#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ASPM	259266	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	197060067	197060067	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:197060067C>G	ENST00000367409.4	-	23	9805	c.9549G>C	c.(9547-9549)agG>agC	p.R3183S	ASPM_ENST00000367408.1_Missense_Mutation_p.R848S|ASPM_ENST00000294732.7_Missense_Mutation_p.R1598S	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	3183	IQ 38. {ECO:0000255|PROSITE- ProRule:PRU00116}.				developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.R3183S(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						CTGATGCAGCCCTATTTCGCT	0.368																																																	1	Substitution - Missense(1)	kidney(1)											117.0	114.0	115.0					1																	197060067		2203	4300	6503	SO:0001583	missense	259266			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.9549G>C	1.37:g.197060067C>G	ENSP00000356379:p.Arg3183Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	16.96	3.264821	0.59431	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408;ENST00000367406	T;T;T	0.72282	-0.64;-0.64;1.26	5.05	-1.69	0.08186	.	0.448404	0.23879	N	0.043664	T	0.70684	0.3252	M	0.73598	2.24	0.09310	N	1	P;P;P	0.43231	0.801;0.684;0.785	B;B;P	0.53988	0.355;0.197;0.739	T	0.62511	-0.6839	10	0.09843	T	0.71	.	6.1004	0.20043	0.1915:0.3341:0.0:0.4744	.	1169;1598;3183	E7EQ84;Q4G1H1;Q8IZT6	.;.;ASPM_HUMAN	S	3183;1598;848;1169	ENSP00000356379:R3183S;ENSP00000294732:R1598S;ENSP00000356378:R848S	ENSP00000294732:R1598S	R	-	3	2	ASPM	195326690	0.000000	0.05858	0.284000	0.24805	0.949000	0.60115	-1.851000	0.01669	-0.241000	0.09681	0.491000	0.48974	AGG		0.368	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1		NM_018136	
BAP1	8314	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52439876	52439876	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:52439876G>T	ENST00000460680.1	-	10	1307	c.836C>A	c.(835-837)tCa>tAa	p.S279*	BAP1_ENST00000296288.5_Nonsense_Mutation_p.S261*	NM_004656.2	NP_004647.1	Q99496	RING2_HUMAN	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)	190					anterior/posterior axis specification (GO:0009948)|gastrulation with mouth forming second (GO:0001702)|histone H2A monoubiquitination (GO:0035518)|histone H2A-K119 monoubiquitination (GO:0036353)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|MLL1 complex (GO:0071339)|nuclear body (GO:0016604)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|RING-like zinc finger domain binding (GO:0071535)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S279*(1)|p.S279L(1)		NS(1)|breast(4)|endometrium(3)|eye(42)|kidney(60)|large_intestine(3)|lung(9)|ovary(4)|pleura(39)|prostate(4)|skin(9)|urinary_tract(2)	180				BRCA - Breast invasive adenocarcinoma(193;1.72e-05)|Kidney(197;0.0018)|KIRC - Kidney renal clear cell carcinoma(197;0.00203)|OV - Ovarian serous cystadenocarcinoma(275;0.0277)		AGGCAGCTGTGACTCTTGAGA	0.557			"""N, Mis, F, S, O"""		"""uveal melanoma, breast, NSCLC, RCC"""	"""mesothelioma, uveal melanoma"""																															GBM(101;493 1458 7992 21037 25532)			Rec	yes		3	3p21.31-p21.2	8314	BRCA1 associated protein-1 (ubiquitin carboxy-terminal hydrolase)		E	2	Substitution - Missense(1)|Substitution - Nonsense(1)	ovary(1)|kidney(1)											70.0	69.0	70.0					3																	52439876		2203	4300	6503	SO:0001587	stop_gained	8314			AF045581	CCDS2853.1	3p21.31-p21.2	2014-09-17			ENSG00000163930	ENSG00000163930			950	protein-coding gene	gene with protein product		603089				9528852	Standard	NM_004656		Approved	hucep-6, KIAA0272, UCHL2	uc003ddx.4	Q92560	OTTHUMG00000158392	ENST00000460680.1:c.836C>A	3.37:g.52439876G>T	ENSP00000417132:p.Ser279*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RBS7|B3KRH1|Q5TEN1|Q5TEN2	Nonsense_Mutation	SNP	ENST00000460680.1	37	CCDS2853.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.917248	0.92249	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	5.35	5.35	0.76521	.	0.678279	0.15439	N	0.262307	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.6419	14.9751	0.71264	0.0:0.1423:0.8577:0.0	.	.	.	.	X	279;261	.	ENSP00000296288:S261X	S	-	2	0	BAP1	52414916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.821000	0.55700	2.663000	0.90544	0.561000	0.74099	TCA		0.557	BAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350895.1			
ATP13A4	84239	broad.mit.edu;hgsc.bcm.edu	37	3	193120483	193120483	+	Silent	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:193120483A>G	ENST00000342695.4	-	30	3871	c.3549T>C	c.(3547-3549)tcT>tcC	p.S1183S	ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.S199S|ATP13A4_ENST00000392443.3_Silent_p.S1164S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1183						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)	p.S1183S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GATTGCTGTAAGACACTCCTC	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											100.0	98.0	99.0					3																	193120483		2203	4300	6503	SO:0001819	synonymous_variant	84239			AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3549T>C	3.37:g.193120483A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																				0.463	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4		NM_032279	
BCAS2	10286	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	115123970	115123970	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:115123970T>G	ENST00000369541.3	-	2	183	c.136A>C	c.(136-138)Act>Cct	p.T46P	BCAS2_ENST00000485021.1_5'UTR	NM_005872.2	NP_005863.1	O75934	SPF27_HUMAN	breast carcinoma amplified sequence 2	46					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cell junction (GO:0030054)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)		p.T46P(1)		biliary_tract(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(4)	13	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		TAGTTCTTAGTAGGTCGGTAT	0.468																																																	1	Substitution - Missense(1)	kidney(1)											206.0	205.0	205.0					1																	115123970		2203	4300	6503	SO:0001583	missense	10286			AB020623	CCDS874.1	1p13.2	2010-01-25			ENSG00000116752	ENSG00000116752			975	protein-coding gene	gene with protein product		605783				9731529, 10403562	Standard	NM_005872		Approved	DAM1, SPF27, Snt309	uc001efa.3	O75934	OTTHUMG00000011898	ENST00000369541.3:c.136A>C	1.37:g.115123970T>G	ENSP00000358554:p.Thr46Pro	Somatic		WXS	Illumina HiSeq	Phase_I	Q6FGS0	Missense_Mutation	SNP	ENST00000369541.3	37	CCDS874.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.491728	0.84962	.	.	ENSG00000116752	ENST00000369541	.	.	.	4.84	4.84	0.62591	.	0.091703	0.85682	D	0.000000	T	0.52273	0.1724	L	0.41079	1.255	0.80722	D	1	P	0.43633	0.813	P	0.57244	0.816	T	0.47497	-0.9113	9	0.20046	T	0.44	-13.1225	14.9298	0.70906	0.0:0.0:0.0:1.0	.	46	O75934	SPF27_HUMAN	P	46	.	ENSP00000358554:T46P	T	-	1	0	BCAS2	114925493	1.000000	0.71417	0.935000	0.37517	0.987000	0.75469	5.431000	0.66507	2.165000	0.68154	0.451000	0.29950	ACT		0.468	BCAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032871.1		NM_005872	
C14orf177	283598	hgsc.bcm.edu	37	14	99182527	99182535	+	Start_Codon_Del	DEL	GGATGCATC	GGATGCATC	-	rs17097718|rs373583218|rs139827156	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	GGATGCATC	GGATGCATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr14:99182527_99182535delGGATGCATC	ENST00000325812.2	+	0	418_426					NM_182560.2	NP_872366.2	Q52M58	CN177_HUMAN	chromosome 14 open reading frame 177											endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	13		Melanoma(154;0.128)				CAGTACGACTGGATGCATCGGAAAGAGCC	0.569														134	0.0267572	0.0356	0.0245	5008	,	,		21205	0.004		0.0567	False		,,,				2504	0.0092																0										127,4135		2,123,2006						1.8	0.0		dbSNP_134	53	465,7787		31,403,3692	no	coding	C14orf177	NM_182560.2		33,526,5698	A1A1,A1R,RR		5.635,2.9798,4.7307				592,11922				SO:0001582	initiator_codon_variant	283598			AK098639	CCDS9948.1	14q32.2	2012-05-30			ENSG00000176605	ENSG00000176605			26375	protein-coding gene	gene with protein product						12477932	Standard	NM_182560		Approved	FLJ25773	uc001yfz.2	Q52M58	OTTHUMG00000167745		14.37:g.99182527_99182535delGGATGCATC		Somatic		WXS	Illumina HiSeq	Phase_I	Q8N7D2	Frame_Shift_Del	DEL	ENST00000325812.2	37	CCDS9948.1																																																																																				0.569	C14orf177-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396078.1		NM_182560	
PRR14L	253143	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	32108234	32108234	+	Missense_Mutation	SNP	C	C	T	rs143043548		TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr22:32108234C>T	ENST00000327423.6	-	4	5780	c.5591G>A	c.(5590-5592)cGg>cAg	p.R1864Q	PRR14L_ENST00000434485.1_Missense_Mutation_p.R1864Q|PRR14L_ENST00000397493.2_Missense_Mutation_p.R1864Q	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1864								p.R1864Q(2)|p.R17Q(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						GGCTGGAGACCGTAACCCTTT	0.532													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20121	0.0		0.0	False		,,,				2504	0.0																3	Substitution - Missense(3)	kidney(3)						C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	131.0	125.0	127.0		5591	3.4	0.3	22	dbSNP_134	127	2,8598	2.2+/-6.3	0,2,4298	no	missense	PRR14L	NM_173566.2	43	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	1864/2152	32108234	3,13003	2203	4300	6503	SO:0001583	missense	0			BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.5591G>A	22.37:g.32108234C>T	ENSP00000331845:p.Arg1864Gln	Somatic		WXS	Illumina HiSeq	Phase_I	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.83	2.653243	0.47362	2.27E-4	2.33E-4	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.35789	1.29;1.29;1.29	5.66	3.36	0.38483	.	0.238980	0.36444	N	0.002596	T	0.47432	0.1445	L	0.45581	1.43	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	P;P;D	0.66497	0.905;0.905;0.944	T	0.30297	-0.9983	10	0.59425	D	0.04	-5.6263	9.575	0.39452	0.0:0.8225:0.0:0.1775	.	1864;1864;1864	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	Q	1864	ENSP00000380630:R1864Q;ENSP00000331845:R1864Q;ENSP00000388314:R1864Q	ENSP00000331845:R1864Q	R	-	2	0	PRR14L	30438234	0.689000	0.27690	0.272000	0.24630	0.483000	0.33249	0.941000	0.29005	0.613000	0.30089	0.655000	0.94253	CGG		0.532	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2		NM_173566	
