64	5.64	4.67	0.58626	Immunoglobulin E-set (1);Transglutaminase, N-terminal (1);Immunoglobulin-like fold (1);	0.104767	0.64402	D	0.000005	D	0.95793	0.8631	M	0.90082	3.085	0.28476	N	0.915166	D;D	0.89917	0.998;1.0	D;D	0.85130	0.952;0.997	D	0.91135	0.4941	10	0.87932	D	0	-35.0121	13.7541	0.62926	0.0:0.8448:0.1552:0.0	.	11;11	O43548-2;O43548	.;TGM5_HUMAN	Y	11;11;10	ENSP00000220420:D11Y;ENSP00000220419:D11Y	ENSP00000220420:D11Y	D	-	1	0	TGM5	41340049	0.996000	0.38824	0.990000	0.47175	0.706000	0.40770	3.463000	0.53050	2.664000	0.90586	0.555000	0.69702	GAC		0.562	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1		NM_004245	
TMC6	11322	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	76116777	76116777	+	Missense_Mutation	SNP	C	C	T	rs199724291		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:76116777C>T	ENST00000590602.1	-	13	1831	c.1672G>A	c.(1672-1674)Gtc>Atc	p.V558I	TMC6_ENST00000589553.1_3'UTR|TMC6_ENST00000322914.3_Missense_Mutation_p.V558I|TMC6_ENST00000591436.1_Intron|TMC6_ENST00000592076.1_Intron|TMC6_ENST00000322933.4_Intron|TMC6_ENST00000392467.3_Missense_Mutation_p.V558I|TMC6_ENST00000306591.7_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	558					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			AACATGAGGACGAAGTCCATC	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16250	0.0		0.001	False		,,,				2504	0.0																0								C	ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	167.0	159.0	162.0		1672,1672	-9.1	0.0	17		162	0,8600		0,0,4300	yes	missense,missense	TMC6	NM_007267.6,NM_001127198.1	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	558/806,558/806	76116777	1,13005	2203	4300	6503	SO:0001583	missense	11322			AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.1672G>A	17.37:g.76116777C>T	ENSP00000465261:p.Val558Ile	Somatic		WXS	Illumina HiSeq	Phase_I	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.008	-1.888457	0.00527	2.27E-4	0.0	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000392466	T;T	0.62639	0.01;0.01	4.55	-9.11	0.00711	.	0.503810	0.20929	N	0.083140	T	0.18425	0.0442	N	0.02391	-0.57	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.003;0.004	T	0.60954	-0.7160	10	0.02654	T	1	-8.9684	1.8191	0.03106	0.169:0.1482:0.3384:0.3443	.	558;558	B3KTU5;Q7Z403	.;TMC6_HUMAN	I	558;558;20	ENSP00000313408:V558I;ENSP00000376260:V558I	ENSP00000313408:V558I	V	-	1	0	TMC6	73628372	0.011000	0.17503	0.002000	0.10522	0.004000	0.04260	-1.158000	0.03153	-4.063000	0.00077	-1.474000	0.01003	GTC		0.637	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			
TMEM184C	55751	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	148555434	148555434	+	Missense_Mutation	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr4:148555434C>T	ENST00000296582.3	+	10	1740	c.1166C>T	c.(1165-1167)tCt>tTt	p.S389F	TMEM184C_ENST00000508208.1_Intron	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	389						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						ATTGCTTCTTCTATGCCACCT	0.418																																																	0													109.0	98.0	102.0					4																	148555434		2203	4300	6503	SO:0001583	missense	55751			AF305823	CCDS3770.1	4q31.22	2008-06-05	2008-06-05	2008-06-05		ENSG00000164168			25587	protein-coding gene	gene with protein product		613937	"""transmembrane protein 34"""	TMEM34			Standard	NM_018241		Approved	FLJ10846	uc003ila.4	Q9NVA4		ENST00000296582.3:c.1166C>T	4.37:g.148555434C>T	ENSP00000296582:p.Ser389Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D3DP04|Q86X84|Q969I7|Q9NXM2	Missense_Mutation	SNP	ENST00000296582.3	37	CCDS3770.1	.	.	.	.	.	.	.	.	.	.	C	19.29	3.799512	0.70567	.	.	ENSG00000164168	ENST00000296582	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.59865	0.2225	L	0.45581	1.43	0.80722	D	1	B	0.24533	0.105	B	0.19666	0.026	T	0.55976	-0.8055	9	0.52906	T	0.07	-27.8557	20.1253	0.97977	0.0:1.0:0.0:0.0	.	389	Q9NVA4	T184C_HUMAN	F	389	.	ENSP00000296582:S389F	S	+	2	0	TMEM184C	148774884	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	4.624000	0.61254	2.832000	0.97577	0.655000	0.94253	TCT		0.418	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1		NM_018241	
TMEM61	199964	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	55457606	55457606	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr1:55457606G>T	ENST00000371268.3	+	3	737	c.463G>T	c.(463-465)Gcc>Tcc	p.A155S	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	155						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						TACGGAGGAAGCCCTGGAGCC	0.627																																																	0													99.0	86.0	90.0					1																	55457606		2203	4300	6503	SO:0001583	missense	199964			BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.463G>T	1.37:g.55457606G>T	ENSP00000360315:p.Ala155Ser	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000371268.3	37	CCDS601.1	.	.	.	.	.	.	.	.	.	.	G	7.393	0.631187	0.14322	.	.	ENSG00000143001	ENST00000371268	T	0.44881	0.91	3.64	1.77	0.24775	.	1.086220	0.07182	N	0.854159	T	0.25344	0.0616	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.24799	-1.0150	10	0.10902	T	0.67	-3.2661	7.453	0.27250	0.2128:0.0:0.7872:0.0	.	155	Q8N0U2	TMM61_HUMAN	S	155	ENSP00000360315:A155S	ENSP00000360315:A155S	A	+	1	0	TMEM61	55230194	0.918000	0.31147	0.004000	0.12327	0.012000	0.07955	1.484000	0.35508	0.532000	0.28657	0.462000	0.41574	GCC		0.627	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1		NM_182532	
