#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVarCov_SOL	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
MAGEC1	9947	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	140994602	140994602	+	Missense_Mutation	SNP	A	A	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:140994602A>T	ENST00000285879.4	+	4	1698	c.1412A>T	c.(1411-1413)gAg>gTg	p.E471V	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	471										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					AGTACTTTTGAGGGTTTTCCC	0.483										HNSCC(15;0.026)																											p.E471V		.											.	.	.	0			c.A1412T						.						109.0	120.0	116.0					X																	140994602		2203	4297	6500	SO:0001583	missense	9947	exon4			CTTTTGAGGGTTT	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1412A>T	X.37:g.140994602A>T	ENSP00000285879:p.Glu471Val	Somatic	76	0		WXS	Illumina HiSeq	.	95	21	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	a	6.493	0.459111	0.12342	.	.	ENSG00000155495	ENST00000285879	T	0.03065	4.06	.	.	.	.	.	.	.	.	T	0.01627	0.0052	N	0.08118	0	0.24060	N	0.996011	P	0.42993	0.797	B	0.31686	0.134	T	0.47799	-0.9089	8	0.87932	D	0	.	4.5587	0.12149	0.9995:0.0:5.0E-4:0.0	.	471	O60732	MAGC1_HUMAN	V	471	ENSP00000285879:E471V	ENSP00000285879:E471V	E	+	2	0	MAGEC1	140822268	0.001000	0.12720	0.023000	0.16930	0.023000	0.10783	-0.120000	0.10660	0.126000	0.18424	0.125000	0.15800	GAG	.		0.483	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
GPS1	2873	hgsc.bcm.edu	37	17	80012466	80012466	+	Missense_Mutation	SNP	C	C	T	rs139982509		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:80012466C>T	ENST00000306823.6	+	4	424	c.401C>T	c.(400-402)aCg>aTg	p.T134M	GPS1_ENST00000392358.2_Missense_Mutation_p.T170M|GPS1_ENST00000355130.2_Missense_Mutation_p.T170M|GPS1_ENST00000320548.4_Missense_Mutation_p.T114M|RFNG_ENST00000310496.4_5'Flank|GPS1_ENST00000578552.1_Missense_Mutation_p.T130M			Q13098	CSN1_HUMAN	G protein pathway suppressor 1	134					cell cycle (GO:0007049)|cullin deneddylation (GO:0010388)|inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase inhibitor activity (GO:0005095)			breast(1)|central_nervous_system(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|skin(2)	13	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0211)			GTGGAGGCCACGCGGAAGAAG	0.647																																					p.T170M		.											.	.	.	0			c.C509T						.	C	MET/THR,MET/THR	0,4382		0,0,2191	27.0	23.0	24.0		401,509	3.8	0.9	17	dbSNP_134	24	2,8586		0,2,4292	no	missense,missense	GPS1	NM_004127.4,NM_212492.1	81,81	0,2,6483	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	134/492,170/528	80012466	2,12968	2191	4294	6485	SO:0001583	missense	2873	exon4			AGGCCACGCGGAA		CCDS11800.1, CCDS32774.1	17q25.3	2013-03-14				ENSG00000169727			4549	protein-coding gene	gene with protein product	"""COP9 signalosome subunit 1"""	601934				9535219	Standard	NM_212492		Approved	COPS1, CSN1	uc002kdl.1	Q13098		ENST00000306823.6:c.401C>T	17.37:g.80012466C>T	ENSP00000302873:p.Thr134Met	Somatic	83	0		WXS	Illumina HiSeq	.	97	4	NM_212492	Q8NA10|Q9BWL1	Missense_Mutation	SNP	ENST00000306823.6	37	CCDS32774.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.223163	0.39300	0.0	2.33E-4	ENSG00000169727	ENST00000392358;ENST00000320548;ENST00000306823;ENST00000355130;ENST00000392357	.	.	.	3.84	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.78578	0.4305	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.72075	0.954;0.976;0.975;0.923;0.965;0.959	T	0.82594	-0.0380	9	0.66056	D	0.02	-25.4788	15.9283	0.79639	0.0:1.0:0.0:0.0	.	126;170;119;130;134;170	B4DND6;A8K070;Q13098-6;Q13098-5;Q13098;Q13098-7	.;.;.;.;CSN1_HUMAN;.	M	170;120;134;170;55	.	ENSP00000302873:T134M	T	+	2	0	GPS1	77605755	1.000000	0.71417	0.916000	0.36221	0.795000	0.44927	6.989000	0.76219	1.981000	0.57761	0.313000	0.20887	ACG	0.000		0.647	GPS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442176.1	NM_212492	
PI4KA	5297	hgsc.bcm.edu;bcgsc.ca	37	22	21153979	21153979	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr22:21153979G>A	ENST00000572273.1	-	15	1856	c.1626C>T	c.(1624-1626)taC>taT	p.Y542Y	PI4KA_ENST00000255882.6_Silent_p.Y600Y			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	542					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CCTGAGAGATGTAGAGCCGGT	0.577																																					p.Y600Y	GBM(136;1332 1831 3115 23601 50806)	.											.	.	.	0			c.C1800T						.						62.0	50.0	54.0					22																	21153979		2162	4220	6382	SO:0001819	synonymous_variant	5297	exon15			AGAGATGTAGAGC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1626C>T	22.37:g.21153979G>A		Somatic	29	0		WXS	Illumina HiSeq	.	45	4	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				.		0.577	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
DLL1	28514	hgsc.bcm.edu	37	6	170597856	170597856	+	Nonsense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:170597856C>A	ENST00000366756.3	-	3	706	c.373G>T	c.(373-375)Gaa>Taa	p.E125*	FAM120B_ENST00000540480.1_5'Flank	NM_005618.3	NP_005609.3	O00548	DLL1_HUMAN	delta-like 1 (Drosophila)	125					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|cell-cell signaling (GO:0007267)|compartment pattern specification (GO:0007386)|determination of left/right symmetry (GO:0007368)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|inner ear development (GO:0048839)|left/right axis specification (GO:0070986)|loop of Henle development (GO:0072070)|negative regulation of auditory receptor cell differentiation (GO:0045608)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of myeloid cell differentiation (GO:0045638)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal tubule development (GO:0072014)|regulation of cell adhesion (GO:0030155)|somite specification (GO:0001757)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|Notch binding (GO:0005112)			NS(2)|breast(1)|endometrium(1)|large_intestine(7)|lung(17)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	33		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.71e-23)|BRCA - Breast invasive adenocarcinoma(81;4.81e-06)|GBM - Glioblastoma multiforme(31;0.0584)		TGGAGAGCTTCAATAATCAGA	0.458																																					p.E125X		.											.	.	.	0			c.G373T						.						207.0	204.0	205.0					6																	170597856		2203	4300	6503	SO:0001587	stop_gained	28514	exon3			GAGCTTCAATAAT	AF003522	CCDS5313.1	6q13-q22.33	2008-07-28	2001-12-03		ENSG00000198719	ENSG00000198719			2908	protein-coding gene	gene with protein product		606582	"""delta (Drosophila)-like 1"""				Standard	NM_005618		Approved		uc003qxm.3	O00548	OTTHUMG00000016078	ENST00000366756.3:c.373G>T	6.37:g.170597856C>A	ENSP00000355718:p.Glu125*	Somatic	91	0		WXS	Illumina HiSeq	.	105	4	NM_005618	B2RAK7|B5M0B3|Q9NU41|Q9UJV2	Nonsense_Mutation	SNP	ENST00000366756.3	37	CCDS5313.1	.	.	.	.	.	.	.	.	.	.	C	40	8.358645	0.98777	.	.	ENSG00000198719	ENST00000366756	.	.	.	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.1365	0.86742	0.0:1.0:0.0:0.0	.	.	.	.	X	125	.	ENSP00000355718:E125X	E	-	1	0	DLL1	170439781	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.257000	0.78362	2.266000	0.75297	0.558000	0.71614	GAA	.		0.458	DLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043254.1		
GREB1	9687	hgsc.bcm.edu	37	2	11735403	11735403	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:11735403G>T	ENST00000381486.2	+	12	2023	c.1723G>T	c.(1723-1725)Gag>Tag	p.E575*	GREB1_ENST00000234142.5_Nonsense_Mutation_p.E575*	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	575						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		gattctttccGAGAGCCTTCT	0.522																																					p.E575X	Ovarian(39;850 945 2785 23371 33093)	.											.	.	.	0			c.G1723T						.						53.0	55.0	54.0					2																	11735403		1823	4090	5913	SO:0001587	stop_gained	9687	exon12			CTTTCCGAGAGCC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.1723G>T	2.37:g.11735403G>T	ENSP00000370896:p.Glu575*	Somatic	57	0		WXS	Illumina HiSeq	.	99	4	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Nonsense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	.	.	.	.	.	.	.	.	.	.	g	41	8.866246	0.98982	.	.	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000432985	.	.	.	4.59	4.59	0.56863	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-33.282	17.782	0.88527	0.0:0.0:1.0:0.0	.	.	.	.	X	575;575;209	.	ENSP00000234142:E575X	E	+	1	0	GREB1	11652854	1.000000	0.71417	0.970000	0.41538	0.625000	0.37756	9.072000	0.93986	2.250000	0.74265	0.450000	0.29827	GAG	.		0.522	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
CAV1	857	hgsc.bcm.edu	37	7	116199003	116199003	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:116199003G>T	ENST00000341049.2	+	3	477	c.199G>T	c.(199-201)Gac>Tac	p.D67Y	CAV1_ENST00000393467.1_Missense_Mutation_p.D36Y|CAV1_ENST00000405348.1_Missense_Mutation_p.D36Y|CAV1_ENST00000393468.1_Missense_Mutation_p.D36Y|CAV1_ENST00000393470.1_Missense_Mutation_p.D56Y	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	67					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			CTTTTAGATTGACTTTGAAGA	0.388																																					p.D67Y		.											CAV1,NS,neuroblastoma,0,1	CAV1	0	0			c.G199T						.						66.0	56.0	60.0					7																	116199003		2203	4300	6503	SO:0001583	missense	857	exon3			TAGATTGACTTTG	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"""caveolin 1, caveolae protein, 22kD"""	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.199G>T	7.37:g.116199003G>T	ENSP00000339191:p.Asp67Tyr	Somatic	29	0		WXS	Illumina HiSeq	.	42	3	NM_001753	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	37	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220622	0.79464	.	.	ENSG00000105974	ENST00000341049;ENST00000393470;ENST00000405348;ENST00000456473;ENST00000393468;ENST00000393467	D;D;D;D;D;D	0.92965	-3.14;-3.14;-3.14;-3.14;-3.14;-3.14	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.95544	0.8552	M	0.78637	2.42	0.80722	D	1	P	0.48407	0.91	P	0.57425	0.82	D	0.95260	0.8368	10	0.59425	D	0.04	-36.0006	19.8309	0.96634	0.0:0.0:1.0:0.0	.	67	Q03135	CAV1_HUMAN	Y	67;56;36;36;36;36	ENSP00000339191:D67Y;ENSP00000377113:D56Y;ENSP00000384348:D36Y;ENSP00000389033:D36Y;ENSP00000377111:D36Y;ENSP00000377110:D36Y	ENSP00000339191:D67Y	D	+	1	0	CAV1	115986239	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.476000	0.97823	2.684000	0.91462	0.650000	0.86243	GAC	.		0.388	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753	
SLC13A3	64849	hgsc.bcm.edu	37	20	45192078	45192078	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr20:45192078G>T	ENST00000279027.4	-	12	1625	c.1607C>A	c.(1606-1608)tCt>tAt	p.S536Y	SLC13A3_ENST00000495082.1_Missense_Mutation_p.S489Y|SLC13A3_ENST00000472148.1_Missense_Mutation_p.S454Y|SLC13A3_ENST00000396360.1_Missense_Mutation_p.S454Y|SLC13A3_ENST00000290317.5_Missense_Mutation_p.S489Y|SLC13A3_ENST00000413164.2_Missense_Mutation_p.S486Y|SLC13A3_ENST00000435032.1_Missense_Mutation_p.S121Y	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	536					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)	p.S536Y(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	CAAGTGTCCAGAGGCGAAGGC	0.622																																					p.S536Y		.											SLC13A3,NS,carcinoma,0,1	SLC13A3	0	1	Substitution - Missense(1)	lung(1)	c.C1607A						.						44.0	40.0	41.0					20																	45192078		2203	4300	6503	SO:0001583	missense	64849	exon12			TGTCCAGAGGCGA	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.1607C>A	20.37:g.45192078G>T	ENSP00000279027:p.Ser536Tyr	Somatic	45	0		WXS	Illumina HiSeq	.	43	2	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	37	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	G	11.69	1.712373	0.30322	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000435032;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082	T;T;T;T;T;T;T	0.03181	4.02;4.02;4.02;4.02;4.02;4.02;4.02	5.36	5.36	0.76844	.	0.177988	0.51477	D	0.000088	T	0.09512	0.0234	L	0.33753	1.03	0.80722	D	1	B;D;P;B;B;D	0.76494	0.399;0.998;0.545;0.138;0.45;0.999	B;D;B;B;B;D	0.74348	0.34;0.983;0.325;0.085;0.33;0.975	T	0.18366	-1.0339	10	0.02654	T	1	-9.1489	19.0927	0.93233	0.0:0.0:1.0:0.0	.	486;121;454;489;438;536	B4DIR8;B4E181;Q8WWT9-3;F6WI18;B4DF27;Q8WWT9	.;.;.;.;.;S13A3_HUMAN	Y	489;454;121;536;454;486;489	ENSP00000290317:S489Y;ENSP00000379648:S454Y;ENSP00000403394:S121Y;ENSP00000279027:S536Y;ENSP00000420177:S454Y;ENSP00000415852:S486Y;ENSP00000419621:S489Y	ENSP00000279027:S536Y	S	-	2	0	SLC13A3	44625485	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	6.445000	0.73456	2.514000	0.84764	0.561000	0.74099	TCT	.		0.622	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
MICALL1	85377	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	22	38323501	38323501	+	Missense_Mutation	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr22:38323501G>C	ENST00000215957.6	+	9	1675	c.1549G>C	c.(1549-1551)Gag>Cag	p.E517Q	MICALL1_ENST00000402631.1_3'UTR	NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	517	Pro-rich.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					CCTGTCGTCTGAGAGCGCCAG	0.677																																					p.E517Q		.											.	.	.	0			c.G1549C						.						62.0	57.0	59.0					22																	38323501		2203	4300	6503	SO:0001583	missense	85377	exon9			TCGTCTGAGAGCG	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.1549G>C	22.37:g.38323501G>C	ENSP00000215957:p.Glu517Gln	Somatic	41	0		WXS	Illumina HiSeq	.	54	5	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.34|14.34	2.506172|2.506172	0.44558|0.44558	.|.	.|.	ENSG00000100139|ENSG00000100139	ENST00000215957|ENST00000454685	T|.	0.55413|.	0.52|.	4.99|4.99	4.99|4.99	0.66335|0.66335	.|.	0.097270|.	0.44688|.	D|.	0.000423|.	T|.	0.74283|.	0.3696|.	M|M	0.67953|0.67953	2.075|2.075	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	P|.	0.60789|.	0.879|.	T|.	0.74028|.	-0.3796|.	10|.	0.39692|.	T|.	0.17|.	.|.	18.3451|18.3451	0.90319|0.90319	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	517|.	Q8N3F8|.	MILK1_HUMAN|.	Q|S	517|94	ENSP00000215957:E517Q|.	ENSP00000215957:E517Q|.	E|X	+|+	1|2	0|2	MICALL1|MICALL1	36653447|36653447	0.998000|0.998000	0.40836|0.40836	0.336000|0.336000	0.25522|0.25522	0.036000|0.036000	0.12997|0.12997	4.377000|4.377000	0.59562|0.59562	2.321000|2.321000	0.78463|0.78463	0.555000|0.555000	0.69702|0.69702	GAG|TGA	.		0.677	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
ZNF208	7757	hgsc.bcm.edu;broad.mit.edu	37	19	22157034	22157034	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:22157034G>A	ENST00000397126.4	-	4	950	c.802C>T	c.(802-804)Caa>Taa	p.Q268*	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	268					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATTGCAGATTGGTTAAAAGCC	0.368																																					p.Q268X		.											.	.	.	0			c.C802T						.						33.0	36.0	35.0					19																	22157034		2134	4262	6396	SO:0001587	stop_gained	7757	exon4			CAGATTGGTTAAA	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.802C>T	19.37:g.22157034G>A	ENSP00000380315:p.Gln268*	Somatic	45	0		WXS	Illumina HiSeq	.	55	5	NM_007153		Nonsense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.851625	0.51270	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	.	.	.	2.89	-5.78	0.02362	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23891	T	0.37	.	3.2759	0.06898	0.3022:0.0:0.3602:0.3376	.	.	.	.	X	268	.	ENSP00000380315:Q268X	Q	-	1	0	ZNF208	21948874	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.038000	0.03553	-2.590000	0.00457	-2.635000	0.00153	CAA	.		0.368	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
SCNN1A	6337	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	6471245	6471245	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:6471245G>T	ENST00000228916.2	-	4	945	c.847C>A	c.(847-849)Cgc>Agc	p.R283S	SCNN1A_ENST00000396966.2_Missense_Mutation_p.R283S|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R306S|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R342S|SCNN1A_ENST00000358945.3_Missense_Mutation_p.R283S|SCNN1A_ENST00000540037.1_5'UTR	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	283					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	TGGTTGAAGCGGCAGGCGAAG	0.627																																					p.R342S		.											.	.	.	0			c.C1024A						.						92.0	90.0	90.0					12																	6471245		2203	4300	6503	SO:0001583	missense	6337	exon3			TGAAGCGGCAGGC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.847C>A	12.37:g.6471245G>T	ENSP00000228916:p.Arg283Ser	Somatic	30	0		WXS	Illumina HiSeq	.	41	6	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	G	13.47	2.246354	0.39697	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07	5.05	5.05	0.67936	.	0.174133	0.37809	N	0.001921	T	0.63570	0.2522	L	0.42008	1.315	0.42866	D	0.994128	D;D;B	0.58970	0.984;0.984;0.185	D;D;B	0.65874	0.939;0.939;0.105	T	0.58549	-0.7617	10	0.20519	T	0.43	-14.1256	11.0678	0.47985	0.0:0.0:0.8147:0.1853	.	306;283;342	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	S	342;283;283;283;306	ENSP00000353292:R342S;ENSP00000351825:R283S;ENSP00000228916:R283S;ENSP00000380166:R283S;ENSP00000438739:R306S	ENSP00000228916:R283S	R	-	1	0	SCNN1A	6341506	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.983000	0.63832	2.334000	0.79466	0.561000	0.74099	CGC	.		0.627	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
SHPRH	257218	hgsc.bcm.edu	37	6	146268687	146268687	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:146268687G>T	ENST00000367505.2	-	6	1418	c.1154C>A	c.(1153-1155)gCt>gAt	p.A385D	SHPRH_ENST00000367503.3_Missense_Mutation_p.A385D|SHPRH_ENST00000275233.7_Missense_Mutation_p.A385D|SHPRH_ENST00000438092.2_Missense_Mutation_p.A385D			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	385	Helicase ATP-binding; first part. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		CAGAATCAGAGCCAAAACCTC	0.483																																					p.A385D		.											.	.	.	0			c.C1154A						.						136.0	132.0	133.0					6																	146268687		1942	4140	6082	SO:0001583	missense	257218	exon6			ATCAGAGCCAAAA	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1154C>A	6.37:g.146268687G>T	ENSP00000356475:p.Ala385Asp	Somatic	67	0		WXS	Illumina HiSeq	.	52	3	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.851758	0.91355	.	.	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233;ENST00000444767	D;D;D;D	0.94576	-3.46;-3.46;-3.46;-3.46	5.62	4.74	0.60224	DEAD-like helicase (1);SNF2-related (1);	0.083002	0.47852	D	0.000211	D	0.95564	0.8558	L	0.58101	1.795	0.45390	D	0.998376	D;D;D;D	0.76494	0.992;0.998;0.994;0.999	P;D;P;D	0.74023	0.856;0.965;0.908;0.982	D	0.96297	0.9218	10	0.87932	D	0	-18.9459	15.1179	0.72419	0.0:0.2679:0.7321:0.0	.	274;385;385;274	Q149N8-2;Q149N8;Q149N8-4;F8WEL0	.;SHPRH_HUMAN;.;.	D	385;385;385;385;274	ENSP00000356475:A385D;ENSP00000356473:A385D;ENSP00000412797:A385D;ENSP00000275233:A385D	ENSP00000275233:A385D	A	-	2	0	SHPRH	146310380	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.831000	0.86748	1.465000	0.48006	0.585000	0.79938	GCT	.		0.483	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78305220	78305220	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:78305220G>T	ENST00000300584.3	-	9	2214	c.2215C>A	c.(2215-2217)Ctc>Atc	p.L739I	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.L739I	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	739	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)			breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						AAGGCGAGGAGGACATTGCGT	0.512																																					p.L739I		.											TBC1D2B_ENST00000300584,colon,carcinoma,0,2	TBC1D2B_ENST00000300584	0	0			c.C2215A						.						136.0	109.0	119.0					15																	78305220		2196	4293	6489	SO:0001583	missense	23102	exon9			CGAGGAGGACATT	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2215C>A	15.37:g.78305220G>T	ENSP00000300584:p.Leu739Ile	Somatic	22	0		WXS	Illumina HiSeq	.	36	2	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	37	CCDS45314.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.043195	0.75732	.	.	ENSG00000167202	ENST00000409931;ENST00000300584	T;T	0.50277	0.75;0.75	5.32	5.32	0.75619	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.78394	0.4276	H	0.94808	3.585	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.998	D	0.84586	0.0664	10	0.87932	D	0	.	18.3439	0.90314	0.0:0.0:1.0:0.0	.	739;191;739	Q9UPU7-2;Q9UPU7-3;Q9UPU7	.;.;TBD2B_HUMAN	I	739	ENSP00000387165:L739I;ENSP00000300584:L739I	ENSP00000300584:L739I	L	-	1	0	TBC1D2B	76092275	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	6.557000	0.73937	2.646000	0.89796	0.655000	0.94253	CTC	.		0.512	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
CDK15	65061	hgsc.bcm.edu;bcgsc.ca	37	2	202672307	202672307	+	Missense_Mutation	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:202672307A>G	ENST00000374598.4	+	2	214	c.214A>G	c.(214-216)Agg>Ggg	p.R72G	CDK15_ENST00000488419.1_3'UTR|Y_RNA_ENST00000365267.1_RNA|CDK15_ENST00000410091.3_Missense_Mutation_p.R21G|CDK15_ENST00000434439.1_Missense_Mutation_p.R72G|CDK15_ENST00000260967.2_Missense_Mutation_p.R21G|CDK15_ENST00000450471.2_Missense_Mutation_p.R72G			Q96Q40	CDK15_HUMAN	cyclin-dependent kinase 15	72							ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|metal ion binding (GO:0046872)			breast(3)|endometrium(2)|kidney(5)|large_intestine(1)|lung(14)|ovary(1)	26					Adenosine triphosphate(DB00171)	CAAGAGTAAAAGGCCACGGAG	0.453																																					p.R72G		.											.	.	.	0			c.A214G						.						128.0	133.0	131.0					2																	202672307		2203	4300	6503	SO:0001583	missense	65061	exon2			AGTAAAAGGCCAC	AB053308	CCDS2350.1, CCDS58746.1, CCDS58747.1	2q33.2	2011-11-08	2009-12-16	2009-12-16	ENSG00000138395	ENSG00000138395		"""Cyclin-dependent kinases"""	14434	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 7"", ""PFTAIRE protein kinase 2"""	ALS2CR7, PFTK2		11586298, 16236519, 19884882	Standard	NM_139158		Approved	PFTAIRE2	uc002uyt.3	Q96Q40	OTTHUMG00000132838	ENST00000374598.4:c.214A>G	2.37:g.202672307A>G	ENSP00000363726:p.Arg72Gly	Somatic	59	0		WXS	Illumina HiSeq	.	79	4	NM_001261435	A8K8R9|B8ZZX0|C9J1N8|C9K003|F8W6H8|Q4ZG86|Q53TV1|Q6ZMR9|Q8IUP1	Missense_Mutation	SNP	ENST00000374598.4	37		.	.	.	.	.	.	.	.	.	.	A	14.14	2.445702	0.43429	.	.	ENSG00000138395	ENST00000410091;ENST00000260967;ENST00000450471;ENST00000434439;ENST00000374598	T;T;T;T;T	0.70516	-0.48;-0.48;-0.49;-0.47;-0.48	5.65	4.51	0.55191	.	0.000000	0.85682	D	0.000000	T	0.52869	0.1761	N	0.17082	0.46	0.53688	D	0.99997	B;B	0.24768	0.111;0.111	B;B	0.22753	0.041;0.041	T	0.54159	-0.8335	10	0.49607	T	0.09	-15.5437	10.0352	0.42125	0.9207:0.0:0.0793:0.0	.	72;72	Q96Q40-2;F8W6H8	.;.	G	21;21;72;72;72	ENSP00000386901:R21G;ENSP00000260967:R21G;ENSP00000406472:R72G;ENSP00000412775:R72G;ENSP00000363726:R72G	ENSP00000260967:R21G	R	+	1	2	CDK15	202380552	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.607000	0.46300	2.169000	0.68431	0.528000	0.53228	AGG	.		0.453	CDK15-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000336053.2		
GABRB3	2562	hgsc.bcm.edu	37	15	26812850	26812850	+	Missense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:26812850C>A	ENST00000311550.5	-	7	824	c.713G>T	c.(712-714)cGg>cTg	p.R238L	GABRB3_ENST00000400188.3_Missense_Mutation_p.R167L|GABRB3_ENST00000541819.2_Missense_Mutation_p.R294L|GABRB3_ENST00000299267.4_Missense_Mutation_p.R238L|GABRB3_ENST00000545868.1_Missense_Mutation_p.R153L	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	238					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)	p.R238L(2)|p.R294L(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CCTCTTCAACCGAAAGCTCAG	0.423																																					p.R238L		.											GABRB3_ENST00000541819,rectum,carcinoma,-1,3	GABRB3_ENST00000541819	-1	3	Substitution - Missense(3)	lung(3)	c.G713T						.						125.0	107.0	113.0					15																	26812850		2203	4300	6503	SO:0001583	missense	2562	exon7			TTCAACCGAAAGC		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.713G>T	15.37:g.26812850C>A	ENSP00000308725:p.Arg238Leu	Somatic	36	0		WXS	Illumina HiSeq	.	46	2	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Missense_Mutation	SNP	ENST00000311550.5	37	CCDS10019.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496539	0.44352	.	.	ENSG00000166206	ENST00000311550;ENST00000541819;ENST00000299267;ENST00000400188;ENST00000545868	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	6.06	5.14	0.70334	Neurotransmitter-gated ion-channel ligand-binding (3);	0.096499	0.64402	D	0.000001	T	0.63153	0.2487	N	0.19112	0.55	0.48762	D	0.999705	B;B;B	0.22541	0.071;0.013;0.028	B;B;B	0.18871	0.023;0.009;0.016	T	0.61744	-0.7000	10	0.62326	D	0.03	.	10.0786	0.42375	0.0:0.8536:0.0:0.1464	.	294;238;238	F5H7N0;P28472-2;P28472	.;.;GBRB3_HUMAN	L	238;294;238;167;153	ENSP00000308725:R238L;ENSP00000442408:R294L;ENSP00000299267:R238L;ENSP00000383049:R167L;ENSP00000439169:R153L	ENSP00000299267:R238L	R	-	2	0	GABRB3	24363943	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.188000	0.50958	2.879000	0.98667	0.650000	0.86243	CGG	.		0.423	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
MAP3K1	4214	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	56178366	56178366	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:56178366C>T	ENST00000399503.3	+	14	3339	c.3339C>T	c.(3337-3339)ttC>ttT	p.F1113F		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1113					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		AGACAGTGTTCACCCCAGTAG	0.433																																					p.F1113F		.											.	.	.	0			c.C3339T						.						122.0	117.0	119.0					5																	56178366		1987	4173	6160	SO:0001819	synonymous_variant	4214	exon14			AGTGTTCACCCCA	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3339C>T	5.37:g.56178366C>T		Somatic	41	0		WXS	Illumina HiSeq	.	57	6	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			.		0.433	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324095	39324095	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:39324095G>A	ENST00000391356.2	-	1	329	c.330C>T	c.(328-330)tgC>tgT	p.C110C		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	110	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		Missing (in allele KAP3-v2). {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			AGGAAGGCCTGCAGCAACTAG	0.612																																					p.C110C		.											.	.	.	0			c.C330T						.						19.0	24.0	22.0					17																	39324095		2123	4254	6377	SO:0001819	synonymous_variant	85290	exon1			AGGCCTGCAGCAA	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.330C>T	17.37:g.39324095G>A		Somatic	88	0		WXS	Illumina HiSeq	.	87	4	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.		0.612	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
CCDC15	80071	hgsc.bcm.edu	37	11	124862504	124862504	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:124862504G>T	ENST00000344762.5	+	10	2319	c.2060G>T	c.(2059-2061)aGa>aTa	p.R687I	CCDC15_ENST00000529051.1_Missense_Mutation_p.R687I	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	687						centrosome (GO:0005813)				central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(3)|skin(1)	23	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.68e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0413)		AGAGAAGAAAGAGTGAGAGAA	0.348																																					p.R687I		.											.	.	.	0			c.G2060T						.						62.0	56.0	58.0					11																	124862504		1819	4085	5904	SO:0001583	missense	80071	exon10			AAGAAAGAGTGAG	BC018540	CCDS44756.1	11q24.2	2008-02-05			ENSG00000149548	ENSG00000149548			25798	protein-coding gene	gene with protein product							Standard	NM_025004		Approved	FLJ13215	uc001qbm.4	Q0P6D6	OTTHUMG00000165940	ENST00000344762.5:c.2060G>T	11.37:g.124862504G>T	ENSP00000341684:p.Arg687Ile	Somatic	48	0		WXS	Illumina HiSeq	.	82	4	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.457590	0.43634	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.36340	1.26;1.26	4.08	-2.28	0.06826	.	1.500960	0.04408	N	0.365584	T	0.31451	0.0797	L	0.55481	1.735	0.09310	N	1	B	0.32829	0.386	B	0.33521	0.165	T	0.30416	-0.9979	10	0.52906	T	0.07	-0.26	3.6121	0.08063	0.4527:0.0:0.3334:0.2139	.	687	Q0P6D6	CCD15_HUMAN	I	687	ENSP00000435403:R687I;ENSP00000341684:R687I	ENSP00000341684:R687I	R	+	2	0	CCDC15	124367714	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	0.437000	0.21543	-0.417000	0.07461	0.655000	0.94253	AGA	.		0.348	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004	
CLDN16	10686	hgsc.bcm.edu	37	3	190106072	190106072	+	Missense_Mutation	SNP	G	G	A	rs386669518|rs201380153|rs56086318|rs368234054	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr3:190106072G>A	ENST00000264734.2	+	1	412	c.164G>A	c.(163-165)aGg>aAg	p.R55K	CLDN16_ENST00000468220.1_Intron|CLDN16_ENST00000456423.1_Missense_Mutation_p.R55K	NM_006580.3	NP_006571.1	Q9Y5I7	CLD16_HUMAN	claudin 16	55					calcium-independent cell-cell adhesion (GO:0016338)|cellular metal ion homeostasis (GO:0006875)|excretion (GO:0007588)|magnesium ion transport (GO:0015693)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|magnesium ion transmembrane transporter activity (GO:0015095)|structural molecule activity (GO:0005198)			breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|skin(1)	19	all_cancers(143;3.61e-10)|Ovarian(172;0.0991)		Lung(62;2.23e-05)|LUSC - Lung squamous cell carcinoma(58;3.15e-05)	GBM - Glioblastoma multiforme(93;0.018)		AGTGGGGCCAGGGCTGGTGTC	0.512																																					p.R55K		.											.,1	.	59	0			c.G164A						.						145.0	107.0	120.0					3																	190106072		2203	4291	6494	SO:0001583	missense	10686	exon1			GGGCCAGGGCTGG	AF152101	CCDS3296.1	3q28	2008-12-10			ENSG00000113946	ENSG00000113946		"""Claudins"""	2037	protein-coding gene	gene with protein product	"""paracellin-1"", ""hypomagnesemia 3, with hypercalciuria and nephrocalcinosis"""	603959				10390358	Standard	NM_006580		Approved	PCLN1, HOMG3	uc003fsi.3	Q9Y5I7	OTTHUMG00000156215	ENST00000264734.2:c.164G>A	3.37:g.190106072G>A	ENSP00000264734:p.Arg55Lys	Somatic	24	0		WXS	Illumina HiSeq	.	38	5	NM_006580		Missense_Mutation	SNP	ENST00000264734.2	37	CCDS3296.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.478634	0.01035	.	.	ENSG00000113946	ENST00000264734;ENST00000456423	D;D	0.92965	-2.78;-3.14	5.61	1.57	0.23409	.	1.365350	0.04318	N	0.350134	D	0.84561	0.5499	N	0.19112	0.55	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.12156	0.007;0.001	T	0.69712	-0.5071	10	0.15066	T	0.55	-18.8536	6.6557	0.22986	0.1665:0.3355:0.498:0.0	.	55;55	A0SDD8;Q9Y5I7	.;CLD16_HUMAN	K	55	ENSP00000264734:R55K;ENSP00000414136:R55K	ENSP00000264734:R55K	R	+	2	0	CLDN16	191588766	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	0.492000	0.22435	0.324000	0.23333	0.460000	0.39030	AGG	.		0.512	CLDN16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343519.1	NM_006580	
FAM193A	8603	hgsc.bcm.edu	37	4	2698243	2698243	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:2698243C>T	ENST00000324666.5	+	16	2908	c.2557C>T	c.(2557-2559)Cag>Tag	p.Q853*	FAM193A_ENST00000505311.1_Nonsense_Mutation_p.Q853*|FAM193A_ENST00000382839.3_Nonsense_Mutation_p.Q853*|FAM193A_ENST00000502458.1_Nonsense_Mutation_p.Q875*|FAM193A_ENST00000545951.1_Nonsense_Mutation_p.Q853*	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	853								p.Q853*(1)		NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GGATTTGTTGCAGTTTATAAA	0.498																																					p.Q875X		.											FAM193A,NS,NS,0,1	FAM193A	0	1	Substitution - Nonsense(1)	NS(1)	c.C2623T						.						115.0	108.0	110.0					4																	2698243		2203	4300	6503	SO:0001587	stop_gained	8603	exon17			TTGTTGCAGTTTA	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.2557C>T	4.37:g.2698243C>T	ENSP00000324587:p.Gln853*	Somatic	70	0		WXS	Illumina HiSeq	.	80	4	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Nonsense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	C	44	11.122394	0.99518	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-21.6609	17.8501	0.88744	0.0:1.0:0.0:0.0	.	.	.	.	X	853;853;853;875;707	.	ENSP00000324587:Q853X	Q	+	1	0	FAM193A	2668041	1.000000	0.71417	0.963000	0.40424	0.951000	0.60555	5.757000	0.68766	2.464000	0.83262	0.603000	0.83216	CAG	.		0.498	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
NUMBL	9253	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	41183174	41183174	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:41183174C>T	ENST00000252891.4	-	7	860	c.693G>A	c.(691-693)ggG>ggA	p.G231G	NUMBL_ENST00000540131.1_Silent_p.G190G|NUMBL_ENST00000598779.1_Silent_p.G190G	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	231					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CAGCAGGCCGCCCACCCCCAG	0.667																																					p.G231G		.											.	.	.	0			c.G693A						.						19.0	18.0	18.0					19																	41183174		2191	4280	6471	SO:0001819	synonymous_variant	9253	exon7			AGGCCGCCCACCC	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.693G>A	19.37:g.41183174C>T		Somatic	65	0		WXS	Illumina HiSeq	.	71	5	NM_004756	Q7Z4J9	Silent	SNP	ENST00000252891.4	37	CCDS12561.1																																																																																			.		0.667	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
SIGLEC16	400709	hgsc.bcm.edu	37	19	50475311	50475311	+	RNA	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:50475311G>A	ENST00000602139.1	+	0	1257							A6NMB1	SIG16_HUMAN	sialic acid binding Ig-like lectin 16 (gene/pseudogene)						cell adhesion (GO:0007155)|innate immune response (GO:0045087)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|lung(6)	10						TGCCACGCTCGGCACCCGCTG	0.672																																					.		.											.	.	.	0			.						.																																					400709	.			ACGCTCGGCACCC	BC030222		19q13.33	2014-03-20	2008-08-04	2008-08-04	ENSG00000161643	ENSG00000161643		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	24851	protein-coding gene	gene with protein product			"""sialic acid binding Ig-like lectin, pseudogene 16"""	SIGLECP16		11986327, 18629938	Standard	NR_002825		Approved	Siglec-P16	uc002prf.3	A6NMB1	OTTHUMG00000183074		19.37:g.50475311G>A		Somatic	34	0		WXS	Illumina HiSeq	.	68	8	.		RNA	SNP	ENST00000602139.1	37		.	.	.	.	.	.	.	.	.	.	G	0.012	-1.652727	0.00785	.	.	ENSG00000161643	ENST00000417280;ENST00000456956	.	.	.	1.92	-0.391	0.12446	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.309190	0.05003	N	0.469577	T	0.15782	0.0380	.	.	.	0.09310	N	1	B	0.14012	0.009	B	0.08055	0.003	T	0.17899	-1.0354	8	0.08381	T	0.77	.	4.27	0.10782	0.6059:0.0:0.3941:0.0	.	411	A6NMB1	SIG16_HUMAN	Q	439;411	.	ENSP00000396157:R439Q	R	+	2	0	SIGLEC16	55167123	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.123000	0.15708	-0.130000	0.11599	-0.628000	0.03992	CGG	.		0.672	SIGLEC16-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000464979.1	NR_002825	
HLA-F	3134	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	29693309	29693309	+	Silent	SNP	C	C	T	rs566982053		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:29693309C>T	ENST00000376861.1	+	6	1356	c.972C>T	c.(970-972)gtC>gtT	p.V324V	HLA-F_ENST00000434407.2_Silent_p.V232V|HLA-F_ENST00000440587.2_Silent_p.V206V|HLA-F_ENST00000259951.7_Silent_p.V324V|HLA-F_ENST00000475996.1_3'UTR|HLA-F_ENST00000334668.4_Silent_p.V324V			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	324					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GAGCTGTGGTCGCTGCTGTGA	0.582													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19989	0.0		0.0	False		,,,				2504	0.0				p.V324V		.											.	.	.	0			c.C972T						.						183.0	179.0	180.0					6																	29693309		1511	2709	4220	SO:0001819	synonymous_variant	3134	exon5			TGTGGTCGCTGCT	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.972C>T	6.37:g.29693309C>T		Somatic	42	0		WXS	Illumina HiSeq	.	76	5	NM_001098479	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	3.586	-0.084569	0.07097	.	.	ENSG00000204642	ENST00000429294	.	.	.	1.76	-3.36	0.04913	.	.	.	.	.	T	0.05960	0.0155	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34601	-0.9822	4	.	.	.	.	0.468	0.00527	0.1952:0.2491:0.3202:0.2355	.	.	.	.	L	203	.	.	S	+	2	0	HLA-F	29801288	0.000000	0.05858	0.007000	0.13788	0.077000	0.17291	-0.939000	0.03933	-0.410000	0.07542	0.205000	0.17691	TCG	.		0.582	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950	
XIRP2	129446	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	168115754	168115754	+	Missense_Mutation	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:168115754G>C	ENST00000409728.1	+	11	2886	c.2797G>C	c.(2797-2799)Gat>Cat	p.D933H	XIRP2_ENST00000409756.2_Missense_Mutation_p.D900H|XIRP2_ENST00000420519.1_Missense_Mutation_p.D933H|XIRP2_ENST00000409043.1_Missense_Mutation_p.D900H|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000409605.1_Missense_Mutation_p.D678H|XIRP2_ENST00000409195.1_3'UTR	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						CACAGGTTTTGATGCTCTGAG	0.428																																					p.D933H		.											.	.	.	0			c.G2797C						.						92.0	85.0	87.0					2																	168115754		1910	4137	6047	SO:0001583	missense	129446	exon11			GGTTTTGATGCTC	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.2797G>C	2.37:g.168115754G>C	ENSP00000386619:p.Asp933His	Somatic	58	0		WXS	Illumina HiSeq	.	56	8	NM_001199143	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.734796	0.48939	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	T;T;T;T;T	0.80994	-1.41;-1.41;-1.41;-1.41;-1.44	5.91	3.07	0.35406	.	.	.	.	.	T	0.73418	0.3584	.	.	.	0.20975	N	0.999811	B;B	0.24368	0.102;0.102	B;B	0.24155	0.051;0.051	T	0.62210	-0.6902	8	0.52906	T	0.07	.	11.4688	0.50254	0.0:0.279:0.5926:0.1284	.	900;933	A4UGR9-4;A4UGR9-6	.;.	H	900;933;900;933;678	ENSP00000386454:D900H;ENSP00000386619:D933H;ENSP00000386724:D900H;ENSP00000415541:D933H;ENSP00000386981:D678H	ENSP00000386454:D900H	D	+	1	0	XIRP2	167824000	0.026000	0.19158	0.016000	0.15963	0.013000	0.08279	1.533000	0.36040	0.352000	0.24053	-0.188000	0.12872	GAT	.		0.428	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
ENTPD1	953	hgsc.bcm.edu	37	10	97582886	97582886	+	Intron	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:97582886C>T	ENST00000371205.4	+	2	299				ENTPD1_ENST00000453258.2_Intron|ENTPD1_ENST00000543964.1_Intron|ENTPD1-AS1_ENST00000416301.1_RNA|ENTPD1_ENST00000371203.5_Intron|ENTPD1_ENST00000539125.1_Intron|ENTPD1_ENST00000371207.3_Intron			P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1						ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		GGCTTTTAATCTGTCTCTGAT	0.353																																					.		.											.	.	.	0			.						.																																			SO:0001627	intron_variant	0	.			TTTAATCTGTCTC	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"""CD molecules"""	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000371205.4:c.17-108C>T	10.37:g.97582886C>T		Somatic	49	0		WXS	Illumina HiSeq	.	77	4	.	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	RNA	SNP	ENST00000371205.4	37	CCDS7444.1																																																																																			.		0.353	ENTPD1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049566.1	NM_001776	