C5orf42	65250	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	37226660	37226660	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr5:37226660C>G	ENST00000508244.1	-	11	2130	c.2037G>C	c.(2035-2037)caG>caC	p.Q679H	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Missense_Mutation_p.Q679H			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	679						integral component of membrane (GO:0016021)		p.Q679H(1)		breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CTGAGAATAACTGACCCTTTT	0.333																																																	1	Substitution - Missense(1)	kidney(1)											42.0	35.0	37.0					5																	37226660		692	1591	2283	SO:0001583	missense	65250				CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.2037G>C	5.37:g.37226660C>G	ENSP00000421690:p.Gln679His	Somatic		WXS	Illumina HiSeq	Phase_I	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	C	8.249	0.808679	0.16467	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	D;D	0.98178	-4.77;-4.77	5.18	-2.75	0.05914	.	0.551148	0.16751	U	0.201042	D	0.95050	0.8397	L	0.59436	1.845	0.20307	N	0.999914	B	0.21071	0.051	B	0.21917	0.037	D	0.87810	0.2631	10	0.52906	T	0.07	9.3987	2.5421	0.04728	0.1069:0.4592:0.1951:0.2389	.	679	E9PH94	.	H	679	ENSP00000421690:Q679H;ENSP00000389014:Q679H	ENSP00000389014:Q679H	Q	-	3	2	C5orf42	37262417	0.434000	0.25570	0.000000	0.03702	0.965000	0.64279	0.138000	0.16016	-1.066000	0.03164	0.586000	0.80456	CAG		0.333	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1		NM_023073	
CCDC47	57003	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	61829787	61829787	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:61829787G>A	ENST00000225726.5	-	11	1478	c.1096C>T	c.(1096-1098)Cct>Tct	p.P366S	CCDC47_ENST00000582252.1_Missense_Mutation_p.P366S|CCDC47_ENST00000403162.3_Missense_Mutation_p.P366S|RP11-51F16.8_ENST00000580553.1_5'Flank	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	366					calcium ion homeostasis (GO:0055074)|ER overload response (GO:0006983)|osteoblast differentiation (GO:0001649)|post-embryonic development (GO:0009791)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.P366S(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	18						CCTGAGCCAGGCACTGGAAAA	0.378																																																	1	Substitution - Missense(1)	kidney(1)											78.0	76.0	77.0					17																	61829787		2203	4300	6503	SO:0001583	missense	57003			AF226054	CCDS11643.1	17q23.3	2005-12-19				ENSG00000108588			24856	protein-coding gene	gene with protein product						12477932	Standard	NM_020198		Approved	GK001	uc002jbs.4	Q96A33		ENST00000225726.5:c.1096C>T	17.37:g.61829787G>A	ENSP00000225726:p.Pro366Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Missense_Mutation	SNP	ENST00000225726.5	37	CCDS11643.1	.	.	.	.	.	.	.	.	.	.	G	14.90	2.674458	0.47781	.	.	ENSG00000108588	ENST00000225726;ENST00000403162	.	.	.	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.75213	0.3819	L	0.52126	1.63	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.75693	-0.3229	9	0.54805	T	0.06	-10.5104	17.7273	0.88369	0.0:0.0:1.0:0.0	.	366;366	Q96A33-2;Q96A33	.;CCD47_HUMAN	S	366	.	ENSP00000225726:P366S	P	-	1	0	CCDC47	59183519	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	9.645000	0.98471	2.658000	0.90341	0.655000	0.94253	CCT		0.378	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2		NM_020198	
CDKN2A	1029	hgsc.bcm.edu	37	9	21970901	21970901	+	Splice_Site	SNP	C	C	T	rs45476696		TCGA-BP-4163-01A-02W-1382-10	TCGA-BP-4163-11A-01W-1244-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	03533768-49b2-4a13-bf8a-cddce7e8aa43	0c0c2e5a-75e4-4968-8e2a-3a6da1cabcc6	g.chr9:21970901C>T	ENST00000304494.5	-	2	727	c.457G>A	c.(457-459)Gac>Aac	p.D153N	CDKN2A_ENST00000361570.3_3'UTR|CDKN2A_ENST00000579122.1_Intron|CDKN2A_ENST00000498628.2_Splice_Site_p.D102N|CDKN2A_ENST00000579755.1_3'UTR|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000497750.1_Missense_Mutation_p.G102S|CDKN2A_ENST00000479692.2_Splice_Site_p.V102I|CDKN2A_ENST00000578845.2_Splice_Site_p.D102N|CDKN2A_ENST00000494262.1_Splice_Site_p.D102N|CDKN2A_ENST00000446177.1_Splice_Site_p.E153K|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498124.1_Splice_Site_p.E153K	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	153					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(16)|p.D153N(1)|p.0(1)|p.E153K(1)|p.D153Y(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CAGTCCTCACCTGAGGGACCT	0.597		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																												.											1335	Whole gene deletion(1316)|Unknown(16)|Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(278)|skin(170)|central_nervous_system(163)|lung(145)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|oesophagus(48)|upper_aerodigestive_tract(47)|ovary(34)|breast(31)|kidney(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	GRCh37	CS972842	CDKN2A	S	rs45476696						34.0	35.0	34.0					9																	21970901		2203	4300	6503	SO:0001630	splice_region_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.457+1G>A	9.37:g.21970901C>T		Somatic		WXS	Illumina MiSeq	Phase_I	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000304494.5	37	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.26|10.26	1.301003|1.301003	0.23650|0.23650	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000304494|ENST00000446177	T|T	0.78126|0.76578	-1.15|-1.03	4.21|4.21	3.31|3.31	0.37934|0.37934	.|.	.|.	.|.	.|.	.|.	T|T	0.75140|0.75140	0.3809|0.3809	L|L	0.39898|0.39898	1.24|1.24	0.80722|0.80722	D|D	1|1	B|.	0.13594|.	0.008|.	B|.	0.12156|.	0.007|.	T|T	0.74266|0.74266	-0.3721|-0.3721	9|7	0.66056|0.48119	D|T	0.02|0.1	.|.	9.7139|9.7139	0.40263|0.40263	0.2066:0.7934:0.0:0.0|0.2066:0.7934:0.0:0.0	rs45476696|rs45476696	153|.	P42771|.	CD2A1_HUMAN|.	N|K	153|153	ENSP00000307101:D153N|ENSP00000394932:E153K	ENSP00000307101:D153N|ENSP00000394932:E153K	D|E	-|-	1|1	0|0	CDKN2A|CDKN2A	21960901|21960901	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.015000|0.015000	0.08874|0.08874	3.892000|3.892000	0.56235|0.56235	1.376000|1.376000	0.46267|0.46267	-0.122000|-0.122000	0.15005|0.15005	GAC|GAA		0.597	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1		NM_000077	Missense_Mutation
CENPE	1062	broad.mit.edu;ucsc.edu	37	4	104061981	104061981	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr4:104061981G>A	ENST00000265148.3	-	36	5833	c.5744C>T	c.(5743-5745)aCc>aTc	p.T1915I	CENPE_ENST00000380026.3_Missense_Mutation_p.T1890I	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1915					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.T1915I(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TCTAGCTTTGGTTTCTTGCAG	0.393																																																	1	Substitution - Missense(1)	kidney(1)											126.0	110.0	116.0					4																	104061981		2203	4300	6503	SO:0001583	missense	1062			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.5744C>T	4.37:g.104061981G>A	ENSP00000265148:p.Thr1915Ile	Somatic		WXS	Illumina GAIIx	Phase_I	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.272140	0.23221	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.69685	-0.42;-0.42	5.21	-1.93	0.07594	.	.	.	.	.	T	0.50769	0.1635	L	0.49350	1.555	0.09310	N	1	P;B	0.38767	0.646;0.04	B;B	0.35859	0.212;0.075	T	0.45629	-0.9248	9	0.59425	D	0.04	.	1.3032	0.02083	0.3282:0.1034:0.3574:0.2109	.	1890;1915	Q02224-3;Q02224	.;CENPE_HUMAN	I	1915;1915;1890	ENSP00000265148:T1915I;ENSP00000369365:T1890I	ENSP00000265148:T1915I	T	-	2	0	CENPE	104281430	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.000000	0.12993	-0.431000	0.07307	-0.874000	0.02982	ACC		0.393	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
DNAH17-AS1	100996295	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	76496393	76496393	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:76496393G>A	ENST00000598378.1	+	1	1483	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	DNAH17_ENST00000389840.5_Silent_p.D1864D|RP11-559N14.5_ENST00000591373.1_RNA|DNAH17_ENST00000585328.1_Silent_p.D1873D					DNAH17 antisense RNA 1									p.D1873D(1)									GTACCTTGTAGTCCATCTGCT	0.617																																																	1	Substitution - coding silent(1)	kidney(1)											21.0	24.0	23.0					17																	76496393		1995	4192	6187	SO:0001583	missense	8632					17q25.3	2014-02-12	2013-05-21		ENSG00000268470	ENSG00000267432		"""Long non-coding RNAs"""	48594	non-coding RNA	RNA, long non-coding							Standard	NR_102401		Approved				OTTHUMG00000177588	ENST00000598378.1:c.325G>A	17.37:g.76496393G>A	ENSP00000472049:p.Val109Ile	Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000598378.1	37																																																																																					0.617	DNAH17-AS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				
DNAJC17	55192	broad.mit.edu;hgsc.bcm.edu	37	15	41065992	41065992	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr15:41065992A>T	ENST00000220496.4	-	10	755	c.725T>A	c.(724-726)cTg>cAg	p.L242Q		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	242	RRM.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.L242Q(1)		endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GGAAATCTTCAGAGGGTTATC	0.592																																																	1	Substitution - Missense(1)	kidney(1)											43.0	37.0	39.0					15																	41065992		2203	4300	6503	SO:0001583	missense	55192			AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"""Heat shock proteins / DNAJ (HSP40)"", ""RNA binding motif (RRM) containing"""	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.725T>A	15.37:g.41065992A>T	ENSP00000220496:p.Leu242Gln	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.303309	0.81136	.	.	ENSG00000104129	ENST00000220496	T	0.26957	1.7	5.17	5.17	0.71159	Nucleotide-binding, alpha-beta plait (1);	0.148390	0.47093	D	0.000251	T	0.59649	0.2209	M	0.91818	3.245	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.69982	-0.4997	10	0.87932	D	0	.	14.8314	0.70151	1.0:0.0:0.0:0.0	.	242	Q9NVM6	DJC17_HUMAN	Q	242	ENSP00000220496:L242Q	ENSP00000220496:L242Q	L	-	2	0	DNAJC17	38853284	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.450000	0.80656	2.181000	0.69327	0.459000	0.35465	CTG		0.592	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2		NM_018163	
FAT3	120114	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	92577387	92577387	+	Silent	SNP	G	G	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr11:92577387G>T	ENST00000298047.6	+	18	10871	c.10854G>T	c.(10852-10854)ctG>ctT	p.L3618L	FAT3_ENST00000525166.1_Silent_p.L3468L|FAT3_ENST00000533797.1_5'Flank|FAT3_ENST00000409404.2_Silent_p.L3618L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3618	Cadherin 33. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L3618L(2)|p.L193L(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGTATGTCCTGAATGTGTCTG	0.507										TCGA Ovarian(4;0.039)																																							3	Substitution - coding silent(3)	kidney(3)											173.0	181.0	178.0					11																	92577387		2152	4258	6410	SO:0001819	synonymous_variant	120114			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10854G>T	11.37:g.92577387G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																					0.507	FAT3-201	KNOWN	basic	protein_coding	protein_coding			NM_001008781	