TMIGD2	126259	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	4298004	4298004	+	Missense_Mutation	SNP	T	T	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:4298004T>C	ENST00000301272.2	-	2	430	c.385A>G	c.(385-387)Aca>Gca	p.T129A	TMIGD2_ENST00000600114.1_Intron|TMIGD2_ENST00000595645.1_Missense_Mutation_p.T129A|TMIGD2_ENST00000600349.1_Intron	NM_001169126.1|NM_144615.2	NP_001162597.1|NP_653216.2	Q96BF3	TMIG2_HUMAN	transmembrane and immunoglobulin domain containing 2	129	Ig-like.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|skin(2)	19				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0339)|STAD - Stomach adenocarcinoma(1328;0.18)		AAGAGCCTTGTTATGTTGCCC	0.587																																																	0													103.0	118.0	113.0					19																	4298004		2203	4300	6503	SO:0001583	missense	126259			BC015655	CCDS12126.1, CCDS59334.1	19p13.3	2014-02-12	2006-07-05					"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28324	protein-coding gene	gene with protein product		614715					Standard	NM_144615		Approved	MGC23244	uc002lzx.2	Q96BF3		ENST00000301272.2:c.385A>G	19.37:g.4298004T>C	ENSP00000301272:p.Thr129Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q6UW59	Missense_Mutation	SNP	ENST00000301272.2	37	CCDS12126.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.325069	0.41197	.	.	ENSG00000167664	ENST00000301272	T	0.37235	1.21	4.09	0.627	0.17675	Immunoglobulin subtype (1);Immunoglobulin-like (1);	.	.	.	.	T	0.19208	0.0461	L	0.29908	0.895	0.09310	N	1	P;P	0.38551	0.582;0.636	B;B	0.32724	0.093;0.151	T	0.18178	-1.0345	9	0.62326	D	0.03	.	1.0833	0.01647	0.1874:0.1084:0.1942:0.51	.	129;129	Q96BF3-2;Q96BF3	.;TMIG2_HUMAN	A	129	ENSP00000301272:T129A	ENSP00000301272:T129A	T	-	1	0	TMIGD2	4249004	0.023000	0.18921	0.000000	0.03702	0.003000	0.03518	0.936000	0.28938	-0.137000	0.11455	0.397000	0.26171	ACA		0.587	TMIGD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458088.1		NM_144615	
TNFRSF1A	7132	hgsc.bcm.edu	37	12	6442919	6442919	+	Silent	SNP	G	G	A	rs104895249		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr12:6442919G>A	ENST00000162749.2	-	3	605	c.306C>T	c.(304-306)tgC>tgT	p.C102C	TNFRSF1A_ENST00000437813.3_5'UTR|TNFRSF1A_ENST00000540022.1_Intron|TNFRSF1A_ENST00000366159.4_Silent_p.C102C	NM_001065.3	NP_001056.1	P19438	TNR1A_HUMAN	tumor necrosis factor receptor superfamily, member 1A	102					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of angiogenesis (GO:0045766)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|prostaglandin metabolic process (GO:0006693)|protein heterooligomerization (GO:0051291)|response to alkaloid (GO:0043279)|response to amino acid (GO:0043200)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|tetrapyrrole metabolic process (GO:0033013)|viral process (GO:0016032)	axon (GO:0030424)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	tumor necrosis factor-activated receptor activity (GO:0005031)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	19						GGCATTTGGAGCAGCTGAGGC	0.602																																																	0			GRCh37	CM035575	TNFRSF1A	M	rs104895249						61.0	51.0	55.0					12																	6442919		2200	4297	6497	SO:0001819	synonymous_variant	7132			M75866	CCDS8542.1	12p13.2	2014-09-17			ENSG00000067182	ENSG00000067182		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11916	protein-coding gene	gene with protein product		191190		TNFR1		1655358, 2158863	Standard	NM_001065		Approved	TNF-R, TNFAR, TNFR60, TNF-R-I, CD120a, TNF-R55	uc001qnu.3	P19438	OTTHUMG00000168267	ENST00000162749.2:c.306C>T	12.37:g.6442919G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K4X3|B2RDE4|B3KPQ1|B4DQB7|B4E309|B5M0B5|D3DUR1|Q9UCA4	Silent	SNP	ENST00000162749.2	37	CCDS8542.1																																																																																				0.602	TNFRSF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399038.1		NM_001065	