SLC19A3	80704	hgsc.bcm.edu	37	2	228564115	228564115	+	Missense_Mutation	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:228564115T>C	ENST00000258403.3	-	3	387	c.316A>G	c.(316-318)Atg>Gtg	p.M106V	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.M102V	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	106					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.M106V(1)		breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	ACAACCTGCATGGTCTTCACT	0.527																																					p.M106V		.											SLC19A3,NS,carcinoma,0,1	SLC19A3	0	1	Substitution - Missense(1)	lung(1)	c.A316G						.						122.0	121.0	122.0					2																	228564115		2203	4300	6503	SO:0001583	missense	80704	exon3			CCTGCATGGTCTT	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.316A>G	2.37:g.228564115T>C	ENSP00000258403:p.Met106Val	Somatic	41	0		WXS	Illumina HiSeq	.	58	4	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.758319	0.89843	.	.	ENSG00000135917	ENST00000258403;ENST00000541617;ENST00000456524	T;T;T	0.80480	-1.38;-1.38;0.37	5.91	5.91	0.95273	Major facilitator superfamily domain, general substrate transporter (1);	0.068694	0.85682	D	0.000000	D	0.89546	0.6746	M	0.92555	3.32	0.80722	D	1	P;P	0.46395	0.743;0.877	P;P	0.51742	0.547;0.678	D	0.90947	0.4802	10	0.49607	T	0.09	-50.9321	16.3351	0.83056	0.0:0.0:0.0:1.0	.	102;106	F5H2M8;Q9BZV2	.;S19A3_HUMAN	V	106;102;106	ENSP00000258403:M106V;ENSP00000445519:M102V;ENSP00000399001:M106V	ENSP00000258403:M106V	M	-	1	0	SLC19A3	228272359	1.000000	0.71417	0.975000	0.42487	0.948000	0.59901	7.882000	0.87258	2.262000	0.75019	0.528000	0.53228	ATG	.		0.527	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
DNAJC2	27000	hgsc.bcm.edu;bcgsc.ca	37	7	102953518	102953518	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:102953518G>T	ENST00000379263.3	-	16	1917	c.1667C>A	c.(1666-1668)aCa>aAa	p.T556K	PMPCB_ENST00000249269.4_3'UTR|PMPCB_ENST00000420236.2_Intron|DNAJC2_ENST00000249270.7_Missense_Mutation_p.T503K	NM_014377.1	NP_055192.1	Q99543	DNJC2_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 2	556	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				'de novo' cotranslational protein folding (GO:0051083)|chromatin modification (GO:0016568)|DNA replication (GO:0006260)|negative regulation of cell growth (GO:0030308)|negative regulation of DNA biosynthetic process (GO:2000279)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone binding (GO:0042393)|Hsp70 protein binding (GO:0030544)|poly(A) RNA binding (GO:0044822)|ubiquitin binding (GO:0043130)			endometrium(1)|kidney(9)|large_intestine(6)|lung(4)|ovary(1)	21						CTGTTCTTCTGTTGTCCAAGG	0.393																																					p.T556K		.											.	.	.	0			c.C1667A						.						197.0	179.0	185.0					7																	102953518		1826	4081	5907	SO:0001583	missense	27000	exon16			TCTTCTGTTGTCC	X98260	CCDS43628.1, CCDS47679.1	7q22-q32	2011-09-02	2008-07-01	2008-07-01	ENSG00000105821	ENSG00000105821		"""Heat shock proteins / DNAJ (HSP40)"""	13192	protein-coding gene	gene with protein product		605502	"""zuotin related factor 1"""	ZRF1		8885239	Standard	NM_001129887		Approved	MPP11, MPHOSPH11, ZUO1, zuotin	uc003vbo.3	Q99543	OTTHUMG00000157202	ENST00000379263.3:c.1667C>A	7.37:g.102953518G>T	ENSP00000368565:p.Thr556Lys	Somatic	52	0		WXS	Illumina HiSeq	.	57	4	NM_014377	A4VCI0|Q9BVX1	Missense_Mutation	SNP	ENST00000379263.3	37	CCDS43628.1	.	.	.	.	.	.	.	.	.	.	G	18.31	3.596915	0.66332	.	.	ENSG00000105821	ENST00000249270;ENST00000379263	T;T	0.46063	0.88;0.88	5.51	5.51	0.81932	Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);SANT, eukarya (1);	0.044478	0.85682	D	0.000000	T	0.23410	0.0566	N	0.01015	-1.05	0.80722	D	1	P;P	0.49559	0.925;0.801	P;B	0.49752	0.621;0.355	T	0.27226	-1.0080	10	0.05833	T	0.94	-26.1583	19.7866	0.96442	0.0:0.0:1.0:0.0	.	503;556	Q99543-2;Q99543	.;DNJC2_HUMAN	K	503;556	ENSP00000249270:T503K;ENSP00000368565:T556K	ENSP00000249270:T503K	T	-	2	0	DNAJC2	102740754	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	9.328000	0.96403	2.756000	0.94617	0.655000	0.94253	ACA	.		0.393	DNAJC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347891.1		
EML5	161436	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	89220900	89220900	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:89220900G>T	ENST00000380664.5	-	2	312	c.313C>A	c.(313-315)Cat>Aat	p.H105N	EML5_ENST00000352093.5_Missense_Mutation_p.H105N|EML5_ENST00000554922.1_Missense_Mutation_p.H105N			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	105						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CCATGTGTATGAACATCCTTT	0.353																																					p.H105N		.											.	.	.	0			c.C313A						.						102.0	92.0	95.0					14																	89220900		1868	4111	5979	SO:0001583	missense	161436	exon2			GTGTATGAACATC	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.313C>A	14.37:g.89220900G>T	ENSP00000370039:p.His105Asn	Somatic	89	0		WXS	Illumina HiSeq	.	110	11	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	37	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055082	0.75960	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.01947	4.54;4.54;4.54	5.8	5.8	0.92144	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.145289	0.48767	D	0.000174	T	0.17831	0.0428	M	0.90252	3.1	0.80722	D	1	D	0.67145	0.996	D	0.70227	0.968	T	0.00595	-1.1653	10	0.44086	T	0.13	-16.7777	20.0716	0.97726	0.0:0.0:1.0:0.0	.	105	Q05BV3	EMAL5_HUMAN	N	105	ENSP00000451998:H105N;ENSP00000298315:H105N;ENSP00000370039:H105N	ENSP00000298315:H105N	H	-	1	0	EML5	88290653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.741000	0.93983	0.585000	0.79938	CAT	.		0.353	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
CHRNB1	1140	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7357773	7357773	+	Silent	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:7357773T>C	ENST00000306071.2	+	8	1045	c.978T>C	c.(976-978)agT>agC	p.S326S	CHRNB1_ENST00000576360.1_Silent_p.S205S|CHRNB1_ENST00000575379.1_5'Flank|CHRNB1_ENST00000536404.2_Silent_p.S254S	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	326					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	TCATCCTTAGTGTCGTGGTTC	0.502																																					p.S326S		.											.	.	.	0			c.T978C						.						234.0	195.0	208.0					17																	7357773		2203	4300	6503	SO:0001819	synonymous_variant	1140	exon8			CCTTAGTGTCGTG	X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1961	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 1 (muscle)"""	100710	"""cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"""	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.978T>C	17.37:g.7357773T>C		Somatic	27	0		WXS	Illumina HiSeq	.	39	5	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Silent	SNP	ENST00000306071.2	37	CCDS11106.1																																																																																			.		0.502	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3		
PTPN14	5784	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	214557314	214557314	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:214557314G>A	ENST00000366956.5	-	13	2078	c.1884C>T	c.(1882-1884)ctC>ctT	p.L628L	PTPN14_ENST00000543945.1_3'UTR	NM_005401.4	NP_005392.2	Q15678	PTN14_HUMAN	protein tyrosine phosphatase, non-receptor type 14	628					lymphangiogenesis (GO:0001946)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of protein export from nucleus (GO:0046825)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)			NS(2)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(9)|liver(3)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	58				OV - Ovarian serous cystadenocarcinoma(81;0.00181)|all cancers(67;0.00194)|Epithelial(68;0.0157)|GBM - Glioblastoma multiforme(131;0.155)		TGGTGGCCGTGAGGGGCTCGC	0.627																																					p.L628L	Colon(92;557 1424 24372 34121 40073)	.											.	.	.	0			c.C1884T						.						46.0	41.0	43.0					1																	214557314		2203	4300	6503	SO:0001819	synonymous_variant	5784	exon13			GGCCGTGAGGGGC	X82676	CCDS1514.1	1q32.2	2011-06-09			ENSG00000152104	ENSG00000152104		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9647	protein-coding gene	gene with protein product		603155				7733990	Standard	NM_005401		Approved	PEZ	uc001hkk.2	Q15678	OTTHUMG00000037039	ENST00000366956.5:c.1884C>T	1.37:g.214557314G>A		Somatic	16	0		WXS	Illumina HiSeq	.	33	7	NM_005401	Q5VSI0	Silent	SNP	ENST00000366956.5	37	CCDS1514.1																																																																																			.		0.627	PTPN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089918.2	NM_005401	
SLC6A18	348932	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	1232354	1232354	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:1232354G>A	ENST00000324642.3	+	2	304	c.181G>A	c.(181-183)Gtc>Atc	p.V61I	SLC6A18_ENST00000296821.4_Missense_Mutation_p.V61I	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	61					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			CATCCCCTACGTCATCGCGCT	0.701																																					p.V61I		.											SLC6A18,NS,carcinoma,0,1	SLC6A18	0	0			c.G181A						.						46.0	46.0	46.0					5																	1232354		2203	4300	6503	SO:0001583	missense	348932	exon2			CCCTACGTCATCG	AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.181G>A	5.37:g.1232354G>A	ENSP00000323549:p.Val61Ile	Somatic	46	0		WXS	Illumina HiSeq	.	53	4	NM_182632		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	G	4.320	0.058715	0.08339	.	.	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.73789	-0.78;-0.78	5.45	-10.9	0.00192	.	0.787886	0.11888	N	0.519895	T	0.39358	0.1075	N	0.04805	-0.155	0.09310	N	1	B	0.21753	0.06	B	0.17722	0.019	T	0.25047	-1.0143	10	0.20046	T	0.44	.	4.6951	0.12800	0.0715:0.2539:0.347:0.3276	.	61	Q96N87	S6A18_HUMAN	I	61	ENSP00000323549:V61I;ENSP00000296821:V61I	ENSP00000296821:V61I	V	+	1	0	SLC6A18	1285354	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	-1.172000	0.03112	-4.056000	0.00078	-1.961000	0.00478	GTC	.		0.701	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
MT-CYB	4519	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	M	15591	15591	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrM:15591G>A	ENST00000361789.2	+	1	845	c.845G>A	c.(844-846)cGa>cAa	p.R282Q	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	282					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CACAATTCTCCGATCCGTCCC	0.478											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.R282Q		.											.	.	.	0			c.G845A						.																																			SO:0001583	missense	0	exon1			TTCTCCGATCCGT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.845G>A	M.37:g.15591G>A	ENSP00000354554:p.Arg282Gln	Somatic	18	0	585	WXS	Illumina HiSeq	.	7	4	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.		0.478	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
KYNU	8942	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	143799625	143799625	+	Missense_Mutation	SNP	C	C	G	rs147475752		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:143799625C>G	ENST00000264170.4	+	14	1540	c.1282C>G	c.(1282-1284)Cgg>Ggg	p.R428G	KYNU_ENST00000409512.1_Missense_Mutation_p.R428G	NM_003937.2	NP_003928.1			kynureninase											large_intestine(10)|liver(1)|lung(18)|prostate(3)|skin(4)	36				BRCA - Breast invasive adenocarcinoma(221;0.072)		GTGTGACAAGCGGAATCCAAA	0.363																																					p.R428G		.											.	.	.	0			c.C1282G						.						130.0	128.0	129.0					2																	143799625		2203	4299	6502	SO:0001583	missense	8942	exon15			GACAAGCGGAATC	U57721	CCDS2183.1, CCDS33299.1	2q22.2	2010-11-23	2010-11-23		ENSG00000115919	ENSG00000115919	3.7.1.3		6469	protein-coding gene	gene with protein product	"""L-kynurenine hydrolase"""	605197	"""kynureninase (L-kynurenine hydrolase)"""			8706755, 9180257	Standard	NM_001199241		Approved		uc002tvl.3	Q16719	OTTHUMG00000131829	ENST00000264170.4:c.1282C>G	2.37:g.143799625C>G	ENSP00000264170:p.Arg428Gly	Somatic	86	0		WXS	Illumina HiSeq	.	107	20	NM_001199241		Missense_Mutation	SNP	ENST00000264170.4	37	CCDS2183.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.171828	0.38315	.	.	ENSG00000115919	ENST00000264170;ENST00000409512	T;T	0.40225	1.04;1.04	5.09	-0.425	0.12317	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.124091	0.53938	D	0.000043	T	0.72614	0.3482	H	0.97158	3.95	0.50632	D	0.999881	D	0.89917	1.0	D	0.87578	0.998	T	0.79612	-0.1731	10	0.87932	D	0	.	13.296	0.60296	0.6938:0.3062:0.0:0.0	.	428	Q16719	KYNU_HUMAN	G	428	ENSP00000264170:R428G;ENSP00000386731:R428G	ENSP00000264170:R428G	R	+	1	2	KYNU	143516095	0.976000	0.34144	0.198000	0.23420	0.497000	0.33675	-0.121000	0.10643	-0.172000	0.10779	-0.188000	0.12872	CGG	.		0.363	KYNU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254772.1	NM_001032998	
Unknown	0	hgsc.bcm.edu	37	16	33503759	33503759	+	IGR	SNP	T	T	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:33503759T>A								BMS1P8 (4667 upstream) : IGHV3OR16-12 (101471 downstream)																							ATGTGCTTTCTCCTTCATCAT	0.388																																					.		.											.	.	.	0			.						.																																			SO:0001628	intergenic_variant	100873777	.			GCTTTCTCCTTCA																													16.37:g.33503759T>A		Somatic	395	0		WXS	Illumina HiSeq	.	527	30	.		RNA	SNP		37																																																																																				.	0	0.388								
DOCK7	85440	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	63018485	63018485	+	Missense_Mutation	SNP	C	C	T	rs573187574		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:63018485C>T	ENST00000340370.5	-	22	2701	c.2684G>A	c.(2683-2685)cGa>cAa	p.R895Q	DOCK7_ENST00000251157.5_Missense_Mutation_p.R895Q	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	895					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ACTAAGGCTTCGAGAACGATT	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		14963	0.001		0.0	False		,,,				2504	0.0				p.R895Q		.											.	.	.	0			c.G2684A						.						99.0	92.0	95.0					1																	63018485		2203	4300	6503	SO:0001583	missense	85440	exon22			AGGCTTCGAGAAC		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.2684G>A	1.37:g.63018485C>T	ENSP00000340742:p.Arg895Gln	Somatic	70	0		WXS	Illumina HiSeq	.	83	10	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.239878	0.79912	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370	T;T	0.14640	2.49;2.51	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.11879	0.0289	N	0.17631	0.505	0.80722	D	1	B;B;B;P;B	0.40602	0.101;0.101;0.101;0.723;0.358	B;B;B;B;B	0.38712	0.038;0.048;0.048;0.28;0.091	T	0.07790	-1.0754	10	0.54805	T	0.06	.	18.3751	0.90433	0.0:1.0:0.0:0.0	.	895;895;895;895;895	Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6	.;.;.;.;.	Q	895	ENSP00000251157:R895Q;ENSP00000340742:R895Q	ENSP00000251157:R895Q	R	-	2	0	DOCK7	62791073	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.831000	0.69330	2.564000	0.86499	0.585000	0.79938	CGA	.		0.453	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
IL12RB2	3595	hgsc.bcm.edu	37	1	67787288	67787288	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:67787288C>T	ENST00000262345.1	+	3	720	c.80C>T	c.(79-81)gCg>gTg	p.A27V	IL12RB2_ENST00000544434.1_Missense_Mutation_p.A27V|IL12RB2_ENST00000371000.1_Missense_Mutation_p.A27V|IL12RB2_ENST00000541374.1_Missense_Mutation_p.A27V	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	27					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.A27G(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						ATTGCAGATGCGTGCAAGAGA	0.378																																					p.A27V		.											IL12RB2,NS,carcinoma,0,1	IL12RB2	0	1	Substitution - Missense(1)	lung(1)	c.C80T						.						105.0	96.0	99.0					1																	67787288		2203	4300	6503	SO:0001583	missense	3595	exon3			CAGATGCGTGCAA	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.80C>T	1.37:g.67787288C>T	ENSP00000262345:p.Ala27Val	Somatic	43	0		WXS	Illumina HiSeq	.	57	3	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.824689	0.00589	.	.	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0	5.56	1.84	0.25277	Immunoglobulin C2-set-like, ligand-binding (1);	0.436821	0.25860	N	0.027824	T	0.19366	0.0465	N	0.03050	-0.425	0.19300	N	0.999979	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.32955	-0.9887	10	0.16896	T	0.51	-3.9302	3.8963	0.09141	0.1587:0.1723:0.0:0.669	.	27;27;27;27	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	V	27	ENSP00000262345:A27V;ENSP00000360039:A27V;ENSP00000445276:A27V;ENSP00000442443:A27V	ENSP00000262345:A27V	A	+	2	0	IL12RB2	67559876	0.138000	0.22547	0.998000	0.56505	0.009000	0.06853	0.049000	0.14099	0.068000	0.16574	-1.878000	0.00547	GCG	.		0.378	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
MUC1	4582	hgsc.bcm.edu	37	1	155161733	155161733	+	Missense_Mutation	SNP	G	G	C	rs113445744		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:155161733G>C	ENST00000368395.1	-	2	471	c.400C>G	c.(400-402)Cca>Gca	p.P134A	MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000342482.4_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368389.2_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	914	42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.			P -> Q (in Ref. 22; AAA35757). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)	p.P134A(2)		breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CCGTGGGCTGGGGGGGCGGTG	0.766			T	IGH@	B-NHL																																p.P143A		.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	MUC1_ENST00000368395,extremity,malignant_melanoma,0,3	MUC1_ENST00000368395	0	2	Substitution - Missense(2)	skin(2)	c.C427G						.																																			SO:0001583	missense	4582	exon2			GGGCTGGGGGGGC	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.400C>G	1.37:g.155161733G>C	ENSP00000357380:p.Pro134Ala	Somatic	10	1		WXS	Illumina HiSeq	.	12	3	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Missense_Mutation	SNP	ENST00000368395.1	37	CCDS55640.1	.	.	.	.	.	.	.	.	.	.	G	9.848	1.192814	0.21954	.	.	ENSG00000185499	ENST00000368395	T	0.20463	2.07	2.51	-2.27	0.06846	.	1.546230	0.04533	N	0.386605	T	0.13586	0.0329	L	0.38175	1.15	0.09310	N	0.999996	D	0.61080	0.989	D	0.69824	0.966	T	0.10177	-1.0641	10	0.52906	T	0.07	4.9504	0.9943	0.01463	0.2432:0.3605:0.2264:0.1698	.	134	P15941	MUC1_HUMAN	A	134	ENSP00000357380:P134A	ENSP00000357380:P134A	P	-	1	0	MUC1	153428357	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.106000	0.01338	-0.523000	0.06409	0.485000	0.47835	CCA	.		0.766	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
AFF4	27125	hgsc.bcm.edu	37	5	132228047	132228047	+	Missense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:132228047C>A	ENST00000265343.5	-	13	2825	c.2446G>T	c.(2446-2448)Gct>Tct	p.A816S	AFF4_ENST00000378595.3_Missense_Mutation_p.A816S	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	816					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACAGGCCCAGCGGGAGAAGGC	0.448																																					p.A816S	Ovarian(126;889 1733 2942 10745 11605)	.											AFF4,right_upper_lobe,carcinoma,0,1	AFF4	0	0			c.G2446T						.						107.0	110.0	109.0					5																	132228047		2203	4300	6503	SO:0001583	missense	27125	exon13			GCCCAGCGGGAGA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2446G>T	5.37:g.132228047C>A	ENSP00000265343:p.Ala816Ser	Somatic	35	0		WXS	Illumina HiSeq	.	40	2	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	.	.	.	.	.	.	.	.	.	.	C	17.80	3.478198	0.63849	.	.	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.62364	0.03;0.03	5.68	5.68	0.88126	.	0.246810	0.41938	D	0.000791	T	0.61739	0.2371	N	0.12569	0.235	0.45139	D	0.998151	D;B	0.76494	0.999;0.367	D;B	0.85130	0.997;0.165	T	0.54970	-0.8213	10	0.06757	T	0.87	-11.7626	17.9742	0.89122	0.0:1.0:0.0:0.0	.	816;816	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	S	816	ENSP00000265343:A816S;ENSP00000367858:A816S	ENSP00000265343:A816S	A	-	1	0	AFF4	132255946	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.243000	0.58721	2.677000	0.91161	0.563000	0.77884	GCT	.		0.448	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
NFKB2	4791	hgsc.bcm.edu	37	10	104157319	104157319	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:104157319G>T	ENST00000369966.3	+	8	788	c.538G>T	c.(538-540)Gaa>Taa	p.E180*	NFKB2_ENST00000189444.6_Nonsense_Mutation_p.E180*|NFKB2_ENST00000428099.1_Nonsense_Mutation_p.E180*	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	180	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	AGAGGCCAAAGAACTGAAGAA	0.587			T	IGH@	B-NHL																																p.E180X		.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	NFKB2,NS,carcinoma,0,1	NFKB2	0	0			c.G538T						.						157.0	190.0	179.0					10																	104157319		2119	4227	6346	SO:0001587	stop_gained	4791	exon8			GCCAAAGAACTGA	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"""Ankyrin repeat domain containing"""	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.538G>T	10.37:g.104157319G>T	ENSP00000358983:p.Glu180*	Somatic	27	0		WXS	Illumina HiSeq	.	33	2	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Nonsense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	G	34	5.386385	0.95967	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	.	.	.	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	18.2059	0.89854	0.0:0.0:1.0:0.0	.	.	.	.	X	180	.	ENSP00000189444:E180X	E	+	1	0	NFKB2	104147309	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.557000	0.98129	2.291000	0.77112	0.561000	0.74099	GAA	.		0.587	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2		
HYDIN	54768	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	71015307	71015307	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:71015307G>A	ENST00000393567.2	-	29	4647	c.4497C>T	c.(4495-4497)ccC>ccT	p.P1499P		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1499					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGAGGTTCCTGGGGAGATCGA	0.468																																					p.P1499P		.											.	.	.	0			c.C4497T						.						89.0	85.0	86.0					16																	71015307		1860	4083	5943	SO:0001819	synonymous_variant	54768	exon29			GTTCCTGGGGAGA	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4497C>T	16.37:g.71015307G>A		Somatic	47	0		WXS	Illumina HiSeq	.	71	9	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			.		0.468	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
MAP3K11	4296	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	11	65373425	65373425	+	Missense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:65373425C>G	ENST00000530153.1	-	7	1481	c.960G>C	c.(958-960)caG>caC	p.Q320H	MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000532507.1_5'UTR|MAP3K11_ENST00000309100.3_Missense_Mutation_p.Q577H					mitogen-activated protein kinase kinase kinase 11									p.Q577H(1)		breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						ACCTCCCATTCTGGGCTTCCC	0.622																																					p.Q577H		.											MAP3K11,NS,carcinoma,0,1	MAP3K11	0	1	Substitution - Missense(1)	lung(1)	c.G1731C						.						27.0	30.0	29.0					11																	65373425		2201	4297	6498	SO:0001583	missense	4296	exon7			CCCATTCTGGGCT		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.960G>C	11.37:g.65373425C>G	ENSP00000433886:p.Gln320His	Somatic	30	0		WXS	Illumina HiSeq	.	62	5	NM_002419		Missense_Mutation	SNP	ENST00000530153.1	37		.	.	.	.	.	.	.	.	.	.	C	20.3	3.973807	0.74246	.	.	ENSG00000173327	ENST00000309100;ENST00000530153	T;T	0.74421	-0.76;-0.84	5.24	5.24	0.73138	.	0.537461	0.17679	N	0.165710	T	0.80025	0.4548	L	0.29908	0.895	0.41414	D	0.987752	D;D	0.69078	0.997;0.981	D;P	0.81914	0.995;0.827	T	0.81369	-0.0964	10	0.59425	D	0.04	.	16.3154	0.82918	0.0:1.0:0.0:0.0	.	84;577	B3KQY4;Q16584	.;M3K11_HUMAN	H	577;320	ENSP00000309597:Q577H;ENSP00000433886:Q320H	ENSP00000309597:Q577H	Q	-	3	2	MAP3K11	65130001	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.008000	0.29872	2.465000	0.83290	0.491000	0.48974	CAG	.		0.622	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
HTT	3064	hgsc.bcm.edu;bcgsc.ca	37	4	3213728	3213728	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:3213728G>T	ENST00000355072.5	+	48	6632	c.6487G>T	c.(6487-6489)Gcc>Tcc	p.A2163S		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2163					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CCAGAAGAGTGCCCTTTTTGA	0.542																																					p.A2163S		.											.	.	.	0			c.G6487T						.						80.0	84.0	83.0					4																	3213728		1965	4168	6133	SO:0001583	missense	3064	exon48			AAGAGTGCCCTTT	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.6487G>T	4.37:g.3213728G>T	ENSP00000347184:p.Ala2163Ser	Somatic	54	0		WXS	Illumina HiSeq	.	56	4	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	6.953	0.545719	0.13312	.	.	ENSG00000197386	ENST00000355072	T	0.05081	3.5	5.73	1.73	0.24493	.	0.579744	0.18754	N	0.132091	T	0.01765	0.0056	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46762	-0.9168	10	0.07325	T	0.83	.	3.8433	0.08923	0.2016:0.3584:0.3561:0.0839	.	2163	P42858	HD_HUMAN	S	2163	ENSP00000347184:A2163S	ENSP00000347184:A2163S	A	+	1	0	HTT	3183526	0.001000	0.12720	0.283000	0.24790	0.786000	0.44442	1.384000	0.34396	0.743000	0.32719	-0.128000	0.14901	GCC	.		0.542	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
ADAMTS17	170691	hgsc.bcm.edu;bcgsc.ca	37	15	100802574	100802574	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:100802574G>T	ENST00000268070.4	-	5	961	c.856C>A	c.(856-858)Ctg>Atg	p.L286M	ADAMTS17_ENST00000559976.1_5'Flank	NM_139057.2	NP_620688.2	Q8TE56	ATS17_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 17	286	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(24)|ovary(3)|prostate(2)	50	Lung NSC(78;0.00299)|all_lung(78;0.00457)|Melanoma(26;0.00571)		OV - Ovarian serous cystadenocarcinoma(32;0.0013)|LUSC - Lung squamous cell carcinoma(107;0.132)|Lung(145;0.161)	COAD - Colon adenocarcinoma(1;0.111)|all cancers(203;0.219)		TGTCGTAGCAGGACAAGCTTG	0.438																																					p.L286M		.											.	.	.	0			c.C856A						.						157.0	151.0	153.0					15																	100802574		2203	4300	6503	SO:0001583	missense	170691	exon5			GTAGCAGGACAAG	AJ315735	CCDS10383.1	15q24	2014-01-28	2005-08-19		ENSG00000140470	ENSG00000140470		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17109	protein-coding gene	gene with protein product		607511	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 17"""			11867212	Standard	NM_139057		Approved	FLJ32769, FLJ16363	uc002bvv.1	Q8TE56	OTTHUMG00000149867	ENST00000268070.4:c.856C>A	15.37:g.100802574G>T	ENSP00000268070:p.Leu286Met	Somatic	48	0		WXS	Illumina HiSeq	.	59	4	NM_139057	Q2I7G4|Q6ZN75	Missense_Mutation	SNP	ENST00000268070.4	37	CCDS10383.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997619	0.74818	.	.	ENSG00000140470	ENST00000268070;ENST00000378898	D	0.87412	-2.25	5.6	5.6	0.85130	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (1);	0.090722	0.45606	D	0.000346	D	0.89839	0.6831	L	0.35854	1.095	0.50039	D	0.99984	D;D	0.71674	0.992;0.998	D;P	0.64237	0.923;0.905	D	0.87893	0.2685	10	0.31617	T	0.26	.	19.6251	0.95674	0.0:0.0:1.0:0.0	.	43;286	Q8TE56-2;Q8TE56	.;ATS17_HUMAN	M	286;43	ENSP00000268070:L286M	ENSP00000268070:L286M	L	-	1	2	ADAMTS17	98620097	1.000000	0.71417	0.995000	0.50966	0.926000	0.56050	5.949000	0.70257	2.636000	0.89361	0.655000	0.94253	CTG	.		0.438	ADAMTS17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313595.1	NM_139057	
GSTK1	373156	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	142960620	142960620	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:142960620C>T	ENST00000358406.5	+	1	85	c.14C>T	c.(13-15)cCg>cTg	p.P5L	GSTK1_ENST00000443571.2_Missense_Mutation_p.P5L|GSTK1_ENST00000479303.1_Missense_Mutation_p.P5L|GSTK1_ENST00000494735.1_3'UTR|GSTK1_ENST00000409500.3_Missense_Mutation_p.P5L|AC073342.12_ENST00000427392.1_RNA	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	5					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)	p.P5Q(2)		lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	GGGCCCCTGCCGCGCACCGTG	0.677																																					p.P5L		.											GSTK1_ENST00000479303,NS,haematopoietic_neoplasm,0,4	GSTK1_ENST00000479303	0	2	Substitution - Missense(2)	lung(2)	c.C14T						.						50.0	54.0	53.0					7																	142960620		2203	4300	6503	SO:0001583	missense	373156	exon1			CCCTGCCGCGCAC		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"""Glutathione S-transferases / Mitochondrial (kappa)"""	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.14C>T	7.37:g.142960620C>T	ENSP00000351181:p.Pro5Leu	Somatic	41	0		WXS	Illumina HiSeq	.	44	5	NM_001143681	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	37	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865764	0.51588	.	.	ENSG00000197448	ENST00000409500;ENST00000443571;ENST00000358406;ENST00000479303	.	.	.	5.49	4.62	0.57501	Thioredoxin-like fold (1);	0.281782	0.36628	N	0.002492	T	0.41119	0.1145	L	0.58669	1.825	0.27073	N	0.963267	B;B;B;B	0.31040	0.218;0.07;0.305;0.001	B;B;B;B	0.21546	0.035;0.016;0.033;0.001	T	0.35525	-0.9785	9	0.40728	T	0.16	-15.7146	11.14	0.48398	0.0:0.9135:0.0:0.0865	.	5;5;5;5	Q9Y2Q3-3;Q9Y2Q3-4;Q9Y2Q3-2;Q9Y2Q3	.;.;.;GSTK1_HUMAN	L	5	.	ENSP00000351181:P5L	P	+	2	0	GSTK1	142670742	0.813000	0.29090	0.341000	0.25589	0.208000	0.24298	1.444000	0.35068	1.302000	0.44855	-0.306000	0.09157	CCG	.		0.677	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917	
FAM205B	389715	hgsc.bcm.edu	37	9	34834808	34834808	+	RNA	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:34834808A>G	ENST00000455647.2	-	0	1585							Q63HN1	F205B_HUMAN	family with sequence similarity 205, member B									p.N227N(1)									GAGACACCCAATTTGGCGAAA	0.517																																					.		.											C9orf144,NS,carcinoma,0,1	C9orf144	0	1	Substitution - coding silent(1)	endometrium(1)	.						.																																					389715	.			CACCCAATTTGGC			9p13.3	2013-05-22	2011-08-15	2011-08-15	ENSG00000257198	ENSG00000257198			24504	other	unknown			"""chromosome 9 open reading frame 144"""	C9orf144			Standard	NR_024481		Approved	DKFZp434J193, C9orf144A	uc003zvp.4	Q63HN1	OTTHUMG00000019839		9.37:g.34834808A>G		Somatic	57	2		WXS	Illumina HiSeq	.	46	3	.	Q6ZRJ7	RNA	SNP	ENST00000455647.2	37																																																																																				.		0.517	FAM205B-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052246.5	NR_024481	
KIAA0195	9772	hgsc.bcm.edu	37	17	73482012	73482012	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:73482012G>T	ENST00000314256.7	+	4	599	c.205G>T	c.(205-207)Ggg>Tgg	p.G69W	KIAA0195_ENST00000579208.1_Intron|KIAA0195_ENST00000375248.5_Missense_Mutation_p.G79W	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	69						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCACTGGCCGGGGGCCTCACT	0.667																																					p.G69W		.											.	.	.	0			c.G205T						.						25.0	24.0	24.0					17																	73482012		2203	4299	6502	SO:0001583	missense	9772	exon4			TGGCCGGGGGCCT		CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.205G>T	17.37:g.73482012G>T	ENSP00000313885:p.Gly69Trp	Somatic	75	0		WXS	Illumina HiSeq	.	100	4	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.843778	0.51164	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	D;D	0.88431	-2.38;-2.38	5.09	5.09	0.68999	.	0.115763	0.56097	D	0.000024	D	0.90820	0.7117	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.98;0.999	D	0.92561	0.6058	10	0.87932	D	0	-24.8321	18.0985	0.89498	0.0:0.0:1.0:0.0	.	79;69	C9JL75;Q12767	.;K0195_HUMAN	W	69;79	ENSP00000313885:G69W;ENSP00000364397:G79W	ENSP00000313885:G69W	G	+	1	0	KIAA0195	70993607	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	7.250000	0.78287	2.363000	0.80096	0.561000	0.74099	GGG	.		0.667	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738	
MUC5B	727897	hgsc.bcm.edu	37	11	1255536	1255536	+	Splice_Site	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:1255536G>T	ENST00000529681.1	+	20	2536		c.e20+1		MUC5B_ENST00000447027.1_Splice_Site	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming						cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGTGGGCTGTGTGAGTTCCAT	0.667																																					.		.											.	.	.	0			c.2478+1G>T						.						10.0	12.0	11.0					11																	1255536		2005	4157	6162	SO:0001630	splice_region_variant	727897	exon20			GGCTGTGTGAGTT	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.2478+1G>T	11.37:g.1255536G>T		Somatic	38	0		WXS	Illumina HiSeq	.	62	5	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Splice_Site	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	15.00	2.702433	0.48307	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	.	.	.	4.11	4.11	0.48088	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.1263	0.81397	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MUC5B	1212112	1.000000	0.71417	0.954000	0.39281	0.426000	0.31534	7.295000	0.78780	2.122000	0.65172	0.457000	0.33378	.	.		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Intron
ZUFSP	221302	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	116957009	116957009	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:116957009C>T	ENST00000368576.3	-	10	1966	c.1723G>A	c.(1723-1725)Gag>Aag	p.E575K		NM_145062.2	NP_659499.2	Q96AP4	ZUFSP_HUMAN	zinc finger with UFM1-specific peptidase domain	575							metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(6)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	21				GBM - Glioblastoma multiforme(226;0.0258)|all cancers(137;0.0368)|OV - Ovarian serous cystadenocarcinoma(136;0.0464)|Epithelial(106;0.186)		GGAATCTTCTCGGCTGTAAAG	0.294																																					p.E575K		.											.	.	.	0			c.G1723A						.						69.0	74.0	72.0					6																	116957009		2203	4298	6501	SO:0001583	missense	221302	exon10			TCTTCTCGGCTGT	AK054582	CCDS5110.1	6q22.31	2013-01-28	2008-03-25	2008-03-25	ENSG00000153975	ENSG00000153975		"""Zinc fingers, C2H2-type"""	21224	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 113"""	C6orf113			Standard	NM_145062		Approved	dJ412I7.3	uc003pxf.2	Q96AP4	OTTHUMG00000015445	ENST00000368576.3:c.1723G>A	6.37:g.116957009C>T	ENSP00000357565:p.Glu575Lys	Somatic	33	0		WXS	Illumina HiSeq	.	42	4	NM_145062	Q5TD92|Q6PJH7|Q96NV6	Missense_Mutation	SNP	ENST00000368576.3	37	CCDS5110.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434687	0.83885	.	.	ENSG00000153975	ENST00000368576	T	0.45668	0.89	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.50274	0.1606	M	0.72118	2.19	0.80722	D	1	D	0.71674	0.998	P	0.60117	0.869	T	0.53802	-0.8387	10	0.56958	D	0.05	-1.189	13.8178	0.63303	0.0:0.8455:0.1545:0.0	.	575	Q96AP4	ZUFSP_HUMAN	K	575	ENSP00000357565:E575K	ENSP00000357565:E575K	E	-	1	0	ZUFSP	117063702	0.991000	0.36638	0.957000	0.39632	0.993000	0.82548	3.198000	0.51035	2.420000	0.82092	0.563000	0.77884	GAG	.		0.294	ZUFSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041961.1	NM_145062	
AZIN2	113451	hgsc.bcm.edu	37	1	33583665	33583665	+	Missense_Mutation	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:33583665T>C	ENST00000294517.6	+	11	1779	c.1192T>C	c.(1192-1194)Ttt>Ctt	p.F398L	ADC_ENST00000398167.1_Missense_Mutation_p.F418L|ADC_ENST00000484656.1_3'UTR|ADC_ENST00000373441.1_Missense_Mutation_p.F418L|ADC_ENST00000373443.3_Missense_Mutation_p.F398L	NM_052998.2	NP_443724.1	Q96A70	AZIN2_HUMAN		398					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of protein catabolic process (GO:0042177)|ornithine metabolic process (GO:0006591)|polyamine biosynthetic process (GO:0006596)|polyamine metabolic process (GO:0006595)|positive regulation of catalytic activity (GO:0043085)|positive regulation of polyamine transmembrane transport (GO:1902269)|putrescine transport (GO:0015847)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|trans-Golgi network membrane organization (GO:0098629)	axon (GO:0030424)|cis-Golgi network (GO:0005801)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|granular vesicle (GO:1990005)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	catalytic activity (GO:0003824)|ornithine decarboxylase activator activity (GO:0042978)|putrescine transmembrane transporter activity (GO:0015489)			NS(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)			L-Arginine(DB00125)	GGGTTCCCCCTTTTGGGGGAC	0.622																																					p.F398L		.											.	.	.	0			c.T1192C						.						42.0	51.0	48.0					1																	33583665		2203	4300	6503	SO:0001583	missense	113451	exon11			TCCCCCTTTTGGG																												ENST00000294517.6:c.1192T>C	1.37:g.33583665T>C	ENSP00000294517:p.Phe398Leu	Somatic	46	0		WXS	Illumina HiSeq	.	96	4	NM_052998	B2RDU5|D3DPQ9|Q5TIF4|Q5TIF5|Q5TIF6|Q8TF56|Q96L54|Q96L55|Q96L56|Q96L57|Q96MD9	Missense_Mutation	SNP	ENST00000294517.6	37	CCDS375.1	.	.	.	.	.	.	.	.	.	.	T	6.387	0.439479	0.12104	.	.	ENSG00000142920	ENST00000294517;ENST00000373443;ENST00000398167;ENST00000373441	T;T;T;T	0.61274	0.12;0.12;0.12;0.12	4.92	-3.2	0.05156	Orn/DAP/Arg decarboxylase 2, C-terminal (1);Alanine racemase/group IV decarboxylase, C-terminal (2);	2.546130	0.01512	N	0.017982	T	0.47322	0.1439	L	0.52905	1.665	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.0;0.003;0.003	T	0.20940	-1.0260	10	0.45353	T	0.12	-0.3489	0.8754	0.01223	0.2324:0.2919:0.1142:0.3615	.	418;303;398	Q96A70-2;D3DPR0;Q96A70	.;.;ADC_HUMAN	L	398;398;418;418	ENSP00000294517:F398L;ENSP00000362542:F398L;ENSP00000381233:F418L;ENSP00000362540:F418L	ENSP00000294517:F398L	F	+	1	0	ADC	33356252	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	0.352000	0.20113	-0.243000	0.09653	-1.016000	0.02456	TTT	.		0.622	ADC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011867.1		
RUNX2	860	hgsc.bcm.edu	37	6	45390463	45390463	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:45390463G>A	ENST00000371438.1	+	2	550	c.192G>A	c.(190-192)caG>caA	p.Q64Q	RUNX2_ENST00000576263.1_Silent_p.Q64Q|RUNX2_ENST00000371432.3_Silent_p.Q50Q|RUNX2_ENST00000541979.1_Silent_p.Q132Q|RUNX2_ENST00000359524.5_Silent_p.Q50Q|RUNX2_ENST00000465038.2_Silent_p.Q64Q|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000352853.5_Silent_p.Q132Q|RUNX2_ENST00000371436.6_Silent_p.Q64Q	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	64	Poly-Gln.				BMP signaling pathway (GO:0030509)|cell maturation (GO:0048469)|cellular response to BMP stimulus (GO:0071773)|chondrocyte development (GO:0002063)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|endochondral ossification (GO:0001958)|gene expression (GO:0010467)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|osteoblast fate commitment (GO:0002051)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|stem cell differentiation (GO:0048863)|T cell differentiation (GO:0030217)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(18)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						agcagcagcagcaacagcagc	0.736																																					p.Q64Q		.											RUNX2_ENST00000352853,NS,carcinoma,0,2	RUNX2_ENST00000352853	0	0			c.G192A						.						11.0	16.0	14.0					6																	45390463		1448	3096	4544	SO:0001819	synonymous_variant	860	exon3			GCAGCAGCAACAG	AF001450	CCDS43467.1, CCDS43468.1, CCDS43467.2, CCDS43468.2	6p21	2010-08-20			ENSG00000124813	ENSG00000124813			10472	protein-coding gene	gene with protein product		600211		CCD, CBFA1, CCD1		7835892	Standard	NM_001024630		Approved	AML3, PEBP2A1, PEBP2aA1	uc011dvx.2	Q13950	OTTHUMG00000014774	ENST00000371438.1:c.192G>A	6.37:g.45390463G>A		Somatic	41	0		WXS	Illumina HiSeq	.	48	3	NM_001024630	O14614|O14615|O95181	Silent	SNP	ENST00000371438.1	37	CCDS43467.2																																																																																			.		0.736	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348	
SSPO	23145	hgsc.bcm.edu	37	7	149503932	149503932	+	RNA	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:149503932C>T	ENST00000378016.2	+	0	8756							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ATAGAGTGTACGGGCTTCTGC	0.657																																					p.T2919M		.											.	.	.	0			c.C8756T						.						23.0	32.0	29.0					7																	149503932		1892	4088	5980			23145	exon60			AGTGTACGGGCTT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149503932C>T		Somatic	61	0		WXS	Illumina HiSeq	.	67	4	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