G6PC	2538	hgsc.bcm.edu;ucsc.edu	37	17	41062994	41062995	+	Frame_Shift_Ins	INS	-	-	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:41062994_41062995insA	ENST00000253801.2	+	5	704_705	c.625_626insA	c.(625-627)tatfs	p.Y209fs	G6PC_ENST00000592383.1_3'UTR|G6PC_ENST00000585489.1_3'UTR	NM_000151.3	NP_000142.2	P35575	G6PC_HUMAN	glucose-6-phosphatase, catalytic subunit	209			Y -> C (in GSD1A; complete loss of activity and reduced enzyme stability). {ECO:0000269|PubMed:15542400}.		carbohydrate metabolic process (GO:0005975)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|gluconeogenesis (GO:0006094)|glucose 6-phosphate metabolic process (GO:0051156)|glucose homeostasis (GO:0042593)|glucose transport (GO:0015758)|glucose-6-phosphate transport (GO:0015760)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|hexose transport (GO:0008645)|multicellular organism growth (GO:0035264)|regulation of gene expression (GO:0010468)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)|urate metabolic process (GO:0046415)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	glucose-6-phosphatase activity (GO:0004346)|phosphate ion binding (GO:0042301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.113)		CCTCAAGAAATATTTTCTCATT	0.475																																																	0			GRCh37	CM043503	G6PC	M																																				SO:0001589	frameshift_variant	2538			U01120	CCDS11446.1, CCDS59291.1	17q21	2014-09-17	2006-06-28			ENSG00000131482	3.1.3.9		4056	protein-coding gene	gene with protein product	"""glycogen storage disease type I, von Gierke disease"""	613742	"""glucose-6-phosphatase, catalytic (glycogen storage disease type I, von Gierke disease)"""	G6PT		7774924	Standard	NM_000151		Approved	GSD1a	uc002icb.2	P35575		ENST00000253801.2:c.626dupA	17.37:g.41062995_41062995dupA	ENSP00000253801:p.Tyr209fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L4C0|B4E1C3|K7EL82	Frame_Shift_Del	INS	ENST00000253801.2	37	CCDS11446.1																																																																																				0.475	G6PC-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452451.1		NM_000151	
HEATR3	55027	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	50120249	50120249	+	Silent	SNP	T	T	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr16:50120249T>G	ENST00000299192.7	+	11	1688	c.1497T>G	c.(1495-1497)ctT>ctG	p.L499L	HEATR3_ENST00000564942.1_3'UTR|HEATR3_ENST00000285767.4_Silent_p.L413L	NM_182922.2	NP_891552.1	Q7Z4Q2	HEAT3_HUMAN	HEAT repeat containing 3	499								p.L499L(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	28						CACAGCTGCTTTTTTCTCAAC	0.473																																																	1	Substitution - coding silent(1)	kidney(1)											31.0	31.0	31.0					16																	50120249		2198	4300	6498	SO:0001819	synonymous_variant	55027			BC018730	CCDS10739.1	16q12.1	2008-02-05			ENSG00000155393	ENSG00000155393			26087	protein-coding gene	gene with protein product		614951				12477932	Standard	XM_005256013		Approved	FLJ20718	uc002efw.3	Q7Z4Q2	OTTHUMG00000133174	ENST00000299192.7:c.1497T>G	16.37:g.50120249T>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K1N4|Q8N525|Q8WV56|Q96CC9|Q9NWN7	Silent	SNP	ENST00000299192.7	37	CCDS10739.1																																																																																				0.473	HEATR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256880.2		NM_182922	
HLA-DQB1	3119	hgsc.bcm.edu;ucsc.edu	37	6	32629137	32629137	+	Missense_Mutation	SNP	T	T	G	rs1140343	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr6:32629137T>G	ENST00000399084.1	-	5	937	c.759A>C	c.(757-759)caA>caC	p.Q253H	HLA-DQB1_ENST00000399082.3_Intron|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000460185.1_5'Flank|HLA-DQB1-AS1_ENST00000419852.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.Q253H|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.Q253H|HLA-DQB1_ENST00000399079.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	253			H -> Q (in allele DQB1*05:01, allele DQB1*05:02, allele DQB1*05:03, allele DQB1*06:01, allele DQB1*06:02, allele DQB1*06:03, allele DQB1*06:04, allele DQB1*06:09, allele DQB1*06:12 and allele DQB1*06:36).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	TCTGACTCCTTTGACGGATGA	0.557									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				.|||	2374	0.474042	0.4115	0.6455	5008	,	,		12639	0.4563		0.502	False		,,,				2504	0.4264				Esophageal Squamous(151;720 1825 15000 40336 43415)												0													29.0	26.0	27.0					6																	32629137		1985	3993	5978	SO:0001583	missense	3119	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399084.1:c.759A>C	6.37:g.32629137T>G	ENSP00000382034:p.Gln253His	Somatic		WXS	Illumina HiSeq	Phase_I	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Silent	SNP	ENST00000399084.1	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.667088	0.00765	.	.	ENSG00000179344	ENST00000374943;ENST00000434651;ENST00000399084	T;T;T	0.00637	6.09;6.05;6.05	4.9	1.89	0.25635	.	0.386589	0.24472	N	0.038227	T	0.00210	0.0006	.	.	.	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.43877	-0.9364	8	0.37606	T	0.19	.	4.3544	0.11170	0.166:0.1331:0.5795:0.1215	rs1140343;rs3204407;rs9273623;rs9273624;rs12722394;rs17404508;rs36092604	218;253;253	A2VCT9;Q5Y7D6;Q5Y7A9	.;.;.	H	253	ENSP00000364080:Q253H;ENSP00000407332:Q253H;ENSP00000382034:Q253H	ENSP00000364080:Q253H	Q	-	3	2	HLA-DQB1	32737115	0.000000	0.05858	0.029000	0.17559	0.566000	0.35808	-0.071000	0.11505	0.152000	0.19188	-0.127000	0.14921	CAA		0.557	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1		NM_002123	
IFI30	10437	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	18286140	18286140	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr19:18286140G>C	ENST00000407280.3	+	3	510	c.335G>C	c.(334-336)aGg>aCg	p.R112T	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	112					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 II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)	p.R112T(1)		endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						GTCAGTGGCAGGTGGGAGTTC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											25.0	30.0	29.0					19																	18286140		2036	4178	6214	SO:0001583	missense	10437			J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.335G>C	19.37:g.18286140G>C	ENSP00000384886:p.Arg112Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Missense_Mutation	SNP	ENST00000407280.3	37	CCDS46015.1	.	.	.	.	.	.	.	.	.	.	G	0.678	-0.799485	0.02841	.	.	ENSG00000216490	ENST00000407280	.	.	.	5.19	-1.63	0.08345	.	.	.	.	.	T	0.16385	0.0394	N	0.05510	-0.035	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.22243	-1.0222	8	0.37606	T	0.19	-44.5345	6.3541	0.21393	0.4257:0.3178:0.2565:0.0	.	112	P13284	GILT_HUMAN	T	112	.	ENSP00000384886:R112T	R	+	2	0	IFI30	18147140	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.124000	0.11724	-0.339000	0.08088	AGG		0.622	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3		NM_006332	
IVD	3712	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	40707145	40707145	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr15:40707145A>T	ENST00000249760.2	+	8	1185	c.842A>T	c.(841-843)gAc>gTc	p.D281V	IVD_ENST00000479013.2_Missense_Mutation_p.D254V|IVD_ENST00000487418.2_Missense_Mutation_p.D284V	NM_002225.3	NP_002216.2	P26440	IVD_HUMAN	isovaleryl-CoA dehydrogenase	281	Substrate binding.				branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	flavin adenine dinucleotide binding (GO:0050660)|isovaleryl-CoA dehydrogenase activity (GO:0008470)	p.D281V(1)		kidney(1)|lung(5)|ovary(2)|prostate(1)	9		all_cancers(109;1.19e-18)|all_epithelial(112;1.52e-15)|Lung NSC(122;5.14e-11)|all_lung(180;1.27e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.65e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0808)	Flavin adenine dinucleotide(DB03147)	AGTGGGCTGGACCTGGAGCGG	0.622																																					GBM(31;293 617 7486 32527 34655)												1	Substitution - Missense(1)	kidney(1)											66.0	57.0	60.0					15																	40707145		2203	4300	6503	SO:0001583	missense	3712			AF038317	CCDS10057.1, CCDS10057.2, CCDS53930.1	15q14-q15	2010-05-11	2010-05-11		ENSG00000128928	ENSG00000128928	1.3.99.10		6186	protein-coding gene	gene with protein product		607036	"""isovaleryl Coenzyme A dehydrogenase"", ""isovaleryl CoA dehydrogenase"""			2063866	Standard	NM_002225		Approved	ACAD2	uc001zls.3	P26440	OTTHUMG00000129984	ENST00000249760.2:c.842A>T	15.37:g.40707145A>T	ENSP00000249760:p.Asp281Val	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCV5|B3KVI7|J3KR54|Q53XZ9|Q96AF6	Missense_Mutation	SNP	ENST00000249760.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.2|25.2	4.613919|4.613919	0.87359|0.87359	.|.	.|.	ENSG00000128928|ENSG00000128928	ENST00000249760;ENST00000479013;ENST00000487418;ENST00000497252|ENST00000473112	D;D;D|.	0.96491|.	-4.03;-4.03;-4.03|.	5.06|5.06	5.06|5.06	0.68205|0.68205	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);|.	0.086607|.	0.85682|.	D|.	0.000000|.	D|D	0.85557|0.85557	0.5724|0.5724	M|M	0.93720|0.93720	3.45|3.45	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.91635|.	0.996;0.999|.	D|D	0.89568|0.89568	0.3811|0.3811	10|5	0.87932|.	D|.	0|.	.|.	14.9454|14.9454	0.71026|0.71026	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	281;254|.	P26440;B3KVI7|.	IVD_HUMAN;.|.	V|S	281;254;284;51|201	ENSP00000249760:D281V;ENSP00000417990:D254V;ENSP00000418397:D284V|.	ENSP00000249760:D281V|.	D|T	+|+	2|1	0|0	IVD|IVD	38494437|38494437	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	8.686000|8.686000	0.91250|0.91250	2.123000|2.123000	0.65237|0.65237	0.402000|0.402000	0.26972|0.26972	GAC|ACC		0.622	IVD-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				
KDM4A	9682	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	44154664	44154664	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:44154664G>C	ENST00000372396.3	+	13	2069	c.1935G>C	c.(1933-1935)caG>caC	p.Q645H		NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	645					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q645H(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						AACTGTGGCAGAACCGACCTC	0.537																																																	1	Substitution - Missense(1)	kidney(1)											93.0	83.0	86.0					1																	44154664		2203	4300	6503	SO:0001583	missense	9682			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.1935G>C	1.37:g.44154664G>C	ENSP00000361473:p.Gln645His	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	37	CCDS491.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.535210	0.85812	.	.	ENSG00000066135	ENST00000372396	T	0.52057	0.68	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.68705	0.3030	M	0.69358	2.11	0.52501	D	0.999958	D	0.71674	0.998	D	0.79784	0.993	T	0.68337	-0.5435	10	0.51188	T	0.08	-23.5947	19.5353	0.95251	0.0:0.0:1.0:0.0	.	645	O75164	KDM4A_HUMAN	H	645	ENSP00000361473:Q645H	ENSP00000361473:Q645H	Q	+	3	2	KDM4A	43927251	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.751000	0.68720	2.608000	0.88229	0.563000	0.77884	CAG		0.537	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1		NM_014663	