TOP1MT	116447	hgsc.bcm.edu	37	8	144403383	144403383	+	Silent	SNP	C	C	A	rs576527377		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr8:144403383C>A	ENST00000329245.4	-	8	1168	c.1134G>T	c.(1132-1134)ccG>ccT	p.P378P	TOP1MT_ENST00000523676.1_Silent_p.P280P|TOP1MT_ENST00000521193.1_Silent_p.P280P|TOP1MT_ENST00000519148.1_Silent_p.P280P	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	378					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GCTTCTCCACCGGCACTCTGT	0.637																																																	0													43.0	42.0	42.0					8																	144403383		2199	4293	6492	SO:0001819	synonymous_variant	116447			AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1134G>T	8.37:g.144403383C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																				0.637	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3		NM_052963	
TOP3A	7156	broad.mit.edu;ucsc.edu	37	17	18188466	18188466	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:18188466T>A	ENST00000321105.5	-	15	2081	c.1867A>T	c.(1867-1869)Aaa>Taa	p.K623*	TOP3A_ENST00000540524.1_Nonsense_Mutation_p.K153*|TOP3A_ENST00000542570.1_Nonsense_Mutation_p.K528*	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	623					DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TTCTTTGCTTTAGCCACCGCT	0.458																																																	0													183.0	183.0	183.0					17																	18188466		2203	4300	6503	SO:0001587	stop_gained	7156			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.1867A>T	17.37:g.18188466T>A	ENSP00000321636:p.Lys623*	Somatic		WXS	Illumina GAIIx	Phase_I	A8KA61|B4DK80|D3DXC7|Q13473	Nonsense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	T	36	5.748643	0.96882	.	.	ENSG00000177302	ENST00000321105;ENST00000540524;ENST00000542570	.	.	.	5.54	4.39	0.52855	.	0.123113	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.5595	13.8713	0.63622	0.0:0.0:0.1355:0.8645	.	.	.	.	X	623;153;528	.	ENSP00000321636:K623X	K	-	1	0	TOP3A	18129191	1.000000	0.71417	0.863000	0.33907	0.975000	0.68041	4.998000	0.63927	2.107000	0.64212	0.491000	0.48974	AAA		0.458	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			
TTN	7273	broad.mit.edu;hgsc.bcm.edu	37	2	179460510	179460510	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr2:179460510A>G	ENST00000591111.1	-	245	52872	c.52648T>C	c.(52648-52650)Ttc>Ctc	p.F17550L	TTN_ENST00000460472.2_Missense_Mutation_p.F10126L|TTN_ENST00000589042.1_Missense_Mutation_p.F19191L|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.F10251L|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.F16623L|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.F10318L|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	17550	Fibronectin type-III 27. {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)			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)			TGAGCTAGGAATGGTGTTCCA	0.393																																																	0													71.0	64.0	66.0					2																	179460510		1884	4122	6006	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.52648T>C	2.37:g.179460510A>G	ENSP00000465570:p.Phe17550Leu	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		.	.	.	.	.	.	.	.	.	.	A	17.38	3.375842	0.61735	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.52057	0.68;0.68;0.68;0.68	6.05	6.05	0.98169	Fibronectin, type III (3);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.29620	0.0739	N	0.04705	-0.18	0.58432	D	0.999993	B;B;B;B	0.20550	0.046;0.046;0.046;0.046	B;B;B;B	0.22601	0.04;0.04;0.04;0.04	T	0.15607	-1.0431	9	0.87932	D	0	.	12.362	0.55209	0.9331:0.0:0.0669:0.0	.	10126;10251;10318;17550	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	16623;10126;10318;10251;10124	ENSP00000343764:F16623L;ENSP00000434586:F10126L;ENSP00000340554:F10318L;ENSP00000352154:F10251L	ENSP00000340554:F10318L	F	-	1	0	TTN	179168756	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.483000	0.81158	2.320000	0.78422	0.528000	0.53228	TTC		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
UMODL1	89766	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	43529671	43529671	+	Splice_Site	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr21:43529671G>A	ENST00000408910.2	+	10	1519		c.e10-1		UMODL1_ENST00000408989.2_Splice_Site|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Splice_Site|UMODL1_ENST00000400424.2_Splice_Site	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1						adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CCCCCTGGCAGACTGGGACGA	0.577																																					Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)												0													91.0	102.0	98.0					21																	43529671		2039	4184	6223	SO:0001630	splice_region_variant	89766				CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1520-1G>A	21.37:g.43529671G>A		Somatic		WXS	Illumina HiSeq	Phase_I	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Splice_Site	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086695	0.55861	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	.	.	.	3.04	3.04	0.35103	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8362	0.40971	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UMODL1	42402740	1.000000	0.71417	0.978000	0.43139	0.974000	0.67602	4.250000	0.58772	2.013000	0.59113	0.655000	0.94253	.		0.577	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			Intron