RSG1	79363	hgsc.bcm.edu	37	1	16563182	16563182	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:16563182G>A	ENST00000375599.3	-	1	475	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_030907.3	NP_112169.2	Q9BU20	RSG1_HUMAN	REM2 and RAB-like small GTPase 1	19					cellular protein localization (GO:0034613)|cilium assembly (GO:0042384)|exocytosis (GO:0006887)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of vesicle fusion (GO:0031338)|small GTPase mediated signal transduction (GO:0007264)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)	GTP binding (GO:0005525)			large_intestine(2)|lung(2)|pancreas(1)|prostate(1)	6						CTTGCCCTCGGCACTCTCGTG	0.632																																					p.A19V		.											.	.	.	0			c.C56T						.						42.0	30.0	34.0					1																	16563182		2184	4247	6431	SO:0001583	missense	79363	exon1			CCCTCGGCACTCT	BC008702	CCDS171.1	1p36.13	2014-02-21	2011-02-22	2011-02-22	ENSG00000132881	ENSG00000132881			28127	protein-coding gene	gene with protein product	"""Rem/Rab-Similar GTPase 1"""		"""chromosome 1 open reading frame 89"""	C1orf89		19767740	Standard	NM_030907		Approved	MGC10731	uc001ayd.3	Q9BU20	OTTHUMG00000002214	ENST00000375599.3:c.56C>T	1.37:g.16563182G>A	ENSP00000364749:p.Ala19Val	Somatic	55	0		WXS	Illumina HiSeq	.	70	4	NM_030907	Q5TEV7	Missense_Mutation	SNP	ENST00000375599.3	37	CCDS171.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.505928	0.26949	.	.	ENSG00000132881	ENST00000375599	T	0.55760	0.5	4.39	2.47	0.30058	.	0.524501	0.19330	N	0.116917	T	0.27241	0.0668	N	0.08118	0	0.20873	N	0.999835	B	0.02656	0.0	B	0.01281	0.0	T	0.13176	-1.0519	10	0.28530	T	0.3	-5.5505	6.3485	0.21363	0.2227:0.0:0.7773:0.0	.	19	Q9BU20	RSG1_HUMAN	V	19	ENSP00000364749:A19V	ENSP00000364749:A19V	A	-	2	0	RSG1	16435769	0.497000	0.26067	0.853000	0.33588	0.515000	0.34225	3.315000	0.51951	0.574000	0.29417	0.305000	0.20034	GCC	.		0.632	RSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006279.2	NM_030907	
PCSK9	255738	hgsc.bcm.edu	37	1	55505552	55505552	+	Silent	SNP	A	A	G	rs35574083|rs371488778|rs113330492|rs45454392	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:55505552A>G	ENST00000302118.5	+	1	332	c.42A>G	c.(40-42)ccA>ccG	p.P14P	PCSK9_ENST00000543384.1_5'Flank|PCSK9_ENST00000452118.2_Silent_p.P14P	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	14					apoptotic process (GO:0006915)|cellular response to insulin stimulus (GO:0032869)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|kidney development (GO:0001822)|lipoprotein metabolic process (GO:0042157)|liver development (GO:0001889)|low-density lipoprotein particle receptor catabolic process (GO:0032802)|lysosomal transport (GO:0007041)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of receptor recycling (GO:0001920)|neurogenesis (GO:0022008)|neuron differentiation (GO:0030182)|phospholipid metabolic process (GO:0006644)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of receptor internalization (GO:0002092)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)|regulation of neuron apoptotic process (GO:0043523)|regulation of receptor activity (GO:0010469)|triglyceride metabolic process (GO:0006641)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|extracellular space (GO:0005615)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)	apolipoprotein binding (GO:0034185)|apolipoprotein receptor binding (GO:0034190)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein particle receptor binding (GO:0050750)|poly(A) RNA binding (GO:0044822)|protein self-association (GO:0043621)|serine-type endopeptidase activity (GO:0004252)|sodium channel inhibitor activity (GO:0019871)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.P14_L15insL(2)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(1)|liver(2)|lung(4)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	32						Ggccgctgccactgctgctgc	0.706																																					p.P14P	Pancreas(137;1454 1827 5886 22361 42375)	.											.,7	.	76	2	Insertion - In frame(2)	breast(1)|central_nervous_system(1)	c.A42G						.						10.0	10.0	10.0					1																	55505552		2070	4074	6144	SO:0001819	synonymous_variant	255738	exon1			GCTGCCACTGCTG	AX207686	CCDS603.1	1p34.1-p32	2014-09-17	2003-05-13		ENSG00000169174	ENSG00000169174			20001	protein-coding gene	gene with protein product		607786	"""hypercholesterolemia, autosomal dominant 3"""	HCHOLA3		12552133, 12730697	Standard	NM_174936		Approved	NARC-1, FH3	uc001cyf.2	Q8NBP7	OTTHUMG00000008136	ENST00000302118.5:c.42A>G	1.37:g.55505552A>G		Somatic	63	0		WXS	Illumina HiSeq	.	69	3	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			.		0.706	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936	
PCDHB8	56128	hgsc.bcm.edu	37	5	140559572	140559572	+	Missense_Mutation	SNP	T	T	C	rs17844504		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:140559572T>C	ENST00000239444.2	+	1	2202	c.1957T>C	c.(1957-1959)Tgc>Cgc	p.C653R	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	653	Cadherin 6. {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.C653R(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGAGCCTCCGTGCTCGGCCAC	0.711																																					p.C653R		.											PCDHB8,NS,malignant_melanoma,0,1	PCDHB8	0	1	Substitution - Missense(1)	NS(1)	c.T1957C						.						22.0	25.0	24.0					5																	140559572		2150	4208	6358	SO:0001583	missense	56128	exon1			CCTCCGTGCTCGG	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.1957T>C	5.37:g.140559572T>C	ENSP00000239444:p.Cys653Arg	Somatic	72	0		WXS	Illumina HiSeq	.	98	5	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	C	0.012	-1.657243	0.00779	.	.	ENSG00000120322	ENST00000239444	T	0.45276	0.9	4.22	3.33	0.38152	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.08044	0.0201	N	0.00096	-2.155	0.36249	D	0.853792	B	0.02656	0.0	B	0.01281	0.0	T	0.25882	-1.0119	9	0.05833	T	0.94	.	8.1883	0.31352	0.1644:0.7506:0.0:0.085	rs17844504	653	Q9UN66	PCDB8_HUMAN	R	653	ENSP00000239444:C653R	ENSP00000239444:C653R	C	+	1	0	PCDHB8	140539756	0.000000	0.05858	0.047000	0.18901	0.446000	0.32137	0.734000	0.26101	0.243000	0.21327	-0.711000	0.03637	TGC	.		0.711	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
GALNTL5	168391	hgsc.bcm.edu	37	7	151680104	151680104	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:151680104G>A	ENST00000392800.2	+	4	656	c.402G>A	c.(400-402)ccG>ccA	p.P134P	GALNTL5_ENST00000431418.2_Silent_p.P134P	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	134	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		CCCGCCTCCCGACTGCCAGCA	0.448																																					p.P134P		.											GALNTL5,NS,carcinoma,0,1	GALNTL5	0	0			c.G402A						.						125.0	117.0	120.0					7																	151680104		2203	4300	6503	SO:0001819	synonymous_variant	168391	exon4			CCTCCCGACTGCC	AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.402G>A	7.37:g.151680104G>A		Somatic	57	0		WXS	Illumina HiSeq	.	64	3	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Silent	SNP	ENST00000392800.2	37	CCDS5929.1																																																																																			.		0.448	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
MGST1	4257	hgsc.bcm.edu	37	12	16516728	16516728	+	Splice_Site	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:16516728G>T	ENST00000396209.1	+	4	364		c.e4-1		MGST1_ENST00000535309.1_Intron|MGST1_ENST00000540056.1_Splice_Site|MGST1_ENST00000010404.2_Splice_Site|MGST1_ENST00000396210.3_Splice_Site|MGST1_ENST00000396207.1_Splice_Site	NM_145791.2	NP_665734.1	P10620	MGST1_HUMAN	microsomal glutathione S-transferase 1						cellular response to lipid hydroperoxide (GO:0071449)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|Leydig cell differentiation (GO:0033327)|oxidation-reduction process (GO:0055114)|protein homotrimerization (GO:0070207)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	apical part of cell (GO:0045177)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	glutathione binding (GO:0043295)|glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)			endometrium(2)|large_intestine(2)|lung(4)|ovary(1)	9		Hepatocellular(102;0.121)			Glutathione(DB00143)	TTTTTCCACAGAGCCCACCTG	0.383																																					.		.											.	.	.	0			c.222-1G>T						.						103.0	101.0	101.0					12																	16516728		2203	4300	6503	SO:0001630	splice_region_variant	4257	exon4			TCCACAGAGCCCA	U46494	CCDS8677.1, CCDS58209.1	12p12.3-p12.1	2012-06-21			ENSG00000008394	ENSG00000008394	2.5.1.18	"""Glutathione S-transferases / Microsomal"""	7061	protein-coding gene	gene with protein product		138330		GST12			Standard	NM_145792		Approved	MGST-I	uc031qgl.1	P10620	OTTHUMG00000168816	ENST00000396209.1:c.222-1G>T	12.37:g.16516728G>T		Somatic	67	0		WXS	Illumina HiSeq	.	95	4	NM_145792	A8K533|G5EA53	Splice_Site	SNP	ENST00000396209.1	37	CCDS8677.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.928431	0.52759	.	.	ENSG00000008394	ENST00000536371;ENST00000010404;ENST00000543076;ENST00000396210;ENST00000540056;ENST00000396209;ENST00000540126;ENST00000396207	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2213	0.93797	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MGST1	16407995	1.000000	0.71417	0.999000	0.59377	0.571000	0.35966	8.503000	0.90509	2.775000	0.95449	0.655000	0.94253	.	.		0.383	MGST1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401189.1	NM_145791	Intron
KIF21A	55605	hgsc.bcm.edu;bcgsc.ca	37	12	39752014	39752014	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:39752014G>T	ENST00000361418.5	-	8	1196	c.1181C>A	c.(1180-1182)aCa>aAa	p.T394K	KIF21A_ENST00000541463.2_Missense_Mutation_p.T394K|KIF21A_ENST00000544797.2_Missense_Mutation_p.T394K|KIF21A_ENST00000395670.3_Missense_Mutation_p.T394K|KIF21A_ENST00000361961.3_Missense_Mutation_p.T394K			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	394					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				CTGAAGTCGTGTGATTTCACT	0.403																																					p.T394K		.											.	.	.	0			c.C1181A						.						382.0	345.0	358.0					12																	39752014		2203	4300	6503	SO:0001583	missense	55605	exon8			AGTCGTGTGATTT	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.1181C>A	12.37:g.39752014G>T	ENSP00000354878:p.Thr394Lys	Somatic	72	0		WXS	Illumina HiSeq	.	90	4	NM_001173463	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Missense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	G	19.40	3.820887	0.71028	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000544797;ENST00000361418;ENST00000541463;ENST00000552908	T;T;T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63;-0.63;-0.63	4.47	4.47	0.54385	.	0.000000	0.53938	D	0.000059	T	0.51109	0.1655	N	0.08118	0	0.45129	D	0.998146	B;P;B;P;B	0.36282	0.007;0.546;0.038;0.469;0.006	B;B;B;B;B	0.33750	0.024;0.073;0.107;0.169;0.001	T	0.54622	-0.8266	10	0.28530	T	0.3	.	17.5127	0.87764	0.0:0.0:1.0:0.0	.	394;394;394;394;394	F5H219;B9EGE4;F5H0C3;Q7Z4S6;Q7Z4S6-2	.;.;.;KI21A_HUMAN;.	K	394;394;394;394;394;394;217	ENSP00000354851:T394K;ENSP00000379029:T394K;ENSP00000445606:T394K;ENSP00000354878:T394K;ENSP00000438075:T394K;ENSP00000449700:T217K	ENSP00000344501:T394K	T	-	2	0	KIF21A	38038281	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.550000	0.98110	2.190000	0.69967	0.655000	0.94253	ACA	.		0.403	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
DPF3	8110	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	73140954	73140954	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:73140954G>A	ENST00000556509.1	-	8	864	c.865C>T	c.(865-867)Cgc>Tgc	p.R289C	DPF3_ENST00000557704.1_5'UTR|DPF3_ENST00000541685.1_Missense_Mutation_p.R289C|DPF3_ENST00000546183.1_Missense_Mutation_p.R299C	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3	289					chromatin modification (GO:0016568)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)	22				BRCA - Breast invasive adenocarcinoma(234;0.00649)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCACCAGAGCGTCCACAGTCT	0.572																																					p.R289C		.											.	.	.	0			c.C865T						.						48.0	55.0	53.0					14																	73140954		2124	4251	6375	SO:0001583	missense	8110	exon8			CAGAGCGTCCACA	U43919	CCDS45133.1, CCDS61495.1, CCDS61496.1, CCDS61497.1	14q24.2	2014-05-13			ENSG00000205683	ENSG00000205683		"""Zinc fingers, PHD-type"""	17427	protein-coding gene	gene with protein product		601672				11845289, 8812431	Standard	NM_012074		Approved	cer-d4, Cerd4, FLJ14079, BAF45c	uc010ari.1	Q92784		ENST00000556509.1:c.865C>T	14.37:g.73140954G>A	ENSP00000450518:p.Arg289Cys	Somatic	48	0		WXS	Illumina HiSeq	.	58	5	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	G	35	5.425849	0.96131	.	.	ENSG00000205683	ENST00000556509;ENST00000398816;ENST00000541685;ENST00000546183	D;T;T	0.91894	-2.93;-1.09;-1.11	5.65	5.65	0.86999	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	D	0.97228	0.9094	M	0.93062	3.375	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.998	D	0.97432	1.0016	9	0.87932	D	0	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	299;289;289	F5H575;Q92784-2;Q92784	.;.;DPF3_HUMAN	C	289;288;289;299	ENSP00000450518:R289C;ENSP00000441640:R289C;ENSP00000444662:R299C	ENSP00000381791:R344C	R	-	1	0	DPF3	72210707	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.595000	0.98260	2.941000	0.99782	0.655000	0.94253	CGC	.		0.572	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2		
RASA1	5921	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	5	86672323	86672323	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:86672323C>T	ENST00000274376.6	+	16	2689	c.2125C>T	c.(2125-2127)Cga>Tga	p.R709*	RASA1_ENST00000456692.2_Nonsense_Mutation_p.R532*|RASA1_ENST00000512763.1_Nonsense_Mutation_p.R542*|RASA1_ENST00000506290.1_Nonsense_Mutation_p.R543*|CTC-428H11.2_ENST00000607486.1_RNA	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	709					blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)	p.R532*(1)|p.R709*(1)		NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CCTGCGTGTTCGAGCACGATA	0.398																																					p.R709X		.											RASA1_ENST00000456692,NS,carcinoma,0,2	RASA1_ENST00000456692	0	2	Substitution - Nonsense(2)	lung(2)	c.C2125T	GRCh37	CM083069	RASA1	M		.						97.0	93.0	94.0					5																	86672323		2203	4300	6503	SO:0001587	stop_gained	5921	exon16			CGTGTTCGAGCAC		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2125C>T	5.37:g.86672323C>T	ENSP00000274376:p.Arg709*	Somatic	114	0		WXS	Illumina HiSeq	.	123	25	NM_002890	B2R6W3|Q9UDI1	Nonsense_Mutation	SNP	ENST00000274376.6	37	CCDS34200.1	.	.	.	.	.	.	.	.	.	.	C	39	7.301230	0.98196	.	.	ENSG00000145715	ENST00000274376;ENST00000534133;ENST00000456692;ENST00000512763;ENST00000506290	.	.	.	5.54	3.51	0.40186	.	0.059655	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8021	0.78458	0.2591:0.7409:0.0:0.0	.	.	.	.	X	709;742;532;542;543	.	ENSP00000274376:R709X	R	+	1	2	RASA1	86708079	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.395000	0.44459	1.292000	0.44672	0.563000	0.77884	CGA	.		0.398	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
DOCK1	1793	hgsc.bcm.edu;bcgsc.ca	37	10	128817096	128817096	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:128817096C>T	ENST00000280333.6	+	13	1370	c.1261C>T	c.(1261-1263)Cct>Tct	p.P421S	RP11-223P11.3_ENST00000594559.1_RNA|RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.2_ENST00000420941.2_RNA|RP11-223P11.3_ENST00000599979.1_RNA|RP11-223P11.3_ENST00000601826.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	421					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		GATAATCATGCCTGGTAAGAA	0.527																																					p.P421S		.											.	.	.	0			c.C1261T						.						44.0	47.0	46.0					10																	128817096		1953	4146	6099	SO:0001583	missense	1793	exon13			ATCATGCCTGGTA	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.1261C>T	10.37:g.128817096C>T	ENSP00000280333:p.Pro421Ser	Somatic	40	0		WXS	Illumina HiSeq	.	67	4	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	C	25.4	4.637835	0.87760	.	.	ENSG00000150760	ENST00000280333	T	0.15256	2.44	4.32	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.50360	0.1611	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.99	T	0.63888	-0.6535	10	0.87932	D	0	.	17.0227	0.86438	0.0:1.0:0.0:0.0	.	421;421	B2RUU3;Q14185	.;DOCK1_HUMAN	S	421	ENSP00000280333:P421S	ENSP00000280333:P421S	P	+	1	0	DOCK1	128707086	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.578000	0.82498	2.226000	0.72624	0.557000	0.71058	CCT	.		0.527	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
ABCC9	10060	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	22089573	22089573	+	Silent	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:22089573T>C	ENST00000261201.4	-	1	35	c.36A>G	c.(34-36)tcA>tcG	p.S12S	ABCC9_ENST00000326684.4_Silent_p.S12S|ABCC9_ENST00000538350.1_Silent_p.S12S|ABCC9_ENST00000261200.4_Silent_p.S12S|ABCC9_ENST00000345162.2_Silent_p.S12S	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	12					defense response to virus (GO:0051607)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	ATP-sensitive potassium channel complex (GO:0008282)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcomere (GO:0030017)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium channel activity (GO:0005267)|potassium channel regulator activity (GO:0015459)|sulfonylurea receptor activity (GO:0008281)|transporter activity (GO:0005215)			NS(2)|breast(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|lung(56)|ovary(4)|pancreas(1)|prostate(4)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(5)	118					Adenosine triphosphate(DB00171)|Glyburide(DB01016)	TGATATTATATGAAGAAATGT	0.338																																					p.S12S		.											.	.	.	0			c.A36G						.						98.0	99.0	98.0					12																	22089573		2203	4300	6503	SO:0001819	synonymous_variant	10060	exon1			ATTATATGAAGAA	AF061323	CCDS8693.1, CCDS8694.1	12p12.1	2014-09-17			ENSG00000069431	ENSG00000069431		"""ATP binding cassette transporters / subfamily C"""	60	protein-coding gene	gene with protein product	"""sulfonylurea receptor 2"""	601439				9457174, 15034580	Standard	NM_020297		Approved	SUR2, CMD1O	uc001rfh.3	O60706	OTTHUMG00000169094	ENST00000261201.4:c.36A>G	12.37:g.22089573T>C		Somatic	58	0		WXS	Illumina HiSeq	.	74	7	NM_005691	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																			.		0.338	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691	
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	51921499	51921499	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:51921499G>A	ENST00000371117.3	-	18	1965	c.1690C>T	c.(1690-1692)Cga>Tga	p.R564*	PKHD1_ENST00000340994.4_Nonsense_Mutation_p.R564*	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	564					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					ACAGCACCTCGTTCAAATCCA	0.403																																					p.R564X		.											.	.	.	0			c.C1690T						.						128.0	132.0	131.0					6																	51921499		2203	4300	6503	SO:0001587	stop_gained	5314	exon18			CACCTCGTTCAAA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1690C>T	6.37:g.51921499G>A	ENSP00000360158:p.Arg564*	Somatic	55	0		WXS	Illumina HiSeq	.	82	13	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Nonsense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	37	6.253145	0.97417	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	.	.	.	5.4	2.53	0.30540	.	0.716247	0.13259	N	0.401389	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1374	0.48383	0.0:0.2543:0.6168:0.1289	.	.	.	.	X	564	.	ENSP00000341097:R564X	R	-	1	2	PKHD1	52029458	0.929000	0.31497	0.967000	0.41034	0.004000	0.04260	0.188000	0.17018	0.262000	0.21774	-1.943000	0.00494	CGA	.		0.403	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
SLC2A10	81031	hgsc.bcm.edu	37	20	45358084	45358084	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr20:45358084G>T	ENST00000359271.2	+	4	1754	c.1504G>T	c.(1504-1506)Ggc>Tgc	p.G502C		NM_030777.3	NP_110404.1	O95528	GTR10_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 10	502					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sugar:proton symporter activity (GO:0005351)			central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	34		Myeloproliferative disorder(115;0.0122)				TGAAACAAAAGGCCAGTCGTT	0.552																																					p.G502C		.											.	.	.	0			c.G1504T						.						67.0	65.0	66.0					20																	45358084		2203	4300	6503	SO:0001583	missense	81031	exon4			ACAAAAGGCCAGT	AL137188	CCDS13402.1	20q13.12	2013-05-22			ENSG00000197496	ENSG00000197496		"""Solute carriers"""	13444	protein-coding gene	gene with protein product		606145				11247674	Standard	NM_030777		Approved	GLUT10	uc002xsl.3	O95528	OTTHUMG00000032657	ENST00000359271.2:c.1504G>T	20.37:g.45358084G>T	ENSP00000352216:p.Gly502Cys	Somatic	41	0		WXS	Illumina HiSeq	.	75	4	NM_030777	A8K4J6|Q3MIX5|Q9H4I6	Missense_Mutation	SNP	ENST00000359271.2	37	CCDS13402.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.955302	0.92726	.	.	ENSG00000197496	ENST00000359271	T	0.80123	-1.34	5.72	5.72	0.89469	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95552	0.8621	10	0.87932	D	0	-22.4576	19.8917	0.96932	0.0:0.0:1.0:0.0	.	502	O95528	GTR10_HUMAN	C	502	ENSP00000352216:G502C	ENSP00000352216:G502C	G	+	1	0	SLC2A10	44791491	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.390000	0.79816	2.705000	0.92388	0.591000	0.81541	GGC	.		0.552	SLC2A10-001	KNOWN	mRNA_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079578.2		
TRUB1	142940	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	116734973	116734973	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:116734973G>A	ENST00000298746.3	+	8	946	c.885G>A	c.(883-885)tgG>tgA	p.W295*		NM_139169.4	NP_631908.1	Q8WWH5	TRUB1_HUMAN	TruB pseudouridine (psi) synthase family member 1	295					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(2)|kidney(2)|large_intestine(1)|lung(5)|urinary_tract(2)	12		Colorectal(252;0.09)|Breast(234;0.174)|Lung NSC(174;0.245)		Epithelial(162;0.00879)|all cancers(201;0.0243)		AAGACAAATGGACAATTGATG	0.433																																					p.W295X		.											TRUB1,NS,carcinoma,0,1	TRUB1	0	0			c.G885A						.						173.0	156.0	161.0					10																	116734973		2203	4300	6503	SO:0001587	stop_gained	142940	exon8			CAAATGGACAATT	AF448144	CCDS7591.1	10q25.3	2013-09-02	2013-09-02		ENSG00000165832	ENSG00000165832			16060	protein-coding gene	gene with protein product		610726	"""TruB pseudouridine (psi) synthase homolog 1 (E. coli)"""			12736709	Standard	NM_139169		Approved	PUS4	uc001lcd.3	Q8WWH5	OTTHUMG00000019094	ENST00000298746.3:c.885G>A	10.37:g.116734973G>A	ENSP00000298746:p.Trp295*	Somatic	54	0		WXS	Illumina HiSeq	.	60	8	NM_139169	B2R716|Q53ES2	Nonsense_Mutation	SNP	ENST00000298746.3	37	CCDS7591.1	.	.	.	.	.	.	.	.	.	.	G	35	5.528866	0.96446	.	.	ENSG00000165832	ENST00000298746	.	.	.	5.56	4.66	0.58398	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-9.347	13.0117	0.58735	0.0749:0.0:0.9251:0.0	.	.	.	.	X	295	.	ENSP00000298746:W295X	W	+	3	0	TRUB1	116724963	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.233000	0.89799	1.485000	0.48380	0.561000	0.74099	TGG	.		0.433	TRUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050504.1	NM_139169	
CENPU	79682	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	185638302	185638302	+	Silent	SNP	A	A	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:185638302A>T	ENST00000281453.5	-	5	439	c.369T>A	c.(367-369)atT>atA	p.I123I	MLF1IP_ENST00000541971.1_Silent_p.I123I	NM_024629.3	NP_078905.2														endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|stomach(1)	13		all_lung(41;7.57e-14)|Lung NSC(41;1.81e-13)|Hepatocellular(41;0.000519)|Colorectal(36;0.00172)|Renal(120;0.00988)|Prostate(90;0.0235)|all_neural(102;0.0299)|all_hematologic(60;0.0592)|Medulloblastoma(177;0.146)		all cancers(43;7.83e-28)|Epithelial(43;2.56e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.5e-11)|Colorectal(24;3.27e-06)|STAD - Stomach adenocarcinoma(60;2.66e-05)|GBM - Glioblastoma multiforme(59;3.16e-05)|BRCA - Breast invasive adenocarcinoma(30;0.000252)|COAD - Colon adenocarcinoma(29;0.000512)|LUSC - Lung squamous cell carcinoma(40;0.01)|READ - Rectum adenocarcinoma(43;0.0419)		TTTTTGCACTAATTTTTACAG	0.299																																					p.I123I		.											.	.	.	0			c.T369A						.						109.0	104.0	105.0					4																	185638302		2203	4299	6502	SO:0001819	synonymous_variant	79682	exon5			TGCACTAATTTTT																												ENST00000281453.5:c.369T>A	4.37:g.185638302A>T		Somatic	46	0		WXS	Illumina HiSeq	.	48	4	NM_024629		Silent	SNP	ENST00000281453.5	37	CCDS3838.1																																																																																			.		0.299	MLF1IP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360841.2		
CHID1	66005	hgsc.bcm.edu	37	11	884165	884165	+	Missense_Mutation	SNP	C	C	A	rs143837907		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:884165C>A	ENST00000449825.1	-	9	1062	c.706G>T	c.(706-708)Gac>Tac	p.D236Y	CHID1_ENST00000526714.1_Intron|CHID1_ENST00000429789.2_Missense_Mutation_p.D205Y|CHID1_ENST00000323578.8_Missense_Mutation_p.D236Y|CHID1_ENST00000323541.7_Missense_Mutation_p.D266Y|CHID1_ENST00000336845.5_Missense_Mutation_p.D261Y|CHID1_ENST00000528581.1_Missense_Mutation_p.D261Y|CHID1_ENST00000436108.2_Missense_Mutation_p.D236Y|CHID1_ENST00000454838.2_Missense_Mutation_p.D261Y	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1	236					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|innate immune response (GO:0045087)|negative regulation of cytokine production involved in inflammatory response (GO:1900016)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	chitinase activity (GO:0004568)|oligosaccharide binding (GO:0070492)			endometrium(4)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	13		all_cancers(49;9.46e-06)|Breast(177;0.00257)|all_epithelial(84;0.0027)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.48e-25)|Epithelial(43;3.75e-24)|BRCA - Breast invasive adenocarcinoma(625;4.65e-05)|Lung(200;0.0624)|LUSC - Lung squamous cell carcinoma(625;0.0735)		CCCAGCTGGTCGGTCCTGTAA	0.607																																					p.D261Y	Pancreas(117;992 2327 5172 41921)	.											CHID1,NS,carcinoma,0,1	CHID1	0	0			c.G781T						.						112.0	77.0	88.0					11																	884165		2203	4299	6502	SO:0001583	missense	66005	exon10			GCTGGTCGGTCCT	AK124697	CCDS7722.1, CCDS44510.1, CCDS44511.1	11p15.5	2005-10-27			ENSG00000177830	ENSG00000177830			28474	protein-coding gene	gene with protein product		615692					Standard	NM_023947		Approved	MGC3234, FLJ42707	uc001lsm.3	Q9BWS9	OTTHUMG00000133314	ENST00000449825.1:c.706G>T	11.37:g.884165C>A	ENSP00000391255:p.Asp236Tyr	Somatic	26	0		WXS	Illumina HiSeq	.	36	3	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Missense_Mutation	SNP	ENST00000449825.1	37	CCDS7722.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.511060	0.27036	.	.	ENSG00000177830	ENST00000323541;ENST00000449825;ENST00000454838;ENST00000323578;ENST00000429789;ENST00000528581;ENST00000336845;ENST00000436108;ENST00000531859	T;T;T;T;T;T;T;T;T	0.43294	3.35;3.35;3.35;3.35;0.95;3.35;3.35;3.35;1.55	5.32	2.3	0.28687	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.347524	0.32002	N	0.006740	T	0.47060	0.1425	L	0.46157	1.445	0.35514	D	0.800894	P;P;D;D;P	0.59767	0.818;0.818;0.985;0.986;0.577	B;B;P;P;B	0.58391	0.331;0.331;0.838;0.788;0.251	T	0.55535	-0.8126	10	0.72032	D	0.01	-17.3777	7.1449	0.25577	0.0:0.5363:0.3086:0.1551	.	297;266;205;261;236	B4DN31;B7Z705;Q9BWS9-3;Q9BWS9-2;Q9BWS9	.;.;.;.;CHID1_HUMAN	Y	266;236;261;236;205;261;261;236;140	ENSP00000324821:D266Y;ENSP00000391255:D236Y;ENSP00000398722:D261Y;ENSP00000325055:D236Y;ENSP00000416034:D205Y;ENSP00000435503:D261Y;ENSP00000338838:D261Y;ENSP00000388156:D236Y;ENSP00000434651:D140Y	ENSP00000324821:D266Y	D	-	1	0	CHID1	874165	0.039000	0.19947	0.474000	0.27266	0.320000	0.28249	0.248000	0.18198	0.199000	0.20427	-0.175000	0.13238	GAC	.		0.607	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947	
CXCR1	3577	hgsc.bcm.edu	37	2	219029811	219029811	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:219029811C>T	ENST00000295683.2	-	2	244	c.124G>A	c.(124-126)Gtg>Atg	p.V42M		NM_000634.2	NP_000625.1	P25024	CXCR1_HUMAN	chemokine (C-X-C motif) receptor 1	42					cell surface receptor signaling pathway (GO:0007166)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|receptor internalization (GO:0031623)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)			endometrium(1)|large_intestine(2)|lung(7)|prostate(3)	13					Ketoprofen(DB01009)	GCGATGATCACAACATACTTG	0.498																																					p.V42M		.											CXCR1,NS,carcinoma,0,1	CXCR1	0	0			c.G124A						.						212.0	196.0	202.0					2																	219029811		2203	4300	6503	SO:0001583	missense	3577	exon2			TGATCACAACATA	U11870	CCDS2409.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000163464	ENSG00000163464		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6026	protein-coding gene	gene with protein product		146929	"""interleukin 8 receptor, alpha"""	CMKAR1, IL8RA		1303245, 1427896	Standard	NM_000634		Approved	CKR-1, CDw128a, CD181	uc002vhc.3	P25024	OTTHUMG00000133108	ENST00000295683.2:c.124G>A	2.37:g.219029811C>T	ENSP00000295683:p.Val42Met	Somatic	24	0		WXS	Illumina HiSeq	.	29	2	NM_000634	B2R6Q3|Q2YEF8|Q2YEG4|Q2YEG5|Q2YEG7|Q2YEG8|Q53R18|Q6IN95|Q8N6T6|Q9P2T8|Q9P2T9|Q9P2U0|Q9P2U1|Q9P2U2	Missense_Mutation	SNP	ENST00000295683.2	37	CCDS2409.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.049664	0.55218	.	.	ENSG00000163464	ENST00000295683;ENST00000421691	T	0.38560	1.13	5.35	2.29	0.28610	.	0.364382	0.26951	N	0.021674	T	0.38108	0.1028	L	0.54323	1.7	0.09310	N	0.999999	B	0.32731	0.382	B	0.35607	0.206	T	0.34925	-0.9809	10	0.72032	D	0.01	.	9.4029	0.38444	0.151:0.5563:0.2927:0.0	.	42	P25024	CXCR1_HUMAN	M	42	ENSP00000295683:V42M	ENSP00000295683:V42M	V	-	1	0	CXCR1	218738056	0.002000	0.14202	0.005000	0.12908	0.007000	0.05969	-0.027000	0.12371	0.585000	0.29608	0.655000	0.94253	GTG	.		0.498	CXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256773.2	NM_000634	
PBK	55872	hgsc.bcm.edu	37	8	27690596	27690596	+	Missense_Mutation	SNP	T	T	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:27690596T>A	ENST00000301905.4	-	2	498	c.35A>T	c.(34-36)aAa>aTa	p.K12I	PBK_ENST00000522944.1_Missense_Mutation_p.K12I	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	12					mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.K12R(2)		endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TTCTGATAATTTGCTTGGTGT	0.308																																					p.K12I		.											PBK_ENST00000301905,colon,carcinoma,0,2	PBK_ENST00000301905	0	2	Substitution - Missense(2)	large_intestine(2)	c.A35T						.						138.0	125.0	129.0					8																	27690596		2203	4300	6503	SO:0001583	missense	55872	exon2			GATAATTTGCTTG	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.35A>T	8.37:g.27690596T>A	ENSP00000301905:p.Lys12Ile	Somatic	36	0		WXS	Illumina HiSeq	.	35	2	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	37	CCDS6063.1	.	.	.	.	.	.	.	.	.	.	T	19.49	3.837914	0.71373	.	.	ENSG00000168078	ENST00000301905;ENST00000522944	D;D	0.86164	-1.95;-2.08	5.4	4.24	0.50183	Protein kinase-like domain (1);	0.141665	0.64402	D	0.000007	D	0.82683	0.5090	M	0.68952	2.095	0.35602	D	0.807957	B;B	0.29481	0.245;0.055	B;B	0.20577	0.03;0.02	T	0.81929	-0.0708	10	0.42905	T	0.14	-16.2635	7.6962	0.28596	0.0:0.0995:0.0:0.9005	.	12;12	B4DX68;Q96KB5	.;TOPK_HUMAN	I	12	ENSP00000301905:K12I;ENSP00000428489:K12I	ENSP00000301905:K12I	K	-	2	0	PBK	27746515	1.000000	0.71417	0.999000	0.59377	0.940000	0.58332	1.551000	0.36233	0.982000	0.38575	0.533000	0.62120	AAA	.		0.308	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
TSPAN16	26526	hgsc.bcm.edu;bcgsc.ca	37	19	11408920	11408920	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:11408920G>T	ENST00000316737.1	+	2	322	c.172G>T	c.(172-174)Ggc>Tgc	p.G58C	CTC-510F12.4_ENST00000586356.1_RNA|TSPAN16_ENST00000592955.1_Missense_Mutation_p.G58C|TSPAN16_ENST00000590327.1_Missense_Mutation_p.G58C	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	58						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						CCTTCACGTTGGCAACCTGTG	0.567																																					p.G58C		.											.	.	.	0			c.G172T						.						161.0	126.0	138.0					19																	11408920		2203	4300	6503	SO:0001583	missense	26526	exon2			CACGTTGGCAACC	BC029908	CCDS12256.1, CCDS62549.1, CCDS62550.1	19p13.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000130167	ENSG00000130167		"""Tetraspanins"""	30725	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 16"""	TM4SF16		10500248	Standard	NM_012466		Approved	TM4-B, TM-8	uc002mqv.1	Q9UKR8	OTTHUMG00000180833	ENST00000316737.1:c.172G>T	19.37:g.11408920G>T	ENSP00000319486:p.Gly58Cys	Somatic	48	0		WXS	Illumina HiSeq	.	64	4	NM_012466	K7EN22|K7EPD8|Q8N6J7	Missense_Mutation	SNP	ENST00000316737.1	37	CCDS12256.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226818	0.39399	.	.	ENSG00000130167	ENST00000316737;ENST00000337994	T;T	0.80214	-1.35;-1.35	3.57	0.144	0.14824	.	0.215088	0.23793	N	0.044507	D	0.84848	0.5563	M	0.72118	2.19	0.09310	N	1	D	0.89917	1.0	D	0.75484	0.986	T	0.73729	-0.3891	10	0.62326	D	0.03	-9.3434	5.5212	0.16933	0.4022:0.0:0.5978:0.0	.	58	Q9UKR8	TSN16_HUMAN	C	58	ENSP00000319486:G58C;ENSP00000338759:G58C	ENSP00000319486:G58C	G	+	1	0	TSPAN16	11269920	0.002000	0.14202	0.001000	0.08648	0.003000	0.03518	0.206000	0.17375	0.113000	0.18004	0.462000	0.41574	GGC	.		0.567	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466	
ZNF610	162963	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	52852438	52852438	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:52852438G>A	ENST00000403906.3	+	3	469	c.13G>A	c.(13-15)Gaa>Aaa	p.E5K	ZNF610_ENST00000321287.8_Missense_Mutation_p.E5K|ZNF610_ENST00000327920.8_Missense_Mutation_p.E5K|ZNF610_ENST00000601151.1_Missense_Mutation_p.E5K	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	5					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		GCTATGTGATGAAGAAGCCCA	0.433																																					p.E5K		.											.	.	.	0			c.G13A						.						172.0	149.0	157.0					19																	52852438		2203	4300	6503	SO:0001583	missense	162963	exon3			TGTGATGAAGAAG	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.13G>A	19.37:g.52852438G>A	ENSP00000383922:p.Glu5Lys	Somatic	28	0		WXS	Illumina HiSeq	.	50	8	NM_001161427	A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	CCDS12851.1	.	.	.	.	.	.	.	.	.	.	G	9.952	1.220534	0.22457	.	.	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T;T	0.05649	3.41;3.41;3.41	1.24	1.24	0.21308	.	.	.	.	.	T	0.11623	0.0283	L	0.38531	1.155	0.09310	N	1	D;D	0.60575	0.988;0.98	P;P	0.62885	0.908;0.811	T	0.19224	-1.0312	9	0.59425	D	0.04	.	5.8612	0.18747	0.0:0.0:1.0:0.0	.	5;5	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	K	5	ENSP00000383922:E5K;ENSP00000324441:E5K;ENSP00000327597:E5K	ENSP00000324441:E5K	E	+	1	0	ZNF610	57544250	0.000000	0.05858	0.036000	0.18154	0.206000	0.24218	-0.702000	0.05069	1.010000	0.39314	0.561000	0.74099	GAA	.		0.433	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
MUC12	10071	hgsc.bcm.edu	37	7	100634194	100634194	+	Missense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:100634194C>G	ENST00000379442.3	+	5	779	c.779C>G	c.(778-780)gCc>gGc	p.A260G	MUC12_ENST00000536621.1_Missense_Mutation_p.A117G			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	260	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						ATCACTTCAGCCTCAATGGAA	0.512																																					p.A117G		.											MUC12,tonsil,carcinoma,0,1	MUC12	0	0			c.C350G						.						154.0	138.0	143.0					7																	100634194		692	1591	2283	SO:0001583	missense	10071	exon2			CTTCAGCCTCAAT	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.779C>G	7.37:g.100634194C>G	ENSP00000368755:p.Ala260Gly	Somatic	84	0		WXS	Illumina HiSeq	.	118	6	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Missense_Mutation	SNP	ENST00000379442.3	37		.	.	.	.	.	.	.	.	.	.	-	0.005	-2.145464	0.00332	.	.	ENSG00000205277	ENST00000379442;ENST00000536621	T;T	0.12984	2.63;2.63	0.499	-0.998	0.10212	.	.	.	.	.	T	0.05273	0.0140	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.42413	-0.9453	7	0.10636	T	0.68	.	7.7982	0.29160	0.0:0.472:0.528:0.0	.	.	.	.	G	260;117	ENSP00000368755:A260G;ENSP00000441929:A117G	ENSP00000368755:A260G	A	+	2	0	MUC12	100420914	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-4.508000	0.00223	-2.408000	0.00573	-2.879000	0.00098	GCC	.		0.512	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
CEL	1056	hgsc.bcm.edu	37	9	135947131	135947131	+	Missense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:135947131C>A	ENST00000372080.4	+	11	2267	c.2251C>A	c.(2251-2253)Cct>Act	p.P751T	CEL_ENST00000351304.7_Missense_Mutation_p.P682T	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	748					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		AGCTCAGATGCCTGCAGTCAT	0.632																																					p.P751T		.											CEL,caecum,carcinoma,0,1	CEL	0	0			c.C2251A						.						19.0	22.0	21.0					9																	135947131		1876	4088	5964	SO:0001583	missense	1056	exon11			CAGATGCCTGCAG	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.2251C>A	9.37:g.135947131C>A	ENSP00000361151:p.Pro751Thr	Somatic	51	0		WXS	Illumina HiSeq	.	48	2	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	c	15.40	2.821406	0.50633	.	.	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71103	-0.3;-0.54	2.8	1.85	0.25348	.	0.163089	0.29293	N	0.012580	T	0.52964	0.1767	N	0.24115	0.695	0.23401	N	0.997752	B	0.20550	0.046	B	0.15870	0.014	T	0.51702	-0.8672	10	0.87932	D	0	.	8.8881	0.35416	0.2247:0.7752:0.0:0.0	.	748	P19835	CEL_HUMAN	T	751;682;717	ENSP00000361151:P751T;ENSP00000342217:P682T	ENSP00000304021:P717T	P	+	1	0	CEL	134936952	0.986000	0.35501	0.864000	0.33941	0.077000	0.17291	1.039000	0.30266	0.711000	0.32018	0.460000	0.39030	CCT	.		0.632	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
AAK1	22848	hgsc.bcm.edu	37	2	69741753	69741753	+	Silent	SNP	C	C	T	rs66931661|rs3832159	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:69741753C>T	ENST00000409085.4	-	13	2002	c.1626G>A	c.(1624-1626)caG>caA	p.Q542Q	AAK1_ENST00000406297.3_Silent_p.Q542Q|RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q542Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	542	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gttgctgttgctgttgttgtt	0.552																																					p.Q542Q		.											.	.	.	0			c.G1626A						.						33.0	35.0	34.0					2																	69741753		2192	4296	6488	SO:0001819	synonymous_variant	22848	exon13			CTGTTGCTGTTGT	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1626G>A	2.37:g.69741753C>T		Somatic	40	0		WXS	Illumina HiSeq	.	41	4	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																			.		0.552	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
BTN3A1	11119	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	26411341	26411341	+	Silent	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:26411341A>G	ENST00000289361.6	+	8	1337	c.969A>G	c.(967-969)ggA>ggG	p.G323G	BTN3A1_ENST00000476549.2_Silent_p.G323G|BTN3A1_ENST00000425234.2_Silent_p.G323G|BTN3A1_ENST00000414912.2_Silent_p.G271G	NM_001145008.1|NM_001145009.1|NM_007048.5	NP_001138480.1|NP_001138481.1|NP_008979.3	O00481	BT3A1_HUMAN	butyrophilin, subfamily 3, member A1	323	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				activated T cell proliferation (GO:0050798)|cytokine secretion (GO:0050663)|interferon-gamma secretion (GO:0072643)|T cell receptor signaling pathway (GO:0050852)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28						TTGTAGGGGGAGAGAGACATT	0.408																																					p.G323G		.											.	.	.	0			c.A969G						.						170.0	169.0	169.0					6																	26411341		2203	4300	6503	SO:0001819	synonymous_variant	11119	exon8			AGGGGGAGAGAGA	U90552	CCDS4608.1, CCDS4609.1, CCDS47388.1, CCDS47389.1	6p22.1	2014-01-14			ENSG00000026950	ENSG00000026950		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1138	protein-coding gene	gene with protein product		613593				9149941	Standard	NM_007048		Approved	BT3.1, BTF5, CD277, BTN3.1	uc003nhv.3	O00481	OTTHUMG00000014449	ENST00000289361.6:c.969A>G	6.37:g.26411341A>G		Somatic	52	0		WXS	Illumina HiSeq	.	74	4	NM_007048	A2A278|A8K2C8|B4DIQ1|B4DRM2|E9PGB4|E9PHG8|Q0P515|Q147X5|Q53F15|Q99420|Q9HCY1	Silent	SNP	ENST00000289361.6	37	CCDS4608.1																																																																																			.		0.408	BTN3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040112.3		