KRT15	3866	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	39673185	39673185	+	Missense_Mutation	SNP	C	C	T	rs138271368	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:39673185C>T	ENST00000254043.3	-	3	4198	c.613G>A	c.(613-615)Gtt>Att	p.V205I	KRT15_ENST00000393976.2_Missense_Mutation_p.V205I|KRT15_ENST00000393974.3_Missense_Mutation_p.V40I|KRT15_ENST00000393981.3_Missense_Mutation_p.V40I	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	205	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)	p.V205I(3)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				TCAGCCTCAACGCCCTGGCGC	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19121	0.001		0.0	False		,,,				2504	0.0																3	Substitution - Missense(3)	prostate(1)|kidney(1)|central_nervous_system(1)						C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	75.0	75.0	75.0		613	2.7	1.0	17	dbSNP_134	75	0,8600		0,0,4300	yes	missense	KRT15	NM_002275.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	205/457	39673185	1,13005	2203	4300	6503	SO:0001583	missense	3866				CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.613G>A	17.37:g.39673185C>T	ENSP00000254043:p.Val205Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	CCDS11398.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	3	0.005244755244755245	1	0.0013192612137203166	C	18.69	3.678865	0.68042	2.27E-4	0.0	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981;ENST00000458290	D;D;D;D;D	0.89617	-2.54;-2.54;-2.54;-2.54;-2.54	4.86	2.74	0.32292	Filament (1);	0.000000	0.41823	D	0.000804	D	0.93288	0.7861	M	0.93150	3.385	0.47037	D	0.99929	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.997;0.997	D	0.93234	0.6620	10	0.87932	D	0	.	10.0097	0.41979	0.1362:0.7907:0.0:0.0731	.	40;205;205	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	I	205;40;205;40;40	ENSP00000254043:V205I;ENSP00000377544:V40I;ENSP00000377546:V205I;ENSP00000377550:V40I;ENSP00000409282:V40I	ENSP00000254043:V205I	V	-	1	0	KRT15	36926711	1.000000	0.71417	0.999000	0.59377	0.185000	0.23345	4.807000	0.62576	1.254000	0.44035	0.650000	0.86243	GTT		0.612	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1		NM_002275	
LAMB4	22798	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	107717486	107717486	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr7:107717486A>T	ENST00000388781.3	-	17	2110	c.2027T>A	c.(2026-2028)aTc>aAc	p.I676N	LAMB4_ENST00000418464.1_Missense_Mutation_p.I676N|LAMB4_ENST00000414450.2_Missense_Mutation_p.I676N|LAMB4_ENST00000205386.4_Missense_Mutation_p.I676N|LAMB4_ENST00000388780.3_Missense_Mutation_p.I676N	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	676	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)		p.I676N(1)		NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						TTCTAAACAGATGGGTGTGGG	0.383																																																	1	Substitution - Missense(1)	kidney(1)											97.0	102.0	100.0					7																	107717486		2203	4300	6503	SO:0001583	missense	22798			AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2027T>A	7.37:g.107717486A>T	ENSP00000373433:p.Ile676Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.238677	0.79800	.	.	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.36157	1.32;1.32;1.34;1.27;1.32	5.06	5.06	0.68205	Laminin IV (1);	0.144445	0.32503	N	0.006008	T	0.47395	0.1443	L	0.55481	1.735	0.39039	D	0.960088	D	0.61080	0.989	P	0.53450	0.726	T	0.54807	-0.8238	10	0.87932	D	0	.	14.6452	0.68756	1.0:0.0:0.0:0.0	.	676	A4D0S4	LAMB4_HUMAN	N	676	ENSP00000205386:I676N;ENSP00000373433:I676N;ENSP00000373432:I676N;ENSP00000402353:I676N;ENSP00000402265:I676N	ENSP00000205386:I676N	I	-	2	0	LAMB4	107504722	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.100000	0.71473	2.134000	0.65973	0.533000	0.62120	ATC		0.383	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1		XM_209857	
MAP1A	4130	broad.mit.edu	37	15	43818938	43818938	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr15:43818938A>G	ENST00000300231.5	+	4	5717	c.5267A>G	c.(5266-5268)aAg>aGg	p.K1756R	MAP1A_ENST00000382031.1_Missense_Mutation_p.K1994R|MAP1A_ENST00000399453.1_Missense_Mutation_p.K1756R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1756					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)	p.K1756R(1)		breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	TCAGACTTCAAGGATTTCCAG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											63.0	65.0	65.0					15																	43818938		1931	4129	6060	SO:0001583	missense	4130			U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5267A>G	15.37:g.43818938A>G	ENSP00000300231:p.Lys1756Arg	Somatic		WXS	Illumina GAIIx	Phase_I	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	A	14.81	2.645349	0.47258	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01629	4.72;4.72;4.72	4.46	4.46	0.54185	.	0.000000	0.35708	N	0.003038	T	0.03783	0.0107	L	0.36672	1.1	0.34321	D	0.686581	D	0.58268	0.982	P	0.58013	0.831	T	0.56920	-0.7899	10	0.14656	T	0.56	-15.1748	12.1342	0.53961	1.0:0.0:0.0:0.0	.	1756	P78559	MAP1A_HUMAN	R	1994;1756;1756	ENSP00000371462:K1994R;ENSP00000382380:K1756R;ENSP00000300231:K1756R	ENSP00000300231:K1756R	K	+	2	0	MAP1A	41606230	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	5.030000	0.64128	1.882000	0.54519	0.374000	0.22700	AAG		0.572	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5		NM_002373	
LRRK1	79705	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	101601457	101601457	+	Silent	SNP	G	G	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr15:101601457G>A	ENST00000388948.3	+	30	5120	c.4761G>A	c.(4759-4761)caG>caA	p.Q1587Q	LRRK1_ENST00000284395.5_Silent_p.Q1584Q|RP11-505E24.2_ENST00000559857.1_RNA	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1									p.Q1599Q(1)|p.Q1587Q(1)		breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			TGAGCTGCCAGCTCCAGGTCC	0.617																																																	2	Substitution - coding silent(2)	kidney(2)											68.0	80.0	76.0					15																	101601457		2090	4222	6312	SO:0001819	synonymous_variant	79705			AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4761G>A	15.37:g.101601457G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																				0.617	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2		NM_024652	
MLX	6945	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	40721610	40721610	+	Silent	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:40721610A>G	ENST00000246912.4	+	6	677	c.624A>G	c.(622-624)ctA>ctG	p.L208L	MLX_ENST00000346833.4_Silent_p.L124L|MLX_ENST00000435881.2_Silent_p.L154L	NM_170607.2	NP_733752.1	Q9UH92	MLX_HUMAN	MLX, MAX dimerization protein	208					energy reserve metabolic process (GO:0006112)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|positive regulation of cellular metabolic process (GO:0031325)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.L208L(1)		kidney(3)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	10		all_cancers(22;4.26e-05)|Breast(137;0.000153)|all_epithelial(22;0.00148)		BRCA - Breast invasive adenocarcinoma(366;0.129)		TCACCGCCCTAAAGATCATGA	0.498																																					GBM(121;657 1601 4665 24731 34640)												1	Substitution - coding silent(1)	kidney(1)											79.0	76.0	77.0					17																	40721610		2203	4300	6503	SO:0001819	synonymous_variant	6945			AF213668	CCDS11430.1, CCDS42341.1, CCDS45687.1	17q21.1	2013-05-21	2012-11-15	2005-02-11		ENSG00000108788		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	11645	protein-coding gene	gene with protein product		602976	"""transcription factor-like 4"", ""MAX-like protein X"""	TCFL4		8973301	Standard	NM_170607		Approved	MAD7, MXD7, bHLHd13	uc002iag.3	Q9UH92		ENST00000246912.4:c.624A>G	17.37:g.40721610A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K2J3|B2RAV8|B2RD73|Q53XM6|Q96FL2|Q9H2V0|Q9H2V1|Q9H2V2|Q9NXN3	Silent	SNP	ENST00000246912.4	37	CCDS11430.1																																																																																				0.498	MLX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450415.1		NM_170607	
MPV17L	255027	broad.mit.edu;hgsc.bcm.edu	37	16	15501819	15501819	+	Silent	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr16:15501819A>G	ENST00000396385.3	+	4	560	c.441A>G	c.(439-441)caA>caG	p.Q147Q	RP11-1021N1.1_ENST00000568222.1_Intron|MPV17L_ENST00000287594.7_Missense_Mutation_p.M124V	NM_001128423.1	NP_001121895.1	Q2QL34	MP17L_HUMAN	MPV17 mitochondrial membrane protein-like	147					negative regulation of hydrogen peroxide biosynthetic process (GO:0010730)|negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901029)|reactive oxygen species metabolic process (GO:0072593)	integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	receptor binding (GO:0005102)	p.M124V(1)|p.Q147Q(1)		kidney(2)|large_intestine(1)|skin(1)	4						TTCCTGTTCAATGGAGAACAG	0.498																																																	2	Substitution - Missense(1)|Substitution - coding silent(1)	kidney(2)											82.0	71.0	75.0					16																	15501819		2197	4300	6497	SO:0001819	synonymous_variant	255027			DQ004255	CCDS10560.1, CCDS45421.1	16p13.11	2009-04-06			ENSG00000156968	ENSG00000156968			26827	protein-coding gene	gene with protein product						16631601	Standard	NM_001128423		Approved	FLJ39599, MLPH1, MLPH2, MPV17L1	uc002ddn.2	Q2QL34	OTTHUMG00000129882	ENST00000396385.3:c.441A>G	16.37:g.15501819A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B4DDY1|Q6P7T6|Q8N8E9	Missense_Mutation	SNP	ENST00000396385.3	37	CCDS45421.1	.	.	.	.	.	.	.	.	.	.	.	10.01	1.233637	0.22626	.	.	ENSG00000156968	ENST00000287594	D	0.91996	-2.95	5.2	-1.57	0.08506	.	.	.	.	.	D	0.82655	0.5084	.	.	.	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.67329	-0.5698	8	0.33940	T	0.23	-7.7033	2.6026	0.04870	0.1384:0.3749:0.3289:0.1578	.	124	Q2QL34-2	.	V	124	ENSP00000287594:M124V	ENSP00000287594:M124V	M	+	1	0	MPV17L	15409320	0.996000	0.38824	0.374000	0.26016	0.585000	0.36419	0.229000	0.17833	-0.098000	0.12285	-2.459000	0.00205	ATG		0.498	MPV17L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422450.1		NM_173803	
MRPL9	65005	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	151732588	151732588	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:151732588A>T	ENST00000368830.3	-	7	826	c.742T>A	c.(742-744)Tat>Aat	p.Y248N	OAZ3_ENST00000321531.5_5'Flank|OAZ3_ENST00000315067.8_5'Flank|RP11-98D18.15_ENST00000601684.1_RNA|MRPL9_ENST00000467306.1_5'UTR|MRPL9_ENST00000368829.3_Missense_Mutation_p.Y214N	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	248					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.Y248N(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			CAGTACTTATATCTTTTGGTC	0.493																																																	1	Substitution - Missense(1)	kidney(1)											86.0	84.0	85.0					1																	151732588		2203	4300	6503	SO:0001583	missense	65005			AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"""Mitochondrial ribosomal proteins / large subunits"""	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.742T>A	1.37:g.151732588A>T	ENSP00000357823:p.Tyr248Asn	Somatic		WXS	Illumina HiSeq	Phase_I	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.637649	0.47049	.	.	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.34667	1.35;1.37	5.16	5.16	0.70880	.	0.589487	0.16610	N	0.206947	T	0.35098	0.0920	L	0.57536	1.79	0.35639	D	0.810843	D	0.61697	0.99	P	0.53146	0.719	T	0.36138	-0.9760	10	0.62326	D	0.03	-1.2972	11.3139	0.49379	1.0:0.0:0.0:0.0	.	248	Q9BYD2	RM09_HUMAN	N	248;214	ENSP00000357823:Y248N;ENSP00000357822:Y214N	ENSP00000357822:Y214N	Y	-	1	0	MRPL9	149999212	1.000000	0.71417	0.986000	0.45419	0.123000	0.20343	5.053000	0.64269	2.157000	0.67596	0.528000	0.53228	TAT		0.493	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2		NM_031420	