VSIG4	11326	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	65253460	65253460	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chrX:65253460G>A	ENST00000374737.4	-	2	376	c.268C>T	c.(268-270)Cac>Tac	p.H90Y	VSIG4_ENST00000455586.2_Missense_Mutation_p.H90Y|VSIG4_ENST00000412866.2_Missense_Mutation_p.H90Y	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	90	Ig-like 1.				complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGAACCTTGTGGCTCACATGC	0.552																																																	0													131.0	111.0	118.0					X																	65253460		2203	4300	6503	SO:0001583	missense	11326			AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.268C>T	X.37:g.65253460G>A	ENSP00000363869:p.His90Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.615|3.615	-0.078798|-0.078798	0.07141|0.07141	.|.	.|.	ENSG00000155659|ENSG00000155659	ENST00000374737;ENST00000455586;ENST00000412866|ENST00000427538	T;T;T|.	0.65178|.	-0.14;-0.14;-0.14|.	4.93|4.93	1.79|1.79	0.24919|0.24919	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	1.086990|.	0.07053|.	N|.	0.832236|.	T|T	0.39489|0.39489	0.1080|0.1080	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	B;P;B;B;B|.	0.40266|.	0.001;0.71;0.107;0.0;0.132|.	B;B;B;B;B|.	0.27796|.	0.001;0.083;0.061;0.0;0.082|.	T|T	0.31641|0.31641	-0.9936|-0.9936	10|5	0.18276|.	T|.	0.48|.	-1.2609|-1.2609	3.494|3.494	0.07648|0.07648	0.1057:0.1517:0.5627:0.1799|0.1057:0.1517:0.5627:0.1799	.|.	90;90;80;90;90|.	C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279|.	.;.;.;.;VSIG4_HUMAN|.	Y|L	90|16	ENSP00000363869:H90Y;ENSP00000411581:H90Y;ENSP00000394143:H90Y|.	ENSP00000363869:H90Y|.	H|P	-|-	1|2	0|0	VSIG4|VSIG4	65170185|65170185	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	0.879000|0.879000	0.28146|0.28146	0.339000|0.339000	0.23719|0.23719	0.594000|0.594000	0.82650|0.82650	CAC|CCA		0.552	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1		NM_007268	
WDR5	11091	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	137007540	137007540	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr9:137007540G>A	ENST00000358625.3	+	6	611	c.440G>A	c.(439-441)gGa>gAa	p.G147E	WDR5_ENST00000425041.1_Missense_Mutation_p.G147E	NM_017588.2	NP_060058.1	P61964	WDR5_HUMAN	WD repeat domain 5	147					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|histone H3-K4 methylation (GO:0051568)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|positive regulation of gluconeogenesis (GO:0045722)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|histone acetyltransferase complex (GO:0000123)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)				endometrium(1)|kidney(1)|large_intestine(2)|lung(5)	9		Myeloproliferative disorder(178;0.0255)|Medulloblastoma(224;0.123)		Epithelial(140;6.61e-13)|all cancers(34;5.66e-12)|OV - Ovarian serous cystadenocarcinoma(145;3.93e-08)|GBM - Glioblastoma multiforme(294;0.00326)|READ - Rectum adenocarcinoma(205;0.154)		ATTGTCTCAGGATCCGTAAGT	0.502																																																	0													105.0	103.0	104.0					9																	137007540		2203	4300	6503	SO:0001583	missense	11091			AJ011376	CCDS6981.1	9q34	2014-09-03			ENSG00000196363	ENSG00000196363		"""WD repeat domain containing"""	12757	protein-coding gene	gene with protein product	"""SWD3, Set1c WD40 repeat protein, homolog (S. cerevisiae)"", ""cilia and flagella associated protein 89"""	609012				11551928	Standard	XM_005272163		Approved	SWD3, CFAP89	uc004cey.3	P61964	OTTHUMG00000131707	ENST00000358625.3:c.440G>A	9.37:g.137007540G>A	ENSP00000351446:p.Gly147Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q91VA5|Q9NWX7|Q9UGP9	Missense_Mutation	SNP	ENST00000358625.3	37	CCDS6981.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.469194	0.63625	.	.	ENSG00000196363	ENST00000358625;ENST00000425041	T;T	0.72051	-0.62;-0.62	3.99	3.99	0.46301	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92874	0.6317	10	0.87932	D	0	.	15.0467	0.71833	0.0:0.0:1.0:0.0	.	147	P61964	WDR5_HUMAN	E	147	ENSP00000351446:G147E;ENSP00000401889:G147E	ENSP00000351446:G147E	G	+	2	0	WDR5	135997361	1.000000	0.71417	0.989000	0.46669	0.336000	0.28762	8.804000	0.91921	1.948000	0.56530	0.455000	0.32223	GGA		0.502	WDR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254621.1		NM_052821	