AKAP1	8165	hgsc.bcm.edu	37	17	55195744	55195744	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:55195744G>A	ENST00000337714.3	+	9	2736	c.2503G>A	c.(2503-2505)Gat>Aat	p.D835N	AKAP1_ENST00000571629.1_Missense_Mutation_p.D835N|AKAP1_ENST00000572557.1_Missense_Mutation_p.D835N|AKAP1_ENST00000539273.1_Missense_Mutation_p.D835N	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	835					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					TCCTGAAGACGATGACCAGTT	0.532																																					p.D835N		.											AKAP1,middle_lobe,carcinoma,0,2	AKAP1	0	0			c.G2503A						.						112.0	97.0	102.0					17																	55195744		2203	4300	6503	SO:0001583	missense	8165	exon10			GAAGACGATGACC	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.2503G>A	17.37:g.55195744G>A	ENSP00000337736:p.Asp835Asn	Somatic	26	0		WXS	Illumina HiSeq	.	46	2	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.782703	0.70222	.	.	ENSG00000121057	ENST00000337714;ENST00000427138;ENST00000539273	T;T	0.15372	2.43;2.43	5.08	5.08	0.68730	.	0.098627	0.64402	D	0.000002	T	0.24812	0.0602	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	P	0.55923	0.787	T	0.00995	-1.1487	10	0.51188	T	0.08	.	17.6397	0.88132	0.0:0.0:1.0:0.0	.	835	Q92667	AKAP1_HUMAN	N	835;877;835	ENSP00000337736:D835N;ENSP00000443139:D835N	ENSP00000337736:D835N	D	+	1	0	AKAP1	52550743	1.000000	0.71417	0.999000	0.59377	0.410000	0.31052	7.846000	0.86887	2.643000	0.89663	0.650000	0.86243	GAT	.		0.532	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
CSF1R	1436	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	149450020	149450020	+	Splice_Site	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:149450020T>C	ENST00000286301.3	-	8	1488	c.1197A>G	c.(1195-1197)cgA>cgG	p.R399R		NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	399	Ig-like C2-type 4.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	AGCACTCACATCGAAGGGTGA	0.657																																					p.R399R		.											.	.	.	0			c.A1197G						.						22.0	24.0	24.0					5																	149450020		2197	4292	6489	SO:0001630	splice_region_variant	1436	exon8			CTCACATCGAAGG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.1198+1A>G	5.37:g.149450020T>C		Somatic	30	0		WXS	Illumina HiSeq	.	38	5	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			.		0.657	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	Silent
PIP4K2C	79837	hgsc.bcm.edu	37	12	57994636	57994636	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:57994636G>T	ENST00000354947.5	+	8	872	c.856G>T	c.(856-858)Ggc>Tgc	p.G286C	PIP4K2C_ENST00000550465.1_Missense_Mutation_p.G268C|PIP4K2C_ENST00000422156.3_Missense_Mutation_p.G238C|PIP4K2C_ENST00000540759.2_Missense_Mutation_p.G286C			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	286	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					CCTTCTGCTAGGCATCCACGA	0.557																																					p.G286C		.											.,1	.	50	0			c.G856T						.						218.0	216.0	217.0					12																	57994636		2203	4300	6503	SO:0001583	missense	79837	exon8			CTGCTAGGCATCC	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"""phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"""	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.856G>T	12.37:g.57994636G>T	ENSP00000347032:p.Gly286Cys	Somatic	23	0		WXS	Illumina HiSeq	.	43	2	NM_001146258	B2RDL3|B4DM11|B4DY44|Q9H6N2	Missense_Mutation	SNP	ENST00000354947.5	37	CCDS8946.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.5|22.5	4.293651|4.293651	0.80914|0.80914	.|.	.|.	ENSG00000166908|ENSG00000166908	ENST00000422156;ENST00000540759;ENST00000550465;ENST00000354947|ENST00000548264	T;T;T;T|.	0.69926|.	-0.44;-0.44;-0.44;-0.44|.	4.47|4.47	4.47|4.47	0.54385|0.54385	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.87350|.	0.6155|.	H|H	0.96080|0.96080	3.765|3.765	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.999;1.0|.	D;D;D|.	0.91635|.	0.999;0.997;0.999|.	D|.	0.91490|.	0.5211|.	10|.	0.87932|.	D|.	0|.	-13.5224|-13.5224	16.433|16.433	0.83860|0.83860	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	238;268;286|.	B4DM11;B4DY44;Q8TBX8|.	.;.;PI42C_HUMAN|.	C|Y	238;286;268;286|93	ENSP00000412035:G238C;ENSP00000439878:G286C;ENSP00000447390:G268C;ENSP00000347032:G286C|.	ENSP00000347032:G286C|.	G|X	+|+	1|3	0|2	PIP4K2C|PIP4K2C	56280903|56280903	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.089000|9.089000	0.94137|0.94137	2.480000|2.480000	0.83734|0.83734	0.555000|0.555000	0.69702|0.69702	GGC|TAG	.		0.557	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779	
SRSF6	6431	hgsc.bcm.edu	37	20	42088724	42088724	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr20:42088724C>T	ENST00000244020.3	+	4	539	c.433C>T	c.(433-435)Cga>Tga	p.R145*		NM_006275.5	NP_006266.2	Q13247	SRSF6_HUMAN	serine/arginine-rich splicing factor 6	145	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.		R -> Q (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell death (GO:0060548)|negative regulation of keratinocyte differentiation (GO:0045617)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of keratinocyte proliferation (GO:0010837)|regulation of wound healing (GO:0061041)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|upper_aerodigestive_tract(2)	5						CCACAAGGAACGAACAAATGA	0.418																																					p.R145X		.											SRSF6_ENST00000244020,caecum,carcinoma,0,3	SRSF6_ENST00000244020	0	0			c.C433T						.						138.0	137.0	137.0					20																	42088724		2203	4300	6503	SO:0001587	stop_gained	6431	exon4			AAGGAACGAACAA	U30883	CCDS13318.1	20q12-q13.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000124193	ENSG00000124193		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10788	protein-coding gene	gene with protein product	"""pre-mRNA splicing factor SRP55"", ""SR splicing factor 6"""	601944	"""splicing factor, arginine/serine-rich 6"""	SFRS6		7556075, 20516191	Standard	NM_006275		Approved	SRP55, B52	uc010zwg.2	Q13247	OTTHUMG00000032502	ENST00000244020.3:c.433C>T	20.37:g.42088724C>T	ENSP00000244020:p.Arg145*	Somatic	43	0		WXS	Illumina HiSeq	.	38	2	NM_006275	B7Z6J3|E1P5W6|Q13244|Q13245|Q96J06|Q9UJB8|Q9Y3N7	Nonsense_Mutation	SNP	ENST00000244020.3	37	CCDS13318.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.017233	0.75161	.	.	ENSG00000124193	ENST00000244020	.	.	.	6.08	6.08	0.98989	.	0.044791	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.4436	0.94836	0.0:1.0:0.0:0.0	.	.	.	.	X	145	.	ENSP00000244020:R145X	R	+	1	2	SRSF6	41522138	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	6.005000	0.70716	2.894000	0.99253	0.591000	0.81541	CGA	.		0.418	SRSF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079292.1	NM_006275	
ASCC1	51008	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	10	73956736	73956736	+	Nonsense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:73956736G>A	ENST00000342444.4	-	6	507	c.406C>T	c.(406-408)Cag>Tag	p.Q136*	ASCC1_ENST00000394915.3_Nonsense_Mutation_p.Q136*|ASCC1_ENST00000394919.1_Nonsense_Mutation_p.Q108*|ASCC1_ENST00000317168.6_Nonsense_Mutation_p.Q108*|ASCC1_ENST00000317126.4_Nonsense_Mutation_p.Q108*|ASCC1_ENST00000545550.1_Nonsense_Mutation_p.Q130*	NM_001198799.2	NP_001185728.1	Q8N9N2	ASCC1_HUMAN	activating signal cointegrator 1 complex subunit 1	136	KH. {ECO:0000255|PROSITE- ProRule:PRU00117}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|transcription factor complex (GO:0005667)	catalytic activity (GO:0003824)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	7						TTTCGATGCTGGCCAGTGATT	0.443																																					p.Q136X		.											.	.	.	0			c.C406T						.						73.0	69.0	71.0					10																	73956736		2202	4299	6501	SO:0001587	stop_gained	51008	exon6			GATGCTGGCCAGT	AY013290	CCDS31219.1, CCDS55713.1	10q22.1	2012-09-20			ENSG00000138303	ENSG00000138303			24268	protein-coding gene	gene with protein product		614215				10810093, 12077347	Standard	NM_001198799		Approved	CGI-18, ASC1p50, Em:AC022392.3	uc001jst.2	Q8N9N2	OTTHUMG00000018434	ENST00000342444.4:c.406C>T	10.37:g.73956736G>A	ENSP00000339404:p.Gln136*	Somatic	75	0		WXS	Illumina HiSeq	.	108	11	NM_001198799	Q5SW06|Q5SW07|Q96EI8|Q9Y307	Nonsense_Mutation	SNP	ENST00000342444.4	37	CCDS55713.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.179589|6.179589	0.97352|0.97352	.|.	.|.	ENSG00000138303|ENSG00000138303	ENST00000486689|ENST00000394919;ENST00000342444;ENST00000317168;ENST00000373101;ENST00000503308;ENST00000317126;ENST00000545550;ENST00000394915;ENST00000530431;ENST00000531048;ENST00000530461;ENST00000527593;ENST00000524829	.|.	.|.	.|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	.|0.313548	.|0.36815	.|N	.|0.002391	T|.	0.49915|.	0.1585|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36383|.	-0.9750|.	3|.	.|0.05620	.|T	.|0.96	.|.	20.0666|20.0666	0.97706|0.97706	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	39|108;136;108;108;23;108;130;136;23;42;69;108;108	.|.	.|ENSP00000320461:Q108X	P|Q	-|-	2|1	0|0	ASCC1|ASCC1	73626742|73626742	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	4.674000|4.674000	0.61612|0.61612	2.826000|2.826000	0.97356|0.97356	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.		0.443	ASCC1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048573.2	NM_015947	
SUPT6H	6830	hgsc.bcm.edu	37	17	27008381	27008381	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:27008381G>A	ENST00000314616.6	+	12	1740	c.1457G>A	c.(1456-1458)cGc>cAc	p.R486H	SUPT6H_ENST00000347486.4_Missense_Mutation_p.R486H	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	486	Interaction with KDM6A. {ECO:0000250}.|Interaction with PAAF1.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R486L(1)		NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					AAAGCTAGCCGCAAGAAGCTG	0.468																																					p.R486H		.											SUPT6H,NS,carcinoma,0,1	SUPT6H	0	1	Substitution - Missense(1)	endometrium(1)	c.G1457A						.						83.0	78.0	79.0					17																	27008381		2203	4300	6503	SO:0001583	missense	6830	exon12			CTAGCCGCAAGAA	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.1457G>A	17.37:g.27008381G>A	ENSP00000319104:p.Arg486His	Somatic	35	0		WXS	Illumina HiSeq	.	46	2	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363395	0.82353	.	.	ENSG00000109111	ENST00000314616;ENST00000347486	.	.	.	5.75	5.75	0.90469	.	0.059124	0.64402	D	0.000002	T	0.28632	0.0709	N	0.08118	0	0.53688	D	0.999979	D	0.58268	0.982	B	0.41036	0.346	T	0.12967	-1.0527	9	0.45353	T	0.12	-12.5539	13.1811	0.59655	0.0728:0.0:0.9272:0.0	.	486	Q7KZ85	SPT6H_HUMAN	H	486	.	ENSP00000319104:R486H	R	+	2	0	SUPT6H	24032508	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.656000	0.74396	2.720000	0.93068	0.655000	0.94253	CGC	.		0.468	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
XIRP2	129446	hgsc.bcm.edu	37	2	168104887	168104887	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:168104887C>T	ENST00000409195.1	+	9	7074	c.6985C>T	c.(6985-6987)Ctg>Ttg	p.L2329L	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Silent_p.L2329L|XIRP2_ENST00000409273.1_Silent_p.L2107L|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2154					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TCTTCCCTCACTGTCCACAGA	0.428																																					p.L2329L		.											.	.	.	0			c.C6985T						.						140.0	138.0	139.0					2																	168104887		1884	4108	5992	SO:0001819	synonymous_variant	129446	exon9			CCCTCACTGTCCA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.6985C>T	2.37:g.168104887C>T		Somatic	51	0		WXS	Illumina HiSeq	.	93	4	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			.		0.428	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
FLNB	2317	hgsc.bcm.edu;bcgsc.ca	37	3	58095323	58095323	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr3:58095323C>T	ENST00000295956.4	+	15	2385	c.2220C>T	c.(2218-2220)agC>agT	p.S740S	FLNB_ENST00000348383.5_Silent_p.S740S|FLNB_ENST00000419752.2_Silent_p.S571S|FLNB_ENST00000429972.2_Silent_p.S740S|FLNB_ENST00000358537.3_Silent_p.S740S|FLNB_ENST00000357272.4_Silent_p.S740S|FLNB_ENST00000490882.1_Silent_p.S740S|FLNB_ENST00000493452.1_Silent_p.S571S	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	740					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGCAAGGTAGCCATCCTCAGA	0.468																																					p.S740S		.											.	.	.	0			c.C2220T						.						123.0	121.0	122.0					3																	58095323		2203	4300	6503	SO:0001819	synonymous_variant	2317	exon15			AGGTAGCCATCCT	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.2220C>T	3.37:g.58095323C>T		Somatic	80	0		WXS	Illumina HiSeq	.	78	5	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			.		0.468	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
TTF1	7270	hgsc.bcm.edu	37	9	135277219	135277219	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:135277219G>T	ENST00000334270.2	-	2	1029	c.990C>A	c.(988-990)aaC>aaA	p.N330K		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	330	Poly-Lys.				chromatin remodeling (GO:0006338)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|negative regulation of DNA replication (GO:0008156)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(3)|kidney(1)|large_intestine(5)|lung(13)|ovary(2)|pancreas(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;4.25e-06)|Epithelial(140;9.09e-05)		TCTTAGACTTGTTTTTATAAG	0.507																																					p.N330K		.											TTF1,NS,lymphoid_neoplasm,0,1	TTF1	0	0			c.C990A						.						89.0	93.0	92.0					9																	135277219		2203	4300	6503	SO:0001583	missense	7270	exon2			AGACTTGTTTTTA	BC050734	CCDS6948.1, CCDS75925.1	9q34.3	2008-02-05			ENSG00000125482	ENSG00000125482			12397	protein-coding gene	gene with protein product		600777				7597036	Standard	NM_007344		Approved		uc004cbl.3	Q15361	OTTHUMG00000020836	ENST00000334270.2:c.990C>A	9.37:g.135277219G>T	ENSP00000333920:p.Asn330Lys	Somatic	22	1		WXS	Illumina HiSeq	.	40	10	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	G	0.016	-1.530365	0.00951	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.09255	3.0	2.75	-2.9	0.05648	.	.	.	.	.	T	0.04407	0.0121	N	0.25647	0.755	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.44605	-0.9317	9	0.05436	T	0.98	.	1.1405	0.01764	0.1334:0.1855:0.3099:0.3712	.	330	Q15361	TTF1_HUMAN	K	330	ENSP00000333920:N330K	ENSP00000245588:N330K	N	-	3	2	TTF1	134267040	0.003000	0.15002	0.023000	0.16930	0.228000	0.25075	-1.803000	0.01740	-0.683000	0.05190	0.467000	0.42956	AAC	.		0.507	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344	
SNX29	92017	hgsc.bcm.edu	37	16	12093200	12093200	+	Silent	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:12093200G>T	ENST00000566228.1	+	2	123	c.54G>T	c.(52-54)ctG>ctT	p.L18L		NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	18						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						AGCGACTGCTGGATGCAGTGA	0.418																																					p.L18L		.											.	.	.	0			c.G54T						.						93.0	84.0	87.0					16																	12093200		2197	4300	6497	SO:0001819	synonymous_variant	92017	exon2			ACTGCTGGATGCA	AK074072	CCDS10553.2	16p13.13-p13.12	2011-08-16			ENSG00000048471	ENSG00000048471		"""Sorting nexins"""	30542	protein-coding gene	gene with protein product			"""RUN domain containing 2A"""	RUNDC2A		16782399	Standard	XM_005255682		Approved	FLJ12363	uc002dby.5	Q8TEQ0		ENST00000566228.1:c.54G>T	16.37:g.12093200G>T		Somatic	46	0		WXS	Illumina HiSeq	.	63	3	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Silent	SNP	ENST00000566228.1	37	CCDS10553.2																																																																																			.		0.418	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1		
SCN7A	6332	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	167269613	167269613	+	Missense_Mutation	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:167269613T>C	ENST00000409855.1	-	21	3559	c.3433A>G	c.(3433-3435)Atc>Gtc	p.I1145V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	1145					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	ATAATAGTGATCCATCCATTA	0.299																																					p.I1145V		.											.	.	.	0			c.A3433G						.						42.0	39.0	40.0					2																	167269613		1811	4059	5870	SO:0001583	missense	6332	exon21			TAGTGATCCATCC	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.3433A>G	2.37:g.167269613T>C	ENSP00000386796:p.Ile1145Val	Somatic	84	0		WXS	Illumina HiSeq	.	94	11	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	10.39	1.336864	0.24253	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.97328	-4.34	5.22	2.63	0.31362	Ion transport (1);	0.141043	0.42294	D	0.000722	D	0.91838	0.7417	N	0.16567	0.415	0.32640	N	0.520829	B	0.34103	0.437	B	0.36885	0.235	D	0.91494	0.5214	10	0.87932	D	0	.	6.2746	0.20973	0.1511:0.0:0.1877:0.6612	.	1145	Q01118	SCN7A_HUMAN	V	1145	ENSP00000386796:I1145V	ENSP00000259060:I1145V	I	-	1	0	SCN7A	166977859	1.000000	0.71417	0.980000	0.43619	0.357000	0.29423	1.696000	0.37773	0.935000	0.37341	0.533000	0.62120	ATC	.		0.299	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
DST	667	hgsc.bcm.edu	37	6	56464980	56464980	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:56464980G>T	ENST00000361203.3	-	41	10955	c.10948C>A	c.(10948-10950)Caa>Aaa	p.Q3650K	DST_ENST00000312431.6_Missense_Mutation_p.Q3650K|DST_ENST00000421834.2_Missense_Mutation_p.Q1564K|DST_ENST00000370769.4_Missense_Mutation_p.Q3652K|DST_ENST00000446842.2_Missense_Mutation_p.Q3326K|DST_ENST00000370754.5_Missense_Mutation_p.Q3830K|DST_ENST00000370788.2_Missense_Mutation_p.Q1564K|DST_ENST00000244364.6_Missense_Mutation_p.Q1238K			Q03001	DYST_HUMAN	dystonin	3650					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CATATCCCTTGGAGTTTCTCT	0.393																																					p.Q1238K		.											.	.	.	0			c.C3712A						.						167.0	157.0	160.0					6																	56464980		1849	4085	5934	SO:0001583	missense	667	exon26			TCCCTTGGAGTTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.10948C>A	6.37:g.56464980G>T	ENSP00000354508:p.Gln3650Lys	Somatic	73	0		WXS	Illumina HiSeq	.	107	5	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	G	17.84	3.487379	0.63962	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	6.05	6.05	0.98169	.	0.000000	0.49916	D	0.000121	T	0.58722	0.2142	M	0.65975	2.015	0.25309	N	0.989213	D;P;P;P;P	0.54964	0.969;0.885;0.943;0.702;0.486	D;P;P;B;B	0.64877	0.93;0.622;0.772;0.217;0.205	T	0.43925	-0.9361	9	0.19590	T	0.45	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	1564;3652;3830;3650;1238	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	K	1238;3830;3652;1564;3326;3650;1564;3650	ENSP00000244364:Q1238K;ENSP00000359790:Q3830K;ENSP00000359805:Q3652K;ENSP00000400883:Q1564K;ENSP00000393645:Q3326K;ENSP00000307959:Q3650K;ENSP00000359824:Q1564K;ENSP00000354508:Q3650K	ENSP00000244364:Q1238K	Q	-	1	0	DST	56572939	1.000000	0.71417	0.937000	0.37676	0.916000	0.54674	5.650000	0.67944	2.878000	0.98634	0.650000	0.86243	CAA	.		0.393	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PKD1L1	168507	hgsc.bcm.edu	37	7	47876572	47876572	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:47876572G>T	ENST00000289672.2	-	37	5940	c.5890C>A	c.(5890-5892)Ctg>Atg	p.L1964M		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1964					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TAGACGCACAGCAGGGAGAAG	0.597																																					p.L1964M		.											PKD1L1,NS,carcinoma,0,1	PKD1L1	0	0			c.C5890A						.						63.0	56.0	58.0					7																	47876572		2203	4300	6503	SO:0001583	missense	168507	exon37			CGCACAGCAGGGA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.5890C>A	7.37:g.47876572G>T	ENSP00000289672:p.Leu1964Met	Somatic	36	0		WXS	Illumina HiSeq	.	45	2	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803967	0.31869	.	.	ENSG00000158683	ENST00000289672	T	0.37411	1.2	5.1	1.9	0.25705	.	0.284658	0.23758	N	0.044856	T	0.50463	0.1617	L	0.56769	1.78	0.21105	N	0.999786	D	0.89917	1.0	D	0.73380	0.98	T	0.27157	-1.0082	10	0.59425	D	0.04	-14.0775	9.7551	0.40498	0.0:0.3452:0.5238:0.131	.	1964	Q8TDX9	PK1L1_HUMAN	M	1964	ENSP00000289672:L1964M	ENSP00000289672:L1964M	L	-	1	2	PKD1L1	47843097	1.000000	0.71417	0.732000	0.30844	0.160000	0.22226	1.028000	0.30128	1.122000	0.41944	0.655000	0.94253	CTG	.		0.597	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
N4BP2	55728	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	40122733	40122733	+	Missense_Mutation	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:40122733A>G	ENST00000261435.6	+	9	3418	c.3002A>G	c.(3001-3003)cAa>cGa	p.Q1001R		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	1001					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)			breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TGTCAAGAGCAAATGCCTAAG	0.413																																					p.Q1001R		.											.	.	.	0			c.A3002G						.						66.0	64.0	65.0					4																	40122733		2203	4300	6503	SO:0001583	missense	55728	exon9			AAGAGCAAATGCC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.3002A>G	4.37:g.40122733A>G	ENSP00000261435:p.Gln1001Arg	Somatic	55	0		WXS	Illumina HiSeq	.	52	11	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	.	.	.	.	.	.	.	.	.	.	A	0.766	-0.767688	0.02974	.	.	ENSG00000078177	ENST00000261435;ENST00000381804	T	0.17370	2.28	6.02	-5.0	0.03001	.	1.364070	0.04241	N	0.336989	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B;B	0.19817	0.039;0.023	B;B	0.18871	0.023;0.01	T	0.29792	-1.0000	10	0.21540	T	0.41	0.2271	4.1072	0.10041	0.4946:0.2774:0.1345:0.0934	.	1001;1001	Q86UW6-2;Q86UW6	.;N4BP2_HUMAN	R	1001;921	ENSP00000261435:Q1001R	ENSP00000261435:Q1001R	Q	+	2	0	N4BP2	39799128	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.212000	0.09319	-1.021000	0.03350	-0.177000	0.13119	CAA	.		0.413	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144879561	144879561	+	Missense_Mutation	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:144879561A>G	ENST00000369354.3	-	27	4078	c.3889T>C	c.(3889-3891)Tgt>Cgt	p.C1297R	PDE4DIP_ENST00000313382.9_Missense_Mutation_p.C1253R|AL138796.1_ENST00000582173.1_RNA|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.C1297R|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.C1433R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.C1433R|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1297					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.C1297R(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGCTCCTCACACTCTGAAAAA	0.502			T	PDGFRB	MPD																																p.C1297R		.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369356,NS,carcinoma,0,7	PDE4DIP_ENST00000369356	0	2	Substitution - Missense(2)	lung(2)	c.T3889C						.						46.0	49.0	48.0					1																	144879561		2203	4290	6493	SO:0001583	missense	9659	exon27			CCTCACACTCTGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3889T>C	1.37:g.144879561A>G	ENSP00000358360:p.Cys1297Arg	Somatic	60	2		WXS	Illumina HiSeq	.	92	6	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	A	16.19	3.052829	0.55218	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01665	4.7;4.79;4.79;4.8;4.8	5.79	5.79	0.91817	.	.	.	.	.	T	0.04048	0.0113	L	0.57536	1.79	0.80722	D	1	D;D	0.71674	0.998;0.96	D;B	0.67548	0.952;0.421	T	0.51568	-0.8689	9	0.44086	T	0.13	.	14.0875	0.64968	1.0:0.0:0.0:0.0	.	1253;1297	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	R	1253;1297;1297;1433;1433	ENSP00000327209:C1253R;ENSP00000358360:C1297R;ENSP00000358363:C1297R;ENSP00000435654:C1433R;ENSP00000358366:C1433R	ENSP00000327209:C1253R	C	-	1	0	PDE4DIP	143590918	1.000000	0.71417	1.000000	0.80357	0.718000	0.41266	5.716000	0.68437	2.207000	0.71202	0.533000	0.62120	TGT	.		0.502	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
FBN2	2201	hgsc.bcm.edu	37	5	127714472	127714472	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:127714472G>T	ENST00000508053.1	-	18	2689	c.1715C>A	c.(1714-1716)gCa>gAa	p.A572E	FBN2_ENST00000511489.1_5'Flank|FBN2_ENST00000262464.4_Missense_Mutation_p.A572E|FBN2_ENST00000508989.1_Missense_Mutation_p.A539E			P35556	FBN2_HUMAN	fibrillin 2	572	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.A572V(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACCAATGCATGCTTGCTTGGT	0.378																																					p.A572E		.											FBN2_ENST00000508053,NS,carcinoma,0,1	FBN2_ENST00000508053	0	2	Substitution - Missense(2)	kidney(2)	c.C1715A						.						97.0	91.0	93.0					5																	127714472		2203	4300	6503	SO:0001583	missense	2201	exon12			ATGCATGCTTGCT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1715C>A	5.37:g.127714472G>T	ENSP00000424571:p.Ala572Glu	Somatic	51	0		WXS	Illumina HiSeq	.	44	2	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	G	9.474	1.096495	0.20552	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.91843	-2.92;-2.92;-2.92	4.26	4.26	0.50523	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.080793	0.49916	D	0.000135	D	0.88258	0.6388	N	0.02842	-0.48	0.51482	D	0.999929	B;D	0.69078	0.17;0.997	B;D	0.75484	0.268;0.986	T	0.83271	-0.0043	10	0.05721	T	0.95	.	17.9883	0.89161	0.0:0.0:1.0:0.0	.	539;572	D6RJI3;P35556	.;FBN2_HUMAN	E	572;572;539	ENSP00000262464:A572E;ENSP00000424571:A572E;ENSP00000425596:A539E	ENSP00000262464:A572E	A	-	2	0	FBN2	127742371	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	4.185000	0.58330	2.654000	0.90174	0.655000	0.94253	GCA	.		0.378	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
CFAP61	26074	hgsc.bcm.edu	37	20	20056250	20056250	+	Missense_Mutation	SNP	G	G	T	rs200143211		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr20:20056250G>T	ENST00000245957.5	+	6	633	c.557G>T	c.(556-558)cGc>cTc	p.R186L	C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_Missense_Mutation_p.R186L|C20orf26_ENST00000451767.2_Missense_Mutation_p.R186L	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		186								p.R186H(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		CTGCACGTTCGCAAAGCCAGG	0.478																																					p.R186L		.											C20orf26,caecum,carcinoma,0,1	C20orf26	0	1	Substitution - Missense(1)	large_intestine(1)	c.G557T						.						139.0	129.0	132.0					20																	20056250		2203	4300	6503	SO:0001583	missense	26074	exon6			ACGTTCGCAAAGC																												ENST00000245957.5:c.557G>T	20.37:g.20056250G>T	ENSP00000245957:p.Arg186Leu	Somatic	44	0		WXS	Illumina HiSeq	.	46	2	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430002	0.62844	.	.	ENSG00000089101	ENST00000340348;ENST00000343997;ENST00000389655;ENST00000245957;ENST00000377306;ENST00000377303;ENST00000451767;ENST00000472660	T;T;T;T;T;T	0.60299	1.1;0.2;1.1;1.1;1.1;0.2	5.9	5.9	0.94986	Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.76786	0.4036	M	0.77313	2.365	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.997;0.999;0.997	T	0.78484	-0.2186	10	0.72032	D	0.01	.	15.7627	0.78101	0.0:0.0:1.0:0.0	.	186;186;140;186	Q8NHU2-3;F8W6K4;F8W6E2;Q8NHU2	.;.;.;CT026_HUMAN	L	140;186;186;186;186;186;186;82	ENSP00000345553:R140L;ENSP00000245957:R186L;ENSP00000366521:R186L;ENSP00000366518:R186L;ENSP00000414537:R186L;ENSP00000420498:R82L	ENSP00000245957:R186L	R	+	2	0	C20orf26	20004250	1.000000	0.71417	0.435000	0.26784	0.167000	0.22549	5.627000	0.67784	2.802000	0.96397	0.650000	0.86243	CGC	.		0.478	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
PCDH20	64881	hgsc.bcm.edu	37	13	61986532	61986532	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr13:61986532C>T	ENST00000409186.1	-	5	3805	c.1700G>A	c.(1699-1701)aGa>aAa	p.R567K	PCDH20_ENST00000409204.4_Missense_Mutation_p.R567K			Q8N6Y1	PCD20_HUMAN	protocadherin 20	567	Cadherin 4. {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)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		AACTTGGCCTCTCTCCTCGCT	0.433																																					p.R567K		.											PCDH20_ENST00000409186,NS,carcinoma,0,2	PCDH20_ENST00000409186	0	0			c.G1700A						.						114.0	117.0	116.0					13																	61986532		2203	4300	6503	SO:0001583	missense	64881	exon2			TGGCCTCTCTCCT	AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.1700G>A	13.37:g.61986532C>T	ENSP00000386653:p.Arg567Lys	Somatic	27	0		WXS	Illumina HiSeq	.	40	2	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	C	14.01	2.408609	0.42715	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.51071	0.72;0.72	6.0	5.14	0.70334	.	0.087629	0.50627	D	0.000112	T	0.47728	0.1461	L	0.50333	1.59	0.47374	D	0.999407	B	0.21147	0.052	B	0.27076	0.076	T	0.46569	-0.9182	10	0.87932	D	0	.	16.2103	0.82150	0.1378:0.8622:0.0:0.0	.	567	A8K1K9	.	K	567;567;313	ENSP00000387250:R567K;ENSP00000386653:R567K	ENSP00000351500:R313K	R	-	2	0	PCDH20	60884533	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	2.574000	0.46016	1.481000	0.48307	0.650000	0.86243	AGA	.		0.433	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
GALNT14	79623	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	31168695	31168695	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:31168695G>A	ENST00000349752.5	-	7	1335	c.696C>T	c.(694-696)aaC>aaT	p.N232N	GALNT14_ENST00000486564.1_5'UTR|GALNT14_ENST00000406653.1_Silent_p.N212N|GALNT14_ENST00000420311.2_Silent_p.N197N|GALNT14_ENST00000324589.5_Silent_p.N237N|GALNT14_ENST00000356174.3_Silent_p.N199N	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	232					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					AGGTGTCCAGGTTAATGATAT	0.542																																					p.N237N		.											.	.	.	0			c.C711T						.						106.0	84.0	92.0					2																	31168695		2203	4300	6503	SO:0001819	synonymous_variant	79623	exon8			GTCCAGGTTAATG	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.696C>T	2.37:g.31168695G>A		Somatic	79	0		WXS	Illumina HiSeq	.	68	10	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Silent	SNP	ENST00000349752.5	37	CCDS1773.2																																																																																			.		0.542	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
KCNJ14	3770	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	48967866	48967866	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:48967866C>T	ENST00000391884.1	+	2	1619	c.1143C>T	c.(1141-1143)ttC>ttT	p.F381F	CTC-273B12.5_ENST00000593476.1_RNA|CTC-273B12.5_ENST00000600529.1_RNA|CTC-273B12.7_ENST00000595676.1_5'Flank|KCNJ14_ENST00000342291.2_Silent_p.F381F|CTC-273B12.6_ENST00000597574.1_lincRNA|CTC-273B12.5_ENST00000600650.1_RNA|CTC-273B12.5_ENST00000596497.1_RNA			Q9UNX9	KCJ14_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 14	381					potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|skin(2)|urinary_tract(1)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000109)|all cancers(93;0.000129)|Epithelial(262;0.0081)|GBM - Glioblastoma multiforme(486;0.0222)	Yohimbine(DB01392)	AGTCTAGTTTCCCCGGCTCTC	0.547																																					p.Q381H	NSCLC(148;170 3504 35216)	.											.	.	.	0			c.G1143T						.						66.0	68.0	67.0					19																	48967866		2203	4300	6503	SO:0001819	synonymous_variant	3770	exon3			TAGTTTCCCCGGC	BC042033	CCDS12721.1	19q13	2011-07-05				ENSG00000182324		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6260	protein-coding gene	gene with protein product		603953				9592090, 10723734, 16382105	Standard	NM_013348		Approved	Kir2.4, IRK4	uc002pje.2	Q9UNX9		ENST00000391884.1:c.1143C>T	19.37:g.48967866C>T		Somatic	24	0		WXS	Illumina HiSeq	.	24	6	NM_013348		Missense_Mutation	SNP	ENST00000391884.1	37	CCDS12721.1																																																																																			.		0.547	KCNJ14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466127.1	NM_013348	
ANKRD32	84250	hgsc.bcm.edu	37	5	93966366	93966366	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:93966366C>T	ENST00000265140.5	+	4	768	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C		NM_032290.3	NP_115666.2	Q9BQI6	ANR32_HUMAN	ankyrin repeat domain 32	117						centrosome (GO:0005813)|nucleus (GO:0005634)				NS(1)|breast(2)|endometrium(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	13		all_cancers(142;1.51e-09)|all_epithelial(76;4.68e-12)|all_lung(232;5.94e-05)|Ovarian(174;0.000953)|Lung NSC(167;0.00105)|Colorectal(57;0.122)|Lung SC(612;0.152)		all cancers(79;3.88e-18)		AGAACTGAAACGCACTGGTGC	0.398																																					p.R117C		.											ANKRD32_ENST00000265140,colon,carcinoma,0,1	ANKRD32_ENST00000265140	0	0			c.C349T						.						115.0	106.0	109.0					5																	93966366		692	1591	2283	SO:0001583	missense	84250	exon4			CTGAAACGCACTG	AL136560	CCDS4071.2	5q15	2013-01-10			ENSG00000133302	ENSG00000133302		"""Ankyrin repeat domain containing"""	25408	protein-coding gene	gene with protein product			"""BRCT domain containing 1"""	BRCTD1			Standard	NM_032290		Approved	DKFZp761C121, DKFZp564C0469	uc003kkr.4	Q9BQI6	OTTHUMG00000121133	ENST00000265140.5:c.349C>T	5.37:g.93966366C>T	ENSP00000265140:p.Arg117Cys	Somatic	50	0		WXS	Illumina HiSeq	.	46	2	NM_032290	B4DMG4|Q3B7K4|Q6NSA5|Q6PHW9|Q9Y402	Missense_Mutation	SNP	ENST00000265140.5	37	CCDS4071.2	.	.	.	.	.	.	.	.	.	.	C	14.94	2.686803	0.48097	.	.	ENSG00000133302	ENST00000265140;ENST00000504099	T;T	0.68025	-0.3;-0.3	5.84	4.9	0.64082	.	0.000000	0.46442	D	0.000291	T	0.62171	0.2406	M	0.73598	2.24	0.41857	D	0.990202	B	0.27450	0.179	B	0.18263	0.021	T	0.63323	-0.6663	10	0.46703	T	0.11	.	8.8602	0.35253	0.2309:0.6868:0.0:0.0823	.	117	Q9BQI6	ANR32_HUMAN	C	117	ENSP00000265140:R117C;ENSP00000425022:R117C	ENSP00000265140:R117C	R	+	1	0	ANKRD32	93992122	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	0.233000	0.17911	2.760000	0.94817	0.591000	0.81541	CGC	.		0.398	ANKRD32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241610.1	NM_032290	
EZH2	2146	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	148523609	148523609	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:148523609G>T	ENST00000460911.1	-	8	932	c.844C>A	c.(844-846)Cat>Aat	p.H282N	EZH2_ENST00000483967.1_Missense_Mutation_p.H273N|EZH2_ENST00000350995.2_Missense_Mutation_p.H243N|EZH2_ENST00000541220.1_Missense_Mutation_p.H273N|EZH2_ENST00000536783.1_Missense_Mutation_p.H173N|EZH2_ENST00000476773.1_Missense_Mutation_p.H273N|EZH2_ENST00000320356.2_Missense_Mutation_p.H282N|EZH2_ENST00000478654.1_Missense_Mutation_p.H273N			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	282	Interaction with DNMT1, DNMT3A and DNMT3B.				cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			AAAAGCGTATGAAAGGAGTGT	0.413			Mis		DLBCL																																p.H282N		.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	.	.	0			c.C844A						.						163.0	135.0	145.0					7																	148523609		2203	4300	6503	SO:0001583	missense	2146	exon8			GCGTATGAAAGGA		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.844C>A	7.37:g.148523609G>T	ENSP00000419711:p.His282Asn	Somatic	44	0		WXS	Illumina HiSeq	.	69	5	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	g	28.2	4.896523	0.91962	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.93281	0.7859	M	0.75447	2.3	0.80722	D	1	D;D;D;D;D;D	0.89917	0.986;0.999;1.0;0.998;0.999;0.994	P;D;D;D;D;D	0.72982	0.82;0.962;0.979;0.965;0.962;0.948	D	0.92777	0.6237	10	0.48119	T	0.1	.	19.4397	0.94813	0.0:0.0:1.0:0.0	.	282;273;273;282;243;282	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	N	273;282;282;243;273;273;273;173	ENSP00000417062:H273N;ENSP00000320147:H282N;ENSP00000419711:H282N;ENSP00000223193:H243N;ENSP00000443219:H273N;ENSP00000419050:H273N;ENSP00000419856:H273N;ENSP00000439305:H173N	ENSP00000320147:H282N	H	-	1	0	EZH2	148154542	1.000000	0.71417	0.846000	0.33378	0.991000	0.79684	9.611000	0.98342	2.582000	0.87167	0.591000	0.81541	CAT	.		0.413	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
PRR11	55771	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	57247159	57247159	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:57247159G>A	ENST00000262293.4	+	2	358	c.46G>A	c.(46-48)Gaa>Aaa	p.E16K		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	16						cytoplasm (GO:0005737)|membrane (GO:0016020)				breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AGCCAAAGCCGAAAGATTATT	0.358																																					p.E16K		.											.	.	.	0			c.G46A						.						75.0	74.0	74.0					17																	57247159		2203	4300	6503	SO:0001583	missense	55771	exon2			AAAGCCGAAAGAT		CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.46G>A	17.37:g.57247159G>A	ENSP00000262293:p.Glu16Lys	Somatic	101	0		WXS	Illumina HiSeq	.	138	11	NM_018304	Q9NUZ7|Q9NXE9	Missense_Mutation	SNP	ENST00000262293.4	37	CCDS11614.1	.	.	.	.	.	.	.	.	.	.	A	8.740	0.918811	0.17982	.	.	ENSG00000068489	ENST00000262293	.	.	.	4.79	3.7	0.42460	.	0.094927	0.45606	N	0.000343	T	0.07458	0.0188	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38672	-0.9650	9	0.02654	T	1	-8.252	5.1752	0.15131	0.726:0.1808:0.0932:0.0	.	16	Q96HE9	PRR11_HUMAN	K	16	.	ENSP00000262293:E16K	E	+	1	0	PRR11	54601941	0.997000	0.39634	0.439000	0.26833	0.366000	0.29705	2.173000	0.42472	0.407000	0.25591	-1.589000	0.00846	GAA	.		0.358	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304	
MAN1C1	57134	hgsc.bcm.edu	37	1	26079974	26079974	+	Splice_Site	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:26079974G>T	ENST00000374332.4	+	5	1164		c.e5-1		MAN1C1_ENST00000263979.3_Splice_Site|MAN1C1_ENST00000374329.1_Splice_Site|MAN1C1_ENST00000473891.1_Splice_Site	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1						cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		CTCCTTTACAGGTGTTCCGAA	0.587																																					.		.											MAN1C1,NS,carcinoma,0,1	MAN1C1	0	0			c.835-1G>T						.						48.0	43.0	45.0					1																	26079974		2203	4300	6503	SO:0001630	splice_region_variant	57134	exon5			TTTACAGGTGTTC	AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.835-1G>T	1.37:g.26079974G>T		Somatic	39	1		WXS	Illumina HiSeq	.	47	2	NM_020379	A6NNE2|B2RNP2|Q9Y545	Splice_Site	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	G	19.96	3.923876	0.73213	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979;ENST00000374329	.	.	.	4.93	4.02	0.46733	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.5501	0.50716	0.085:0.0:0.915:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MAN1C1	25952561	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	8.617000	0.90927	1.202000	0.43218	0.561000	0.74099	.	.		0.587	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	Intron
RNF212	285498	hgsc.bcm.edu	37	4	1087255	1087255	+	Intron	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:1087255G>T	ENST00000433731.2	-	4	308				RNF212_ENST00000382968.5_Intron|RNF212_ENST00000333673.5_Missense_Mutation_p.A265E			Q495C1	RN212_HUMAN	ring finger protein 212						chiasma assembly (GO:0051026)|meiotic gene conversion (GO:0006311)|protein sumoylation (GO:0016925)|reciprocal meiotic recombination (GO:0007131)	synaptonemal complex (GO:0000795)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	10			OV - Ovarian serous cystadenocarcinoma(23;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (64;0.151)		ACTCCACCCTGCGTTTGTGAT	0.493																																					p.A265E		.											.	.	.	0			c.C794A						.																																			SO:0001627	intron_variant	285498	exon4			CACCCTGCGTTTG	AK096160	CCDS3345.1, CCDS46996.1, CCDS54704.1	4p16.3	2013-02-27	2007-01-19	2007-01-19	ENSG00000178222	ENSG00000178222		"""RING-type (C3HC4) zinc fingers"""	27729	protein-coding gene	gene with protein product		612041	"""hypothetical protein LOC285498"""	LOC285498		23396135	Standard	NM_001131034		Approved	FLJ38841	uc003gcj.3	Q495C1	OTTHUMG00000118997	ENST00000433731.2:c.247-2629C>A	4.37:g.1087255G>T		Somatic	112	0		WXS	Illumina HiSeq	.	109	4	NM_001193318	C9J8N0|Q495C0|Q86W82|Q8IY99|Q8N8U7	Missense_Mutation	SNP	ENST00000433731.2	37	CCDS46996.1	.	.	.	.	.	.	.	.	.	.	G	1.273	-0.612415	0.03690	.	.	ENSG00000178222	ENST00000333673	.	.	.	1.03	-1.76	0.08006	.	.	.	.	.	T	0.17662	0.0424	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.23368	-1.0190	6	0.87932	D	0	.	4.556	0.12136	0.4669:0.0:0.5331:0.0	.	.	.	.	E	265	.	ENSP00000327481:A265E	A	-	2	0	RNF212	1077255	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.274000	0.08537	-0.691000	0.05135	-0.379000	0.06801	GCA	.		0.493	RNF212-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359124.2	NM_194439	