MRPS7	51081	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73258639	73258639	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:73258639G>C	ENST00000245539.6	+	2	372	c.145G>C	c.(145-147)Gaa>Caa	p.E49Q	GGA3_ENST00000537686.1_5'Flank|GGA3_ENST00000579743.1_5'Flank|GGA3_ENST00000538886.1_5'Flank|GGA3_ENST00000578348.1_5'Flank|MRPS7_ENST00000579761.1_Missense_Mutation_p.E49Q|GGA3_ENST00000245541.6_5'Flank|GGA3_ENST00000582486.1_5'Flank|GGA3_ENST00000351904.7_5'Flank|MRPS7_ENST00000579002.1_Missense_Mutation_p.E78Q|GGA3_ENST00000582717.1_5'Flank	NM_015971.3	NP_057055.2	Q9Y2R9	RT07_HUMAN	mitochondrial ribosomal protein S7	49					translation (GO:0006412)	cytosolic small ribosomal subunit (GO:0022627)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)	p.E49Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)	6	all_cancers(13;1.25e-07)|all_epithelial(9;2.63e-08)|Breast(9;1.06e-07)		all cancers(21;3.02e-07)|Epithelial(20;2.92e-06)			GATTGACAAGGAATATTATCG	0.512																																																	1	Substitution - Missense(1)	kidney(1)											145.0	150.0	149.0					17																	73258639		2203	4300	6503	SO:0001583	missense	51081			AB051348	CCDS11718.1	17q25.1	2012-09-13				ENSG00000125445		"""Mitochondrial ribosomal proteins / small subunits"""	14499	protein-coding gene	gene with protein product		611974					Standard	NM_015971		Approved	MRP-S, RP-S7, RPMS7	uc002jnm.4	Q9Y2R9		ENST00000245539.6:c.145G>C	17.37:g.73258639G>C	ENSP00000245539:p.Glu49Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B2R9N5|Q53GD6	Missense_Mutation	SNP	ENST00000245539.6	37	CCDS11718.1	.	.	.	.	.	.	.	.	.	.	G	9.833	1.189043	0.21954	.	.	ENSG00000125445	ENST00000245539	T	0.46819	0.86	5.57	3.59	0.41128	Ribosomal protein S7 domain (2);	0.368824	0.33496	N	0.004851	T	0.39279	0.1072	L	0.42686	1.345	0.48087	D	0.999586	B	0.26672	0.156	B	0.25759	0.063	T	0.17653	-1.0362	10	0.40728	T	0.16	-3.2929	11.9433	0.52913	0.1407:0.0:0.8593:0.0	.	49	Q9Y2R9	RT07_HUMAN	Q	49	ENSP00000245539:E49Q	ENSP00000245539:E49Q	E	+	1	0	MRPS7	70770234	1.000000	0.71417	0.474000	0.27266	0.033000	0.12548	7.756000	0.85195	0.720000	0.32209	-0.142000	0.14014	GAA		0.512	MRPS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446666.1		NM_015971	
MUC4	4585	broad.mit.edu	37	3	195505855	195505855	+	Missense_Mutation	SNP	G	G	T	rs201422998		TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:195505855G>T	ENST00000463781.3	-	2	13055	c.12596C>A	c.(12595-12597)tCc>tAc	p.S4199Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S4199Y	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.S4199Y(6)		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)		GGATGCTGAGGAAGTGTCGGT	0.597																																																	6	Substitution - Missense(6)	kidney(4)|endometrium(2)																																								SO:0001583	missense	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12596C>A	3.37:g.195505855G>T	ENSP00000417498:p.Ser4199Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	1.831	-0.469745	0.04445	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.26;1.38	.	.	.	.	.	.	.	.	T	0.36826	0.0981	N	0.19112	0.55	0.19300	N	0.999978	D	0.57571	0.98	D	0.66847	0.947	T	0.18241	-1.0343	7	.	.	.	.	6.6097	0.22745	2.0E-4:0.0:0.9998:0.0	.	4071	E7ESK3	.	Y	4199	ENSP00000417498:S4199Y;ENSP00000420243:S4199Y	.	S	-	2	0	MUC4	196990634	0.001000	0.12720	0.030000	0.17652	0.035000	0.12851	-0.256000	0.08757	0.452000	0.26830	0.074000	0.15403	TCC		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
NFRKB	4798	broad.mit.edu;hgsc.bcm.edu	37	11	129754640	129754640	+	Splice_Site	SNP	C	C	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr11:129754640C>T	ENST00000446488.3	-	6	845	c.742G>A	c.(742-744)Gat>Aat	p.D248N	NFRKB_ENST00000524746.1_Splice_Site_p.D248N|NFRKB_ENST00000524794.1_Splice_Site_p.D273N|NFRKB_ENST00000304521.5_Splice_Site_p.D248N	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	248					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)	p.D273N(1)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TGGTTCTCACCTGCAGTTTTC	0.572																																																	1	Substitution - Missense(1)	kidney(1)											65.0	73.0	70.0					11																	129754640		2201	4297	6498	SO:0001630	splice_region_variant	4798				CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.742+1G>A	11.37:g.129754640C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q12869|Q15312|Q9H048	Missense_Mutation	SNP	ENST00000446488.3	37	CCDS44770.1	.	.	.	.	.	.	.	.	.	.	C	16.92	3.256144	0.59321	.	.	ENSG00000170322	ENST00000304521;ENST00000446488;ENST00000524794;ENST00000524746;ENST00000531755	.	.	.	5.46	5.46	0.80206	.	0.059119	0.64402	D	0.000001	T	0.63710	0.2534	L	0.27053	0.805	0.54753	D	0.999988	D;D;D;D	0.67145	0.993;0.993;0.996;0.996	D;D;D;D	0.79784	0.984;0.984;0.993;0.993	T	0.55655	-0.8107	9	0.10636	T	0.68	-14.3712	19.3138	0.94204	0.0:1.0:0.0:0.0	.	260;248;248;273	B4DSL1;Q6P4R8;Q6P4R8-3;Q6P4R8-2	.;NFRKB_HUMAN;.;.	N	248;248;273;248;260	.	ENSP00000303800:D248N	D	-	1	0	NFRKB	129259850	1.000000	0.71417	1.000000	0.80357	0.514000	0.34195	5.699000	0.68310	2.561000	0.86390	0.655000	0.94253	GAT		0.572	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2		NM_006165	Missense_Mutation
NIPBL	25836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	37022178	37022178	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr5:37022178C>G	ENST00000282516.8	+	28	5853	c.5354C>G	c.(5353-5355)gCa>gGa	p.A1785G	NIPBL_ENST00000448238.2_Missense_Mutation_p.A1785G	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1785					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.A1785G(2)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GGTGAAAATGCAATTGCTGTT	0.338																																																	2	Substitution - Missense(2)	kidney(2)											128.0	117.0	121.0					5																	37022178		2203	4300	6503	SO:0001583	missense	25836			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.5354C>G	5.37:g.37022178C>G	ENSP00000282516:p.Ala1785Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789291	0.90367	.	.	ENSG00000164190	ENST00000282516;ENST00000448238	T;T	0.64991	-0.13;-0.13	5.09	5.09	0.68999	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.75110	0.3805	L	0.55481	1.735	0.80722	D	1	D;D	0.63046	0.976;0.992	P;D	0.64410	0.844;0.925	T	0.76669	-0.2874	10	0.59425	D	0.04	.	18.8683	0.92301	0.0:1.0:0.0:0.0	.	1785;1785	Q6KC79;Q6KC79-2	NIPBL_HUMAN;.	G	1785	ENSP00000282516:A1785G;ENSP00000406266:A1785G	ENSP00000282516:A1785G	A	+	2	0	NIPBL	37057935	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.418000	0.80167	2.504000	0.84457	0.650000	0.86243	GCA		0.338	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1		NM_015384	
OR14A16	284532	hgsc.bcm.edu	37	1	247978544	247978544	+	Missense_Mutation	SNP	G	G	A	rs113112592|rs35979231|rs375198428	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:247978544G>A	ENST00000357627.1	-	1	487	c.488C>T	c.(487-489)tCc>tTc	p.S163F		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	163						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						GTAGGATAAGGAGAAGGTGCC	0.453																																					Ovarian(112;180 1586 15073 21914 33526)												0													75.0	25.0	48.0					1																	247978544		2085	2469	4554	SO:0001583	missense	284532			BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.488C>T	1.37:g.247978544G>A	ENSP00000350248:p.Ser163Phe	Somatic		WXS	Illumina HiSeq	Phase_I	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	37	CCDS31097.1	386	0.17673992673992675	6	0.012195121951219513	71	0.19613259668508287	166	0.2902097902097902	143	0.18865435356200527	G	14.49	2.550057	0.45383	.	.	ENSG00000196772	ENST00000357627	T	0.00235	8.48	3.51	3.51	0.40186	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	U	0.000467	T	0.00012	0.0000	M	0.87180	2.865	0.09310	N	1	P	0.49862	0.929	P	0.60173	0.87	T	0.15723	-1.0427	10	0.62326	D	0.03	.	11.4452	0.50118	0.0:0.1832:0.8168:0.0	.	163	Q8NHC5	O14AG_HUMAN	F	163	ENSP00000350248:S163F	ENSP00000350248:S163F	S	-	2	0	OR14A16	246045167	0.000000	0.05858	0.037000	0.18230	0.057000	0.15508	-2.127000	0.01315	2.010000	0.58986	0.590000	0.80494	TCC		0.453	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1		NM_001001966	
OR1D5	8386	broad.mit.edu	37	17	2966855	2966855	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:2966855C>T	ENST00000575751.1	-	1	46	c.47G>A	c.(46-48)gGg>gAg	p.G16E		NM_014566.1	NP_055381.1	P58170	OR1D5_HUMAN	olfactory receptor, family 1, subfamily D, member 5	16					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|G-protein coupled receptor signaling pathway (GO:0007186)|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.G16E(2)		kidney(1)|lung(10)	11						CTCTGAGATCCCCAGGAGAAG	0.483																																																	2	Substitution - Missense(2)	kidney(2)											35.0	29.0	31.0					17																	2966855		1824	3403	5227	SO:0001583	missense	653166			AF087923	CCDS58499.1	17p13.3	2012-10-09			ENSG00000262628	ENSG00000262628		"""GPCR / Class A : Olfactory receptors"""	8186	protein-coding gene	gene with protein product						10673334	Standard	NM_014566		Approved	OR17-31	uc021tns.1	P58170	OTTHUMG00000177676	ENST00000575751.1:c.47G>A	17.37:g.2966855C>T	ENSP00000459028:p.Gly16Glu	Somatic		WXS	Illumina GAIIx	Phase_I	Q96RA6	Missense_Mutation	SNP	ENST00000575751.1	37	CCDS58499.1																																																																																				0.483	OR1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438410.2		NM_014566	
OR56A4	120793	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	6023936	6023936	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr11:6023936C>G	ENST00000330728.4	-	1	488	c.443G>C	c.(442-444)aGc>aCc	p.S148T		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, subfamily A, member 4	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S148T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(4)|large_intestine(5)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	32		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;7.01e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCTGGGAAGCTGATCGACCT	0.542																																																	1	Substitution - Missense(1)	kidney(1)											95.0	87.0	90.0					11																	6023936		2201	4296	6497	SO:0001583	missense	120793			BK004255	CCDS31404.1	11p15.4	2012-08-09			ENSG00000183389	ENSG00000183389		"""GPCR / Class A : Olfactory receptors"""	14791	protein-coding gene	gene with protein product							Standard	NM_001005179		Approved		uc010qzv.2	Q8NGH8	OTTHUMG00000165376	ENST00000330728.4:c.443G>C	11.37:g.6023936C>G	ENSP00000328215:p.Ser148Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B9EH17	Missense_Mutation	SNP	ENST00000330728.4	37	CCDS31404.1	.	.	.	.	.	.	.	.	.	.	C	1.876	-0.458993	0.04508	.	.	ENSG00000183389	ENST00000330728	T	0.01323	5.01	3.34	2.4	0.29515	GPCR, rhodopsin-like superfamily (1);	0.222293	0.22638	U	0.057481	T	0.02494	0.0076	M	0.77103	2.36	0.09310	N	1	B	0.17038	0.02	B	0.24269	0.052	T	0.34403	-0.9830	10	0.32370	T	0.25	.	7.2699	0.26250	0.1915:0.6224:0.1861:0.0	.	96	Q8NGH8	O56A4_HUMAN	T	148	ENSP00000328215:S148T	ENSP00000328215:S148T	S	-	2	0	OR56A4	5980512	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	-0.393000	0.07305	0.698000	0.31739	0.555000	0.69702	AGC		0.542	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2		NM_001005179	