WSCD1	23302	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	6023803	6023803	+	Missense_Mutation	SNP	T	T	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:6023803T>A	ENST00000574946.1	+	9	1940	c.1550T>A	c.(1549-1551)cTg>cAg	p.L517Q	WSCD1_ENST00000573634.1_Missense_Mutation_p.L401Q|WSCD1_ENST00000574232.1_Missense_Mutation_p.L517Q|WSCD1_ENST00000317744.5_Missense_Mutation_p.L517Q|WSCD1_ENST00000539421.1_Missense_Mutation_p.L517Q			Q658N2	WSCD1_HUMAN	WSC domain containing 1	517						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						GAGGAGCGGCTGCTCTGCGTG	0.652																																																	0													73.0	70.0	71.0					17																	6023803		2203	4300	6503	SO:0001583	missense	23302				CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1550T>A	17.37:g.6023803T>A	ENSP00000460825:p.Leu517Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.765954	0.90020	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	D;D	0.85556	-2.0;-2.0	5.54	5.54	0.83059	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.92645	0.7663	M	0.85630	2.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93668	0.6987	10	0.87932	D	0	-20.955	13.6284	0.62181	0.0:0.0:0.0:1.0	.	517	Q658N2	WSCD1_HUMAN	Q	517	ENSP00000323087:L517Q;ENSP00000446032:L517Q	ENSP00000323087:L517Q	L	+	2	0	WSCD1	5964527	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.668000	0.83897	2.107000	0.64212	0.533000	0.62120	CTG		0.652	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4		NM_015253	
ZBTB10	65986	broad.mit.edu;hgsc.bcm.edu	37	8	81412314	81412314	+	Missense_Mutation	SNP	G	G	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr8:81412314G>A	ENST00000430430.1	+	3	2337	c.1558G>A	c.(1558-1560)Ggt>Agt	p.G520S	ZBTB10_ENST00000379091.4_Missense_Mutation_p.G228S|ZBTB10_ENST00000455036.3_Missense_Mutation_p.G520S|ZBTB10_ENST00000426744.2_Missense_Mutation_p.G520S	NM_001277145.1	NP_001264074.1	Q96DT7	ZBT10_HUMAN	zinc finger and BTB domain containing 10	520					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)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|upper_aerodigestive_tract(4)	20	all_cancers(3;1.68e-09)|all_epithelial(4;5.13e-11)|Lung NSC(7;1.75e-07)|all_lung(9;7.38e-07)|Breast(3;2.96e-06)		BRCA - Breast invasive adenocarcinoma(6;0.000434)|Epithelial(68;0.00486)|all cancers(69;0.0296)			TGAAAATGATGGTTGTAATGT	0.403																																																	0													100.0	98.0	99.0					8																	81412314		1846	4095	5941	SO:0001583	missense	65986			AK022814	CCDS47880.1, CCDS64920.1	8q13-q21.1	2013-01-09			ENSG00000205189	ENSG00000205189		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	30953	protein-coding gene	gene with protein product						12477932	Standard	NM_001105539		Approved	RINZF, FLJ12752	uc003ybx.5	Q96DT7	OTTHUMG00000155016	ENST00000430430.1:c.1558G>A	8.37:g.81412314G>A	ENSP00000387462:p.Gly520Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A4FVD0|Q86W96|Q8IXI9|Q96MH9	Missense_Mutation	SNP	ENST00000430430.1	37	CCDS47880.1	.	.	.	.	.	.	.	.	.	.	G	14.35	2.509641	0.44660	.	.	ENSG00000205189	ENST00000379091;ENST00000430430;ENST00000455036;ENST00000426744;ENST00000519370	T;T;T;T	0.10288	2.96;2.91;2.91;2.89	5.41	5.41	0.78517	.	0.366079	0.28841	N	0.013975	T	0.10337	0.0253	L	0.27053	0.805	0.41498	D	0.988264	B;P;P;P	0.41848	0.201;0.651;0.763;0.554	B;B;B;B	0.39660	0.026;0.162;0.306;0.154	T	0.10382	-1.0632	10	0.42905	T	0.14	.	16.551	0.84473	0.0:0.1303:0.8697:0.0	.	376;520;520;228	A8E4L4;Q96DT7;Q96DT7-2;Q96DT7-4	.;ZBT10_HUMAN;.;.	S	228;520;520;520;348	ENSP00000368384:G228S;ENSP00000387462:G520S;ENSP00000412036:G520S;ENSP00000416134:G520S	ENSP00000368384:G228S	G	+	1	0	ZBTB10	81574869	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.008000	0.49544	2.706000	0.92434	0.650000	0.86243	GGT		0.403	ZBTB10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338055.2		NM_023929	
ZNF474	133923	hgsc.bcm.edu	37	5	121488450	121488461	+	In_Frame_Del	DEL	TGTGGAGCTCCA	TGTGGAGCTCCA	-	rs199779243|rs561842196	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	TGTGGAGCTCCA	TGTGGAGCTCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr5:121488450_121488461delTGTGGAGCTCCA	ENST00000296600.4	+	2	1148_1159	c.765_776delTGTGGAGCTCCA	c.(763-777)cctgtggagctccac>ccc	p.VELH256del	CTC-441N14.2_ENST00000504829.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.1_ENST00000505209.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	256							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		ACCGGCTCCCTGTGGAGCTCCACCAGCCACTC	0.524																																																	0																																										SO:0001651	inframe_deletion	133923			AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.765_776delTGTGGAGCTCCA	5.37:g.121488450_121488461delTGTGGAGCTCCA	ENSP00000296600:p.Val256_His259del	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4M0|Q96M07	In_Frame_Del	DEL	ENST00000296600.4	37	CCDS4130.1																																																																																				0.524	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2		NM_207317	