TMED8	283578	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	14	77810058	77810058	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:77810058G>A	ENST00000216468.7	-	4	491	c.436C>T	c.(436-438)Ctg>Ttg	p.L146L		NM_213601.1	NP_998766.1	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain containing 8	146					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)	15			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		TGGTCCCCCAGAAGATCTGCA	0.458																																					p.L146L		.											.	.	.	0			c.C436T						.						190.0	195.0	193.0					14																	77810058		2203	4300	6503	SO:0001819	synonymous_variant	283578	exon4			CCCCCAGAAGATC	AK095650	CCDS32125.1	14q24.3	2005-08-26	2005-08-26	2005-01-07		ENSG00000100580			18633	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member B"", ""transmembrane emp24 domain containing 8"""	FAM15B			Standard	NM_213601		Approved		uc001xto.1	Q6PL24		ENST00000216468.7:c.436C>T	14.37:g.77810058G>A		Somatic	62	0		WXS	Illumina HiSeq	.	69	7	NM_213601	B3KTI6|Q3MJB0|Q9P1V9	Silent	SNP	ENST00000216468.7	37	CCDS32125.1																																																																																			.		0.458	TMED8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414100.1	NM_213601	
ELK1	2002	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	47496463	47496463	+	Missense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:47496463C>G	ENST00000247161.3	-	5	1236	c.1137G>C	c.(1135-1137)tgG>tgC	p.W379C	ELK1_ENST00000376983.3_Missense_Mutation_p.W379C|ELK1_ENST00000343894.4_Intron|ELK1_ENST00000592066.1_Missense_Mutation_p.W325C	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	379	Sufficient for interaction with MAD2L2.				cell differentiation (GO:0030154)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	10						TCAGGGTGCTCCAGAAGTGAA	0.597																																					p.W379C		.											.	.	.	0			c.G1137C						.						49.0	46.0	47.0					X																	47496463		2202	4299	6501	SO:0001583	missense	2002	exon6			GGTGCTCCAGAAG	M25269	CCDS14283.1, CCDS59165.1	Xp11.23	2010-07-20			ENSG00000126767	ENSG00000126767			3321	protein-coding gene	gene with protein product		311040				2539641	Standard	NM_001114123		Approved		uc010nhv.4	P19419	OTTHUMG00000021452	ENST00000247161.3:c.1137G>C	X.37:g.47496463C>G	ENSP00000247161:p.Trp379Cys	Somatic	30	0		WXS	Illumina HiSeq	.	55	6	NM_001114123	B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	37	CCDS14283.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.144777	0.77888	.	.	ENSG00000126767	ENST00000247161;ENST00000542746;ENST00000376983	T;T	0.49432	0.78;0.78	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.69169	0.3081	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74216	-0.3737	10	0.87932	D	0	.	14.7251	0.69339	0.0:1.0:0.0:0.0	.	379	P19419	ELK1_HUMAN	C	379;72;379	ENSP00000247161:W379C;ENSP00000366182:W379C	ENSP00000247161:W379C	W	-	3	0	ELK1	47381407	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.716000	0.84723	2.058000	0.61347	0.506000	0.49869	TGG	.		0.597	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1	NM_005229	
CLCA2	9635	hgsc.bcm.edu	37	1	86913194	86913194	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:86913194G>T	ENST00000370565.4	+	11	1879	c.1717G>T	c.(1717-1719)Ggg>Tgg	p.G573W		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	573					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)			NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TTTACAGCCTGGGCACTGGAC	0.438																																					p.G573W	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	.											CLCA2,NS,carcinoma,0,1	CLCA2	0	0			c.G1717T						.						126.0	124.0	125.0					1																	86913194		2203	4300	6503	SO:0001583	missense	9635	exon11			CAGCCTGGGCACT		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.1717G>T	1.37:g.86913194G>T	ENSP00000359596:p.Gly573Trp	Somatic	58	0		WXS	Illumina HiSeq	.	69	3	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.692417	0.48202	.	.	ENSG00000137975	ENST00000370565	T	0.63096	-0.02	5.61	5.61	0.85477	Domain of unknown function DUF1973 (1);	0.061916	0.64402	D	0.000005	T	0.81800	0.4899	M	0.90082	3.085	0.51233	D	0.999912	D	0.89917	1.0	D	0.97110	1.0	D	0.85025	0.0914	10	0.87932	D	0	-14.5965	19.2426	0.93889	0.0:0.0:1.0:0.0	.	573	Q9UQC9	CLCA2_HUMAN	W	573	ENSP00000359596:G573W	ENSP00000359596:G573W	G	+	1	0	CLCA2	86685782	1.000000	0.71417	0.871000	0.34182	0.075000	0.17131	6.295000	0.72744	2.653000	0.90120	0.655000	0.94253	GGG	.		0.438	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
PIWIL2	55124	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	22145050	22145050	+	Silent	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:22145050G>T	ENST00000454009.2	+	7	1262	c.753G>T	c.(751-753)gtG>gtT	p.V251V	PIWIL2_ENST00000521356.1_Silent_p.V251V|PIWIL2_ENST00000356766.6_Silent_p.V251V	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	251					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		GCCCCAATGTGGAGTGCAAAA	0.453											OREG0018608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V251V		.											.	.	.	0			c.G753T						.						148.0	122.0	131.0					8																	22145050		2203	4300	6503	SO:0001819	synonymous_variant	55124	exon7			CAATGTGGAGTGC	AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"""Argonaute/PIWI family"""	17644	protein-coding gene	gene with protein product	"""Hiwi-like"", ""cancer/testis antigen 80"""	610312	"""piwi-like 2 (Drosophila)"""			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.753G>T	8.37:g.22145050G>T		Somatic	47	0	753	WXS	Illumina HiSeq	.	61	6	NM_001135721	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Silent	SNP	ENST00000454009.2	37	CCDS6029.1																																																																																			.		0.453	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1		
SV2A	9900	hgsc.bcm.edu	37	1	149879665	149879665	+	Silent	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:149879665G>T	ENST00000369146.3	-	9	1963	c.1473C>A	c.(1471-1473)cgC>cgA	p.R491R	SV2A_ENST00000369145.1_Silent_p.R491R	NM_001278719.1|NM_014849.3	NP_001265648.1|NP_055664.3	Q7L0J3	SV2A_HUMAN	synaptic vesicle glycoprotein 2A	491					cellular calcium ion homeostasis (GO:0006874)|neurotransmitter transport (GO:0006836)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	protein kinase binding (GO:0019901)|receptor activity (GO:0004872)|transmembrane transporter activity (GO:0022857)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(16)|ovary(6)|pancreas(1)|prostate(8)|skin(2)|urinary_tract(2)	55	Breast(34;0.00769)|all_hematologic(923;0.127)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)		Levetiracetam(DB01202)	CATGCTCTACGCGCTCCCCGG	0.512																																					p.R491R		.											SV2A,colon,carcinoma,0,1	SV2A	0	0			c.C1473A						.						164.0	161.0	162.0					1																	149879665		2203	4300	6503	SO:0001819	synonymous_variant	9900	exon9			CTCTACGCGCTCC	AB018279	CCDS940.1	1q21.2	2008-02-05			ENSG00000159164	ENSG00000159164			20566	protein-coding gene	gene with protein product		185860				7681585, 10611374	Standard	NM_014849		Approved	SV2, KIAA0736	uc001etg.3	Q7L0J3	OTTHUMG00000012209	ENST00000369146.3:c.1473C>A	1.37:g.149879665G>T		Somatic	32	0		WXS	Illumina HiSeq	.	41	2	NM_014849	D3DUZ7|O94841|Q5QNX8|Q7Z3L6|Q8NBJ6|Q9BVZ9	Silent	SNP	ENST00000369146.3	37	CCDS940.1																																																																																			.		0.512	SV2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033754.1		
ALPK3	57538	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	85401487	85401487	+	Missense_Mutation	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:85401487G>C	ENST00000258888.5	+	6	4291	c.4124G>C	c.(4123-4125)aGa>aCa	p.R1375T		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1375					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CCTAAGGTCAGAGCAGCAGGA	0.642																																					p.R1375T		.											.	.	.	0			c.G4124C						.						18.0	24.0	22.0					15																	85401487		2201	4295	6496	SO:0001583	missense	57538	exon6			AGGTCAGAGCAGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.4124G>C	15.37:g.85401487G>C	ENSP00000258888:p.Arg1375Thr	Somatic	120	0		WXS	Illumina HiSeq	.	187	15	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	.	.	.	.	.	.	.	.	.	.	g	15.73	2.919145	0.52546	.	.	ENSG00000136383	ENST00000258888	T	0.64260	-0.09	5.92	2.63	0.31362	.	0.293421	0.34603	N	0.003838	T	0.50205	0.1602	L	0.57536	1.79	0.25840	N	0.984065	P	0.43094	0.799	B	0.38378	0.272	T	0.50516	-0.8819	10	0.52906	T	0.07	-12.5367	3.8078	0.08785	0.2382:0.2029:0.5588:0.0	.	1375	Q96L96	ALPK3_HUMAN	T	1375	ENSP00000258888:R1375T	ENSP00000258888:R1375T	R	+	2	0	ALPK3	83202491	0.985000	0.35326	0.368000	0.25939	0.893000	0.52053	1.349000	0.33998	0.816000	0.34421	0.651000	0.88453	AGA	.		0.642	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
PRG4	10216	hgsc.bcm.edu	37	1	186276262	186276262	+	Missense_Mutation	SNP	A	A	C	rs572823944|rs554943190	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:186276262A>C	ENST00000445192.2	+	7	1456	c.1411A>C	c.(1411-1413)Acc>Ccc	p.T471P	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Missense_Mutation_p.T428P|PRG4_ENST00000367483.4_Missense_Mutation_p.T430P|PRG4_ENST00000367485.4_Missense_Mutation_p.T378P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	471	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						TGCACCCACCACCAAGGAGCC	0.652														9	0.00179712	0.0038	0.0	5008	,	,		9353	0.0		0.002	False		,,,				2504	0.002				p.T471P		.											.,1	.	259	0			c.A1411C						.						86.0	94.0	92.0					1																	186276262		2203	4298	6501	SO:0001583	missense	10216	exon7			CCCACCACCAAGG	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1411A>C	1.37:g.186276262A>C	ENSP00000399679:p.Thr471Pro	Somatic	56	0		WXS	Illumina HiSeq	.	63	0	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	4.705	0.131095	0.08981	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.05925	3.37;3.49;3.38;3.47	2.65	-5.29	0.02747	.	0.892392	0.09179	N	0.837745	T	0.03783	0.0107	L	0.33189	0.99	0.21762	N	0.999557	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.42632	-0.9440	9	.	.	.	-0.0017	3.2687	0.06874	0.5477:0.2197:0.1343:0.0983	.	337;378;471;430	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	P	428;337;430;378;471	ENSP00000356456:T428P;ENSP00000356453:T430P;ENSP00000356455:T378P;ENSP00000399679:T471P	.	T	+	1	0	PRG4	184542885	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.223000	0.17719	-1.906000	0.01089	0.092000	0.15492	ACC	.		0.652	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
OR7A5	26659	hgsc.bcm.edu	37	19	14938184	14938184	+	Silent	SNP	A	A	G	rs200531878		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:14938184A>G	ENST00000322301.3	-	2	957	c.870T>C	c.(868-870)taT>taC	p.Y290Y	OR7A5_ENST00000594432.1_Silent_p.Y290Y|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	290					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y290Y(2)		breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						TCCTCAGACTATAGATAAAGG	0.478																																					p.Y290Y		.											OR7A5,NS,carcinoma,0,1	OR7A5	0	2	Substitution - coding silent(2)	kidney(2)	c.T870C						.						74.0	72.0	72.0					19																	14938184		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			CAGACTATAGATA	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.870T>C	19.37:g.14938184A>G		Somatic	53	0		WXS	Illumina HiSeq	.	75	3	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			0.001		0.478	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
ACACB	32	hgsc.bcm.edu	37	12	109644547	109644547	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:109644547G>T	ENST00000338432.7	+	20	3065	c.2946G>T	c.(2944-2946)caG>caT	p.Q982H	ACACB_ENST00000377854.5_Missense_Mutation_p.Q982H|ACACB_ENST00000377848.3_Missense_Mutation_p.Q982H			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	982					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	TCCCTGCCCAGCAGACACTGC	0.557																																					p.Q982H		.											ACACB,right_upper_lobe,carcinoma,0,1	ACACB	0	0			c.G2946T						.						170.0	169.0	169.0					12																	109644547		2203	4300	6503	SO:0001583	missense	32	exon19			TGCCCAGCAGACA	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.2946G>T	12.37:g.109644547G>T	ENSP00000341044:p.Gln982His	Somatic	48	0		WXS	Illumina HiSeq	.	50	2	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	G	9.022	0.985160	0.18889	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.42513	0.97;0.97;0.97	5.16	4.27	0.50696	Acetyl-CoA carboxylase, central domain (1);	0.000000	0.85682	D	0.000000	T	0.43433	0.1247	M	0.62723	1.935	0.80722	D	1	B	0.32382	0.368	B	0.36092	0.217	T	0.32666	-0.9898	10	0.33141	T	0.24	.	13.9196	0.63923	0.0734:0.0:0.9266:0.0	.	982	O00763	ACACB_HUMAN	H	982;982;982;213	ENSP00000341044:Q982H;ENSP00000367079:Q982H;ENSP00000367085:Q982H	ENSP00000341044:Q982H	Q	+	3	2	ACACB	108128930	1.000000	0.71417	0.945000	0.38365	0.511000	0.34104	4.042000	0.57347	1.190000	0.43042	0.561000	0.74099	CAG	.		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
ADAMTS18	170692	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	77353780	77353780	+	Missense_Mutation	SNP	G	G	A	rs147816593		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:77353780G>A	ENST00000282849.5	-	16	2916	c.2498C>T	c.(2497-2499)gCg>gTg	p.A833V		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	833	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGGCCCTGGCGCGTACAGACG	0.542																																					p.A833V		.											ADAMTS18,rectum,carcinoma,0,3	ADAMTS18	0	0			c.C2498T						.	G	VAL/ALA	1,4395	2.1+/-5.4	0,1,2197	61.0	60.0	60.0		2498	5.5	0.2	16	dbSNP_134	60	0,8600		0,0,4300	no	missense	ADAMTS18	NM_199355.2	64	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	833/1222	77353780	1,12995	2198	4300	6498	SO:0001583	missense	170692	exon16			CCTGGCGCGTACA	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2498C>T	16.37:g.77353780G>A	ENSP00000282849:p.Ala833Val	Somatic	49	0		WXS	Illumina HiSeq	.	70	6	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141924	0.77775	2.27E-4	0.0	ENSG00000140873	ENST00000282849	T	0.56941	0.43	5.54	5.54	0.83059	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.81914	0.897;0.995	T	0.81191	-0.1045	10	0.87932	D	0	.	18.4764	0.90793	0.0:0.0:1.0:0.0	.	833;833	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	833	ENSP00000282849:A833V	ENSP00000282849:A833V	A	-	2	0	ADAMTS18	75911281	1.000000	0.71417	0.242000	0.24170	0.254000	0.26022	9.378000	0.97191	2.618000	0.88619	0.563000	0.77884	GCG	0.000		0.542	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
LFNG	3955	hgsc.bcm.edu	37	7	2552881	2552881	+	Silent	SNP	A	A	G	rs34637446|rs61564232|rs397694506|rs373004749		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr7:2552881A>G	ENST00000402506.1	+	2	264	c.138A>G	c.(136-138)acA>acG	p.T46T		NM_001166355.1	NP_001159827.1	Q8NES3	LFNG_HUMAN	LFNG O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase	0					compartment pattern specification (GO:0007386)|female meiotic division (GO:0007143)|metabolic process (GO:0008152)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|ovarian follicle development (GO:0001541)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein binding (GO:0032092)|regulation of Notch signaling pathway (GO:0008593)|regulation of somitogenesis (GO:0014807)|somitogenesis (GO:0001756)	extracellular region (GO:0005576)|integral component of Golgi membrane (GO:0030173)|vesicle (GO:0031982)	metal ion binding (GO:0046872)|O-fucosylpeptide 3-beta-N-acetylglucosaminyltransferase activity (GO:0033829)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|urinary_tract(2)	6		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;2.54e-14)		acagatggacagatggatgga	0.562																																					p.T46T		.											LFNG_ENST00000402506,caecum,carcinoma,0,2	LFNG_ENST00000402506	0	0			c.A138G						.						131.0	123.0	126.0					7																	2552881		1568	3582	5150	SO:0001819	synonymous_variant	3955	exon2			ATGGACAGATGGA	BC014851	CCDS34586.1, CCDS34587.1, CCDS55081.1, CCDS55082.1	7p22.3	2013-02-19	2006-11-13		ENSG00000106003	ENSG00000106003	2.4.1.222	"""Beta 3-glycosyltransferases"""	6560	protein-coding gene	gene with protein product		602576	"""lunatic fringe (Drosophila) homolog"", ""lunatic fringe homolog (Drosophila)"""			9878264, 9187150	Standard	NM_001166355		Approved	SCDO3	uc003smf.3	Q8NES3	OTTHUMG00000152043	ENST00000402506.1:c.138A>G	7.37:g.2552881A>G		Somatic	28	0		WXS	Illumina HiSeq	.	38	5	NM_001166355	B3KTY6|B5MCR5|O00589|Q96C39|Q9UJW5	Silent	SNP	ENST00000402506.1	37	CCDS55081.1																																																																																			.		0.562	LFNG-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000325023.1	NM_002304	
TRHDE	29953	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	73015434	73015434	+	Missense_Mutation	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:73015434A>G	ENST00000261180.4	+	15	2539	c.2443A>G	c.(2443-2445)Aga>Gga	p.R815G		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	815					cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(38)|ovary(2)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	79						AGAACTACGTAGAGAAGTTAT	0.343																																					p.R815G		.											.	.	.	0			c.A2443G						.						69.0	64.0	66.0					12																	73015434		2203	4300	6503	SO:0001583	missense	29953	exon15			CTACGTAGAGAAG	AF126372	CCDS9004.1	12q15-q21	2012-07-25		2005-08-09		ENSG00000072657	3.4.19.6		30748	protein-coding gene	gene with protein product	"""pyroglutamyl-peptidase II"", ""pyroglutamyl aminopeptidase II"", ""TRH-specific aminopeptidase"""	606950				10491199, 12975309	Standard	NM_013381		Approved	PGPEP2, TRH-DE, PAP-II	uc001sxa.3	Q9UKU6		ENST00000261180.4:c.2443A>G	12.37:g.73015434A>G	ENSP00000261180:p.Arg815Gly	Somatic	46	0		WXS	Illumina HiSeq	.	47	7	NM_013381	A5PL19|Q6UWJ4	Missense_Mutation	SNP	ENST00000261180.4	37	CCDS9004.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.476955	0.84640	.	.	ENSG00000072657	ENST00000261180	T	0.04862	3.54	5.58	-1.85	0.07784	.	0.050867	0.64402	N	0.000001	T	0.05593	0.0147	L	0.39020	1.185	0.41522	D	0.988405	B	0.20550	0.046	B	0.20184	0.028	T	0.30268	-0.9984	10	0.51188	T	0.08	.	12.4052	0.55434	0.3377:0.5926:0.0696:0.0	.	815	Q9UKU6	TRHDE_HUMAN	G	815	ENSP00000261180:R815G	ENSP00000261180:R815G	R	+	1	2	TRHDE	71301701	0.083000	0.21467	0.107000	0.21349	0.884000	0.51177	0.597000	0.24059	-0.122000	0.11766	0.533000	0.62120	AGA	.		0.343	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381	
MT-ND1	4535	hgsc.bcm.edu	37	M	689	689	+	5'Flank	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrM:689T>C	ENST00000361390.2	+	0	0				MT-RNR1_ENST00000389680.2_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TL1_ENST00000386347.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1						cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CTCTTAGTAAGATTACACATG	0.448																																					.		.											.	.	.	0			.						.																																			SO:0001631	upstream_gene_variant	6052	.			GTAAGATTACACA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886			M.37:g.689T>C	Exception_encountered	Somatic	495	0		WXS	Illumina HiSeq	.	490	118	.	C0JKH6|Q37523	RNA	SNP	ENST00000361390.2	37																																																																																				.		0.448	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
NES	10763	hgsc.bcm.edu	37	1	156642556	156642556	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:156642556G>T	ENST00000368223.3	-	4	1556	c.1424C>A	c.(1423-1425)tCc>tAc	p.S475Y		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	475	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CTCTAAACTGGAGTGGTCAGG	0.597																																					p.S475Y		.											NES,NS,haematopoietic_neoplasm,+1,1	NES	+1	0			c.C1424A						.						84.0	86.0	85.0					1																	156642556		2203	4300	6503	SO:0001583	missense	10763	exon4			AAACTGGAGTGGT	X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.1424C>A	1.37:g.156642556G>T	ENSP00000357206:p.Ser475Tyr	Somatic	49	0		WXS	Illumina HiSeq	.	39	3	NM_006617	O00552|Q3LIF5|Q5SYZ6	Missense_Mutation	SNP	ENST00000368223.3	37	CCDS1151.1	.	.	.	.	.	.	.	.	.	.	G	14.56	2.571598	0.45798	.	.	ENSG00000132688	ENST00000368223;ENST00000255024	D	0.86097	-2.07	5.17	0.318	0.15867	.	1.628260	0.04248	N	0.338068	T	0.65375	0.2685	L	0.47716	1.5	0.09310	N	1	P	0.35982	0.531	B	0.30646	0.118	T	0.60782	-0.7195	10	0.66056	D	0.02	.	6.4288	0.21784	0.094:0.0:0.4606:0.4453	.	475	P48681	NEST_HUMAN	Y	475	ENSP00000357206:S475Y	ENSP00000255024:S475Y	S	-	2	0	NES	154909180	0.000000	0.05858	0.006000	0.13384	0.842000	0.47809	0.060000	0.14342	0.503000	0.28060	0.467000	0.42956	TCC	.		0.597	NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
CEP95	90799	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	62533848	62533848	+	Missense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:62533848C>G	ENST00000556440.2	+	20	2927	c.2417C>G	c.(2416-2418)tCt>tGt	p.S806C	CEP95_ENST00000553412.1_Missense_Mutation_p.S642C	NM_138363.1	NP_612372.1	Q96GE4	CEP95_HUMAN	centrosomal protein 95kDa	806						centrosome (GO:0005813)|cytoplasm (GO:0005737)|spindle pole (GO:0000922)				endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)	13						CGCTTCAGATCTCGGCTTCAG	0.468																																					p.S806C		.											.	.	.	0			c.C2417G						.						49.0	49.0	49.0					17																	62533848		1895	4118	6013	SO:0001583	missense	90799	exon20			TCAGATCTCGGCT	AL832822	CCDS45763.1	17q24.1	2014-02-20	2011-05-06	2011-05-06	ENSG00000258890	ENSG00000258890			25141	protein-coding gene	gene with protein product			"""coiled-coil domain containing 45"""	CCDC45		21399614	Standard	NM_138363		Approved	DKFZp667E1824	uc002jem.3	Q96GE4	OTTHUMG00000179174	ENST00000556440.2:c.2417C>G	17.37:g.62533848C>G	ENSP00000450461:p.Ser806Cys	Somatic	75	0		WXS	Illumina HiSeq	.	76	6	NM_138363	B4DMD2|Q96M81	Missense_Mutation	SNP	ENST00000556440.2	37	CCDS45763.1	.	.	.	.	.	.	.	.	.	.	C	12.89	2.074966	0.36566	.	.	ENSG00000258890	ENST00000553956;ENST00000556440;ENST00000553412	T;T	0.34275	1.37;1.38	5.91	4.93	0.64822	.	0.793280	0.12105	N	0.499108	T	0.33990	0.0882	L	0.36672	1.1	0.09310	N	1	B	0.15473	0.013	B	0.17098	0.017	T	0.27434	-1.0074	10	0.52906	T	0.07	-1.9385	15.4492	0.75259	0.0:0.7374:0.2626:0.0	.	806	Q96GE4	CEP95_HUMAN	C	741;806;642	ENSP00000450461:S806C;ENSP00000450906:S642C	ENSP00000438458:S741C	S	+	2	0	CEP95	59964310	0.921000	0.31238	0.093000	0.20910	0.996000	0.88848	2.791000	0.47829	1.495000	0.48549	0.462000	0.41574	TCT	.		0.468	CEP95-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445100.2	NM_138363	
TOX3	27324	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	52473515	52473515	+	Silent	SNP	C	C	T	rs374335680|rs546327959	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:52473515C>T	ENST00000219746.9	-	7	1637	c.1353G>A	c.(1351-1353)caG>caA	p.Q451Q	TOX3_ENST00000407228.3_Silent_p.Q446Q	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	451	Gln-rich.				apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						gttgttgttgctgctgctgct	0.552																																					p.Q451Q		.											.	.	.	0			c.G1353A						.	C	,	0,4390		0,0,2195	51.0	49.0	50.0		1353,1338	1.6	0.9	16		50	2,8596		0,2,4297	no	coding-synonymous,coding-synonymous	TOX3	NM_001080430.2,NM_001146188.1	,	0,2,6492	TT,TC,CC		0.0233,0.0,0.0154	,	451/577,446/572	52473515	2,12986	2195	4299	6494	SO:0001819	synonymous_variant	27324	exon7			TTGTTGCTGCTGC	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.1353G>A	16.37:g.52473515C>T		Somatic	34	0		WXS	Illumina HiSeq	.	48	4	NM_001080430	B4DRD0|B5MCW4	Silent	SNP	ENST00000219746.9	37	CCDS54009.1																																																																																			.		0.552	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
TENM2	57451	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	167675119	167675119	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:167675119C>T	ENST00000518659.1	+	27	7214	c.7175C>T	c.(7174-7176)aCg>aTg	p.T2392M	TENM2_ENST00000403607.2_Missense_Mutation_p.T2216M|TENM2_ENST00000545108.1_Missense_Mutation_p.T2391M|TENM2_ENST00000519204.1_Missense_Mutation_p.T2271M|TENM2_ENST00000520394.1_Missense_Mutation_p.T2153M	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2392					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										CTGCAGTACACGGCCTATGGG	0.532																																					p.T2383M		.											.	.	.	0			c.C7148T						.						163.0	163.0	163.0					5																	167675119		2001	4174	6175	SO:0001583	missense	57451	exon27			AGTACACGGCCTA	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7175C>T	5.37:g.167675119C>T	ENSP00000429430:p.Thr2392Met	Somatic	32	0		WXS	Illumina HiSeq	.	58	4	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	18.59	3.656207	0.67586	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90563	-2.22;-2.21;-2.32;-2.66;-2.69	4.62	4.62	0.57501	Rhs repeat-associated core (1);	0.000000	0.85682	D	0.000000	D	0.96300	0.8793	M	0.91300	3.195	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.76071	0.987;0.97;0.855	D	0.97151	0.9831	10	0.87932	D	0	.	17.997	0.89187	0.0:1.0:0.0:0.0	.	2391;2392;2153	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	M	2392;2391;2271;2153;2216	ENSP00000429430:T2392M;ENSP00000438635:T2391M;ENSP00000428964:T2271M;ENSP00000427874:T2153M;ENSP00000384905:T2216M	ENSP00000384905:T2216M	T	+	2	0	ODZ2	167607697	1.000000	0.71417	0.978000	0.43139	0.992000	0.81027	7.609000	0.82925	2.556000	0.86216	0.561000	0.74099	ACG	.		0.532	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
ZNF292	23036	hgsc.bcm.edu	37	6	87964852	87964852	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:87964852G>T	ENST00000369577.3	+	8	1548	c.1505G>T	c.(1504-1506)gGt>gTt	p.G502V	ZNF292_ENST00000339907.4_Missense_Mutation_p.G497V	NM_015021.1	NP_055836.1	O60281	ZN292_HUMAN	zinc finger protein 292	502						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(27)|lung(21)|ovary(4)|prostate(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	89		all_cancers(76;3.82e-09)|Prostate(29;1.34e-10)|Acute lymphoblastic leukemia(125;2.17e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;5.31e-05)		BRCA - Breast invasive adenocarcinoma(108;0.0199)		GGTGGAGTTGGTGCTAATTCT	0.378																																					p.G502V		.											.	.	.	0			c.G1505T						.						111.0	105.0	107.0					6																	87964852		1875	4114	5989	SO:0001583	missense	23036	exon8			GAGTTGGTGCTAA	AB011102	CCDS47457.1	6q15	2008-10-23			ENSG00000188994	ENSG00000188994		"""Zinc fingers, C2H2-type"""	18410	protein-coding gene	gene with protein product						9628581	Standard	NM_015021		Approved	KIAA0530, ZFP292, bA393I2.3, Zn-15, Zn-16	uc003plm.4	O60281	OTTHUMG00000015164	ENST00000369577.3:c.1505G>T	6.37:g.87964852G>T	ENSP00000358590:p.Gly502Val	Somatic	38	0		WXS	Illumina HiSeq	.	64	3	NM_015021	Q5W0B2|Q7Z3L7|Q9H8G3|Q9H8J4	Missense_Mutation	SNP	ENST00000369577.3	37	CCDS47457.1	.	.	.	.	.	.	.	.	.	.	G	6.358	0.434117	0.12045	.	.	ENSG00000188994	ENST00000369577;ENST00000339907	T;T	0.35236	1.32;1.32	5.87	3.84	0.44239	.	0.312456	0.35179	N	0.003399	T	0.09512	0.0234	N	0.22421	0.69	0.58432	D	0.999994	B	0.11235	0.004	B	0.10450	0.005	T	0.19192	-1.0313	10	0.33141	T	0.24	.	3.0989	0.06319	0.2199:0.2748:0.5053:0.0	.	502	O60281	ZN292_HUMAN	V	502;497	ENSP00000358590:G502V;ENSP00000342847:G497V	ENSP00000342847:G497V	G	+	2	0	ZNF292	88021571	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	4.016000	0.57159	2.775000	0.95449	0.650000	0.86243	GGT	.		0.378	ZNF292-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376192.2	NM_015021	
TARBP1	6894	hgsc.bcm.edu	37	1	234569297	234569297	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:234569297G>T	ENST00000040877.1	-	14	2252	c.2253C>A	c.(2251-2253)tgC>tgA	p.C751*		NM_005646.3	NP_005637.3	Q13395	TARB1_HUMAN	TAR (HIV-1) RNA binding protein 1	751					regulation of transcription from RNA polymerase II promoter (GO:0006357)|RNA processing (GO:0006396)	nucleus (GO:0005634)	RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(7)|large_intestine(6)|lung(22)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	55	Ovarian(103;0.0339)	all_cancers(173;0.00995)|Prostate(94;0.0115)|all_epithelial(177;0.172)	OV - Ovarian serous cystadenocarcinoma(106;0.000263)			GGTATAAATGGCAACGATCCA	0.393																																					p.C751X		.											.	.	.	0			c.C2253A						.						106.0	103.0	104.0					1																	234569297		2203	4300	6503	SO:0001587	stop_gained	6894	exon14			TAAATGGCAACGA		CCDS1601.1	1q42.2	2012-06-12	2007-06-26		ENSG00000059588	ENSG00000059588			11568	protein-coding gene	gene with protein product	"""tRNA methyltransferase 3 homolog (S. cerevisiae)"""	605052	"""Tar (HIV-1) RNA binding protein 1"""			1936997	Standard	NM_005646		Approved	TRP-185, TRM3	uc001hwd.3	Q13395	OTTHUMG00000037947	ENST00000040877.1:c.2253C>A	1.37:g.234569297G>T	ENSP00000040877:p.Cys751*	Somatic	58	0		WXS	Illumina HiSeq	.	99	4	NM_005646	Q9H581	Nonsense_Mutation	SNP	ENST00000040877.1	37	CCDS1601.1	.	.	.	.	.	.	.	.	.	.	G	38	6.817497	0.97861	.	.	ENSG00000059588	ENST00000040877	.	.	.	5.68	2.34	0.29019	.	0.102535	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.3545	6.9121	0.24340	0.4686:0.0:0.5314:0.0	.	.	.	.	X	751	.	ENSP00000040877:C751X	C	-	3	2	TARBP1	232635920	1.000000	0.71417	0.803000	0.32268	0.679000	0.39708	0.892000	0.28322	0.751000	0.32900	0.655000	0.94253	TGC	.		0.393	TARBP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092616.1	NM_005646	
C2CD2	25966	hgsc.bcm.edu	37	21	43327232	43327232	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr21:43327232G>T	ENST00000380486.3	-	10	1428	c.1187C>A	c.(1186-1188)cCt>cAt	p.P396H	C2CD2_ENST00000329623.7_Missense_Mutation_p.P241H	NM_015500.1	NP_056315.1	Q9Y426	CU025_HUMAN	C2 calcium-dependent domain containing 2	396						cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)		p.P396fs*9(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|stomach(1)	15						AACAGGGGGAGGGATGGGCCA	0.522																																					p.P396H		.											.,1	.	47	1	Deletion - Frameshift(1)	ovary(1)	c.C1187A						.						68.0	65.0	66.0					21																	43327232		2203	4300	6503	SO:0001583	missense	25966	exon10			GGGGGAGGGATGG	AB047784	CCDS13677.1, CCDS42933.1	21q22.3	2008-11-24	2007-10-17	2007-10-17	ENSG00000157617	ENSG00000157617			1266	protein-coding gene	gene with protein product	"""TMEM24-like"""		"""chromosome 21 open reading frame 25"""	C21orf25		15289880	Standard	NM_015500		Approved	TMEM24L, DKFZP586F0422, C21orf258	uc002yzw.3	Q9Y426	OTTHUMG00000086779	ENST00000380486.3:c.1187C>A	21.37:g.43327232G>T	ENSP00000369853:p.Pro396His	Somatic	36	0		WXS	Illumina HiSeq	.	35	3	NM_015500	Q5R2V7|Q6AHX8|Q9NSE6	Missense_Mutation	SNP	ENST00000380486.3	37	CCDS42933.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.151242	0.78001	.	.	ENSG00000157617	ENST00000329623;ENST00000380486	T;T	0.76709	-1.04;-1.04	4.9	4.9	0.64082	C2 calcium/lipid-binding domain, CaLB (1);	0.107611	0.64402	D	0.000003	D	0.84374	0.5458	L	0.48642	1.525	0.54753	D	0.999985	D;D	0.89917	1.0;1.0	D;D	0.67231	0.95;0.95	D	0.86081	0.1544	10	0.72032	D	0.01	-12.32	18.0791	0.89437	0.0:0.0:1.0:0.0	.	241;396	Q6P6D1;Q9Y426	.;CU025_HUMAN	H	241;396	ENSP00000329302:P241H;ENSP00000369853:P396H	ENSP00000329302:P241H	P	-	2	0	C2CD2	42200301	1.000000	0.71417	0.028000	0.17463	0.036000	0.12997	6.024000	0.70857	2.413000	0.81919	0.655000	0.94253	CCT	.		0.522	C2CD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195228.2	NM_015500	
DFNB59	494513	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	2	179318221	179318221	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:179318221G>A	ENST00000409117.3	+	2	441	c.85G>A	c.(85-87)Gac>Aac	p.D29N	PRKRA_ENST00000470200.1_5'Flank|DFNB59_ENST00000375129.4_Missense_Mutation_p.D29N|PRKRA_ENST00000438687.3_5'Flank|PRKRA_ENST00000325748.4_5'Flank|PRKRA_ENST00000432031.2_5'Flank|PRKRA_ENST00000487082.1_5'Flank	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	29					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			CAGTGAAGCTGACAAATATCA	0.378																																					p.D29N		.											.	.	.	0			c.G85A						.						126.0	113.0	117.0					2																	179318221		1858	4110	5968	SO:0001583	missense	494513	exon2			GAAGCTGACAAAT	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.85G>A	2.37:g.179318221G>A	ENSP00000386647:p.Asp29Asn	Somatic	68	0		WXS	Illumina HiSeq	.	94	5	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	G	35	5.448543	0.96205	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.26518	1.73;1.73	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.50497	0.1619	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.28744	-1.0034	10	0.49607	T	0.09	-13.0937	20.6397	0.99537	0.0:0.0:1.0:0.0	.	29	Q0ZLH3	PJVK_HUMAN	N	29	ENSP00000386647:D29N;ENSP00000364271:D29N	ENSP00000364271:D29N	D	+	1	0	DFNB59	179026467	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.880000	0.98712	0.650000	0.86243	GAC	.		0.378	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
CDC27	996	hgsc.bcm.edu	37	17	45234357	45234357	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:45234357G>T	ENST00000066544.3	-	7	857	c.764C>A	c.(763-765)tCt>tAt	p.S255Y	CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.S255Y|CDC27_ENST00000446365.2_Missense_Mutation_p.S194Y|CDC27_ENST00000527547.1_Missense_Mutation_p.S255Y	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	255					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						AACCTGTTTAGATAATATGGA	0.383																																					p.S255Y		.											.	.	.	0			c.C764A						.						55.0	61.0	59.0					17																	45234357		2199	4295	6494	SO:0001583	missense	996	exon7			TGTTTAGATAATA	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.764C>A	17.37:g.45234357G>T	ENSP00000066544:p.Ser255Tyr	Somatic	79	0		WXS	Illumina HiSeq	.	120	4	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	16.82	3.227484	0.58668	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.70631	-0.49;-0.45;-0.17;-0.5;0.76	5.64	5.64	0.86602	.	0.127889	0.52532	D	0.000064	T	0.57695	0.2071	N	0.14661	0.345	0.51767	D	0.999938	B;B;B;B	0.26081	0.055;0.141;0.001;0.001	B;B;B;B	0.25884	0.03;0.064;0.003;0.001	T	0.58070	-0.7701	10	0.62326	D	0.03	-1.7126	17.2083	0.86924	0.0:0.0:1.0:0.0	.	194;255;255;255	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	Y	255;255;194;255;255	ENSP00000066544:S255Y;ENSP00000434614:S255Y;ENSP00000392802:S194Y;ENSP00000437339:S255Y;ENSP00000432105:S255Y	ENSP00000066544:S255Y	S	-	2	0	CDC27	42589356	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.145000	0.71769	2.665000	0.90641	0.460000	0.39030	TCT	.		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
DMXL2	23312	hgsc.bcm.edu	37	15	51809289	51809289	+	Missense_Mutation	SNP	C	C	T	rs199866251		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:51809289C>T	ENST00000251076.5	-	14	2799	c.2512G>A	c.(2512-2514)Gca>Aca	p.A838T	DMXL2_ENST00000449909.3_Missense_Mutation_p.A838T|DMXL2_ENST00000543779.2_Missense_Mutation_p.A838T	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	838						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTGGTTATTGCGTCGAGTTCA	0.333																																					p.A838T		.											DMXL2,colon,carcinoma,0,2	DMXL2	0	0			c.G2512A						.	C	THR/ALA,THR/ALA,THR/ALA	0,4390		0,0,2195	152.0	147.0	149.0		2512,2512,2512	5.4	1.0	15		149	1,8585	1.2+/-3.3	0,1,4292	yes	missense,missense,missense	DMXL2	NM_001174116.1,NM_001174117.1,NM_015263.3	58,58,58	0,1,6487	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	838/3038,838/2401,838/3037	51809289	1,12975	2195	4293	6488	SO:0001583	missense	23312	exon14			TTATTGCGTCGAG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.2512G>A	15.37:g.51809289C>T	ENSP00000251076:p.Ala838Thr	Somatic	80	0		WXS	Illumina HiSeq	.	87	3	NM_001174117	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	37	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.113075	0.77210	0.0	1.16E-4	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909	T;T;T	0.32023	1.47;1.47;1.47	5.4	5.4	0.78164	.	0.049962	0.85682	D	0.000000	T	0.30417	0.0764	L	0.37750	1.13	0.34491	D	0.704933	P;D;D	0.57899	0.807;0.976;0.981	B;B;P	0.44597	0.087;0.353;0.454	T	0.27739	-1.0065	10	0.26408	T	0.33	.	19.2061	0.93730	0.0:1.0:0.0:0.0	.	838;838;838	F5GWF1;B2RTR3;Q8TDJ6	.;.;DMXL2_HUMAN	T	838	ENSP00000251076:A838T;ENSP00000441858:A838T;ENSP00000400855:A838T	ENSP00000251076:A838T	A	-	1	0	DMXL2	49596581	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.445000	0.80570	2.536000	0.85505	0.650000	0.86243	GCA	.		0.333	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
TCHH	7062	hgsc.bcm.edu	37	1	152084627	152084627	+	Missense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:152084627C>G	ENST00000368804.1	-	2	1065	c.1066G>C	c.(1066-1068)Gag>Cag	p.E356Q		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	356	5 X 13 AA tandem repeats of R-R-E-Q-E-E- E-R-R-E-Q-Q-L.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E356Q(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ctctcctcctcctgctcgcgc	0.716																																					p.E356Q		.											TCHH,NS,carcinoma,0,2	TCHH	0	1	Substitution - Missense(1)	kidney(1)	c.G1066C						.																																			SO:0001583	missense	7062	exon3			CCTCCTCCTGCTC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1066G>C	1.37:g.152084627C>G	ENSP00000357794:p.Glu356Gln	Somatic	19	1		WXS	Illumina HiSeq	.	36	4	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	N	7.510	0.654399	0.14580	.	.	ENSG00000159450	ENST00000368804	T	0.05319	3.46	3.05	-0.676	0.11361	.	.	.	.	.	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.06405	0.002	T	0.47509	-0.9112	9	0.21540	T	0.41	.	6.5749	0.22560	0.0:0.3165:0.5607:0.1228	.	356	Q07283	TRHY_HUMAN	Q	356	ENSP00000357794:E356Q	ENSP00000357794:E356Q	E	-	1	0	TCHH	150351251	0.000000	0.05858	0.021000	0.16686	0.029000	0.11900	-0.248000	0.08854	0.122000	0.18314	0.441000	0.28932	GAG	.		0.716	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TMEM178A	130733	hgsc.bcm.edu	37	2	39944386	39944386	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:39944386G>T	ENST00000281961.2	+	4	945	c.889G>T	c.(889-891)Gta>Tta	p.V297L	TMEM178A_ENST00000482239.1_3'UTR	NM_152390.2	NP_689603.2	Q8NBL3	T178A_HUMAN	transmembrane protein 178A	297						integral component of membrane (GO:0016021)											AGACTCCACGGTATGACTGTC	0.532																																					p.V297L		.											TMEM178,NS,malignant_melanoma,0,1	TMEM178	0	0			c.G889T						.						89.0	82.0	85.0					2																	39944386		2203	4300	6503	SO:0001583	missense	130733	exon4			TCCACGGTATGAC	BC029530	CCDS1804.1	2p22.1	2012-06-29	2012-06-29	2012-06-29	ENSG00000152154	ENSG00000152154			28517	protein-coding gene	gene with protein product			"""transmembrane protein 178"""	TMEM178		12975309	Standard	NM_001167959		Approved	MGC33926	uc002rrt.3	Q8NBL3	OTTHUMG00000128591	ENST00000281961.2:c.889G>T	2.37:g.39944386G>T	ENSP00000281961:p.Val297Leu	Somatic	26	0		WXS	Illumina HiSeq	.	31	2	NM_152390	Q6UWI6|Q8N6N4	Missense_Mutation	SNP	ENST00000281961.2	37	CCDS1804.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.949897	0.92660	.	.	ENSG00000152154	ENST00000281961	T	0.50277	0.75	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.30166	0.0756	N	0.08118	0	0.80722	D	1	P	0.41929	0.765	B	0.38921	0.285	T	0.10497	-1.0627	9	.	.	.	.	17.7923	0.88558	0.0:0.0:1.0:0.0	.	297	Q8NBL3	TM178_HUMAN	L	297	ENSP00000281961:V297L	.	V	+	1	0	TMEM178	39797890	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.923000	0.87546	2.793000	0.96121	0.655000	0.94253	GTA	.		0.532	TMEM178A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250445.2	NM_152390	