OTOL1	131149	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	161221212	161221212	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:161221212C>A	ENST00000327928.4	+	4	916	c.916C>A	c.(916-918)Cct>Act	p.P306T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	306	Collagen-like 3.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)		p.P306T(1)		central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TCTCCTGGGACCTACTGGGCC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											28.0	29.0	29.0					3																	161221212		1913	4114	6027	SO:0001583	missense	131149				CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.916C>A	3.37:g.161221212C>A	ENSP00000330808:p.Pro306Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.513797	0.27123	.	.	ENSG00000182447	ENST00000327928	D	0.96651	-4.08	5.03	4.16	0.48862	.	0.162448	0.56097	D	0.000033	D	0.94840	0.8333	M	0.61703	1.905	0.40023	D	0.975436	P	0.47604	0.898	P	0.45167	0.472	D	0.92802	0.6257	10	0.25751	T	0.34	.	11.9216	0.52795	0.0:0.9151:0.0:0.0849	.	306	A6NHN0	OTOL1_HUMAN	T	306	ENSP00000330808:P306T	ENSP00000330808:P306T	P	+	1	0	OTOL1	162703906	0.992000	0.36948	0.568000	0.28447	0.299000	0.27559	2.148000	0.42235	1.106000	0.41623	0.557000	0.71058	CCT		0.567	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1		NM_001080440	
PCNX	22990	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	71571970	71571970	+	Silent	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr14:71571970A>T	ENST00000304743.2	+	33	6560	c.6114A>T	c.(6112-6114)ggA>ggT	p.G2038G	PCNX_ENST00000439984.3_Silent_p.G1927G|PCNX_ENST00000556272.1_3'UTR|PCNX_ENST00000238570.5_Silent_p.G1966G	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	2038						integral component of membrane (GO:0016021)		p.G2038G(1)		NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		AAGGTTGCGGAGCTGGATGTA	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											99.0	89.0	92.0					14																	71571970		2203	4300	6503	SO:0001819	synonymous_variant	22990			AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.6114A>T	14.37:g.71571970A>T		Somatic		WXS	Illumina HiSeq	Phase_I	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	A	9.885	1.202588	0.22121	.	.	ENSG00000100731	ENST00000554691	.	.	.	5.51	-1.63	0.08345	.	.	.	.	.	T	0.43411	0.1246	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.30446	-0.9978	4	.	.	.	.	4.1021	0.10018	0.3564:0.0:0.2206:0.423	.	.	.	.	V	1025	.	.	E	+	2	0	PCNX	70641723	0.989000	0.36119	0.996000	0.52242	0.988000	0.76386	0.294000	0.19047	-0.187000	0.10516	0.533000	0.62120	GAG		0.428	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1		NM_014982	
RP11-337C18.8	0	broad.mit.edu	37	1	146649788	146649788	+	RNA	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr1:146649788C>G	ENST00000607149.1	+	0	350				RP11-337C18.8_ENST00000606757.1_RNA|RP11-337C18.9_ENST00000606152.1_RNA|RP11-337C18.10_ENST00000606856.1_RNA																							GACTCAGGGACGACAACTTGG	0.687																																																	0																																												171423																															1.37:g.146649788C>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000607149.1	37																																																																																					0.687	RP11-337C18.8-004	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000471324.1			
PHKA1	5255	broad.mit.edu	37	X	71933736	71933736	+	De_novo_Start_OutOfFrame	SNP	C	C	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chrX:71933736C>T	ENST00000373542.4	-	0	152				PHKA1_ENST00000373545.3_De_novo_Start_OutOfFrame|PHKA1_ENST00000339490.3_De_novo_Start_OutOfFrame|PHKA1-AS1_ENST00000420998.1_RNA|PHKA1_ENST00000541944.1_De_novo_Start_OutOfFrame|PHKA1_ENST00000373539.3_De_novo_Start_OutOfFrame	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)						carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(2)|lung(18)|ovary(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	52	Renal(35;0.156)					CATGGCGACACGTTACTAATT	0.607																																																	0													50.0	41.0	44.0					X																	71933736		2203	4300	6503			5255				CCDS14421.1, CCDS48137.1, CCDS55453.1	Xq12-q13	2009-07-10			ENSG00000067177	ENSG00000067177	2.7.11.19		8925	protein-coding gene	gene with protein product		311870		PHKA			Standard	NM_002637		Approved		uc004eax.4	P46020	OTTHUMG00000022696	ENST00000373542.4:c.-8G>A	X.37:g.71933736C>T		Somatic		WXS	Illumina GAIIx	Phase_I	B7ZL05|B7ZL07|Q2M3D7	Translation_Start_Site	SNP	ENST00000373542.4	37	CCDS14421.1																																																																																				0.607	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			
PKD2L2	27039	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	137228267	137228267	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr5:137228267T>G	ENST00000508883.1	+	3	258	c.232T>G	c.(232-234)Ttt>Gtt	p.F78V	PKD2L2_ENST00000350250.4_Missense_Mutation_p.F44V|PKD2L2_ENST00000508638.1_Missense_Mutation_p.F78V|PKD2L2_ENST00000502810.1_Missense_Mutation_p.F78V|PKD2L2_ENST00000290431.5_Missense_Mutation_p.F78V			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	78					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.F78V(1)		breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AAGAACCAACTTTAAGTCCAT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											163.0	155.0	157.0					5																	137228267		1878	4119	5997	SO:0001583	missense	27039			AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.232T>G	5.37:g.137228267T>G	ENSP00000424725:p.Phe78Val	Somatic		WXS	Illumina HiSeq	Phase_I	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	37		.	.	.	.	.	.	.	.	.	.	T	28.6	4.934628	0.92458	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7	5.84	5.84	0.93424	Polycystin cation channel, PKD1/PKD2 (1);	0.000000	0.64402	D	0.000002	D	0.84028	0.5382	M	0.82323	2.585	0.54753	D	0.999986	P;D;P	0.58268	0.931;0.982;0.787	P;P;B	0.62560	0.861;0.904;0.322	D	0.86549	0.1833	10	0.87932	D	0	-23.0712	15.8842	0.79232	0.0:0.0:0.0:1.0	.	78;78;78	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	V	44;78;78;78;78	ENSP00000344177:F44V;ENSP00000423382:F78V;ENSP00000425513:F78V;ENSP00000424725:F78V;ENSP00000290431:F78V	ENSP00000290431:F78V	F	+	1	0	PKD2L2	137256166	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.173000	0.77612	2.233000	0.73108	0.496000	0.49642	TTT		0.388	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1		NM_014386	
PLIN4	729359	hgsc.bcm.edu	37	19	4511479	4511479	+	Silent	SNP	A	A	T	rs386806133|rs386806132|rs138464610	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr19:4511479A>T	ENST00000301286.3	-	3	2450	c.2451T>A	c.(2449-2451)acT>acA	p.T817T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	817	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CACTGCAGACAGTGTCCTTGG	0.597													a|||	397	0.0792732	0.1377	0.0735	5008	,	,		23517	0.0734		0.0586	False		,,,				2504	0.0317																0													86.0	109.0	102.0					19																	4511479		1995	4194	6189	SO:0001819	synonymous_variant	729359			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2451T>A	19.37:g.4511479A>T		Somatic		WXS	Illumina HiSeq	Phase_I	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																				0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1		XM_170901	
PLS3	5358	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	114864223	114864223	+	Silent	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chrX:114864223A>G	ENST00000420625.2	+	5	578	c.444A>G	c.(442-444)ccA>ccG	p.P148P	PLS3_ENST00000539310.1_Silent_p.P103P|PLS3_ENST00000537301.1_Silent_p.P126P|PLS3_ENST00000289290.3_Silent_p.P103P|PLS3_ENST00000355899.3_Silent_p.P148P	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	148	Actin-binding 1.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)	p.P148P(1)		NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						ATGTTATACCAATGAACCCTA	0.333																																					Colon(160;1047 1864 8490 12969 29601)												1	Substitution - coding silent(1)	kidney(1)											222.0	197.0	205.0					X																	114864223		2203	4300	6503	SO:0001819	synonymous_variant	5358			L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"""EF-hand domain containing"""	9091	protein-coding gene	gene with protein product		300131	"""plastin 3 (T isoform)"""			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.444A>G	X.37:g.114864223A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	37	CCDS14568.1																																																																																				0.333	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			
PSMA3	5684	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	58737146	58737146	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr14:58737146G>A	ENST00000216455.4	+	9	691	c.601G>A	c.(601-603)Gta>Ata	p.V201I	PSMA3_ENST00000557508.1_Missense_Mutation_p.V126I|RP11-349A22.5_ENST00000555707.1_RNA|RP11-349A22.5_ENST00000554360.1_RNA|RP11-349A22.5_ENST00000556225.1_RNA|PSMA3_ENST00000412908.2_Missense_Mutation_p.V194I|RP11-349A22.5_ENST00000555162.1_RNA|CTD-2002H8.2_ENST00000557322.1_RNA|RP11-349A22.5_ENST00000556002.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA|RP11-349A22.5_ENST00000555275.1_RNA	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	201					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)	p.V201I(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						AATTTACATAGTACATGACGA	0.343																																																	1	Substitution - Missense(1)	kidney(1)											129.0	129.0	129.0					14																	58737146		2203	4299	6502	SO:0001583	missense	5684				CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"""Proteasome (prosome, macropain) subunits"""	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.601G>A	14.37:g.58737146G>A	ENSP00000216455:p.Val201Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	37	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427429	0.62733	.	.	ENSG00000100567	ENST00000216455;ENST00000412908;ENST00000557508;ENST00000553677	T;T;T	0.23348	1.91;1.91;1.91	5.0	5.0	0.66597	.	0.053954	0.64402	D	0.000001	T	0.35189	0.0923	M	0.72624	2.21	0.80722	D	1	B;B	0.24533	0.086;0.105	B;B	0.29077	0.059;0.098	T	0.20840	-1.0263	10	0.56958	D	0.05	7.8973	18.4404	0.90665	0.0:0.0:1.0:0.0	.	194;201	P25788-2;P25788	.;PSA3_HUMAN	I	201;194;126;29	ENSP00000216455:V201I;ENSP00000390491:V194I;ENSP00000452056:V126I	ENSP00000216455:V201I	V	+	1	0	PSMA3	57806899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.036000	0.88901	2.762000	0.94881	0.591000	0.81541	GTA		0.343	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1		NM_002788	