FAT4	79633	broad.mit.edu	37	4	126238838	126238838	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr4:126238838C>A	ENST00000394329.3	+	1	1285	c.1272C>A	c.(1270-1272)agC>agA	p.S424R		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	424	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S424R(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						AGGTGGCCAGCGCCTTGGACC	0.597											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					2	Substitution - Missense(2)	prostate(2)											36.0	39.0	38.0					4																	126238838		2035	4190	6225	SO:0001583	missense	79633			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.1272C>A	4.37:g.126238838C>A	ENSP00000377862:p.Ser424Arg	Somatic	1548	WXS	Illumina GAIIx	Phase_I	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	12.35	1.911205	0.33721	.	.	ENSG00000196159	ENST00000394329	T	0.50001	0.76	4.66	2.94	0.34122	Cadherin (4);Cadherin-like (1);	0.430293	0.17056	U	0.188732	T	0.30572	0.0769	N	0.03903	-0.33	0.80722	D	1	D	0.58970	0.984	P	0.53450	0.726	T	0.03017	-1.1082	10	0.15952	T	0.53	.	7.8532	0.29468	0.0:0.6096:0.0:0.3904	.	424	Q6V0I7	FAT4_HUMAN	R	424	ENSP00000377862:S424R	ENSP00000377862:S424R	S	+	3	2	FAT4	126458288	0.987000	0.35691	1.000000	0.80357	0.967000	0.64934	0.195000	0.17155	0.587000	0.29643	0.561000	0.74099	AGC		0.597	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2		NM_024582	
KCNA7	3743	broad.mit.edu	37	19	49575301	49575301	+	Missense_Mutation	SNP	G	G	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:49575301G>T	ENST00000221444.1	-	1	897	c.542C>A	c.(541-543)gCc>gAc	p.A181D		NM_031886.2	NP_114092.2	Q96RP8	KCNA7_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 7	181					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|skin(2)	11		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_epithelial(76;3.83e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000397)|OV - Ovarian serous cystadenocarcinoma(262;0.000519)|GBM - Glioblastoma multiforme(486;0.00541)|Epithelial(262;0.0441)	Dalfampridine(DB06637)	GCCGGCTGCGGCTGCAGCAGC	0.697																																					Colon(74;686 1235 3793 23366 48562)												0													7.0	8.0	8.0					19																	49575301		1979	3930	5909	SO:0001583	missense	3743			AF315818	CCDS12755.1	19q13.3	2012-07-05				ENSG00000104848		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6226	protein-coding gene	gene with protein product		176268				16382104	Standard	NM_031886		Approved	Kv1.7, HAK6	uc002pmg.3	Q96RP8		ENST00000221444.1:c.542C>A	19.37:g.49575301G>T	ENSP00000221444:p.Ala181Asp	Somatic		WXS	Illumina GAIIx	Phase_I	A1KYX7|Q9BYS4	Missense_Mutation	SNP	ENST00000221444.1	37	CCDS12755.1	.	.	.	.	.	.	.	.	.	.	G	7.554	0.663340	0.14710	.	.	ENSG00000104848	ENST00000221444	D	0.97710	-4.5	4.28	3.14	0.36123	.	1.068620	0.07144	N	0.847932	D	0.94192	0.8136	L	0.38175	1.15	0.09310	N	1	B	0.30763	0.294	B	0.19666	0.026	D	0.86626	0.1882	10	0.14252	T	0.57	.	10.852	0.46775	0.0:0.0:0.8105:0.1895	.	181	Q96RP8	KCNA7_HUMAN	D	181	ENSP00000221444:A181D	ENSP00000221444:A181D	A	-	2	0	KCNA7	54267113	0.151000	0.22747	0.061000	0.19648	0.006000	0.05464	2.391000	0.44424	2.134000	0.65973	0.485000	0.47835	GCC		0.697	KCNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466263.1		NM_031886	
MRPL38	64978	broad.mit.edu	37	17	73898001	73898001	+	Splice_Site	SNP	G	G	C			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr17:73898001G>C	ENST00000309352.3	-	4	920	c.383C>G	c.(382-384)gCc>gGc	p.A128G	RP11-552F3.10_ENST00000587267.1_RNA|MRPL38_ENST00000409963.3_5'UTR|MRPL38_ENST00000585475.1_5'UTR	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	128						mitochondrion (GO:0005739)|ribosome (GO:0005840)				ovary(1)|pancreas(1)|prostate(2)|skin(1)	5			all cancers(21;0.000154)|Epithelial(20;0.000156)|BRCA - Breast invasive adenocarcinoma(9;0.00936)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGACACTGGCTAGACAGGA	0.642																																																	0													22.0	20.0	20.0					17																	73898001		2203	4298	6501	SO:0001630	splice_region_variant	64978			AB051345	CCDS11733.2	17q23-q25	2012-09-13			ENSG00000204316	ENSG00000204316		"""Mitochondrial ribosomal proteins / large subunits"""	14033	protein-coding gene	gene with protein product		611844				11543634	Standard	NM_032478		Approved	RPML3, MRP-L3, HSPC262, MGC4810	uc010wso.1	Q96DV4	OTTHUMG00000152977	ENST00000309352.3:c.383-1C>G	17.37:g.73898001G>C		Somatic		WXS	Illumina GAIIx	Phase_I	B3KN96|Q96Q66|Q9P0B9	Missense_Mutation	SNP	ENST00000309352.3	37	CCDS11733.2	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606826	0.28623	.	.	ENSG00000204316	ENST00000309352	T	0.23348	1.91	5.06	2.7	0.31948	.	0.400442	0.27922	N	0.017320	T	0.21631	0.0521	L	0.54323	1.7	0.80722	D	1	P	0.39665	0.682	B	0.35240	0.198	T	0.05937	-1.0855	10	0.87932	D	0	.	8.5288	0.33321	0.363:0.0:0.637:0.0	.	128	Q96DV4	RM38_HUMAN	G	128	ENSP00000308275:A128G	ENSP00000308275:A128G	A	-	2	0	MRPL38	71409596	0.997000	0.39634	0.719000	0.30619	0.149000	0.21700	3.025000	0.49681	1.121000	0.41925	0.650000	0.86243	GCC		0.642	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1		NM_032478	Missense_Mutation