BGN	633	hgsc.bcm.edu;bcgsc.ca	37	X	152771327	152771327	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:152771327G>T	ENST00000331595.4	+	4	544	c.358G>T	c.(358-360)Gtc>Ttc	p.V120F	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	120					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCAGGCCCTCGTCCTGGTGAA	0.617																																					p.V120F		.											.	.	.	0			c.G358T						.						40.0	32.0	35.0					X																	152771327		2203	4297	6500	SO:0001583	missense	633	exon4			GCCCTCGTCCTGG	AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.358G>T	X.37:g.152771327G>T	ENSP00000327336:p.Val120Phe	Somatic	35	0		WXS	Illumina HiSeq	.	53	4	NM_001711	D3DWU3|P13247	Missense_Mutation	SNP	ENST00000331595.4	37	CCDS14721.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436776	0.25900	.	.	ENSG00000182492	ENST00000331595;ENST00000431891;ENST00000370204;ENST00000430380	T;T;T	0.57907	0.37;0.39;0.37	4.87	4.87	0.63330	.	0.134859	0.49916	D	0.000122	T	0.34366	0.0895	N	0.05441	-0.05	0.40391	D	0.979541	B	0.14012	0.009	B	0.12156	0.007	T	0.14337	-1.0476	10	0.33141	T	0.24	-43.3383	16.1375	0.81497	0.0:0.0:1.0:0.0	.	120	P21810	PGS1_HUMAN	F	120;137;59;59	ENSP00000327336:V120F;ENSP00000402525:V137F;ENSP00000359223:V59F	ENSP00000327336:V120F	V	+	1	0	BGN	152424521	0.198000	0.23374	0.924000	0.36721	0.853000	0.48598	1.376000	0.34306	2.148000	0.66965	0.476000	0.43555	GTC	.		0.617	BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711	
SPTBN1	6711	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	54858390	54858390	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:54858390G>T	ENST00000356805.4	+	16	3487	c.3206G>T	c.(3205-3207)cGg>cTg	p.R1069L	SPTBN1_ENST00000333896.5_Missense_Mutation_p.R1056L	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1069					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			CAGTTCCTACGGGACTTGGAC	0.617																																					p.R1069L		.											.	.	.	0			c.G3206T						.						69.0	75.0	73.0					2																	54858390		2203	4300	6503	SO:0001583	missense	6711	exon16			TCCTACGGGACTT		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3206G>T	2.37:g.54858390G>T	ENSP00000349259:p.Arg1069Leu	Somatic	39	0		WXS	Illumina HiSeq	.	35	7	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	G	32	5.160668	0.94727	.	.	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.54675	0.56;0.56	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.59280	0.2182	L	0.60845	1.875	0.80722	D	1	B;P	0.37997	0.194;0.614	B;B	0.42771	0.143;0.397	T	0.62459	-0.6850	10	0.72032	D	0.01	.	19.5375	0.95260	0.0:0.0:1.0:0.0	.	1056;1069	Q01082-3;Q01082	.;SPTB2_HUMAN	L	1069;1056	ENSP00000349259:R1069L;ENSP00000334156:R1056L	ENSP00000334156:R1056L	R	+	2	0	SPTBN1	54711894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.807000	0.99171	2.620000	0.88729	0.655000	0.94253	CGG	.		0.617	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
CLNK	116449	hgsc.bcm.edu;bcgsc.ca	37	4	10560060	10560060	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:10560060G>T	ENST00000226951.6	-	8	655	c.416C>A	c.(415-417)tCc>tAc	p.S139Y	CLNK_ENST00000507719.1_Missense_Mutation_p.S97Y|CLNK_ENST00000442825.2_Missense_Mutation_p.S97Y	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	139					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						GACGTCCTTGGAAATGGGTTT	0.383																																					p.S139Y	GBM(87;402 1286 6949 13902 35851)	.											.	.	.	0			c.C416A						.						215.0	202.0	206.0					4																	10560060		1918	4135	6053	SO:0001583	missense	116449	exon8			TCCTTGGAAATGG	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.416C>A	4.37:g.10560060G>T	ENSP00000226951:p.Ser139Tyr	Somatic	82	0		WXS	Illumina HiSeq	.	91	4	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	.	.	.	.	.	.	.	.	.	.	G	9.336	1.061874	0.19987	.	.	ENSG00000109684	ENST00000226951;ENST00000429087;ENST00000442825;ENST00000507719	T;T;T	0.48522	1.8;0.81;0.81	4.53	2.75	0.32379	.	2.803700	0.01019	N	0.003945	T	0.52789	0.1756	L	0.32530	0.975	0.09310	N	1	D;P	0.53462	0.96;0.785	P;B	0.55303	0.773;0.275	T	0.40289	-0.9571	10	0.59425	D	0.04	-10.0761	6.7454	0.23458	0.2141:0.0:0.7859:0.0	.	97;139	Q7Z7G1-2;Q7Z7G1	.;CLNK_HUMAN	Y	139;139;97;97	ENSP00000226951:S139Y;ENSP00000390744:S97Y;ENSP00000427208:S97Y	ENSP00000226951:S139Y	S	-	2	0	CLNK	10169158	0.036000	0.19791	0.300000	0.25030	0.451000	0.32288	0.454000	0.21827	1.222000	0.43521	0.551000	0.68910	TCC	.		0.383	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964	
ARHGEF38	54848	hgsc.bcm.edu;broad.mit.edu	37	4	106552107	106552107	+	Nonsense_Mutation	SNP	C	C	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:106552107C>G	ENST00000420470.2	+	4	705	c.561C>G	c.(559-561)taC>taG	p.Y187*	ARHGEF38_ENST00000265154.2_Nonsense_Mutation_p.Y187*	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	187	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						ATAAAATCTACTGCTATCACC	0.383																																					p.Y187X		.											.	.	.	0			c.C561G						.						120.0	114.0	116.0					4																	106552107		2203	4300	6503	SO:0001587	stop_gained	54848	exon4			AATCTACTGCTAT	AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"""Rho guanine nucleotide exchange factors"""	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.561C>G	4.37:g.106552107C>G	ENSP00000416125:p.Tyr187*	Somatic	43	0		WXS	Illumina HiSeq	.	50	5	NM_001242729	C9JIB4	Nonsense_Mutation	SNP	ENST00000420470.2	37	CCDS56338.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.745906	0.89663	.	.	ENSG00000236699	ENST00000265154;ENST00000420470	.	.	.	4.92	4.06	0.47325	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6034	11.7701	0.51953	0.0:0.8498:0.0:0.1502	.	.	.	.	X	187	.	ENSP00000265154:Y187X	Y	+	3	2	ARHGEF38	106771556	0.999000	0.42202	1.000000	0.80357	0.954000	0.61252	0.664000	0.25068	1.036000	0.39998	0.591000	0.81541	TAC	.		0.383	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700	
PRMT7	54496	hgsc.bcm.edu	37	16	68355328	68355328	+	Splice_Site	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:68355328G>T	ENST00000339507.5	+	4	925		c.e4-1		PRMT7_ENST00000449359.3_Splice_Site|PRMT7_ENST00000441236.1_Splice_Site|PRMT7_ENST00000348497.4_Splice_Site|PRMT7_ENST00000564441.1_Splice_Site|RP11-96D1.3_ENST00000563203.1_RNA			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7						cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		TTGTTTTTTAGGTCATCTTAT	0.338																																					.		.											.	.	.	0			c.96-1G>T						.						265.0	240.0	248.0					16																	68355328		2198	4300	6498	SO:0001630	splice_region_variant	54496	exon3			TTTTTAGGTCATC	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.96-1G>T	16.37:g.68355328G>T		Somatic	100	0		WXS	Illumina HiSeq	.	99	4	NM_001184824	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Splice_Site	SNP	ENST00000339507.5	37	CCDS10866.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708414	0.68615	.	.	ENSG00000132600	ENST00000449359;ENST00000441236;ENST00000348497;ENST00000339507	.	.	.	5.16	5.16	0.70880	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5181	0.84306	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PRMT7	66912829	1.000000	0.71417	0.999000	0.59377	0.735000	0.41995	9.149000	0.94659	2.574000	0.86865	0.462000	0.41574	.	.		0.338	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	Intron
FCRLA	84824	hgsc.bcm.edu	37	1	161682007	161682007	+	Splice_Site	SNP	G	G	T	rs569112764		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:161682007G>T	ENST00000236938.6	+	4	1076	c.834G>T	c.(832-834)caG>caT	p.Q278H	FCRLA_ENST00000367957.2_Splice_Site_p.Q138H|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000309691.6_Splice_Site_p.Q172H|FCRLA_ENST00000367950.1_Intron|FCRLA_ENST00000540926.1_Splice_Site_p.Q267H|FCRLA_ENST00000367959.2_Splice_Site_p.Q284H|FCRLA_ENST00000367953.3_Splice_Site_p.Q267H|FCRLA_ENST00000349527.4_Intron|FCRLA_ENST00000367949.2_Intron|FCRLA_ENST00000540521.1_Splice_Site_p.Q144H|FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000546024.1_Splice_Site_p.Q189H|FCRLA_ENST00000294796.4_Splice_Site_p.Q127H	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	261	Pro-rich.				cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)		p.Q284H(1)|p.Q261H(1)		breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			TCAGAGTGCAGGGTGAGTTCG	0.527																																					p.Q284H		.											FCRLA_ENST00000367959,NS,carcinoma,0,2	FCRLA_ENST00000367959	0	2	Substitution - Missense(2)	lung(2)	c.G852T						.						69.0	67.0	68.0					1																	161682007		2203	4300	6503	SO:0001630	splice_region_variant	84824	exon5			AGTGCAGGGTGAG	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18504	protein-coding gene	gene with protein product		606891	"""Fc receptor-like and mucin-like 1"""	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.835+1G>T	1.37:g.161682007G>T		Somatic	12	0		WXS	Illumina HiSeq	.	22	2	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Missense_Mutation	SNP	ENST00000236938.6	37	CCDS30926.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.169710	0.38315	.	.	ENSG00000132185	ENST00000236938;ENST00000367959;ENST00000546024;ENST00000540521;ENST00000540926;ENST00000367957;ENST00000309691;ENST00000294796;ENST00000367953	T;T;T;T;T;T;T;T;T	0.59083	0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29;0.29	5.81	1.63	0.23807	.	0.410667	0.21013	N	0.081659	T	0.23532	0.0569	L	0.34521	1.04	0.31787	N	0.630172	B;B;B;B;B	0.24258	0.086;0.064;0.1;0.013;0.018	B;B;B;B;B	0.33196	0.159;0.052;0.034;0.005;0.067	T	0.07102	-1.0790	10	0.48119	T	0.1	.	2.3675	0.04323	0.1673:0.1395:0.528:0.1653	.	144;138;189;284;278	F5H720;Q5VXB1;G3V1J2;A6NC03;Q7L513-9	.;.;.;.;.	H	278;284;189;144;267;138;172;127;267	ENSP00000236938:Q278H;ENSP00000356936:Q284H;ENSP00000439838:Q189H;ENSP00000442870:Q144H;ENSP00000446380:Q267H;ENSP00000356934:Q138H;ENSP00000309596:Q172H;ENSP00000294796:Q127H;ENSP00000356930:Q267H	ENSP00000236938:Q278H	Q	+	3	2	FCRLA	159948631	0.996000	0.38824	0.999000	0.59377	0.938000	0.57974	0.131000	0.15870	0.312000	0.23038	0.591000	0.81541	CAG	.		0.527	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738	Missense_Mutation
MARK4	57787	hgsc.bcm.edu;bcgsc.ca	37	19	45790748	45790748	+	Silent	SNP	G	G	T	rs112982501		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:45790748G>T	ENST00000262891.4	+	13	1651	c.1320G>T	c.(1318-1320)acG>acT	p.T440T	MARK4_ENST00000300843.4_Silent_p.T440T	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	440					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)			NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GCAGCCCGACGAGCACGGGGG	0.701																																					p.T440T		.											.	.	.	0			c.G1320T						.						9.0	11.0	11.0					19																	45790748		2154	4233	6387	SO:0001819	synonymous_variant	57787	exon13			CCCGACGAGCACG	AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"""MAP/microtubule affinity-regulating kinase like 1"""	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1320G>T	19.37:g.45790748G>T		Somatic	63	0		WXS	Illumina HiSeq	.	70	4	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Silent	SNP	ENST00000262891.4	37	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	G	9.848	1.192819	0.21954	.	.	ENSG00000007047	ENST00000262893	.	.	.	5.06	0.439	0.16567	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	1.904	0.03273	0.1401:0.332:0.3416:0.1863	.	.	.	.	X	405	.	ENSP00000262893:E405X	E	+	1	0	MARK4	50482588	0.774000	0.28592	1.000000	0.80357	0.891000	0.51852	-0.158000	0.10070	0.737000	0.32582	0.591000	0.81541	GAG	.		0.701	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417	
LRRC71	149499	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	156901798	156901798	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:156901798C>T	ENST00000337428.7	+	13	1574	c.1420C>T	c.(1420-1422)Ctt>Ttt	p.L474F	LRRC71_ENST00000490146.1_3'UTR|ARHGEF11_ENST00000487682.1_5'Flank	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	474										endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						GAACAAGGTCCTTTTGCACCT	0.572																																					p.L474F		.											.	.	.	0			c.C1420T						.						78.0	82.0	81.0					1																	156901798		2055	4188	6243	SO:0001583	missense	149499	exon13			AAGGTCCTTTTGC	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1420C>T	1.37:g.156901798C>T	ENSP00000336661:p.Leu474Phe	Somatic	52	0		WXS	Illumina HiSeq	.	76	8	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.726647	0.89298	.	.	ENSG00000160838	ENST00000337428	T	0.80123	-1.34	5.68	5.68	0.88126	.	0.000000	0.45126	D	0.000384	D	0.87525	0.6199	M	0.70275	2.135	0.47441	D	0.999426	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.88266	0.2926	10	0.72032	D	0.01	-12.4493	16.7107	0.85384	0.0:1.0:0.0:0.0	.	474;260	Q8N4P6;Q8N4P6-2	LRC71_HUMAN;.	F	474	ENSP00000336661:L474F	ENSP00000336661:L474F	L	+	1	0	LRRC71	155168422	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	5.511000	0.67024	2.668000	0.90789	0.563000	0.77884	CTT	.		0.572	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
APOB	338	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	21246522	21246522	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:21246522G>T	ENST00000233242.1	-	17	2606	c.2479C>A	c.(2479-2481)Ctt>Att	p.L827I		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	827					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.L827V(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGTAGTGAAGAAAAAAGTCA	0.433																																					p.L827I		.											APOB,NS,carcinoma,0,1	APOB	0	1	Substitution - Missense(1)	cervix(1)	c.C2479A						.						80.0	74.0	76.0					2																	21246522		2203	4300	6503	SO:0001583	missense	338	exon17			AGTGAAGAAAAAA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2479C>A	2.37:g.21246522G>T	ENSP00000233242:p.Leu827Ile	Somatic	64	0		WXS	Illumina HiSeq	.	84	10	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368844	0.61624	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.14766	2.48	5.35	4.42	0.53409	Lipid transport protein, beta-sheet shell (1);Vitellinogen, open beta-sheet (1);Vitellinogen, open beta-sheet, subdomain 2 (1);	0.125341	0.35235	N	0.003356	T	0.25121	0.0610	M	0.76574	2.34	0.80722	D	1	P	0.52842	0.956	P	0.48982	0.597	T	0.01401	-1.1364	10	0.40728	T	0.16	.	14.5927	0.68378	0.0:0.2318:0.7682:0.0	.	827	P04114	APOB_HUMAN	I	827	ENSP00000233242:L827I	ENSP00000233242:L827I	L	-	1	0	APOB	21100027	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.305000	0.59110	2.675000	0.91044	0.655000	0.94253	CTT	.		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
KHK	3795	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	27310211	27310211	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:27310211G>A	ENST00000260599.6	+	1	597	c.84G>A	c.(82-84)tcG>tcA	p.S28S	KHK_ENST00000490823.1_3'UTR|KHK_ENST00000260598.5_Silent_p.S28S	NM_000221.2	NP_000212.1	P50053	KHK_HUMAN	ketohexokinase (fructokinase)	28					carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose catabolic process (GO:0006001)|regulation of glycogen metabolic process (GO:0070873)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ketohexokinase activity (GO:0004454)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGAGGACTCGGAGATAAGGT	0.627																																					p.S28S		.											.	.	.	0			c.G84A						.						77.0	67.0	70.0					2																	27310211		2199	4299	6498	SO:0001819	synonymous_variant	3795	exon1			GGACTCGGAGATA		CCDS1734.1, CCDS1735.1	2p23.3-p23.2	2008-02-05			ENSG00000138030	ENSG00000138030	2.7.1.3		6315	protein-coding gene	gene with protein product		614058				7833921	Standard	NM_000221		Approved		uc002rim.2	P50053	OTTHUMG00000097077	ENST00000260599.6:c.84G>A	2.37:g.27310211G>A		Somatic	59	0		WXS	Illumina HiSeq	.	61	18	NM_006488	Q6IBK2|Q99532|Q9BRJ3|Q9UMN1	Silent	SNP	ENST00000260599.6	37	CCDS1734.1																																																																																			.		0.627	KHK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214196.1		
LAMA4	3910	hgsc.bcm.edu	37	6	112510361	112510361	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:112510361G>T	ENST00000230538.7	-	7	1162	c.765C>A	c.(763-765)tgC>tgA	p.C255*	LAMA4_ENST00000524032.1_5'Flank|LAMA4_ENST00000424408.2_Nonsense_Mutation_p.C255*|LAMA4_ENST00000522006.1_Nonsense_Mutation_p.C255*|LAMA4_ENST00000389463.4_Nonsense_Mutation_p.C255*	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	255	Laminin EGF-like 4; truncated. {ECO:0000255|PROSITE-ProRule:PRU00460}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CTTCTTCCAAGCATTCTCCGG	0.443																																					p.C255X		.											.	.	.	0			c.C765A						.						114.0	102.0	106.0					6																	112510361		2203	4300	6503	SO:0001587	stop_gained	3910	exon7			TTCCAAGCATTCT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.765C>A	6.37:g.112510361G>T	ENSP00000230538:p.Cys255*	Somatic	57	0		WXS	Illumina HiSeq	.	87	3	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Nonsense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	39|39|39	7.872090|7.872090|7.872090	0.98537|0.98537|0.98537	.|.|.	.|.|.	ENSG00000112769|ENSG00000112769|ENSG00000112769	ENST00000368640|ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408;ENST00000454881;ENST00000521398;ENST00000542588|ENST00000521732	.|.|.	.|.|.	.|.|.	5.5|5.5|5.5	2.76|2.76|2.76	0.32466|0.32466|0.32466	.|.|.	.|0.047545|.	.|0.85682|.	.|D|.	.|0.000000|.	T|.|T	0.44540|.|0.44540	0.1298|.|0.1298	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|.|T	0.37842|.|0.37842	-0.9688|.|-0.9688	4|.|4	.|0.02654|.	.|T|.	.|1|.	.|.|.	8.7189|8.7189|8.7189	0.34428|0.34428|0.34428	0.287:0.0:0.713:0.0|0.287:0.0:0.713:0.0|0.287:0.0:0.713:0.0	.|.|.	.|.|.	.|.|.	.|.|.	D|X|I	59|255|75	.|.|.	.|ENSP00000230538:C255X|.	A|C|L	-|-|-	2|3|1	0|2|0	LAMA4|LAMA4|LAMA4	112617054|112617054|112617054	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.985000|0.985000|0.985000	0.73830|0.73830|0.73830	1.169000|1.169000|1.169000	0.31871|0.31871|0.31871	0.821000|0.821000|0.821000	0.34540|0.34540|0.34540	-0.126000|-0.126000|-0.126000	0.14955|0.14955|0.14955	GCT|TGC|CTT	.		0.443	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
GLG1	2734	hgsc.bcm.edu	37	16	74502875	74502875	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:74502875C>T	ENST00000422840.2	-	17	2404	c.2405G>A	c.(2404-2406)cGc>cAc	p.R802H	GLG1_ENST00000205061.5_Missense_Mutation_p.R802H|GLG1_ENST00000447066.2_Missense_Mutation_p.R791H	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1	802					blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.R802H(1)		breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						GAGCTGCCTGCGGCACTTCAG	0.612																																					p.R802H		.											GLG1,NS,carcinoma,0,1	GLG1	0	1	Substitution - Missense(1)	breast(1)	c.G2405A						.						60.0	50.0	54.0					16																	74502875		2198	4300	6498	SO:0001583	missense	2734	exon17			TGCCTGCGGCACT		CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2405G>A	16.37:g.74502875C>T	ENSP00000405984:p.Arg802His	Somatic	39	0		WXS	Illumina HiSeq	.	42	3	NM_001145667	B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Missense_Mutation	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	C	35	5.544072	0.96488	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.80014	0.4546	M	0.76574	2.34	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72075	0.973;0.975;0.976	T	0.81571	-0.0872	9	0.72032	D	0.01	-19.6127	19.456	0.94889	0.0:1.0:0.0:0.0	.	802;802;791	Q92896;Q92896-2;B7Z8Y4	GSLG1_HUMAN;.;.	H	802;791;802	.	ENSP00000205061:R802H	R	-	2	0	GLG1	73060376	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.814000	0.86154	2.598000	0.87819	0.467000	0.42956	CGC	.		0.612	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1	NM_012201	
CROCCP3	114819	broad.mit.edu	37	1	16812982	16812982	+	RNA	SNP	A	A	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:16812982A>C	ENST00000263511.4	-	0	1329					NR_023386.1		Q8IVE0	CROL2_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 3						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											AGGTCCTTCTAGTGGAGCACC	0.667																																					.													.	.	.	0			.						.																																					0	.			CCTTCTAGTGGAG	AB067509		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000080947	ENSG00000080947			29405	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 2"""	CROCCL2		11572484	Standard	NR_023386		Approved	KIAA1922	uc001ayt.2	Q8IVE0	OTTHUMG00000037885		1.37:g.16812982A>C		Somatic	38	1		WXS	Illumina GAIIx	Phase_I	51	8	.	Q96PW6	RNA	SNP	ENST00000263511.4	37																																																																																				.		0.667	CROCCP3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000458172.1	XM_057040	
CROCCP2	84809	broad.mit.edu	37	1	16957311	16957311	+	lincRNA	SNP	A	A	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:16957311A>C	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											ACACGCCCCCACCCCCACCTG	0.662																																					.													.	.	.	0			.						.																																					0	.			GCCCCCACCCCCA	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16957311A>C		Somatic	44	2		WXS	Illumina GAIIx	Phase_I	53	7	.	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																				.		0.662	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000092784.1	NR_026752.1	
RP5-965F6.2	0	broad.mit.edu	37	1	112810518	112810518	+	lincRNA	DEL	G	G	-			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:112810518delG	ENST00000427290.1	-	0	167																											ctttttttttgactggtttta	0.378																																					.													.	.	.	0			.						.						102.0	80.0	86.0					1																	112810518		692	1591	2283			0	.			TTTTTTGACTGGT																													1.37:g.112810518delG		Somatic	101	0		WXS	Illumina GAIIx	Phase_I	159	14	.		RNA	DEL	ENST00000427290.1	37																																																																																				.		0.378	RP5-965F6.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000033693.1		
OR2T12	127064	broad.mit.edu;bcgsc.ca	37	1	248458309	248458309	+	Missense_Mutation	SNP	G	G	A	rs138674715		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr1:248458309G>A	ENST00000317996.1	-	1	571	c.572C>T	c.(571-573)tCa>tTa	p.S191L		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TTCGAAGACTGAAGTGTCAGC	0.537																																					p.S191L													.	OR2T12	113	0			c.C572T						.	G	LEU/SER	0,4402		0,0,2201	113.0	87.0	96.0		572	0.3	0.1	1	dbSNP_134	96	1,8595	1.2+/-3.3	0,1,4297	no	missense	OR2T12	NM_001004692.1	145	0,1,6498	AA,AG,GG		0.0116,0.0,0.0077	benign	191/321	248458309	1,12997	2201	4298	6499	SO:0001583	missense	127064	exon1			AAGACTGAAGTGT	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.572C>T	1.37:g.248458309G>A	ENSP00000324583:p.Ser191Leu	Somatic	64	0		WXS	Illumina GAIIx	Phase_I	83	12	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	9.564	1.119291	0.20877	0.0	1.16E-4	ENSG00000177201	ENST00000317996	T	0.00152	8.66	1.55	0.316	0.15857	GPCR, rhodopsin-like superfamily (1);	0.311562	0.17801	U	0.161576	T	0.00144	0.0004	L	0.45581	1.43	0.09310	N	1	B	0.14012	0.009	B	0.20384	0.029	T	0.18555	-1.0333	10	0.37606	T	0.19	.	6.3399	0.21316	0.0:0.0:0.4592:0.5408	.	191	Q8NG77	O2T12_HUMAN	L	191	ENSP00000324583:S191L	ENSP00000324583:S191L	S	-	2	0	OR2T12	246524932	0.000000	0.05858	0.080000	0.20451	0.369000	0.29798	-3.982000	0.00320	0.645000	0.30675	0.175000	0.17021	TCA	G|1.000;A|0.000		0.537	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
OR51A4	401666	broad.mit.edu	37	11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	rs201205025	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:4967834C>G	ENST00000380373.2	-	1	522	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(15)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;3.22e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0284)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTCAAGTTTCTTAAAGTGAA	0.413													.|||	12	0.00239617	0.003	0.0029	5008	,	,		24981	0.0		0.003	False		,,,				2504	0.0031				p.R166T													OR51A4,colon,carcinoma,-1,1	OR51A4	73	0			c.G497C						.						212.0	198.0	203.0					11																	4967834		2177	4245	6422	SO:0001583	missense	401666	exon1			AAGTTTCTTAAAG	AB065798	CCDS31367.1	11p15.4	2012-08-09			ENSG00000205497	ENSG00000205497		"""GPCR / Class A : Olfactory receptors"""	14795	protein-coding gene	gene with protein product							Standard	NM_001005329		Approved		uc010qys.2	Q8NGJ6	OTTHUMG00000066614	ENST00000380373.2:c.497G>C	11.37:g.4967834C>G	ENSP00000369731:p.Arg166Thr	Somatic	54	1		WXS	Illumina GAIIx	Phase_I	70	3	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080491	0.20309	.	.	ENSG00000205497	ENST00000380373	T	0.71817	-0.6	3.44	-3.66	0.04489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59046	0.2165	L	0.41027	1.25	0.09310	N	1	B	0.23249	0.082	B	0.27608	0.081	T	0.52041	-0.8628	9	0.66056	D	0.02	.	9.2359	0.37466	0.0:0.303:0.0:0.697	.	166	Q8NGJ6	O51A4_HUMAN	T	166	ENSP00000369731:R166T	ENSP00000369731:R166T	R	-	2	0	OR51A4	4924410	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.905000	0.04075	-1.059000	0.03193	0.479000	0.44913	AGA	.		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329	
OR10A5	144124	broad.mit.edu	37	11	6867462	6867462	+	Silent	SNP	G	G	A	rs543931840		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:6867462G>A	ENST00000299454.4	+	1	580	c.549G>A	c.(547-549)ccG>ccA	p.P183P	OR10A5_ENST00000379831.2_Silent_p.P187P			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	183					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P183P(2)		endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(1)|skin(2)|urinary_tract(2)	21		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.68e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		GTGACAGCCCGCCTGTGCTGA	0.527													A|||	1	0.000199681	0.0	0.0	5008	,	,		23000	0.001		0.0	False		,,,				2504	0.0				p.P183P	Pancreas(44;21 1072 25662 28041 45559)												OR10A5,NS,carcinoma,0,3	OR10A5	48	2	Substitution - coding silent(2)	kidney(2)	c.G549A						.						180.0	152.0	161.0					11																	6867462		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			CAGCCCGCCTGTG	AF324499	CCDS7773.1	11p15.4	2012-08-09			ENSG00000166363	ENSG00000166363		"""GPCR / Class A : Olfactory receptors"""	15131	protein-coding gene	gene with protein product		608493		OR10A1			Standard	NM_178168		Approved	OR11-403, JCG6	uc001met.1	Q9H207	OTTHUMG00000165738	ENST00000299454.4:c.549G>A	11.37:g.6867462G>A		Somatic	42	0		WXS	Illumina GAIIx	Phase_I	57	4	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																			.		0.527	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168	
SLC43A3	29015	broad.mit.edu	37	11	57177487	57177487	+	Missense_Mutation	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:57177487G>C	ENST00000395123.2	-	12	1472	c.1168C>G	c.(1168-1170)Ctc>Gtc	p.L390V	RP11-872D17.8_ENST00000529411.1_Missense_Mutation_p.L34V|SLC43A3_ENST00000529554.1_Missense_Mutation_p.L390V|SLC43A3_ENST00000352187.1_Missense_Mutation_p.L390V|SLC43A3_ENST00000395124.1_Missense_Mutation_p.L390V|SLC43A3_ENST00000533524.1_Missense_Mutation_p.L403V	NM_001278201.1|NM_014096.2	NP_001265130.1|NP_054815.2	Q8NBI5	S43A3_HUMAN	solute carrier family 43, member 3	390					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(10)|lung(4)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	27						AGGTACTGGAGAGGGAGGATG	0.642																																					p.L390V													.	SLC43A3	54	0			c.C1168G						.						101.0	78.0	86.0					11																	57177487		2201	4296	6497	SO:0001583	missense	29015	exon12			ACTGGAGAGGGAG	AL157431	CCDS7956.1, CCDS60784.1	11q11	2013-05-22			ENSG00000134802	ENSG00000134802		"""Solute carriers"""	17466	protein-coding gene	gene with protein product	"""likely ortholog of mouse embryonic epithelial gene 1"""					7531438, 11704567	Standard	NM_017611		Approved	SEEEG-1, Eeg1, DKFZp762A227, FOAP-13, PRO1659	uc001nki.3	Q8NBI5	OTTHUMG00000167113	ENST00000395123.2:c.1168C>G	11.37:g.57177487G>C	ENSP00000378555:p.Leu390Val	Somatic	31	0		WXS	Illumina GAIIx	Phase_I	55	3	NM_017611	B4DNR8|E7EQD2|Q9NSS4	Missense_Mutation	SNP	ENST00000395123.2	37	CCDS7956.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.355579	0.41700	.	.	ENSG00000254979;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802;ENSG00000134802	ENST00000529411;ENST00000395123;ENST00000395124;ENST00000352187;ENST00000529554;ENST00000533524	D;T;T;T;T;T	0.81996	-1.56;0.25;0.25;0.25;0.25;0.25	5.65	4.69	0.59074	Major facilitator superfamily domain, general substrate transporter (1);	0.133678	0.51477	D	0.000089	D	0.84813	0.5555	L	0.55834	1.745	0.41843	D	0.990136	P;P	0.41848	0.701;0.763	P;P	0.54706	0.759;0.479	T	0.83029	-0.0163	10	0.39692	T	0.17	-37.2769	8.7871	0.34827	0.0:0.162:0.6702:0.1678	.	403;390	E7EQD2;Q8NBI5	.;S43A3_HUMAN	V	34;390;390;390;390;403	ENSP00000431536:L34V;ENSP00000378555:L390V;ENSP00000378556:L390V;ENSP00000337561:L390V;ENSP00000436254:L390V;ENSP00000434515:L403V	ENSP00000431536:L34V	L	-	1	0	RP11-872D17.8;SLC43A3	56934063	0.999000	0.42202	0.945000	0.38365	0.189000	0.23516	3.225000	0.51246	2.656000	0.90262	0.655000	0.94253	CTC	.		0.642	SLC43A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393057.1	NM_017611	
ANKRD33	341405	broad.mit.edu	37	12	52284827	52284827	+	Intron	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:52284827C>T	ENST00000340970.4	+	5	1035				ANKRD33_ENST00000301190.6_Missense_Mutation_p.S366F|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Intron			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		CCCCAGAGGTCCCCGTGGGTC	0.657																																					p.S366F													.	ANKRD33	33	0			c.C1097T						.						32.0	33.0	32.0					12																	52284827		2203	4300	6503	SO:0001627	intron_variant	341405	exon5			AGAGGTCCCCGTG		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.664+58C>T	12.37:g.52284827C>T		Somatic	21	0		WXS	Illumina GAIIx	Phase_I	20	3	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	.	.	.	.	.	.	.	.	.	.	C	2.321	-0.355616	0.05138	.	.	ENSG00000167612	ENST00000301190	T	0.24350	1.86	0.235	0.235	0.15431	.	4.767820	0.02797	U	0.122803	T	0.24774	0.0601	.	.	.	0.09310	N	0.999998	P	0.43094	0.799	B	0.41813	0.367	T	0.27806	-1.0063	9	0.72032	D	0.01	-17.1012	5.932	0.19144	0.0:1.0:0.0:0.0	.	366	Q7Z3H0-2	.	F	366	ENSP00000301190:S366F	ENSP00000301190:S366F	S	+	2	0	ANKRD33	50571094	0.002000	0.14202	0.002000	0.10522	0.005000	0.04900	0.441000	0.21611	0.308000	0.22923	0.313000	0.20887	TCC	.		0.657	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
NAP1L1	4673	broad.mit.edu	37	12	76444323	76444323	+	Missense_Mutation	SNP	A	A	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:76444323A>T	ENST00000261182.8	-	12	1533	c.1047T>A	c.(1045-1047)gaT>gaA	p.D349E	NAP1L1_ENST00000393263.3_Missense_Mutation_p.D349E|NAP1L1_ENST00000547993.1_Missense_Mutation_p.D166E|NAP1L1_ENST00000542344.1_Missense_Mutation_p.D307E|NAP1L1_ENST00000549596.1_Missense_Mutation_p.D349E|NAP1L1_ENST00000535020.2_Missense_Mutation_p.D349E|NAP1L1_ENST00000548044.1_Missense_Mutation_p.D308E|NAP1L1_ENST00000431879.3_Missense_Mutation_p.D281E|NAP1L1_ENST00000552342.1_Missense_Mutation_p.D360E|NAP1L1_ENST00000547773.1_Missense_Mutation_p.D286E|NAP1L1_ENST00000544816.1_Missense_Mutation_p.D166E	NM_004537.4|NM_139207.2	NP_004528.1|NP_631946.1	P55209	NP1L1_HUMAN	nucleosome assembly protein 1-like 1	349	Asp/Glu-rich (acidic).				DNA replication (GO:0006260)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)|prostate(1)|skin(1)	9		Colorectal(145;0.09)				CATCATCATCATCTTCAATAG	0.358																																					p.D349E													.	NAP1L1	33	0			c.T1047A						.						71.0	72.0	72.0					12																	76444323		2203	4300	6503	SO:0001583	missense	4673	exon12			ATCATCATCTTCA		CCDS9013.1	12q21.1	2010-03-17			ENSG00000187109	ENSG00000187109			7637	protein-coding gene	gene with protein product		164060				8297347	Standard	NM_004537		Approved	NRP, NAP1, NAP1L, MGC8688, MGC23410	uc001sxx.2	P55209		ENST00000261182.8:c.1047T>A	12.37:g.76444323A>T	ENSP00000261182:p.Asp349Glu	Somatic	60	0		WXS	Illumina GAIIx	Phase_I	70	3	NM_004537	B3KNT8	Missense_Mutation	SNP	ENST00000261182.8	37	CCDS9013.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605005	0.46423	.	.	ENSG00000187109	ENST00000261182;ENST00000552056;ENST00000393263;ENST00000431879;ENST00000547773;ENST00000544816;ENST00000542344;ENST00000535020;ENST00000549596;ENST00000547993;ENST00000552342;ENST00000548044	T;T;T;T;T;T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;1.3;0.98;0.98;0.98;0.98;0.98;0.98	5.65	0.802	0.18686	.	0.000000	0.85682	D	0.000000	T	0.40595	0.1123	N	0.21282	0.65	0.52099	D	0.99994	D;D;D;D;D;B;D	0.61697	0.99;0.984;0.99;0.984;0.984;0.157;0.984	D;D;D;D;D;B;D	0.73380	0.971;0.935;0.98;0.935;0.935;0.082;0.935	T	0.17806	-1.0357	10	0.12103	T	0.63	.	8.9291	0.35659	0.7101:0.0:0.2899:0.0	.	349;307;360;349;281;286;349	F5H4R6;B7Z9C2;F8W0J6;B3KNT8;B3KV44;F8W543;P55209	.;.;.;.;.;.;NP1L1_HUMAN	E	349;343;349;281;286;166;307;349;349;166;360;308	ENSP00000261182:D349E;ENSP00000450236:D343E;ENSP00000376947:D349E;ENSP00000409795:D281E;ENSP00000448167:D286E;ENSP00000437507:D166E;ENSP00000444759:D307E;ENSP00000445008:D349E;ENSP00000447793:D349E;ENSP00000448007:D166E;ENSP00000447196:D360E;ENSP00000449649:D308E	ENSP00000261182:D349E	D	-	3	2	NAP1L1	74730590	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.558000	0.45879	0.108000	0.17862	0.482000	0.46254	GAT	.		0.358	NAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405850.3	NM_139207	
NBEA	26960	broad.mit.edu	37	13	36220028	36220028	+	Intron	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr13:36220028G>C	ENST00000400445.3	+	50	8151				NBEA_ENST00000540320.1_Intron|NBEA_ENST00000379939.2_Intron|NBEA_ENST00000310336.4_Intron|NBEA_ENST00000379922.3_Missense_Mutation_p.R104T|NBEA_ENST00000537702.1_Intron	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin						protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TATTTCATTAGAGACCCCCAC	0.328																																					.													.	.	.	0			.						.						12.0	12.0	12.0					13																	36220028		874	1988	2862	SO:0001627	intron_variant	26960	.			TCATTAGAGACCC	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.7618-368G>C	13.37:g.36220028G>C		Somatic	35	0		WXS	Illumina GAIIx	Phase_I	44	3	.	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	4.251	0.045545	0.08196	.	.	ENSG00000172915	ENST00000402346;ENST00000379922	T	0.57595	0.39	5.14	4.29	0.51040	.	.	.	.	.	T	0.38957	0.1060	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14924	-1.0455	8	0.13853	T	0.58	.	15.6128	0.76740	0.0:0.1379:0.8621:0.0	.	104	Q8NFP9-2	.	T	104	ENSP00000369254:R104T	ENSP00000369254:R104T	R	+	2	0	NBEA	35118028	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	5.903000	0.69877	1.151000	0.42436	0.563000	0.77884	AGA	.		0.328	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
ENOX1	55068	broad.mit.edu	37	13	43930059	43930059	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr13:43930059C>T	ENST00000261488.6	-	8	1396	c.819G>A	c.(817-819)ctG>ctA	p.L273L	ENOX1_ENST00000540032.1_Silent_p.L86L|ENOX1_ENST00000412891.1_Silent_p.L273L	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	273					rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		CCATACCTTTCAGCTTTTCAG	0.622																																					p.L273L													ENOX1_ENST00000261488,NS,carcinoma,-1,2	ENOX1	158	0			c.G819A						.						92.0	101.0	98.0					13																	43930059		2201	4297	6498	SO:0001819	synonymous_variant	55068	exon8			ACCTTTCAGCTTT	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.819G>A	13.37:g.43930059C>T		Somatic	34	0		WXS	Illumina GAIIx	Phase_I	39	4	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Silent	SNP	ENST00000261488.6	37	CCDS9389.1																																																																																			.		0.622	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
OTX2	5015	broad.mit.edu	37	14	57269033	57269033	+	Missense_Mutation	SNP	T	T	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:57269033T>A	ENST00000555006.1	-	4	698	c.290A>T	c.(289-291)cAg>cTg	p.Q97L	OTX2_ENST00000554559.1_3'UTR|OTX2_ENST00000408990.3_Missense_Mutation_p.Q97L|OTX2_ENST00000554788.1_3'UTR|OTX2_ENST00000339475.5_Missense_Mutation_p.Q105L|RP11-1085N6.6_ENST00000602485.1_lincRNA			P32243	OTX2_HUMAN	orthodenticle homeobox 2	97	Poly-Gln.				axon guidance (GO:0007411)|cell fate specification (GO:0001708)|diencephalon morphogenesis (GO:0048852)|dorsal/ventral pattern formation (GO:0009953)|endoderm development (GO:0007492)|eye photoreceptor cell fate commitment (GO:0042706)|forebrain development (GO:0030900)|inner ear morphogenesis (GO:0042472)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|neuron fate determination (GO:0048664)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|protein complex assembly (GO:0006461)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of smoothened signaling pathway (GO:0008589)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|nucleus (GO:0005634)|protein complex (GO:0043234)	eukaryotic initiation factor 4E binding (GO:0008190)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	19	Medulloblastoma(1;0.00184)|all_neural(1;0.00414)					CTGTTGTTGCTGTTGTTGGCG	0.438																																					p.Q105L													.	OTX2	47	0			c.A314T						.						113.0	117.0	116.0					14																	57269033		2203	4300	6503	SO:0001583	missense	5015	exon3			TGTTGCTGTTGTT	AF298117	CCDS9728.1, CCDS41960.1	14q22.3	2014-09-17	2007-02-15		ENSG00000165588	ENSG00000165588		"""Homeoboxes / PRD class"""	8522	protein-coding gene	gene with protein product		600037	"""orthodenticle homolog 2 (Drosophila)"""			7959790	Standard	NM_021728		Approved		uc031qor.1	P32243	OTTHUMG00000152338	ENST00000555006.1:c.290A>T	14.37:g.57269033T>A	ENSP00000452336:p.Gln97Leu	Somatic	44	0		WXS	Illumina GAIIx	Phase_I	54	5	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	37	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	T	17.62	3.435683	0.62955	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006;ENST00000554845;ENST00000555804	D;D;D;D;D	0.96300	-3.97;-3.97;-3.97;-3.97;-3.97	5.78	5.78	0.91487	Homeodomain-related (1);Homeobox (1);Homeodomain-like (1);	0.000000	0.43110	D	0.000612	D	0.96027	0.8706	M	0.79693	2.465	0.80722	D	1	P;B	0.38420	0.63;0.446	B;B	0.38803	0.282;0.197	D	0.96174	0.9125	10	0.72032	D	0.01	.	14.9485	0.71050	0.0:0.0:0.0:1.0	.	105;97	F1T0D1;P32243	.;OTX2_HUMAN	L	105;97;97;105;97	ENSP00000343819:Q105L;ENSP00000386185:Q97L;ENSP00000452336:Q97L;ENSP00000451357:Q105L;ENSP00000451272:Q97L	ENSP00000343819:Q105L	Q	-	2	0	OTX2	56338786	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	7.698000	0.84413	2.212000	0.71576	0.374000	0.22700	CAG	.		0.438	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.	