RAB8B	51762	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	63555808	63555808	+	Missense_Mutation	SNP	C	C	T	rs373850007		TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr15:63555808C>T	ENST00000321437.4	+	8	770	c.614C>T	c.(613-615)tCg>tTg	p.S205L	RAB8B_ENST00000448330.2_Missense_Mutation_p.S188L	NM_016530.2	NP_057614.1	Q92930	RAB8B_HUMAN	RAB8B, member RAS oncogene family	205					adherens junction organization (GO:0034332)|antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|positive regulation of cell projection organization (GO:0031346)|positive regulation of corticotropin secretion (GO:0051461)|protein import into peroxisome membrane (GO:0045046)|small GTPase mediated signal transduction (GO:0007264)	cell tip (GO:0051286)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|receptor binding (GO:0005102)	p.S205L(1)		kidney(3)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9						TTTCGTTGCTCGCTACTTTGA	0.458																																																	1	Substitution - Missense(1)	kidney(1)											94.0	82.0	86.0					15																	63555808		2203	4300	6503	SO:0001583	missense	51762			AL833365	CCDS10183.1	15q22	2008-11-18			ENSG00000166128	ENSG00000166128		"""RAB, member RAS oncogene"""	30273	protein-coding gene	gene with protein product		613532				9030196, 18772196	Standard	XM_006720569		Approved		uc002alz.3	Q92930	OTTHUMG00000132862	ENST00000321437.4:c.614C>T	15.37:g.63555808C>T	ENSP00000312734:p.Ser205Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5JPC4|Q9P293	Missense_Mutation	SNP	ENST00000321437.4	37	CCDS10183.1	.	.	.	.	.	.	.	.	.	.	C	5.636	0.301976	0.10678	.	.	ENSG00000166128	ENST00000321437;ENST00000448330	T;T	0.65549	0.03;-0.16	5.79	2.95	0.34219	.	0.771549	0.12463	N	0.466661	T	0.40119	0.1104	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.25916	-1.0118	10	0.41790	T	0.15	.	8.6988	0.34312	0.0:0.7123:0.0:0.2877	.	188;205	F5GY21;Q92930	.;RAB8B_HUMAN	L	205;188	ENSP00000312734:S205L;ENSP00000405463:S188L	ENSP00000312734:S205L	S	+	2	0	RAB8B	61342861	0.011000	0.17503	0.764000	0.31436	0.239000	0.25481	0.620000	0.24403	0.392000	0.25172	-0.918000	0.02743	TCG		0.458	RAB8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256336.1		NM_016530	
RALGAPA1	253959	hgsc.bcm.edu	37	14	36140605	36140611	+	Frame_Shift_Del	DEL	GCTGAAG	GCTGAAG	-	rs201831397	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	GCTGAAG	GCTGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr14:36140605_36140611delGCTGAAG	ENST00000389698.3	-	25	4058_4064	c.3668_3674delCTTCAGC	c.(3667-3675)tcttcagctfs	p.SSA1223fs	RALGAPA1_ENST00000382366.3_Frame_Shift_Del_p.SSA1236fs|RALGAPA1_ENST00000307138.6_Frame_Shift_Del_p.SSA1223fs|RALGAPA1_ENST00000258840.6_Frame_Shift_Del_p.SSA1270fs	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1223					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)	p.S1223F(2)		breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						ATTGAGAAAAGCTGAAGAAGCCACTCT	0.362																																																	2	Substitution - Missense(2)	lung(2)							,	28,4236		0,28,2104					,	3.1	1.0			48	61,8193		0,61,4066	no	frameshift,frameshift	RALGAPA1	NM_194301.2,NM_014990.1	,	0,89,6170	A1A1,A1R,RR		0.739,0.6567,0.711	,	,		89,12429				SO:0001589	frameshift_variant	253959			AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.3668_3674delCTTCAGC	14.37:g.36140605_36140611delGCTGAAG	ENSP00000374348:p.Ser1223fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Frame_Shift_Del	DEL	ENST00000389698.3	37	CCDS32065.1																																																																																				0.362	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1		XM_210022	
RARA	5914	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	38508302	38508302	+	Missense_Mutation	SNP	C	C	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr17:38508302C>A	ENST00000254066.5	+	5	1065	c.610C>A	c.(610-612)Cag>Aag	p.Q204K	RARA_ENST00000394081.3_Missense_Mutation_p.Q199K|RARA_ENST00000394089.2_Missense_Mutation_p.Q204K|RARA_ENST00000420042.1_3'UTR|RARA_ENST00000425707.3_Missense_Mutation_p.Q107K|RARA_ENST00000394086.3_Missense_Mutation_p.Q220K	NM_000964.3	NP_000955.1	P10276	RARA_HUMAN	retinoic acid receptor, alpha	204	Ligand-binding.				apoptotic cell clearance (GO:0043277)|cellular response to estrogen stimulus (GO:0071391)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to retinoic acid (GO:0071300)|chondroblast differentiation (GO:0060591)|embryonic camera-type eye development (GO:0031076)|face development (GO:0060324)|female pregnancy (GO:0007565)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|intracellular estrogen receptor signaling pathway (GO:0030520)|limb development (GO:0060173)|liver development (GO:0001889)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translational initiation (GO:0045947)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of binding (GO:0051099)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein phosphorylation (GO:0006468)|regulation of myelination (GO:0031641)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to retinoic acid (GO:0032526)|response to vitamin A (GO:0033189)|retinoic acid receptor signaling pathway (GO:0048384)|Sertoli cell fate commitment (GO:0060010)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|trachea cartilage development (GO:0060534)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	chromatin DNA binding (GO:0031490)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|mRNA 5'-UTR binding (GO:0048027)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|protein kinase A binding (GO:0051018)|protein kinase B binding (GO:0043422)|receptor binding (GO:0005102)|retinoic acid binding (GO:0001972)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|translation repressor activity, nucleic acid binding (GO:0000900)|zinc ion binding (GO:0008270)	p.Q204K(1)		breast(1)|kidney(4)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|urinary_tract(2)	16		Breast(137;0.00328)	STAD - Stomach adenocarcinoma(5;0.00143)		Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Isotretinoin(DB00982)|Tamibarotene(DB04942)|Tazarotene(DB00799)	TGCCCTCTGCCAGCTGGGCAA	0.642			T	"""PML, ZNF145, TIF1, NUMA1, NPM1"""	APL																																			Dom	yes		17	17q12	5914	"""retinoic acid receptor, alpha"""		L	1	Substitution - Missense(1)	kidney(1)											29.0	28.0	29.0					17																	38508302		2203	4298	6501	SO:0001583	missense	5914			X06538	CCDS11366.1, CCDS42317.1, CCDS45671.1	17q21.1	2014-01-20			ENSG00000131759	ENSG00000131759		"""Nuclear hormone receptors"""	9864	protein-coding gene	gene with protein product		180240				2825036, 8244378	Standard	NM_001145301		Approved	RAR, NR1B1	uc002huk.2	P10276	OTTHUMG00000133328	ENST00000254066.5:c.610C>A	17.37:g.38508302C>A	ENSP00000254066:p.Gln204Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B8Y636|P78456|Q13440|Q13441|Q96S41|Q9NQS0	Missense_Mutation	SNP	ENST00000254066.5	37	CCDS11366.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.706879	0.48412	.	.	ENSG00000131759	ENST00000254066;ENST00000425707;ENST00000394089;ENST00000394086;ENST00000394081;ENST00000420042	T;D;T;T;T	0.92647	1.34;-3.08;1.34;1.34;1.34	4.69	4.69	0.59074	Nuclear hormone receptor, ligand-binding (2);	.	.	.	.	D	0.90051	0.6893	M	0.78916	2.43	0.80722	D	1	P;B;B	0.51933	0.949;0.001;0.017	B;B;B	0.33392	0.163;0.001;0.008	D	0.91668	0.5348	9	0.54805	T	0.06	.	16.3889	0.83525	0.0:1.0:0.0:0.0	.	107;199;204	B8Y636;F1D8N9;P10276	.;.;RARA_HUMAN	K	204;107;204;220;199;91	ENSP00000254066:Q204K;ENSP00000389993:Q107K;ENSP00000377649:Q204K;ENSP00000377648:Q220K;ENSP00000377643:Q199K	ENSP00000254066:Q204K	Q	+	1	0	RARA	35761828	1.000000	0.71417	1.000000	0.80357	0.751000	0.42716	7.755000	0.85180	2.140000	0.66376	0.467000	0.42956	CAG		0.642	RARA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257136.2			
RIC8A	60626	hgsc.bcm.edu	37	11	209895	209897	+	In_Frame_Del	DEL	CCC	CCC	-	rs201633036|rs200641500|rs3832797|rs398102296|rs571957041	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr11:209895_209897delCCC	ENST00000526104.1	+	3	1965_1967	c.621_623delCCC	c.(619-624)aacccc>aac	p.P210del	BET1L_ENST00000332865.6_5'Flank|BET1L_ENST00000529614.2_5'Flank|BET1L_ENST00000325147.9_5'Flank|BET1L_ENST00000382762.3_5'Flank|RIC8A_ENST00000527696.1_In_Frame_Del_p.P204del|RIC8A_ENST00000325207.5_In_Frame_Del_p.P210del|BET1L_ENST00000486280.1_5'Flank|BET1L_ENST00000410108.1_5'Flank			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	210					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		CTGAAGGGAACCCCCCACCCACG	0.601														2073	0.413938	0.2519	0.428	5008	,	,		21433	0.7629		0.327	False		,,,				2504	0.3528																0										1167,8,3089		173,0,821,4,0,1134						1.2	0.0		dbSNP_107	49	2820,12,5422		493,0,1834,6,0,1794	no	codingComplex	RIC8A	NM_021932.4		666,0,2655,10,0,2928	A1A1,A1A2,A1R,A2A2,A2R,RR		34.3106,27.5563,32.0099				3987,20,8511				SO:0001651	inframe_deletion	60626			AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.621_623delCCC	11.37:g.209898_209900delCCC	ENSP00000432008:p.Pro210del	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	In_Frame_Del	DEL	ENST00000526104.1	37																																																																																					0.601	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1		NM_021932	
SHARPIN	81858	broad.mit.edu;ucsc.edu	37	8	145154959	145154959	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr8:145154959G>C	ENST00000398712.2	-	3	826	c.390C>G	c.(388-390)aaC>aaG	p.N130K	SHARPIN_ENST00000533948.1_5'UTR	NM_030974.3	NP_112236.3	Q9H0F6	SHRPN_HUMAN	SHANK-associated RH domain interactor	130	Self-association. {ECO:0000250}.				apoptotic nuclear changes (GO:0030262)|brain development (GO:0007420)|keratinization (GO:0031424)|mitochondrion organization (GO:0007005)|negative regulation of inflammatory response (GO:0050728)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein homooligomerization (GO:0051260)|protein linear polyubiquitination (GO:0097039)|regulation of CD40 signaling pathway (GO:2000348)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendrite (GO:0030425)|LUBAC complex (GO:0071797)|postsynaptic density (GO:0014069)	polyubiquitin binding (GO:0031593)|zinc ion binding (GO:0008270)	p.N130K(1)		breast(1)|endometrium(1)|kidney(1)|lung(2)|ovary(2)	7	all_cancers(97;2.87e-11)|all_epithelial(106;2.16e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;4.1e-42)|Epithelial(56;1.58e-40)|all cancers(56;6.12e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CTGGTGGTGAGTTGCTCTTGC	0.602																																																	1	Substitution - Missense(1)	kidney(1)											226.0	237.0	233.0					8																	145154959		2174	4267	6441	SO:0001583	missense	81858			AL136816	CCDS43777.1	8q24.3	2005-08-09				ENSG00000179526			25321	protein-coding gene	gene with protein product		611885				11178875, 12753155	Standard	NM_030974		Approved	DKFZP434N1923, SIPL1	uc003zba.3	Q9H0F6		ENST00000398712.2:c.390C>G	8.37:g.145154959G>C	ENSP00000381698:p.Asn130Lys	Somatic		WXS	Illumina GAIIx	Phase_I	A6NEG3|C0L3L2|D3DWL3|Q8IXF5|Q8IXF6|Q8N2E7|Q8TB25|Q9BUE4	Missense_Mutation	SNP	ENST00000398712.2	37	CCDS43777.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.261735	0.00021	.	.	ENSG00000179526	ENST00000398712;ENST00000359551	T;T	0.28895	2.03;1.59	0.235	0.235	0.15431	.	0.726607	0.12311	N	0.480220	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35450	-0.9788	9	0.06625	T	0.88	.	.	.	.	.	130	Q9H0F6	SHRPN_HUMAN	K	130	ENSP00000381698:N130K;ENSP00000352551:N130K	ENSP00000352551:N130K	N	-	3	2	SHARPIN	145226947	0.047000	0.20315	0.016000	0.15963	0.059000	0.15707	1.598000	0.36740	0.308000	0.22923	0.313000	0.20887	AAC		0.602	SHARPIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382901.1		NM_030974	