OR9G1	390174	broad.mit.edu	37	11	56468430	56468430	+	Silent	SNP	C	C	T			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr11:56468430C>T	ENST00000312153.1	+	1	567	c.567C>T	c.(565-567)ggC>ggT	p.G189G		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	189						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						TGGCCTGTGGCGAGAAGGGCG	0.473																																																	0													114.0	116.0	115.0					11																	56468430		2201	4296	6497	SO:0001819	synonymous_variant	504191			AB065500	CCDS31536.1	11q11	2012-08-09			ENSG00000174914	ENSG00000174914		"""GPCR / Class A : Olfactory receptors"""	15319	protein-coding gene	gene with protein product				OR9G5			Standard	NM_001005213		Approved			Q8NH87	OTTHUMG00000167112	ENST00000312153.1:c.567C>T	11.37:g.56468430C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q6IEU9|Q8NGQ0	Silent	SNP	ENST00000312153.1	37	CCDS31536.1																																																																																				0.473	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1		NM_001005213	
SDHAP1	255812	broad.mit.edu	37	3	195692311	195692311	+	RNA	SNP	T	T	C	rs62282793	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:195692311T>C	ENST00000427841.1	-	0	2191					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		TTCCCAGTGCTGACGTCCACA	0.607																																					Ovarian(67;1158 1227 12109 20189 43170)												0																																												255812			BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195692311T>C		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000427841.1	37																																																																																					0.607	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			
CFAP46	54777	broad.mit.edu	37	10	134650414	134650414	+	Missense_Mutation	SNP	C	C	A			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr10:134650414C>A	ENST00000368586.5	-	45	6543	c.6443G>T	c.(6442-6444)tGg>tTg	p.W2148L	TTC40_ENST00000263170.5_Missense_Mutation_p.W309L	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						GAGATTTTGCCAAGCCTGTGT	0.537																																																	0													102.0	89.0	93.0					10																	134650414		2203	4300	6503	SO:0001583	missense	0																														ENST00000368586.5:c.6443G>T	10.37:g.134650414C>A	ENSP00000357575:p.Trp2148Leu	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	C	13.65	2.299273	0.40694	.	.	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.18960	2.35;2.18	4.3	3.39	0.38822	.	0.140217	0.31734	N	0.007141	T	0.38719	0.1051	M	0.66939	2.045	0.80722	D	1	D	0.67145	0.996	D	0.64776	0.929	T	0.15723	-1.0427	10	0.87932	D	0	.	9.2352	0.37461	0.0:0.895:0.0:0.105	.	309	Q8IYW2	CJ092_HUMAN	L	2148;309	ENSP00000357575:W2148L;ENSP00000263170:W309L	ENSP00000263170:W309L	W	-	2	0	C10orf93	134500404	1.000000	0.71417	0.993000	0.49108	0.085000	0.17905	3.695000	0.54749	0.795000	0.33922	0.561000	0.74099	TGG		0.537	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3			
CTC-338M12.4	101928649	broad.mit.edu	37	5	180699086	180699087	+	RNA	INS	-	-	A	rs11377959|rs199570993|rs55791940		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr5:180699086_180699087insA	ENST00000511331.1	+	0	918_919				TRIM52-AS1_ENST00000507434.1_RNA																							CTTTCCATCAGAAAAAAAAAAA	0.406																																																	0																																												0																															5.37:g.180699097_180699097dupA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	INS	ENST00000511331.1	37																																																																																					0.406	CTC-338M12.4-004	KNOWN	basic	antisense	antisense	OTTHUMT00000371318.1			
VHL	7428	broad.mit.edu	37	3	10183725	10183725	+	Nonsense_Mutation	SNP	C	C	A	rs5030826		TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina Miseq			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr3:10183725C>A	ENST00000256474.2	+	1	1034	c.194C>A	c.(193-195)tCg>tAg	p.S65*	snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Nonsense_Mutation_p.S65*	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	65			S -> A (in pheochromocytoma). {ECO:0000269|PubMed:12000816}.|S -> L (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829912}.|S -> W (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911}.		