JAG2	3714	broad.mit.edu	37	14	105612177	105612177	+	Missense_Mutation	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:105612177T>C	ENST00000331782.3	-	23	3246	c.2843A>G	c.(2842-2844)gAg>gGg	p.E948G	JAG2_ENST00000347004.2_Missense_Mutation_p.E910G	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	948					auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		TGCGCCGCACTCCCCCCAGGC	0.687																																					p.E948G													.	JAG2	69	0			c.A2843G						.						27.0	21.0	23.0					14																	105612177		2144	4260	6404	SO:0001583	missense	3714	exon23			CCGCACTCCCCCC	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.2843A>G	14.37:g.105612177T>C	ENSP00000328169:p.Glu948Gly	Somatic	73	1		WXS	Illumina GAIIx	Phase_I	94	3	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Missense_Mutation	SNP	ENST00000331782.3	37	CCDS9998.1	.	.	.	.	.	.	.	.	.	.	T	13.63	2.294824	0.40594	.	.	ENSG00000184916	ENST00000331782;ENST00000347004	D;D	0.87334	-2.23;-2.24	3.6	2.39	0.29439	.	0.356734	0.25762	U	0.028466	D	0.82724	0.5099	L	0.52573	1.65	0.38453	D	0.947009	B;B	0.29646	0.253;0.164	B;B	0.32980	0.156;0.075	T	0.78130	-0.2324	10	0.56958	D	0.05	.	8.9426	0.35740	0.0:0.0:0.1887:0.8113	.	910;948	Q9Y219-2;Q9Y219	.;JAG2_HUMAN	G	948;910	ENSP00000328169:E948G;ENSP00000328566:E910G	ENSP00000328169:E948G	E	-	2	0	JAG2	104683222	0.885000	0.30320	0.990000	0.47175	0.797000	0.45037	1.450000	0.35134	0.254000	0.21573	0.358000	0.22013	GAG	.		0.687	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
IGHD	3495	broad.mit.edu	37	14	106304711	106304711	+	RNA	SNP	C	C	T	rs377697988		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:106304711C>T	ENST00000390556.2	-	0	1125							P01880	IGHD_HUMAN	immunoglobulin heavy constant delta						immune response (GO:0006955)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)										TGCTGAGTGGCGGGTGTGGAC	0.463													C|||	1	0.000199681	0.0008	0.0	5008	,	,		10959	0.0		0.0	False		,,,				2504	0.0				.													.	.	.	0			.						.	C		2,3940		0,2,1969	58.0	76.0	70.0			-0.9	0.0	14		70	1,8231		0,1,4115	no	intergenic				0,3,6084	TT,TC,CC		0.0121,0.0507,0.0246			106304711	3,12171	1971	4116	6087			0	.			GAGTGGCGGGTGT	K02875		14q32.33	2012-03-09			ENSG00000211898	ENSG00000211898		"""Immunoglobulins / IGH locus"""	5480	other	immunoglobulin gene	"""immunoglobulin delta"", ""constant region of heavy chain of IgD"""	147170				3922054	Standard	NG_001019		Approved	FLJ00382, FLJ46727, MGC29633	uc001ysj.3	P01880	OTTHUMG00000152538		14.37:g.106304711C>T		Somatic	89	0		WXS	Illumina GAIIx	Phase_I	81	7	.	Q6P4I8|Q8WU38	RNA	SNP	ENST00000390556.2	37																																																																																				.		0.463	IGHD-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	IG_C_gene	IG_C_gene	OTTHUMT00000326652.1	NG_001019	
DNM1P47	100216544	broad.mit.edu	37	15	102304262	102304264	+	RNA	DEL	GCT	GCT	-	rs56043818|rs373408686		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:102304262_102304264delGCT	ENST00000561463.1	+	0	12308_12310									DNM1 pseudogene 47																		TCTTCTCAGAGCTGCTGTCCAAC	0.581																																					.													.	.	.	0			.						.																																					0	.			CTCAGAGCTGCTG	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102304265_102304267delGCT		Somatic	57	8		WXS	Illumina GAIIx	Phase_I	85	9	.		RNA	DEL	ENST00000561463.1	37																																																																																				.		0.581	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149	
WASH3P	374666	broad.mit.edu	37	15	102506815	102506816	+	RNA	DEL	CC	CC	-	rs151176585		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr15:102506815_102506816delCC	ENST00000557932.1	+	0	172							C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						tacctctccacctggagcgcac	0.421																																					.													.	WASH3P	56	0			.						.																																					0	.			TCTCCACCTGGAG			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102506815_102506816delCC		Somatic	103	10		WXS	Illumina GAIIx	Phase_I	121	18	.		RNA	DEL	ENST00000557932.1	37																																																																																				CC|0.500;-|0.500		0.421	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163	
RRN3P2	653390	broad.mit.edu	37	16	29088010	29088010	+	RNA	SNP	T	T	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:29088010T>G	ENST00000564580.1	+	0	180							A6NIE6	RN3P2_HUMAN	RNA polymerase I transcription factor homolog (S. cerevisiae) pseudogene 2																		AGAATGATTTTTTCAATTCTC	0.348																																					.													.	.	.	0			.						.																																					0	.			TGATTTTTTCAAT			16p11.2	2011-12-02			ENSG00000103472	ENSG00000103472			37619	pseudogene	pseudogene							Standard	NR_003369		Approved		uc002dsf.4	A6NIE6			16.37:g.29088010T>G		Somatic	152	0		WXS	Illumina GAIIx	Phase_I	198	6	.		RNA	SNP	ENST00000564580.1	37		.	.	.	.	.	.	.	.	.	.	t	10.28	1.305725	0.23736	.	.	ENSG00000103472	ENST00000415221;ENST00000427965;ENST00000219758	.	.	.	1.58	-0.368	0.12537	.	0.145650	0.46758	N	0.000262	T	0.34135	0.0887	.	.	.	.	.	.	.	.	.	.	.	.	T	0.30937	-0.9961	5	0.27082	T	0.32	.	4.7545	0.13077	0.0:0.4299:0.0:0.5701	.	.	.	.	L	41	.	ENSP00000219758:F41L	F	+	3	2	AC009093.1	28995511	1.000000	0.71417	0.998000	0.56505	0.775000	0.43874	0.756000	0.26419	-0.076000	0.12775	0.155000	0.16302	TTT	.		0.348	RRN3P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000433243.1	NR_003369	
LRRC37A4P	55073	broad.mit.edu	37	17	43587569	43587569	+	RNA	SNP	G	G	C	rs202189074		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:43587569G>C	ENST00000579913.1	-	0	1444				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		aactccgtctgaaaagaaaag	0.443																																					.													.	.	.	0			.						.																																					0	.			CCGTCTGAAAAGA	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587569G>C		Somatic	70	1		WXS	Illumina GAIIx	Phase_I	100	3	.		RNA	SNP	ENST00000579913.1	37																																																																																				G|1.000;|0.000		0.443	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940	
KIF19	124602	broad.mit.edu	37	17	72340424	72340424	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr17:72340424G>T	ENST00000389916.4	+	6	657	c.519G>T	c.(517-519)gaG>gaT	p.E173D		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	173	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						AGCTGCGGGAGGACTCTAAGG	0.627																																					p.E173D													.	KIF19	102	0			c.G519T						.						44.0	44.0	44.0					17																	72340424		2202	4300	6502	SO:0001583	missense	124602	exon6			GCGGGAGGACTCT	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.519G>T	17.37:g.72340424G>T	ENSP00000374566:p.Glu173Asp	Somatic	21	0		WXS	Illumina GAIIx	Phase_I	34	3	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	37	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	14.39	2.519928	0.44866	.	.	ENSG00000196169	ENST00000389916	T	0.77877	-1.13	5.79	1.54	0.23209	Kinesin, motor domain (4);	.	.	.	.	D	0.83064	0.5173	L	0.60455	1.87	0.53005	D	0.999966	D;D	0.71674	0.998;0.958	D;P	0.77557	0.99;0.9	T	0.81165	-0.1057	9	0.62326	D	0.03	.	9.4361	0.38639	0.3724:0.0:0.6276:0.0	.	173;173	Q2TAC6;Q2TAC6-2	KIF19_HUMAN;.	D	173	ENSP00000374566:E173D	ENSP00000374566:E173D	E	+	3	2	KIF19	69852019	1.000000	0.71417	0.999000	0.59377	0.136000	0.21042	2.316000	0.43761	0.376000	0.24707	-0.274000	0.10170	GAG	.		0.627	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
ROCK1	6093	broad.mit.edu	37	18	18608854	18608854	+	Missense_Mutation	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr18:18608854G>C	ENST00000399799.2	-	10	2034	c.1094C>G	c.(1093-1095)aCt>aGt	p.T365S		NM_005406.2	NP_005397.1	Q13464	ROCK1_HUMAN	Rho-associated, coiled-coil containing protein kinase 1	365	AGC-kinase C-terminal.				actin cytoskeleton organization (GO:0030036)|apical constriction (GO:0003383)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|bleb assembly (GO:0032060)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of focal adhesion assembly (GO:0051894)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(8)|lung(2)	16	Melanoma(1;0.165)					AAAATTACTAGTATCAATGTC	0.338																																					p.T365S													.	ROCK1	162	0			c.C1094G						.						142.0	144.0	143.0					18																	18608854		2203	4299	6502	SO:0001583	missense	6093	exon10			TTACTAGTATCAA		CCDS11870.2	18q11.2	2013-01-10			ENSG00000067900	ENSG00000067900	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10251	protein-coding gene	gene with protein product		601702				8617235	Standard	NM_005406		Approved	p160ROCK	uc002kte.3	Q13464	OTTHUMG00000131723	ENST00000399799.2:c.1094C>G	18.37:g.18608854G>C	ENSP00000382697:p.Thr365Ser	Somatic	39	0		WXS	Illumina GAIIx	Phase_I	67	3	NM_005406	B0YJ91|Q2KHM4|Q59GZ4	Missense_Mutation	SNP	ENST00000399799.2	37	CCDS11870.2	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204312	0.58234	.	.	ENSG00000067900	ENST00000399799	T	0.68903	-0.36	5.67	4.8	0.61643	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);Protein kinase-like domain (1);	0.051730	0.85682	N	0.000000	T	0.77818	0.4187	M	0.83384	2.64	0.80722	D	1	P	0.49635	0.926	P	0.51895	0.683	T	0.79918	-0.1600	10	0.41790	T	0.15	.	16.7135	0.85392	0.0:0.1294:0.8706:0.0	.	365	Q13464	ROCK1_HUMAN	S	365	ENSP00000382697:T365S	ENSP00000382697:T365S	T	-	2	0	ROCK1	16862852	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.639000	0.74314	1.375000	0.46248	0.655000	0.94253	ACT	.		0.338	ROCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254641.2	NM_005406	
PRR22	163154	broad.mit.edu	37	19	5784655	5784655	+	Missense_Mutation	SNP	G	G	A	rs543083484		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:5784655G>A	ENST00000419421.2	-	1	121	c.17C>T	c.(16-18)cCg>cTg	p.P6L	CTB-54O9.9_ENST00000586012.1_Intron	NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	6										endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGCACAGAACGGTTTGGGGTG	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		14608	0.001		0.0	False		,,,				2504	0.0				p.P6L													.	PRR22	25	0			c.C17T						.						12.0	13.0	13.0					19																	5784655		690	1587	2277	SO:0001583	missense	163154	exon1			CAGAACGGTTTGG	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.17C>T	19.37:g.5784655G>A	ENSP00000407653:p.Pro6Leu	Somatic	14	0		WXS	Illumina GAIIx	Phase_I	30	3	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	.	.	.	.	.	.	.	.	.	.	G	8.716	0.913177	0.17907	.	.	ENSG00000212123	ENST00000419421	T	0.17054	2.3	4.57	2.32	0.28847	.	.	.	.	.	T	0.07999	0.0200	N	0.08118	0	0.23704	N	0.997069	P	0.46327	0.876	B	0.36766	0.232	T	0.17961	-1.0352	9	0.66056	D	0.02	.	9.2513	0.37557	0.0:0.1585:0.6773:0.1642	.	6	E9PB31	.	L	6	ENSP00000407653:P6L	ENSP00000407653:P6L	P	-	2	0	PRR22	5735655	0.008000	0.16893	0.369000	0.25952	0.010000	0.07245	1.565000	0.36386	0.597000	0.29811	0.555000	0.69702	CCG	.		0.682	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
CRIM1	51232	broad.mit.edu	37	2	36583501	36583503	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:36583501_36583503delGCT	ENST00000280527.2	+	1	433_435	c.66_68delGCT	c.(64-69)gggctg>ggg	p.L27del	RP11-490M8.1_ENST00000565283.1_lincRNA	NM_016441.2	NP_057525.1	Q9NZV1	CRIM1_HUMAN	cysteine rich transmembrane BMP regulator 1 (chordin-like)	27					insulin-like growth factor receptor signaling pathway (GO:0048009)|nervous system development (GO:0007399)|regulation of cell growth (GO:0001558)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	insulin-like growth factor-activated receptor activity (GO:0005010)|PDZ domain binding (GO:0030165)|serine-type endopeptidase inhibitor activity (GO:0004867)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(15)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	45		all_hematologic(82;0.131)|Acute lymphoblastic leukemia(82;0.154)				CGCTGCTGGGGCTGCTGCTGCTG	0.734																																					p.22_23del													.	CRIM1	88	0			c.66_68del						.			89,3815		5,79,1868						0.6	1.0			9	194,7436		1,192,3622	no	coding	CRIM1	NM_016441.2		6,271,5490	A1A1,A1R,RR		2.5426,2.2797,2.4536				283,11251				SO:0001651	inframe_deletion	51232	exon1			GCTGGGGCTGCTG	AF168681	CCDS1783.1	2p21	2010-06-29	2005-07-25		ENSG00000150938	ENSG00000150938			2359	protein-coding gene	gene with protein product		606189	"""cysteine-rich motor neuron 1"""	S52		10642437	Standard	NM_016441		Approved		uc002rpd.3	Q9NZV1	OTTHUMG00000099419	ENST00000280527.2:c.66_68delGCT	2.37:g.36583510_36583512delGCT	ENSP00000280527:p.Leu27del	Somatic	9	0		WXS	Illumina GAIIx	Phase_I	10	3	NM_016441	Q2M2G4|Q59GH0|Q7LCQ5|Q9H318	In_Frame_Del	DEL	ENST00000280527.2	37	CCDS1783.1																																																																																			.		0.734	CRIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216878.2	NM_016441	
USP34	9736	broad.mit.edu	37	2	61484067	61484067	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:61484067G>T	ENST00000398571.2	-	47	6143	c.6067C>A	c.(6067-6069)Caa>Aaa	p.Q2023K		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2023	USP.				positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TCAGCAGTTTGACTAACATGT	0.249																																					p.Q2023K													.	USP34	334	0			c.C6067A						.						36.0	32.0	33.0					2																	61484067		1810	4067	5877	SO:0001583	missense	9736	exon47			CAGTTTGACTAAC	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.6067C>A	2.37:g.61484067G>T	ENSP00000381577:p.Gln2023Lys	Somatic	125	0		WXS	Illumina GAIIx	Phase_I	148	4	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097983	0.56183	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.05081	3.5;3.5	5.93	5.93	0.95920	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	N	0.02120	-0.675	0.80722	D	1	B	0.31040	0.305	P	0.53185	0.72	T	0.61758	-0.6997	10	0.35671	T	0.21	.	20.3311	0.98718	0.0:0.0:1.0:0.0	.	2023	Q70CQ2	UBP34_HUMAN	K	1871;1871;2023;301	ENSP00000381577:Q2023K;ENSP00000410559:Q301K	ENSP00000263989:Q1871K	Q	-	1	0	USP34	61337571	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.845000	0.99498	2.803000	0.96430	0.650000	0.86243	CAA	.		0.249	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
RPL23AP7	118433	broad.mit.edu	37	2	114369811	114369811	+	RNA	SNP	G	G	A	rs373861612	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:114369811G>A	ENST00000416673.2	-	0	345					NR_000029.3				ribosomal protein L23a pseudogene 7																		AGCTTCCTTCGCTTTCGGTGC	0.413																																					.													.	.	.	0			.						.																																					0	.			TCCTTCGCTTTCG	BC000596		2q14	2009-03-11				ENSG00000240356		"""L ribosomal proteins"""	17336	pseudogene	pseudogene						19123937	Standard	NR_000029		Approved	RPL23AL1, bA395L14.9	uc010yxy.1				2.37:g.114369811G>A		Somatic	102	0		WXS	Illumina GAIIx	Phase_I	165	5	.		RNA	SNP	ENST00000416673.2	37																																																																																				.		0.413	RPL23AP7-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000397215.1		
RPL23AP7	118433	broad.mit.edu	37	2	114369818	114369818	+	RNA	SNP	G	G	A	rs201486476		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:114369818G>A	ENST00000416673.2	-	0	338					NR_000029.3				ribosomal protein L23a pseudogene 7																		TTCGCTTTCGGTGCCATCTTG	0.413																																					.													.	.	.	0			.						.																																					0	.			CTTTCGGTGCCAT	BC000596		2q14	2009-03-11				ENSG00000240356		"""L ribosomal proteins"""	17336	pseudogene	pseudogene						19123937	Standard	NR_000029		Approved	RPL23AL1, bA395L14.9	uc010yxy.1				2.37:g.114369818G>A		Somatic	98	1		WXS	Illumina GAIIx	Phase_I	168	7	.		RNA	SNP	ENST00000416673.2	37																																																																																				.		0.413	RPL23AP7-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000397215.1		
FAM126B	285172	broad.mit.edu	37	2	201846200	201846200	+	Silent	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:201846200G>T	ENST00000418596.3	-	12	1573	c.1386C>A	c.(1384-1386)ggC>ggA	p.G462G	AC005037.3_ENST00000332935.6_RNA|AC005037.3_ENST00000413848.1_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	462						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						TTGCTTGACTGCCATTTACAT	0.473																																					p.G462G													.	FAM126B	34	0			c.C1386A						.						108.0	86.0	94.0					2																	201846200		2203	4300	6503	SO:0001819	synonymous_variant	285172	exon12			TTGACTGCCATTT	BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1386C>A	2.37:g.201846200G>T		Somatic	44	1		WXS	Illumina GAIIx	Phase_I	52	3	NM_173822	B2RCG7|Q4ZG87|Q53TX6	Silent	SNP	ENST00000418596.3	37	CCDS2335.1																																																																																			.		0.473	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822	
MUC4	4585	broad.mit.edu	37	3	195506007	195506007	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr3:195506007G>A	ENST00000463781.3	-	2	12903	c.12444C>T	c.(12442-12444)acC>acT	p.T4148T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4148T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4148T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGATGGTGACAGGAA	0.587																																					p.T4148T													MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	Substitution - coding silent(2)	kidney(1)|endometrium(1)	c.C12444T						.						40.0	22.0	27.0					3																	195506007		646	1562	2208	SO:0001819	synonymous_variant	4585	exon2			AGGGATGGTGACA	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12444C>T	3.37:g.195506007G>A		Somatic	79	1		WXS	Illumina GAIIx	Phase_I	134	10	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|1.000;|0.000		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LARP1B	55132	broad.mit.edu	37	4	129121738	129121738	+	Missense_Mutation	SNP	T	T	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:129121738T>C	ENST00000326639.6	+	17	2438	c.2227T>C	c.(2227-2229)Ttt>Ctt	p.F743L	LARP1B_ENST00000506199.1_3'UTR|LARP1B_ENST00000441387.1_Missense_Mutation_p.F743L|LARP1B_ENST00000264584.5_Missense_Mutation_p.F684L|LARP1B_ENST00000354456.3_Missense_Mutation_p.F162L	NM_018078.2	NP_060548.2	Q659C4	LAR1B_HUMAN	La ribonucleoprotein domain family, member 1B	743						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|lung(11)|ovary(1)|prostate(3)	34						TTTCTGGTCCTTTTTCCTCAG	0.308																																					p.F743L													.	LARP1B	120	0			c.T2227C						.						40.0	40.0	40.0					4																	129121738		2202	4299	6501	SO:0001583	missense	55132	exon17			TGGTCCTTTTTCC		CCDS3738.1, CCDS47133.1, CCDS64057.1	4q28.2	2009-06-09	2009-06-09	2009-06-09	ENSG00000138709	ENSG00000138709		"""La ribonucleoprotein domain containing"""	24704	protein-coding gene	gene with protein product			"""La ribonucleoprotein domain family, member 2"""	LARP2		12045101	Standard	NM_018078		Approved	FLJ10378, DKFZp434K245, DKFZp686E0316	uc003iga.3	Q659C4	OTTHUMG00000133343	ENST00000326639.6:c.2227T>C	4.37:g.129121738T>C	ENSP00000321997:p.Phe743Leu	Somatic	278	0		WXS	Illumina GAIIx	Phase_I	300	6	NM_018078	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Missense_Mutation	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.092258	0.76756	.	.	ENSG00000138709	ENST00000326639;ENST00000264584;ENST00000441387;ENST00000354456	T;T;T;T	0.28069	1.63;1.63;1.69;1.63	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.61451	0.2348	M	0.88450	2.955	0.52099	D	0.999945	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.70182	-0.4942	10	0.72032	D	0.01	.	14.4138	0.67135	0.0:0.0:0.0:1.0	.	162;743	Q659C4-5;Q659C4	.;LAR1B_HUMAN	L	743;684;743;162	ENSP00000321997:F743L;ENSP00000264584:F684L;ENSP00000396521:F743L;ENSP00000346444:F162L	ENSP00000264584:F684L	F	+	1	0	LARP1B	129341188	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.506000	0.81665	1.999000	0.58509	0.459000	0.35465	TTT	.		0.308	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	
GTF2H2B	653238	broad.mit.edu	37	5	69719461	69719461	+	RNA	DEL	T	T	-			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:69719461delT	ENST00000513202.1	+	0	468					NR_033417.1				general transcription factor IIH, polypeptide 2B (pseudogene)																		ttttctttccttttttttttt	0.353																																					.													.	.	.	0			.						.																																					0	.			CTTTCCTTTTTTT			5q13.2	2011-09-01	2011-09-01		ENSG00000226259	ENSG00000226259		"""General transcription factors"""	31393	pseudogene	pseudogene			"""general transcription factor IIH, polypeptide 2B"""				Standard	NR_033417		Approved	DKFZP686M0199	uc021yab.1		OTTHUMG00000162394		5.37:g.69719461delT		Somatic	19	0		WXS	Illumina GAIIx	Phase_I	32	4	.		RNA	DEL	ENST00000513202.1	37																																																																																				.		0.353	GTF2H2B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000396209.1	NM_001098729	
ZDHHC11	79844	broad.mit.edu	37	5	825360	825360	+	Silent	SNP	T	T	C	rs201174878		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:825360T>C	ENST00000283441.8	-	8	1325	c.942A>G	c.(940-942)aaA>aaG	p.K314K	ZDHHC11_ENST00000424784.2_Silent_p.K314K|ZDHHC11_ENST00000503758.2_5'UTR	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	314						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			AGCTCTTGGCTTTGACTCTGG	0.552																																					p.K314K													.	ZDHHC11	97	0			c.A942G						.						168.0	117.0	134.0					5																	825360		2203	4296	6499	SO:0001819	synonymous_variant	79844	exon8			CTTGGCTTTGACT	AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.942A>G	5.37:g.825360T>C		Somatic	48	1		WXS	Illumina GAIIx	Phase_I	47	4	NM_024786	Q6UWR9	Silent	SNP	ENST00000283441.8	37	CCDS3857.1																																																																																			T|0.999;C|0.001		0.552	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3	NM_024786	
TRIO	7204	broad.mit.edu	37	5	14399006	14399006	+	Nonsense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr5:14399006G>T	ENST00000344204.4	+	30	4465	c.4441G>T	c.(4441-4443)Gag>Tag	p.E1481*	TRIO_ENST00000509967.2_Nonsense_Mutation_p.E1432*|TRIO_ENST00000537187.1_Nonsense_Mutation_p.E1481*	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1481	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					TGAAAACATTGAGTCTCAGGG	0.363																																					p.E1481X													.	TRIO	305	0			c.G4441T						.						100.0	103.0	102.0					5																	14399006		2203	4300	6503	SO:0001587	stop_gained	7204	exon30			AACATTGAGTCTC	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.4441G>T	5.37:g.14399006G>T	ENSP00000339299:p.Glu1481*	Somatic	70	0		WXS	Illumina GAIIx	Phase_I	82	3	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Nonsense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	46	12.115611	0.99637	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	.	.	.	5.39	5.39	0.77823	.	0.105591	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	19.1797	0.93617	0.0:0.0:1.0:0.0	.	.	.	.	X	1481;1481;1432;1168	.	ENSP00000339299:E1481X	E	+	1	0	TRIO	14452006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.524000	0.85096	0.591000	0.81541	GAG	.		0.363	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
C8orf34	116328	broad.mit.edu;bcgsc.ca	37	8	69621314	69621314	+	Splice_Site	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:69621314G>A	ENST00000539993.1	+	9	1618	c.1069G>A	c.(1069-1071)Gat>Aat	p.D357N	C8orf34_ENST00000325233.3_Splice_Site_p.D101N|C8orf34_ENST00000337103.4_Splice_Site_p.D332N|C8orf34_ENST00000518698.1_Splice_Site_p.D443N			Q49A92	CH034_HUMAN	chromosome 8 open reading frame 34	357										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(12)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	36			Epithelial(68;0.0117)|OV - Ovarian serous cystadenocarcinoma(28;0.0227)|all cancers(69;0.0502)			AGATTCATTCGGTAAGTTTTA	0.343																																					p.D443N													.	C8orf34	170	0			c.G1327A						.						63.0	60.0	61.0					8																	69621314		2203	4299	6502	SO:0001630	splice_region_variant	116328	exon9			TCATTCGGTAAGT	AB056652	CCDS6203.1, CCDS6203.2	8q13	2009-10-01			ENSG00000165084	ENSG00000165084			30905	protein-coding gene	gene with protein product	"""vestibule 1"""						Standard	NM_052958		Approved	vest-1, VEST1	uc010lyz.3	Q49A92	OTTHUMG00000164438	ENST00000539993.1:c.1069+1G>A	8.37:g.69621314G>A		Somatic	39	0		WXS	Illumina GAIIx	Phase_I	34	4	NM_052958	A8K5X1|G3XAM6|Q8N1X0|Q8N9M7|Q8ND19|Q96Q28	Splice_Site	SNP	ENST00000539993.1	37		.	.	.	.	.	.	.	.	.	.	G	9.651	1.141589	0.21205	.	.	ENSG00000165084	ENST00000518698;ENST00000539993;ENST00000337103;ENST00000325233	T;T;T;T	0.46063	0.9;0.93;0.93;0.88	5.2	5.2	0.72013	.	0.975127	0.08428	N	0.947302	T	0.33000	0.0848	L	0.29908	0.895	0.30488	N	0.771617	P	0.38420	0.63	B	0.32928	0.155	T	0.16600	-1.0397	9	.	.	.	-3.7292	14.5749	0.68238	0.0:0.0:1.0:0.0	.	357	Q49A92	CH034_HUMAN	N	443;357;332;101	ENSP00000427820:D443N;ENSP00000438159:D357N;ENSP00000337174:D332N;ENSP00000319532:D101N	.	D	+	1	0	C8orf34	69783868	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	2.882000	0.48546	2.572000	0.86782	0.655000	0.94253	GAT	.		0.343	C8orf34-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_052958	Missense_Mutation
PCM1	5108	broad.mit.edu	37	8	17797227	17797227	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:17797227G>A	ENST00000519253.1	+	6	891	c.640G>A	c.(640-642)Gat>Aat	p.D214N	PCM1_ENST00000524226.1_Missense_Mutation_p.D214N|PCM1_ENST00000325083.8_Missense_Mutation_p.D214N|PCM1_ENST00000518537.1_Missense_Mutation_p.D214N			Q15154	PCM1_HUMAN	pericentriolar material 1	214					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TCAAATTCGCGATTATATTAC	0.328			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.D214N				Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	0			c.G640A						.						42.0	35.0	37.0					8																	17797227		1799	4052	5851	SO:0001583	missense	5108	exon6			ATTCGCGATTATA		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.640G>A	8.37:g.17797227G>A	ENSP00000431099:p.Asp214Asn	Somatic	106	0		WXS	Illumina GAIIx	Phase_I	101	4	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	G	23.8	4.461693	0.84425	.	.	ENSG00000078674	ENST00000325083;ENST00000325126;ENST00000517730;ENST00000518537;ENST00000523055;ENST00000519253;ENST00000524226	T;T;T;T;T;T	0.33216	3.13;2.34;1.5;1.42;3.14;2.89	5.36	5.36	0.76844	.	0.145914	0.64402	D	0.000009	T	0.34308	0.0893	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.60575	0.988;0.964;0.988;0.988	P;P;P;P	0.51016	0.656;0.54;0.656;0.656	T	0.04255	-1.0965	10	0.46703	T	0.11	-9.0456	18.4529	0.90710	0.0:0.0:1.0:0.0	.	214;214;214;214	E7ETA6;E7EV93;E7EV56;Q15154	.;.;.;PCM1_HUMAN	N	214	ENSP00000327077:D214N;ENSP00000428131:D214N;ENSP00000428123:D214N;ENSP00000429941:D214N;ENSP00000431099:D214N;ENSP00000430521:D214N	ENSP00000327077:D214N	D	+	1	0	PCM1	17841507	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.673000	0.90976	0.650000	0.86243	GAT	.		0.328	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
NBN	4683	broad.mit.edu	37	8	90983510	90983510	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:90983510G>T	ENST00000265433.3	-	6	747	c.593C>A	c.(592-594)cCa>cAa	p.P198Q	NBN_ENST00000409330.1_Missense_Mutation_p.P116Q	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	198	Mediates interaction with SP100. {ECO:0000250}.				blastocyst growth (GO:0001832)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|DNA damage checkpoint (GO:0000077)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intrinsic apoptotic signaling pathway (GO:0097193)|isotype switching (GO:0045190)|meiotic nuclear division (GO:0007126)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G2 DNA damage checkpoint (GO:0007095)|neuromuscular process controlling balance (GO:0050885)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|telomere maintenance (GO:0000723)	Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nuclear inclusion body (GO:0042405)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)	damaged DNA binding (GO:0003684)|protein N-terminus binding (GO:0047485)|transcription factor binding (GO:0008134)			autonomic_ganglia(1)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27			BRCA - Breast invasive adenocarcinoma(11;0.0344)			ATCAAGAGGTGGGTAAAAACT	0.299								Homologous recombination																													p.P198Q													.	NBN	86	0			c.C593A						.						45.0	46.0	46.0					8																	90983510		2201	4294	6495	SO:0001583	missense	4683	exon6			AGAGGTGGGTAAA	AF058696	CCDS6249.1	8q21-q24	2014-09-17	2005-06-02	2005-06-02	ENSG00000104320	ENSG00000104320			7652	protein-coding gene	gene with protein product		602667	"""Nijmegen breakage syndrome 1 (nibrin)"""	NBS, NBS1		9590181, 9590180	Standard	XM_005250923		Approved	ATV, AT-V2, AT-V1	uc003yej.1	O60934	OTTHUMG00000153546	ENST00000265433.3:c.593C>A	8.37:g.90983510G>T	ENSP00000265433:p.Pro198Gln	Somatic	158	0		WXS	Illumina GAIIx	Phase_I	173	5	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.382702	0.82792	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387;ENST00000519426;ENST00000517772	T;T;T;T	0.79940	-1.32;-1.11;1.31;-1.14	5.84	5.84	0.93424	.	0.050989	0.85682	D	0.000000	D	0.91633	0.7356	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92172	0.5744	10	0.87932	D	0	-17.6889	20.1346	0.98019	0.0:0.0:1.0:0.0	.	198;198	A6H8Y5;O60934	.;NBN_HUMAN	Q	198;116;198;110;116	ENSP00000265433:P198Q;ENSP00000386924:P116Q;ENSP00000430983:P110Q;ENSP00000428717:P116Q	ENSP00000265433:P198Q	P	-	2	0	NBN	91052686	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.987000	0.76206	2.765000	0.95021	0.655000	0.94253	CCA	.		0.299	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688	
PDP1	54704	broad.mit.edu;ucsc.edu	37	8	94935050	94935050	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:94935050G>A	ENST00000297598.4	+	2	1032	c.763G>A	c.(763-765)Gat>Aat	p.D255N	PDP1_ENST00000520728.1_Missense_Mutation_p.D255N|PDP1_ENST00000517764.1_Missense_Mutation_p.D255N|PDP1_ENST00000396200.3_Missense_Mutation_p.D280N	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	255					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						GCAAGTTGGTGATCCTAATTC	0.473																																					p.D280N													.	PDP1	97	0			c.G838A						.						121.0	122.0	122.0					8																	94935050		2203	4300	6503	SO:0001583	missense	54704	exon3			GTTGGTGATCCTA	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.763G>A	8.37:g.94935050G>A	ENSP00000297598:p.Asp255Asn	Somatic	13	0		WXS	Illumina GAIIx	Phase_I	29	4	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.062297	0.36373	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.5	5.5	0.81552	Protein phosphatase 2C-like (5);	0.146062	0.64402	N	0.000011	T	0.19886	0.0478	L	0.29908	0.895	0.80722	D	1	P;P	0.52170	0.951;0.905	P;P	0.48166	0.569;0.569	T	0.01657	-1.1302	10	0.19147	T	0.46	-17.3182	19.7663	0.96342	0.0:0.0:1.0:0.0	.	306;255	B4DYX8;Q9P0J1	.;PDP1_HUMAN	N	255;255;280;255	ENSP00000297598:D255N;ENSP00000428317:D255N;ENSP00000379503:D280N;ENSP00000430380:D255N	ENSP00000297598:D255N	D	+	1	0	PDP1	95004226	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.679000	0.74513	2.741000	0.93983	0.650000	0.86243	GAT	.		0.473	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
SCRIB	23513	broad.mit.edu	37	8	144887183	144887183	+	Splice_Site	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr8:144887183C>T	ENST00000320476.3	-	20	2678	c.2672G>A	c.(2671-2673)gGc>gAc	p.G891D	SCRIB_ENST00000356994.2_Splice_Site_p.G891D|SCRIB_ENST00000377533.3_Splice_Site_p.G810D	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	891	Interaction with ARHGEF7.|PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GACGAAGATGCCCTGCAGGGG	0.721																																					p.G891D	Pancreas(51;966 1133 10533 14576 29674)												.	SCRIB	192	0			c.G2672A						.						9.0	10.0	9.0					8																	144887183		2165	4251	6416	SO:0001630	splice_region_variant	23513	exon20			AAGATGCCCTGCA	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.2671-1G>A	8.37:g.144887183C>T		Somatic	15	0		WXS	Illumina GAIIx	Phase_I	25	3	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Splice_Site	SNP	ENST00000320476.3	37	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252149	0.80135	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.35236	1.32;1.32;1.32	4.48	4.48	0.54585	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.60637	0.2284	M	0.76328	2.33	0.47949	D	0.999551	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.66909	-0.5804	9	0.87932	D	0	.	15.7543	0.78013	0.0:1.0:0.0:0.0	.	891;891	Q14160;Q14160-3	SCRIB_HUMAN;.	D	891;891;810;260	ENSP00000349486:G891D;ENSP00000322938:G891D;ENSP00000366756:G810D	ENSP00000322938:G891D	G	-	2	0	SCRIB	144959171	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	5.359000	0.66074	2.031000	0.59945	0.442000	0.29010	GGC	.		0.721	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	Missense_Mutation
KCNV2	169522	broad.mit.edu	37	9	2718784	2718784	+	Nonsense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:2718784C>T	ENST00000382082.3	+	1	1283	c.1045C>T	c.(1045-1047)Cag>Tag	p.Q349*		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	349					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)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		GCTCTACCTTCAGCTGCTGCT	0.682																																					p.Q349X													.	KCNV2	72	0			c.C1045T						.						65.0	66.0	66.0					9																	2718784		2203	4293	6496	SO:0001587	stop_gained	169522	exon1			TACCTTCAGCTGC	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1045C>T	9.37:g.2718784C>T	ENSP00000371514:p.Gln349*	Somatic	36	0		WXS	Illumina GAIIx	Phase_I	51	3	NM_133497	Q5T6X0	Nonsense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.406786|8.406786	0.98799|0.98799	.|.	.|.	ENSG00000168263|ENSG00000168263	ENST00000382082|ENST00000423608	.|.	.|.	.|.	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	0.109916|.	0.64402|.	D|.	0.000005|.	.|T	.|0.78654	.|0.4317	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.81267	.|-0.1010	.|4	0.62326|0.66056	D|D	0.03|0.02	.|.	18.8074|18.8074	0.92043|0.92043	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	X|L	349|299	.|.	ENSP00000371514:Q349X|ENSP00000409635:S299L	Q|S	+|+	1|2	0|0	KCNV2|KCNV2	2708784|2708784	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	5.920000|5.920000	0.70017|0.70017	2.434000|2.434000	0.82447|0.82447	0.563000|0.563000	0.77884|0.77884	CAG|TCA	.		0.682	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
MLLT3	4300	broad.mit.edu	37	9	20414346	20414346	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:20414346G>A	ENST00000380338.4	-	5	784	c.498C>T	c.(496-498)agC>agT	p.S166S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S163S|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	166	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S166S(4)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctactgctgctgctgc	0.527			T	MLL	ALL																																p.S166S				Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	MLLT3,NS,carcinoma,0,7	MLLT3	125	4	Substitution - coding silent(4)	urinary_tract(2)|lung(1)|prostate(1)	c.C498T						.						8.0	15.0	13.0					9																	20414346		1434	3114	4548	SO:0001819	synonymous_variant	4300	exon5			GCTACTGCTGCTG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.498C>T	9.37:g.20414346G>A		Somatic	53	1		WXS	Illumina GAIIx	Phase_I	61	10	NM_004529	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																			.		0.527	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
LINC01410	103352539	broad.mit.edu	37	9	66457314	66457314	+	lincRNA	SNP	G	G	C			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr9:66457314G>C	ENST00000424345.1	+	0	26				RNA5SP283_ENST00000365604.1_RNA																							gggagttgtggagcgacagcg	0.627																																					.													.	.	.	0			.						.																																					0	.			GTTGTGGAGCGAC																													9.37:g.66457314G>C		Somatic	39	1		WXS	Illumina GAIIx	Phase_I	51	5	.		RNA	SNP	ENST00000424345.1	37																																																																																				.		0.627	RP11-262H14.1-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000128851.1		