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.S65L(11)|p.S65*(10)|p.S65W(4)|p.E52_S65del(2)|p.S65_N67del(2)|p.R64fs*63(2)|p.A56_R69>G(1)|p.R60fs*35(1)|p.S65>Q(1)|p.S65fs*92(1)|p.P61fs*61(1)|p.V62fs*1(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)		GTGCTGCGCTCGGTGAACTCG	0.721		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"""	37	Substitution - Missense(15)|Substitution - Nonsense(10)|Deletion - Frameshift(6)|Deletion - In frame(4)|Complex - deletion inframe(1)|Complex - compound substitution(1)	kidney(37)	GRCh37	CM941362|CM941363|CM941364	VHL	M	rs5030826						7.0	11.0	9.0					3																	10183725		2133	4211	6344	SO:0001587	stop_gained	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.194C>A	3.37:g.10183725C>A	ENSP00000256474:p.Ser65*	Somatic		WXS	Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Nonsense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.576281	0.86645	.	.	ENSG00000134086	ENST00000256474;ENST00000345392	.	.	.	5.54	4.67	0.58626	.	0.055860	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.717	12.339	0.55083	0.0:0.9181:0.0:0.0819	rs5030826	.	.	.	X	65	.	ENSP00000256474:S65X	S	+	2	0	VHL	10158725	0.998000	0.40836	0.982000	0.44146	0.307000	0.27823	4.868000	0.63021	1.351000	0.45789	0.550000	0.68814	TCG		0.721	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VPS41	27072	broad.mit.edu	37	7	38807138	38807138	+	Splice_Site	SNP	G	G	A	rs139485137	byFrequency	TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr7:38807138G>A	ENST00000310301.4	-	15	1300	c.1246C>T	c.(1246-1248)Cgc>Tgc	p.R416C	VPS41_ENST00000395969.2_Splice_Site_p.R391C	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	416					Golgi vesicle transport (GO:0048193)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	cytosol (GO:0005829)|early endosome (GO:0005769)|Golgi-associated vesicle (GO:0005798)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	44						CATCATTACCGTGCTGCTATG	0.318													G|||	6	0.00119808	0.0	0.0	5008	,	,		13683	0.0		0.006	False		,,,				2504	0.0																0								G	CYS/ARG,CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	88.0	83.0	85.0		1246,1171	4.8	1.0	7	dbSNP_134	85	35,8565	23.4+/-69.3	0,35,4265	yes	missense-near-splice,missense-near-splice	VPS41	NM_014396.3,NM_080631.3	180,180	0,39,6464	AA,AG,GG		0.407,0.0908,0.2999	probably-damaging,probably-damaging	416/855,391/830	38807138	39,12967	2203	4300	6503	SO:0001630	splice_region_variant	27072			U87309	CCDS5457.1, CCDS5458.2	7p14.1-p13	2009-05-08	2006-12-19		ENSG00000006715	ENSG00000006715			12713	protein-coding gene	gene with protein product		605485	"""vacuolar protein sorting 41 (yeast homolog)"", ""vacuolar protein sorting 41 (yeast)"""			9159129	Standard	NM_080631		Approved	HVSP41	uc003tgy.3	P49754	OTTHUMG00000023629	ENST00000310301.4:c.1247+1C>T	7.37:g.38807138G>A		Somatic		WXS	Illumina GAIIx	Phase_I	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	17.08	3.297691	0.60086	9.08E-4	0.00407	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.18960	2.18;2.18	5.64	4.75	0.60458	.	0.046740	0.85682	D	0.000000	T	0.30665	0.0772	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	P;P;P	0.59221	0.854;0.854;0.854	T	0.12708	-1.0537	10	0.59425	D	0.04	-13.3768	13.971	0.64240	0.0:0.0:0.6125:0.3875	.	416;391;416	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	C	416;391	ENSP00000309457:R416C;ENSP00000379297:R391C	ENSP00000309457:R416C	R	-	1	0	VPS41	38773663	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	2.242000	0.43106	1.359000	0.45940	0.655000	0.94253	CGC		0.318	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			Missense_Mutation
WDR18	57418	broad.mit.edu	37	19	994079	994079	+	Missense_Mutation	SNP	A	A	G			TCGA-AK-3444-01A-01D-0966-08	TCGA-AK-3444-10A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	ea794170-156d-4251-b899-abfd60b213b0	333c5bbe-e69c-408e-ac80-91b0d8ad44c1	g.chr19:994079A>G	ENST00000251289.5	+	9	1182	c.1159A>G	c.(1159-1161)Atg>Gtg	p.M387V	WDR18_ENST00000587001.2_Intron	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	387					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GTGCAGCACCATGGAGAAGGT	0.721																																																	0													12.0	12.0	12.0					19																	994079		2154	4247	6401	SO:0001583	missense	57418				CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.1159A>G	19.37:g.994079A>G	ENSP00000251289:p.Met387Val	Somatic		WXS	Illumina GAIIx	Phase_I	O60390|Q9BWR2	Missense_Mutation	SNP	ENST00000251289.5	37	CCDS12051.1	.	.	.	.	.	.	.	.	.	.	A	1.687	-0.504929	0.04261	.	.	ENSG00000065268	ENST00000251289	T	0.66638	-0.22	4.06	-5.15	0.02866	.	0.536026	0.20589	N	0.089381	T	0.40347	0.1113	L	0.29908	0.895	0.51233	D	0.999914	B	0.12013	0.005	B	0.16722	0.016	T	0.02781	-1.1111	10	0.27785	T	0.31	.	1.368	0.02205	0.3307:0.3226:0.0923:0.2545	.	387	Q9BV38	WDR18_HUMAN	V	387	ENSP00000251289:M387V	ENSP00000251289:M387V	M	+	1	0	WDR18	945079	0.000000	0.05858	0.032000	0.17829	0.785000	0.44390	-0.707000	0.05041	-0.770000	0.04614	0.379000	0.24179	ATG		0.721	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2			