BCOR	54880	broad.mit.edu	37	X	39933623	39933623	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:39933623G>T	ENST00000378444.4	-	4	1204	c.976C>A	c.(976-978)Ccg>Acg	p.P326T	BCOR_ENST00000342274.4_Missense_Mutation_p.P326T|BCOR_ENST00000397354.3_Missense_Mutation_p.P326T|BCOR_ENST00000378455.4_Missense_Mutation_p.P326T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	326					heart development (GO:0007507)|histone H2A monoubiquitination (GO:0035518)|negative regulation of bone mineralization (GO:0030502)|negative regulation of histone H3-K36 methylation (GO:0000415)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of tooth mineralization (GO:0070171)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|odontogenesis (GO:0042476)|palate development (GO:0060021)|specification of axis polarity (GO:0065001)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	heat shock protein binding (GO:0031072)|histone deacetylase binding (GO:0042826)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(4)|central_nervous_system(11)|cervix(1)|endometrium(24)|eye(6)|haematopoietic_and_lymphoid_tissue(33)|kidney(2)|large_intestine(11)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	126						GTGTCCCCCGGCAGGCCACTG	0.637			"""F, N, S, T"""	RARA	"""retinoblastoma, AML, APL(translocation)"""		oculo-facio-cardio-dental genetic																														p.P326T				Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	0			c.C976A						.						28.0	25.0	26.0					X																	39933623		2202	4299	6501	SO:0001583	missense	54880	exon4			CCCCCGGCAGGCC	AF317391	CCDS14250.1, CCDS48092.1, CCDS48093.1	Xp11.4	2014-09-17	2010-06-10		ENSG00000183337	ENSG00000183337		"""Ankyrin repeat domain containing"""	20893	protein-coding gene	gene with protein product		300485	"""BCL6 co-repressor"""			10898795	Standard	NM_017745		Approved	FLJ20285, KIAA1575	uc004den.4	Q6W2J9	OTTHUMG00000024100	ENST00000378444.4:c.976C>A	X.37:g.39933623G>T	ENSP00000367705:p.Pro326Thr	Somatic	21	0		WXS	Illumina GAIIx	Phase_I	32	4	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Missense_Mutation	SNP	ENST00000378444.4	37	CCDS48093.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.268785	0.40095	.	.	ENSG00000183337	ENST00000378455;ENST00000397354;ENST00000378444;ENST00000342274;ENST00000406200	T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01	5.56	5.56	0.83823	.	.	.	.	.	T	0.28699	0.0711	N	0.24115	0.695	0.33254	D	0.558915	D;D;D;D	0.71674	0.971;0.998;0.991;0.995	P;D;P;D	0.65987	0.779;0.94;0.873;0.94	T	0.38499	-0.9658	9	0.87932	D	0	-13.3399	9.2956	0.37813	0.0788:0.1421:0.779:0.0	.	326;326;326;326	Q6W2J9-3;Q6W2J9-4;Q6W2J9;Q6W2J9-2	.;.;BCOR_HUMAN;.	T	326	ENSP00000367716:P326T;ENSP00000380512:P326T;ENSP00000367705:P326T;ENSP00000345923:P326T;ENSP00000384485:P326T	ENSP00000345923:P326T	P	-	1	0	BCOR	39818567	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	1.178000	0.31981	2.331000	0.79229	0.600000	0.82982	CCG	.		0.637	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745	
TMEM258	746	ucsc.edu	37	11	61563066	61563066	+	5'Flank	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:61563066G>A	ENST00000537328.1	-	0	0				FADS2_ENST00000574708.1_Intron|TMEM258_ENST00000543510.1_5'Flank|FEN1_ENST00000305885.2_Missense_Mutation_p.G78D	NM_014206.3	NP_055021.1	P61165	TM258_HUMAN	transmembrane protein 258							integral component of membrane (GO:0016021)											ATGGAGAACGGCATCAAGCCC	0.602																																					p.G78D													.	FEN1	15	0			c.G233A						.						71.0	65.0	67.0					11																	61563066		2202	4299	6501	SO:0001631	upstream_gene_variant	2237	exon2			AGAACGGCATCAA		CCDS8009.1	11q12.2	2012-12-03	2012-12-03	2012-12-03	ENSG00000134825	ENSG00000134825			1164	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 10"""	C11orf10		12427278	Standard	NM_014206		Approved		uc001nsf.3	P61165	OTTHUMG00000168172		11.37:g.61563066G>A	Exception_encountered	Somatic	21	0		WXS	Illumina HiSeq		42	4	NM_004111	A8K6L8|Q9D953|Q9Y2Q7	Missense_Mutation	SNP	ENST00000537328.1	37	CCDS8009.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.038861	0.75617	.	.	ENSG00000168496	ENST00000305885;ENST00000535723	T;T	0.54071	0.59;0.59	5.44	5.44	0.79542	XPG N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.78629	0.4313	M	0.88450	2.955	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.82250	-0.0550	10	0.87932	D	0	-20.2556	19.6661	0.95893	0.0:0.0:1.0:0.0	.	78	P39748	FEN1_HUMAN	D	78	ENSP00000305480:G78D;ENSP00000445692:G78D	ENSP00000305480:G78D	G	+	2	0	FEN1	61319642	1.000000	0.71417	0.999000	0.59377	0.583000	0.36354	9.205000	0.95048	2.724000	0.93272	0.561000	0.74099	GGC	.		0.602	TMEM258-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398577.1	NM_014206	
GXYLT1	283464	ucsc.edu;bcgsc.ca	37	12	42512938	42512938	+	Missense_Mutation	SNP	T	T	A	rs200822565		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:42512938T>A	ENST00000398675.3	-	3	582	c.350A>T	c.(349-351)cAt>cTt	p.H117L	GXYLT1_ENST00000280876.6_Missense_Mutation_p.H86L	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	117					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.H117L(1)|p.H86L(1)		kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						TACAGCTAGATGCATTTTCTC	0.348																																					p.H117L													Q8IXV1_HUMAN,NS,carcinoma,0,4	GXYLT1	47	2	Substitution - Missense(2)	liver(2)	c.A350T						.						98.0	89.0	91.0					12																	42512938		1891	4131	6022	SO:0001583	missense	283464	exon3			GCTAGATGCATTT	BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.350A>T	12.37:g.42512938T>A	ENSP00000381666:p.His117Leu	Somatic	71	1		WXS	Illumina HiSeq		87	12	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Missense_Mutation	SNP	ENST00000398675.3	37	CCDS41772.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.926250	0.92319	.	.	ENSG00000151233	ENST00000398675;ENST00000280876	T;T	0.25749	1.78;1.78	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.52191	0.1719	M	0.86805	2.84	0.80722	D	1	P;D	0.56035	0.937;0.974	P;P	0.57620	0.805;0.824	T	0.61579	-0.7034	10	0.72032	D	0.01	8.6287	15.6136	0.76748	0.0:0.0:0.0:1.0	.	86;117	Q4G148-2;Q4G148	.;GXLT1_HUMAN	L	117;86	ENSP00000381666:H117L;ENSP00000280876:H86L	ENSP00000280876:H86L	H	-	2	0	GXYLT1	40799205	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.428000	0.80296	2.097000	0.63578	0.482000	0.46254	CAT	.		0.348	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
ADAMTS10	81794	ucsc.edu	37	19	8651483	8651483	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr19:8651483G>T	ENST00000597188.1	-	20	2632	c.2362C>A	c.(2362-2364)Ctc>Atc	p.L788I	ADAMTS10_ENST00000595838.1_Missense_Mutation_p.L275I|ADAMTS10_ENST00000270328.4_Missense_Mutation_p.L788I	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	788	Spacer.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						AGGGCTTCGAGGCTCTGGACC	0.612											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L788I													.	ADAMTS10	132	0			c.C2362A						.						69.0	72.0	71.0					19																	8651483		2203	4300	6503	SO:0001583	missense	81794	exon20			CTTCGAGGCTCTG	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2362C>A	19.37:g.8651483G>T	ENSP00000471851:p.Leu788Ile	Somatic	23	0	81	WXS	Illumina HiSeq		32	4	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	G	17.67	3.447569	0.63178	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.60299	0.2	5.01	3.98	0.46160	ADAM-TS Spacer 1 (1);	0.000000	0.64402	U	0.000016	T	0.69070	0.3070	M	0.63169	1.94	0.80722	D	1	D;D;D	0.89917	0.977;1.0;1.0	P;D;D	0.91635	0.852;0.999;0.999	T	0.65368	-0.6185	10	0.15499	T	0.54	.	12.4962	0.55929	0.0809:0.0:0.9191:0.0	.	542;788;275	Q59FE5;Q9H324;E9PCI6	.;ATS10_HUMAN;.	I	788;542	ENSP00000270328:L788I	ENSP00000270328:L788I	L	-	1	0	ADAMTS10	8557483	1.000000	0.71417	0.956000	0.39512	0.262000	0.26303	4.527000	0.60573	1.113000	0.41760	0.655000	0.94253	CTC	.		0.612	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
MAGEC3	139081	ucsc.edu;bcgsc.ca	37	X	140984709	140984709	+	Missense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:140984709C>A	ENST00000298296.1	+	7	1165	c.1165C>A	c.(1165-1167)Cag>Aag	p.Q389K	MAGEC3_ENST00000483584.1_3'UTR|MAGEC3_ENST00000544766.1_Missense_Mutation_p.Q91K|MAGEC3_ENST00000409007.1_Missense_Mutation_p.Q91K|MAGEC3_ENST00000443323.2_Missense_Mutation_p.Q11K|MAGEC3_ENST00000536088.1_Missense_Mutation_p.Q91K	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	389	Pro-rich.									NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					ACCTCTTCCCCAGAGTCCTCC	0.587																																					p.Q389K													.	MAGEC3	228	0			c.C1165A						.						47.0	39.0	42.0					X																	140984709		2175	4257	6432	SO:0001583	missense	139081	exon7			CTTCCCCAGAGTC	AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1165C>A	X.37:g.140984709C>A	ENSP00000298296:p.Gln389Lys	Somatic	26	0		WXS	Illumina HiSeq		34	4	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	c	5.540	0.284552	0.10513	.	.	ENSG00000165509	ENST00000298296;ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T;T	0.03468	4.15;3.92;3.97;3.92;3.92	0.225	0.225	0.15325	.	.	.	.	.	T	0.02380	0.0073	N	0.24115	0.695	0.09310	N	1	P;P	0.38110	0.618;0.458	B;B	0.39152	0.153;0.292	T	0.33752	-0.9856	8	0.06236	T	0.91	.	.	.	.	.	389;91	Q8TD91;Q3SYA7	MAGC3_HUMAN;.	K	389;91;11;91;91	ENSP00000298296:Q389K;ENSP00000441107:Q91K;ENSP00000438254:Q11K;ENSP00000440444:Q91K;ENSP00000386566:Q91K	ENSP00000298296:Q389K	Q	+	1	0	MAGEC3	140812375	0.005000	0.15991	0.036000	0.18154	0.158000	0.22134	0.582000	0.23834	0.280000	0.22209	0.284000	0.19432	CAG	.		0.587	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
KIAA2012	100652824	bcgsc.ca	37	2	202938380	202938380	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:202938380C>T	ENST00000541917.1	+	1	403	c.30C>T	c.(28-30)ggC>ggT	p.G10G	AC079354.1_ENST00000295844.3_Silent_p.G10G|AC079354.1_ENST00000409515.3_3'UTR																							TGAGCCGGGGCCACGGGAAGC	0.542																																					.													.	.	.	0			.						.																																			SO:0001819	synonymous_variant	0	.			CCGGGGCCACGGG																												ENST00000541917.1:c.30C>T	2.37:g.202938380C>T		Somatic	89	0		WXS	Illumina HiSeq	Phase_1	72	4	.		Silent	SNP	ENST00000541917.1	37																																																																																				.		0.542	AC079354.1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
ABCA12	26154	bcgsc.ca	37	2	215851337	215851337	+	Silent	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr2:215851337G>T	ENST00000272895.7	-	28	4311	c.4092C>A	c.(4090-4092)ctC>ctA	p.L1364L	ABCA12_ENST00000389661.4_Silent_p.L1046L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1364	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)	p.L1364L(1)		NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		AGTTCAGATTGAGGTTATCAA	0.428																																					p.L1364L	Ovarian(66;664 1488 5121 34295)												ABCA12,NS,carcinoma,0,1	ABCA12	368	1	Substitution - coding silent(1)	lung(1)	c.C4092A						.						89.0	84.0	86.0					2																	215851337		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon28			CAGATTGAGGTTA	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4092C>A	2.37:g.215851337G>T		Somatic	63	0		WXS	Illumina HiSeq	Phase_1	72	4	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	37	CCDS33372.1																																																																																			.		0.428	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
ANKRD28	23243	bcgsc.ca	37	3	15749477	15749477	+	Missense_Mutation	SNP	C	C	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr3:15749477C>A	ENST00000399451.2	-	14	1778	c.1411G>T	c.(1411-1413)Ggc>Tgc	p.G471C	ANKRD28_ENST00000383777.1_Missense_Mutation_p.G504C|ANKRD28_ENST00000497037.1_5'UTR	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	471						nucleus (GO:0005634)				breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						GGTGTGCAGCCTCTTTCATCA	0.473																																					p.G471C													.	ANKRD28	121	0			c.G1411T						.						102.0	97.0	98.0					3																	15749477		2052	4205	6257	SO:0001583	missense	23243	exon14			TGCAGCCTCTTTC	AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.1411G>T	3.37:g.15749477C>A	ENSP00000382379:p.Gly471Cys	Somatic	29	0		WXS	Illumina HiSeq	Phase_1	31	4	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Missense_Mutation	SNP	ENST00000399451.2	37	CCDS46769.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.289196	0.80914	.	.	ENSG00000206560	ENST00000399451;ENST00000383777;ENST00000412318	D;D;D	0.86366	-2.11;-2.11;-2.11	6.07	5.2	0.72013	Ankyrin repeat-containing domain (3);	0.043967	0.85682	D	0.000000	D	0.95433	0.8517	H	0.95504	3.68	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96611	0.9452	10	0.72032	D	0.01	.	15.145	0.72643	0.0:0.9329:0.0:0.0671	.	504;501;471	O15084-1;O15084-4;O15084	.;.;ANR28_HUMAN	C	471;504;471	ENSP00000382379:G471C;ENSP00000373287:G504C;ENSP00000397341:G471C	ENSP00000373287:G504C	G	-	1	0	ANKRD28	15724481	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.959000	0.70339	1.582000	0.49881	0.655000	0.94253	GGC	.		0.473	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199	
TLR9	54106	bcgsc.ca	37	3	52255277	52255277	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr3:52255277G>T	ENST00000360658.2	-	2	3688	c.3055C>A	c.(3055-3057)Cac>Aac	p.H1019N	TLR9_ENST00000597542.1_Missense_Mutation_p.H1043N|TLR9_ENST00000494383.1_Missense_Mutation_p.P1172Q	NM_017442.3	NP_059138.1	Q9NR96	TLR9_HUMAN	toll-like receptor 9	1019					defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|maintenance of gastrointestinal epithelium (GO:0030277)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to molecule of bacterial origin (GO:0002237)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			endometrium(4)|large_intestine(11)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(193;2.41e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	Chloroquine(DB00608)|Hydroxychloroquine(DB01611)	TTATAGAAGTGGTGGTTGTCC	0.657																																					p.H1019N													.	TLR9	72	0			c.C3055A						.						85.0	92.0	90.0					3																	52255277		2203	4300	6503	SO:0001583	missense	54106	exon2			AGAAGTGGTGGTT	AF259262	CCDS2848.1	3p21.3	2006-02-23			ENSG00000239732	ENSG00000239732		"""CD molecules"""	15633	protein-coding gene	gene with protein product		605474				11022119	Standard	NM_017442		Approved	CD289	uc003ddb.3	Q9NR96	OTTHUMG00000158106	ENST00000360658.2:c.3055C>A	3.37:g.52255277G>T	ENSP00000353874:p.His1019Asn	Somatic	36	0		WXS	Illumina HiSeq	Phase_1	23	4	NM_017442	B3Y661|D1CS56|Q6UVZ2|Q9HD68|Q9HD69|Q9HD70|Q9NYC2|Q9NYC3	Missense_Mutation	SNP	ENST00000360658.2	37	CCDS2848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.54|14.54	2.567125|2.567125	0.45694|0.45694	.|.	.|.	ENSG00000239732|ENSG00000173366	ENST00000360658|ENST00000494383	T|.	0.26373|.	1.74|.	4.87|4.87	3.92|3.92	0.45320|0.45320	.|.	0.165249|.	0.28877|.	N|.	0.013859|.	T|T	0.44477|0.44477	0.1295|0.1295	L|L	0.47716|0.47716	1.5|1.5	0.09310|0.09310	N|N	1|1	B;P|.	0.50443|.	0.118;0.935|.	B;P|.	0.44597|.	0.037;0.454|.	T|T	0.26677|0.26677	-1.0096|-1.0096	10|5	0.22109|.	T|.	0.4|.	.|.	12.1132|12.1132	0.53850|0.53850	0.0:0.0:0.818:0.182|0.0:0.0:0.818:0.182	.|.	1116;1019|.	B4E0A1;Q9NR96|.	.;TLR9_HUMAN|.	N|Q	1019|1172	ENSP00000353874:H1019N|.	ENSP00000353874:H1019N|.	H|P	-|-	1|2	0|0	TLR9|RP11-330H6.5	52230317|52230317	0.936000|0.936000	0.31750|0.31750	0.975000|0.975000	0.42487|0.42487	0.906000|0.906000	0.53458|0.53458	3.428000|3.428000	0.52792|0.52792	2.532000|2.532000	0.85374|0.85374	0.467000|0.467000	0.42956|0.42956	CAC|CCA	.		0.657	TLR9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000350203.1		
ADAM29	11086	bcgsc.ca	37	4	175898005	175898005	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr4:175898005C>T	ENST00000359240.3	+	5	1999	c.1329C>T	c.(1327-1329)tgC>tgT	p.C443C	ADAM29_ENST00000445694.1_Silent_p.C443C|RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000404450.4_Silent_p.C443C|ADAM29_ENST00000514159.1_Silent_p.C443C	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	443	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GGCTTTGTTGCAAAGACTGCA	0.453																																					p.C443C	Ovarian(140;1727 1835 21805 25838 41440)												.	ADAM29	262	0			c.C1329T						.						154.0	142.0	146.0					4																	175898005		2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TTGTTGCAAAGAC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1329C>T	4.37:g.175898005C>T		Somatic	39	0		WXS	Illumina HiSeq	Phase_1	50	4	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																			.		0.453	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
MUC21	394263	bcgsc.ca	37	6	30954572	30954572	+	Missense_Mutation	SNP	C	C	T	rs146037191		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:30954572C>T	ENST00000376296.3	+	2	861	c.620C>T	c.(619-621)gCc>gTc	p.A207V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	207	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.A207V(2)		NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGTGGGGCCAGCACAGCC	0.627																																					p.A207V													MUC21,NS,malignant_melanoma,0,2	MUC21	98	2	Substitution - Missense(2)	NS(1)|skin(1)	c.C620T						.						152.0	149.0	150.0					6																	30954572		2203	4300	6503	SO:0001583	missense	394263	exon2			GTGGGGCCAGCAC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.620C>T	6.37:g.30954572C>T	ENSP00000365473:p.Ala207Val	Somatic	86	2		WXS	Illumina HiSeq	Phase_1	151	13	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	C	8.950	0.968056	0.18659	.	.	ENSG00000204544	ENST00000376296	T	0.02737	4.18	3.86	-1.98	0.07480	.	.	.	.	.	T	0.00356	0.0011	N	0.04508	-0.205	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.45190	-0.9278	8	.	.	.	-2.1025	0.8413	0.01150	0.1528:0.2516:0.2999:0.2958	.	207	Q5SSG8	MUC21_HUMAN	V	207	ENSP00000365473:A207V	.	A	+	2	0	MUC21	31062551	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.003000	0.12901	-0.201000	0.10284	-0.424000	0.05967	GCC	C|0.998;T|0.002		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
POLH	5429	bcgsc.ca	37	6	43581551	43581551	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:43581551G>T	ENST00000372236.4	+	11	1694	c.1399G>T	c.(1399-1401)Ggc>Tgc	p.G467C	POLH_ENST00000372226.1_3'UTR|POLH_ENST00000535400.1_Missense_Mutation_p.G405C	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			CCAGGGAAGTGGCCCAGCGGT	0.493								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																												p.G467C													.	POLH	54	0			c.G1399T						.						54.0	57.0	56.0					6																	43581551		2203	4300	6503	SO:0001583	missense	5429	exon11	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAAGTGGCCCAG	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.1399G>T	6.37:g.43581551G>T	ENSP00000361310:p.Gly467Cys	Somatic	36	0		WXS	Illumina HiSeq	Phase_1	44	4	NM_006502	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	G	7.821	0.717686	0.15372	.	.	ENSG00000170734	ENST00000372236;ENST00000535400	T;T	0.59364	0.39;0.27	5.33	2.08	0.27032	.	0.671825	0.16262	N	0.222168	T	0.29914	0.0748	L	0.56769	1.78	0.09310	N	0.999999	P;P	0.50710	0.621;0.938	B;B	0.40101	0.219;0.319	T	0.11842	-1.0571	10	0.59425	D	0.04	-26.0822	5.0747	0.14625	0.4912:0.0:0.5088:0.0	.	405;467	B4DG64;Q9Y253	.;POLH_HUMAN	C	467;405	ENSP00000361310:G467C;ENSP00000442102:G405C	ENSP00000361310:G467C	G	+	1	0	POLH	43689529	0.669000	0.27502	0.040000	0.18447	0.051000	0.14879	1.046000	0.30354	0.750000	0.32877	0.491000	0.48974	GGC	.		0.493	POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502	
AIG1	51390	bcgsc.ca	37	6	143382350	143382350	+	Intron	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr6:143382350G>T	ENST00000275235.4	+	1	166				AIG1_ENST00000367596.1_Splice_Site|AIG1_ENST00000344492.5_Intron|AIG1_ENST00000367598.5_Intron|AIG1_ENST00000494282.2_Intron|AIG1_ENST00000357847.4_Intron			Q9NVV5	AIG1_HUMAN	androgen-induced 1							integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(155;2.34e-05)|GBM - Glioblastoma multiforme(68;0.0246)		CTCTTCCCCAGTGATTGCGTG	0.627																																					.													.	AIG1	24	0			.						.																																			SO:0001627	intron_variant	51390	.			TCCCCAGTGATTG	AF153605	CCDS5198.1, CCDS69216.1	6q24.1	2008-02-05			ENSG00000146416	ENSG00000146416			21607	protein-coding gene	gene with protein product		608514				11266118	Standard	NM_001286587		Approved	dJ95L4.1, AIG-1, FLJ10485	uc003qjh.3	Q9NVV5	OTTHUMG00000015721	ENST00000275235.4:c.141+147G>T	6.37:g.143382350G>T		Somatic	42	0		WXS	Illumina HiSeq	Phase_1	58	4	.	B4DPX2|C9J569|Q5T2H2|Q6N047|Q7Z378|Q8TB14|Q9Y3A9|Q9Y5B4	Splice_Site	SNP	ENST00000275235.4	37																																																																																				.		0.627	AIG1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000042510.1	NM_016108	
MUC6	4588	bcgsc.ca	37	11	1016916	1016916	+	Missense_Mutation	SNP	A	A	G			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	A	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:1016916A>G	ENST00000421673.2	-	31	5935	c.5885T>C	c.(5884-5886)cTa>cCa	p.L1962P		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1962	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTGTGGGTAGCCTGCTGCT	0.577																																					p.L1962P													.	MUC6	408	0			c.T5885C						.						729.0	746.0	740.0					11																	1016916		2203	4295	6498	SO:0001583	missense	4588	exon31			GTGGGTAGCCTGC	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5885T>C	11.37:g.1016916A>G	ENSP00000406861:p.Leu1962Pro	Somatic	213	3		WXS	Illumina HiSeq	Phase_1	292	14	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	A	2.952	-0.216493	0.06101	.	.	ENSG00000184956	ENST00000421673	T	0.13538	2.58	3.12	1.08	0.20341	.	.	.	.	.	T	0.03520	0.0101	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41627	-0.9498	9	0.32370	T	0.25	.	8.7677	0.34713	0.1288:0.0:0.8712:0.0	.	1962	Q6W4X9	MUC6_HUMAN	P	1962	ENSP00000406861:L1962P	ENSP00000406861:L1962P	L	-	2	0	MUC6	1006916	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.846000	0.04336	0.550000	0.28991	-1.351000	0.01236	CTA	.		0.577	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
MUC6	4588	bcgsc.ca	37	11	1017307	1017307	+	Missense_Mutation	SNP	G	G	A	rs372717767		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:1017307G>A	ENST00000421673.2	-	31	5544	c.5494C>T	c.(5494-5496)Cct>Tct	p.P1832S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1832	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTGGTGTGAGGGTGTGATGGG	0.552																																					p.P1832S													MUC6_ENST00000421673,NS,carcinoma,0,2	MUC6	408	0			c.C5494T						.	G	SER/PRO	152,4250		0,152,2049	780.0	761.0	767.0		5494	-1.4	0.0	11		767	139,8451		0,139,4156	no	missense	MUC6	NM_005961.2	74	0,291,6205	AA,AG,GG		1.6182,3.453,2.2398	benign	1832/2440	1017307	291,12701	2201	4295	6496	SO:0001583	missense	4588	exon31			TGTGAGGGTGTGA	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5494C>T	11.37:g.1017307G>A	ENSP00000406861:p.Pro1832Ser	Somatic	142	2		WXS	Illumina HiSeq	Phase_1	203	11	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	11.67	1.706398	0.30232	0.03453	0.016182	ENSG00000184956	ENST00000421673	T	0.20200	2.09	3.21	-1.4	0.08968	.	.	.	.	.	T	0.10035	0.0246	M	0.65975	2.015	0.09310	N	1	P	0.45078	0.85	P	0.51657	0.676	T	0.08868	-1.0701	9	0.35671	T	0.21	.	3.0139	0.06053	0.3177:0.0:0.3661:0.3162	.	1832	Q6W4X9	MUC6_HUMAN	S	1832	ENSP00000406861:P1832S	ENSP00000406861:P1832S	P	-	1	0	MUC6	1007307	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.644000	0.02002	-0.414000	0.07495	-0.643000	0.03959	CCT	.		0.552	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
MUC2	4583	bcgsc.ca	37	11	1092845	1092845	+	Missense_Mutation	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr11:1092845C>T	ENST00000441003.2	+	30	4691	c.4664C>T	c.(4663-4665)aCa>aTa	p.T1555I	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1556I|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCCACCGGCACACAGACCCCA	0.632																																					p.T1555I													.	MUC2	614	0			c.C4664T						.						94.0	126.0	114.0					11																	1092845		1882	3484	5366	SO:0001583	missense	4583	exon30			CCGGCACACAGAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4664C>T	11.37:g.1092845C>T	ENSP00000415183:p.Thr1555Ile	Somatic	325	3		WXS	Illumina HiSeq	Phase_1	628	17	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.039	-0.197860	0.06219	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.58;2.91	1.59	1.59	0.23543	.	7739.210000	0.00610	U	0.000401	T	0.10508	0.0257	.	.	.	0.09310	N	1	P	0.34699	0.464	B	0.24269	0.052	T	0.33369	-0.9871	9	0.42905	T	0.14	.	10.2908	0.43594	0.0:1.0:0.0:0.0	.	1555	E7EUV1	.	I	1555;1556	ENSP00000415183:T1555I;ENSP00000351956:T1556I	ENSP00000351956:T1556I	T	+	2	0	MUC2	1082845	0.000000	0.05858	0.001000	0.08648	0.338000	0.28826	0.112000	0.15479	0.906000	0.36621	0.109000	0.15622	ACA	.		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TMED2	10959	bcgsc.ca	37	12	124069354	124069354	+	Silent	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr12:124069354C>T	ENST00000262225.3	+	1	277	c.171C>T	c.(169-171)atC>atT	p.I57I	RP11-486O12.2_ENST00000498967.2_lincRNA|TMED2_ENST00000509052.2_5'Flank	NM_006815.3	NP_006806.1	Q15363	TMED2_HUMAN	transmembrane emp24 domain trafficking protein 2	57	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.|Interaction with F2RL1.				cargo loading into vesicle (GO:0035459)|COPI coating of Golgi vesicle (GO:0048205)|COPII vesicle coating (GO:0048208)|embryonic morphogenesis (GO:0048598)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|intracellular protein transport (GO:0006886)|maternal placenta development (GO:0001893)|negative regulation of GTPase activity (GO:0034260)|protein targeting to plasma membrane (GO:0072661)	COPI-coated vesicle (GO:0030137)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|zymogen granule membrane (GO:0042589)				kidney(1)|large_intestine(4)|lung(1)|prostate(1)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000138)|Epithelial(86;0.000613)|all cancers(50;0.00745)		TCCTGGACATCGACGTGGAGG	0.677																																					p.I57I													.	TMED2	19	0			c.C171T						.						50.0	49.0	49.0					12																	124069354		2203	4300	6503	SO:0001819	synonymous_variant	10959	exon1			GGACATCGACGTG	X92098	CCDS9250.1	12q24.31	2006-03-27			ENSG00000086598	ENSG00000086598			16996	protein-coding gene	gene with protein product						8663407	Standard	NM_006815		Approved	RNP24, P24A	uc001ufg.3	Q15363	OTTHUMG00000168694	ENST00000262225.3:c.171C>T	12.37:g.124069354C>T		Somatic	33	0		WXS	Illumina HiSeq	Phase_1	44	4	NM_006815		Silent	SNP	ENST00000262225.3	37	CCDS9250.1																																																																																			.		0.677	TMED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400606.1	NM_006815	
IGHV3-19	28446	bcgsc.ca	37	14	106653388	106653388	+	IGR	SNP	C	C	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr14:106653388C>T								IGHV1-18 (11332 upstream) : AB019440.50 (9857 downstream)																							CAGTAATACACAGCCATGTCC	0.532																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	28446	.			AATACACAGCCAT																													14.37:g.106653388C>T		Somatic	56	0		WXS	Illumina HiSeq	Phase_1	61	8	.		RNA	SNP		37																																																																																				.	0	0.532								
ZCCHC14	23174	bcgsc.ca	37	16	87446484	87446484	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr16:87446484G>T	ENST00000268616.4	-	12	1649	c.1432C>A	c.(1432-1434)Cct>Act	p.P478T		NM_015144.2	NP_055959.1	Q8WYQ9	ZCH14_HUMAN	zinc finger, CCHC domain containing 14	478							nucleic acid binding (GO:0003676)|phosphatidylinositol binding (GO:0035091)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	36				BRCA - Breast invasive adenocarcinoma(80;0.0285)		TTCTGCACAGGGAGAACCTGG	0.592																																					p.P478T													.	ZCCHC14	87	0			c.C1432A						.						69.0	72.0	71.0					16																	87446484		2198	4300	6498	SO:0001583	missense	23174	exon12			GCACAGGGAGAAC	AB011151	CCDS10961.1	16q24.2	2013-01-10			ENSG00000140948	ENSG00000140948		"""Zinc fingers, CCHC domain containing"", ""Sterile alpha motif (SAM) domain containing"""	24134	protein-coding gene	gene with protein product						9628581	Standard	XM_005255858		Approved	BDG29, MGC14139	uc002fjz.1	Q8WYQ9	OTTHUMG00000137655	ENST00000268616.4:c.1432C>A	16.37:g.87446484G>T	ENSP00000268616:p.Pro478Thr	Somatic	30	0		WXS	Illumina HiSeq	Phase_1	41	4	NM_015144	D3DUN1|O60324|Q3MJD8|Q9UFP0	Missense_Mutation	SNP	ENST00000268616.4	37	CCDS10961.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.062649	0.76187	.	.	ENSG00000140948	ENST00000268616	T	0.21932	1.98	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.39332	0.1074	L	0.34521	1.04	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.11060	-1.0603	10	0.62326	D	0.03	-21.9659	19.8234	0.96607	0.0:0.0:1.0:0.0	.	478;478	Q8WYQ9-2;Q8WYQ9	.;ZCH14_HUMAN	T	478	ENSP00000268616:P478T	ENSP00000268616:P478T	P	-	1	0	ZCCHC14	86003985	1.000000	0.71417	0.891000	0.34965	0.812000	0.45895	8.724000	0.91462	2.677000	0.91161	0.462000	0.41574	CCT	.		0.592	ZCCHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269107.1	NM_015144	
TUBB1	81027	bcgsc.ca	37	20	57594614	57594614	+	Missense_Mutation	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr20:57594614G>A	ENST00000217133.1	+	1	306	c.37G>A	c.(37-39)Ggc>Agc	p.G13S		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	13					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	TGGCCAGTGTGGCAACCAGAT	0.463																																					p.G13S													.	TUBB1	42	0			c.G37A						.						159.0	139.0	145.0					20																	57594614		2203	4300	6503	SO:0001583	missense	81027	exon1			CAGTGTGGCAACC	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"""Tubulins"""	16257	protein-coding gene	gene with protein product	"""class VI beta-tubulin"""	612901	"""tubulin, beta 1"""				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.37G>A	20.37:g.57594614G>A	ENSP00000217133:p.Gly13Ser	Somatic	36	0		WXS	Illumina HiSeq	Phase_1	53	4	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	G	36	5.917551	0.97105	.	.	ENSG00000101162	ENST00000217133	D	0.89746	-2.56	5.51	5.51	0.81932	Tubulin/FtsZ, GTPase domain (3);	0.000000	0.85682	D	0.000000	D	0.97692	0.9243	H	0.99973	5.135	0.80722	D	1	D	0.76494	0.999	D	0.67725	0.953	D	0.99675	1.0997	10	0.87932	D	0	.	18.3873	0.90471	0.0:0.0:1.0:0.0	.	13	Q9H4B7	TBB1_HUMAN	S	13	ENSP00000217133:G13S	ENSP00000217133:G13S	G	+	1	0	TUBB1	57028009	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.764000	0.98949	2.592000	0.87571	0.563000	0.77884	GGC	.		0.463	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773	
Unknown	0	bcgsc.ca	37	22	16402212	16402212	+	IGR	SNP	C	C	T	rs112569416		TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr22:16402212C>T								LA16c-2F2.8 (25157 upstream) : LA16c-23H5.4 (15056 downstream)																							CAATGGAGGGCCTTATGATGG	0.498																																					.													.	.	.	0			.						.																																			SO:0001628	intergenic_variant	0	.			GGAGGGCCTTATG																													22.37:g.16402212C>T		Somatic	68	0		WXS	Illumina HiSeq	Phase_1	77	21	.		RNA	SNP		37																																																																																				.	0	0.498								
PKDREJ	10343	bcgsc.ca	37	22	46653730	46653730	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr22:46653730G>T	ENST00000253255.5	-	1	5489	c.5490C>A	c.(5488-5490)gaC>gaA	p.D1830E		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1830					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TGTCTTCTGGGTCAATGCCAT	0.388																																					p.D1830E													.	PKDREJ	195	0			c.C5490A						.						170.0	176.0	174.0					22																	46653730		2203	4300	6503	SO:0001583	missense	10343	exon1			TTCTGGGTCAATG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5490C>A	22.37:g.46653730G>T	ENSP00000253255:p.Asp1830Glu	Somatic	50	0		WXS	Illumina HiSeq	Phase_1	48	4	NM_006071	B1AJY3|O95850	Missense_Mutation	SNP	ENST00000253255.5	37	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.877361	0.72294	.	.	ENSG00000130943	ENST00000253255	T	0.69685	-0.42	5.19	1.89	0.25635	Polycystin cation channel, PKD1/PKD2 (1);	0.093377	0.45867	D	0.000323	T	0.71247	0.3317	M	0.72118	2.19	0.09310	N	1	D	0.57257	0.979	P	0.56278	0.795	T	0.61153	-0.7120	10	0.28530	T	0.3	-23.9253	8.5621	0.33516	0.2491:0.0:0.7509:0.0	.	1830	Q9NTG1	PKDRE_HUMAN	E	1830	ENSP00000253255:D1830E	ENSP00000253255:D1830E	D	-	3	2	PKDREJ	45032394	0.943000	0.32029	0.314000	0.25224	0.643000	0.38383	2.157000	0.42320	0.281000	0.22233	0.455000	0.32223	GAC	.		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
SRPX2	27286	bcgsc.ca	37	X	99925824	99925824	+	Missense_Mutation	SNP	G	G	T			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chrX:99925824G>T	ENST00000373004.3	+	11	1666	c.1238G>T	c.(1237-1239)cGc>cTc	p.R413L	RP11-524D16__A.3_ENST00000568809.1_RNA	NM_014467.2	NP_055282.1	O60687	SRPX2_HUMAN	sushi-repeat containing protein, X-linked 2	413					angiogenesis (GO:0001525)|cell motility (GO:0048870)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of synapse assembly (GO:0051965)|regulation of phosphorylation (GO:0042325)|single organismal cell-cell adhesion (GO:0016337)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|excitatory synapse (GO:0060076)|extracellular space (GO:0005615)|synaptic membrane (GO:0097060)	hepatocyte growth factor binding (GO:0036458)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)	19						CGCCTCACTCGCTCCTACTTC	0.517											OREG0019890	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R413L													.	SRPX2	41	0			c.G1238T						.						158.0	123.0	135.0					X																	99925824		2203	4300	6503	SO:0001583	missense	27286	exon11			TCACTCGCTCCTA	AF393649	CCDS14471.1	Xq21.33-q23	2011-01-25	2011-01-25		ENSG00000102359	ENSG00000102359			30668	protein-coding gene	gene with protein product		300642	"""sushi-repeat-containing protein, X-linked 2"""			9864177	Standard	NM_014467		Approved	SRPUL	uc004egb.3	O60687	OTTHUMG00000022003	ENST00000373004.3:c.1238G>T	X.37:g.99925824G>T	ENSP00000362095:p.Arg413Leu	Somatic	32	0	1347	WXS	Illumina HiSeq	Phase_1	50	4	NM_014467	B3KQT3|Q8WW85	Missense_Mutation	SNP	ENST00000373004.3	37	CCDS14471.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.379930	0.61845	.	.	ENSG00000102359	ENST00000373004	T	0.42513	0.97	5.1	3.32	0.38043	.	0.102319	0.64402	D	0.000008	T	0.44871	0.1314	L	0.33485	1.01	0.46356	D	0.999	P	0.43909	0.821	P	0.52710	0.707	T	0.16247	-1.0409	9	.	.	.	-2.7336	14.5827	0.68302	0.0:0.2856:0.7144:0.0	.	413	O60687	SRPX2_HUMAN	L	413	ENSP00000362095:R413L	.	R	+	2	0	SRPX2	99812480	0.981000	0.34729	0.992000	0.48379	0.997000	0.91878	1.600000	0.36762	0.534000	0.28695	0.529000	0.55759	CGC	.		0.517	SRPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057486.1	NM_014467	
CPXM2	119587	hgsc.bcm.edu	37	10	125601975	125601975	+	Missense_Mutation	SNP	G	G	T	rs17679897	byFrequency	TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr10:125601975G>T	ENST00000241305.3	-	4	697	c.543C>A	c.(541-543)gaC>gaA	p.D181E	CPXM2_ENST00000368854.3_5'UTR	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	181	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		ACCACGCTCCGTCATAAAAAT	0.443																																					p.D181E		.											CPXM2,NS,carcinoma,0,1	CPXM2	0	0			c.C543A						.						61.0	59.0	60.0					10																	125601975		2203	4300	6503	SO:0001583	missense	119587	exon4			CGCTCCGTCATAA	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.543C>A	10.37:g.125601975G>T	ENSP00000241305:p.Asp181Glu	Somatic	36	0		WXS	Illumina HiSeq	.	52	3	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297835	0.40694	.	.	ENSG00000121898	ENST00000241305;ENST00000540123;ENST00000418782	D	0.98221	-4.8	5.24	-10.5	0.00291	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	D	0.96685	0.8918	M	0.65677	2.01	0.80722	D	1	P	0.38223	0.623	B	0.41813	0.367	D	0.89291	0.3619	10	0.87932	D	0	-10.9178	20.2883	0.98536	0.3391:0.0:0.6609:0.0	.	181	Q8N436	CPXM2_HUMAN	E	181;14;181	ENSP00000241305:D181E	ENSP00000241305:D181E	D	-	3	2	CPXM2	125591965	0.000000	0.05858	0.077000	0.20336	0.221000	0.24807	-1.636000	0.02016	-2.422000	0.00563	-1.532000	0.00920	GAC	.		0.443	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
TXNRD2	10587	hgsc.bcm.edu	37	22	19865952	19865952	+	Silent	SNP	G	G	A			TCGA-3X-AAV9-01A-72D-A417-09	TCGA-3X-AAV9-10A-01D-A41A-09	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	dd621b60-9752-48be-967c-43ee49990150	0c81b1b7-c24e-4b40-a844-bf702966e4a1	g.chr22:19865952G>A	ENST00000400521.1	-	15	1290	c.1284C>T	c.(1282-1284)caC>caT	p.H428H	TXNRD2_ENST00000400519.1_Silent_p.H427H|TXNRD2_ENST00000535882.1_Silent_p.H427H|TXNRD2_ENST00000400518.1_Silent_p.H398H|TXNRD2_ENST00000542719.1_Silent_p.H398H	NM_006440.3	NP_006431.2	Q9NNW7	TRXR2_HUMAN	thioredoxin reductase 2	428					cell redox homeostasis (GO:0045454)|heart development (GO:0007507)|hemopoiesis (GO:0030097)|response to oxygen radical (GO:0000305)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|NADP binding (GO:0050661)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|urinary_tract(2)	30	Colorectal(54;0.0993)					TATAATGGGCGTGATAGACCT	0.562																																					.		.											TXNRD2,NS,carcinoma,0,1	TXNRD2	0	0			.						.						138.0	150.0	146.0					22																	19865952		2111	4241	6352	SO:0001819	synonymous_variant	10587	p.H428H			ATGGGCGTGATAG	AF106697	CCDS42981.1, CCDS63402.1	22q11.21	2014-09-17			ENSG00000184470	ENSG00000184470			18155	protein-coding gene	gene with protein product	"""thioredoxin reductase beta"", ""selenoprotein Z"""	606448				9923614, 10215850, 11012661	Standard	NM_006440		Approved	TR, TRXR2, TR3	uc021wlj.1	Q9NNW7	OTTHUMG00000149975	ENST00000400521.1:c.1284C>T	22.37:g.19865952G>A		Somatic	34	0		WXS	Illumina HiSeq	Phase_I	31	2	.	O95840|Q96IJ2|Q9H2Z5|Q9NZV3|Q9NZV4|Q9P2Y0|Q9P2Y1|Q9UQU8	Silent	SNP	ENST00000400521.1	37	CCDS42981.1																																																																																			.		0.562	TXNRD2-003	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS|seleno	protein_coding	protein_coding	OTTHUMT00000314903.3	NM_006440	