SLC25A45	283130	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	65144051	65144051	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr11:65144051C>T	ENST00000527174.1	-	6	749	c.694G>A	c.(694-696)Gat>Aat	p.D232N	SLC25A45_ENST00000526432.1_Missense_Mutation_p.D170N|SLC25A45_ENST00000360662.3_Missense_Mutation_p.D208N|SLC25A45_ENST00000294187.6_Missense_Mutation_p.D190N|SLC25A45_ENST00000417511.2_Missense_Mutation_p.D190N|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000398802.1_Missense_Mutation_p.D232N|SLC25A45_ENST00000534028.1_Missense_Mutation_p.D208N|SLC25A45_ENST00000377152.2_Missense_Mutation_p.D128N			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	232					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.D232N(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						CTCAGTCCATCCATCTGCATC	0.612																																																	1	Substitution - Missense(1)	kidney(1)											99.0	105.0	103.0					11																	65144051		2167	4261	6428	SO:0001583	missense	283130			BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.694G>A	11.37:g.65144051C>T	ENSP00000435489:p.Asp232Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.983234	0.74474	.	.	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	T;T;T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	4.58	4.58	0.56647	Mitochondrial carrier domain (2);	.	.	.	.	D	0.86514	0.5951	M	0.79011	2.435	0.50313	D	0.99986	B;P;D	0.54397	0.324;0.813;0.966	B;P;P	0.62089	0.224;0.76;0.898	D	0.88182	0.2871	9	0.72032	D	0.01	5.0032	15.256	0.73585	0.0:1.0:0.0:0.0	.	170;208;232	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	N	232;208;232;208;128;190;190;170	ENSP00000435489:D232N;ENSP00000431769:D208N;ENSP00000381782:D232N;ENSP00000353879:D208N;ENSP00000366357:D128N;ENSP00000294187:D190N;ENSP00000407530:D190N;ENSP00000435547:D170N	ENSP00000294187:D190N	D	-	1	0	SLC25A45	64900627	1.000000	0.71417	0.967000	0.41034	0.661000	0.39034	3.761000	0.55242	2.550000	0.86006	0.561000	0.74099	GAT		0.612	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3		NM_182556	
STEAP1	26872	broad.mit.edu	37	7	89790291	89790291	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr7:89790291T>C	ENST00000297205.2	+	3	457	c.257T>C	c.(256-258)tTt>tCt	p.F86S	STEAP2-AS1_ENST00000478318.2_RNA	NM_012449.2	NP_036581.1	Q9UHE8	STEA1_HUMAN	six transmembrane epithelial antigen of the prostate 1	86					ion transport (GO:0006811)|iron ion homeostasis (GO:0055072)|transmembrane transport (GO:0055085)	cell-cell junction (GO:0005911)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	channel activity (GO:0015267)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|transporter activity (GO:0005215)	p.F86S(1)		kidney(2)|large_intestine(3)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	14	all_hematologic(106;0.112)					TCTCTGACTTTTCTTTACACT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											116.0	115.0	116.0					7																	89790291		2203	4300	6503	SO:0001583	missense	26872			AF186249	CCDS5614.1	7q21	2011-08-31	2005-02-21	2005-02-24	ENSG00000164647	ENSG00000164647		"""Serine peptidases / Serine peptidases"""	11378	protein-coding gene	gene with protein product		604415	"""six transmembrane epithelial antigen of the prostate"""	STEAP			Standard	NM_012449		Approved	PRSS24	uc003ujx.3	Q9UHE8	OTTHUMG00000023006	ENST00000297205.2:c.257T>C	7.37:g.89790291T>C	ENSP00000297205:p.Phe86Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A4D1E0|O95034	Missense_Mutation	SNP	ENST00000297205.2	37	CCDS5614.1	.	.	.	.	.	.	.	.	.	.	T	14.03	2.413480	0.42817	.	.	ENSG00000164647	ENST00000297205	T	0.11930	2.73	5.02	5.02	0.67125	.	0.076437	0.56097	D	0.000031	T	0.19208	0.0461	M	0.83953	2.67	0.40481	D	0.980443	P;P	0.48503	0.911;0.787	B;B	0.39840	0.311;0.219	T	0.06285	-1.0835	10	0.59425	D	0.04	-18.7857	9.4178	0.38532	0.0:0.0795:0.0:0.9205	.	86;86	B4E221;Q9UHE8	.;STEA1_HUMAN	S	86	ENSP00000297205:F86S	ENSP00000297205:F86S	F	+	2	0	STEAP1	89628227	1.000000	0.71417	0.843000	0.33291	0.759000	0.43091	5.307000	0.65762	2.099000	0.63709	0.533000	0.62120	TTT		0.388	STEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059327.3		NM_012449	
SULT2B1	6820	broad.mit.edu;ucsc.edu	37	19	49096055	49096055	+	Silent	SNP	C	C	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr19:49096055C>G	ENST00000201586.2	+	5	805	c.627C>G	c.(625-627)acC>acG	p.T209T	SULT2B1_ENST00000323090.4_Silent_p.T194T|SULT2B1_ENST00000594274.1_3'UTR	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	209					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)	p.T209T(1)|p.T194T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		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;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		TATTTATCACCTACGAGGAGC	0.597																																																	2	Substitution - coding silent(2)	kidney(2)											95.0	66.0	76.0					19																	49096055		2203	4299	6502	SO:0001819	synonymous_variant	6820			U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"""Sulfotransferases, cytosolic"""	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.627C>G	19.37:g.49096055C>G		Somatic		WXS	Illumina GAIIx	Phase_I	O00205|O75814	Silent	SNP	ENST00000201586.2	37	CCDS12723.1																																																																																				0.597	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1		NM_004605	
SYTL3	94120	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	159184435	159184435	+	Silent	SNP	C	C	A	rs140709967	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr6:159184435C>A	ENST00000297239.9	+	16	1811	c.1617C>A	c.(1615-1617)ggC>ggA	p.G539G	SYTL3_ENST00000367081.3_Silent_p.G265G|SYTL3_ENST00000360448.3_Silent_p.G471G|MIR3918_ENST00000581555.1_RNA			Q4VX76	SYTL3_HUMAN	synaptotagmin-like 3	539	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)	membrane (GO:0016020)	calcium-dependent phospholipid binding (GO:0005544)	p.G471G(1)		endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|urinary_tract(1)	20		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;1.54e-17)|BRCA - Breast invasive adenocarcinoma(81;8.24e-06)		TCTTCAGTGGCGTAACCCCAG	0.537																																																	1	Substitution - coding silent(1)	kidney(1)											110.0	101.0	104.0					6																	159184435		2203	4300	6503	SO:0001819	synonymous_variant	94120			AK055750	CCDS34563.1, CCDS56458.1	6q25.3	2008-07-04			ENSG00000164674	ENSG00000164674			15587	protein-coding gene	gene with protein product						11773082	Standard	NM_001242384		Approved	SLP3, exophilin-6	uc003qrp.3	Q4VX76	OTTHUMG00000015916	ENST00000297239.9:c.1617C>A	6.37:g.159184435C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q496J4|Q496J6|Q5U3B9	Silent	SNP	ENST00000297239.9	37	CCDS56458.1																																																																																				0.537	SYTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042876.1			
TENC1	23371	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	53448982	53448982	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr12:53448982T>G	ENST00000314250.6	+	8	825	c.535T>G	c.(535-537)Tca>Gca	p.S179A	RP11-983P16.4_ENST00000551890.1_RNA|TENC1_ENST00000314276.3_Missense_Mutation_p.S189A|TENC1_ENST00000549700.1_Missense_Mutation_p.S179A|TENC1_ENST00000546602.1_Missense_Mutation_p.S179A|RP11-983P16.4_ENST00000550601.1_RNA|TENC1_ENST00000552570.1_Missense_Mutation_p.S179A|TENC1_ENST00000451358.1_Missense_Mutation_p.S179A|TENC1_ENST00000379902.3_Missense_Mutation_p.S55A|RP11-983P16.4_ENST00000546793.1_RNA	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	179	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.S179A(1)|p.S189A(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						CTTCAACCTTTCAGAGAAAAG	0.512																																																	2	Substitution - Missense(2)	kidney(2)											112.0	111.0	112.0					12																	53448982		2203	4300	6503	SO:0001583	missense	23371			AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.535T>G	12.37:g.53448982T>G	ENSP00000319684:p.Ser179Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Missense_Mutation	SNP	ENST00000314250.6	37	CCDS8843.1	.	.	.	.	.	.	.	.	.	.	T	14.88	2.666846	0.47677	.	.	ENSG00000111077	ENST00000379902;ENST00000314276;ENST00000314250;ENST00000451358;ENST00000443113;ENST00000546602;ENST00000552570;ENST00000549700	D;D;D;D;D;D;D	0.98567	-5.0;-5.0;-5.0;-5.0;-5.0;-5.0;-5.0	4.0	4.0	0.46444	Phosphatase tensin type (1);	0.081738	0.50627	D	0.000113	D	0.98658	0.9550	M	0.83692	2.655	0.44316	D	0.997196	D;B;B;B	0.58970	0.984;0.115;0.003;0.0	D;B;B;B	0.68192	0.956;0.238;0.005;0.001	D	0.98974	1.0802	10	0.59425	D	0.04	-9.1291	11.1733	0.48584	0.0:0.0:0.0:1.0	.	179;179;189;156	Q63HR2;F8W661;Q63HR2-4;Q6ZMJ1	TENC1_HUMAN;.;.;.	A	55;189;179;179;179;179;179;179	ENSP00000369232:S55A;ENSP00000319756:S189A;ENSP00000319684:S179A;ENSP00000393362:S179A;ENSP00000449363:S179A;ENSP00000447021:S179A;ENSP00000449361:S179A	ENSP00000319684:S179A	S	+	1	0	TENC1	51735249	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.411000	0.66386	1.814000	0.52955	0.247000	0.18012	TCA		0.512	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1		NM_170754	
TDG	6996	hgsc.bcm.edu	37	12	104376608	104376608	+	Silent	SNP	G	G	A	rs61937629	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr12:104376608G>A	ENST00000392872.3	+	5	744	c.510G>A	c.(508-510)gaG>gaA	p.E170E	TDG_ENST00000266775.9_Silent_p.E166E|TDG_ENST00000542036.1_5'UTR|TDG_ENST00000544861.1_Silent_p.E27E|AC078819.1_ENST00000401157.1_RNA	NM_003211.4	NP_003202.3	Q13569	TDG_HUMAN	thymine-DNA glycosylase	170					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|chromatin modification (GO:0016568)|depyrimidination (GO:0045008)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|embryo development (GO:0009790)|mismatch repair (GO:0006298)|negative regulation of chromatin binding (GO:0035562)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression, epigenetic (GO:0040029)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|double-stranded DNA binding (GO:0003690)|mismatched DNA binding (GO:0030983)|protein homodimerization activity (GO:0042803)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|RNA polymerase II transcription cofactor activity (GO:0001104)|structure-specific DNA binding (GO:0043566)	p.E170E(1)		large_intestine(2)|lung(14)|ovary(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24				BRCA - Breast invasive adenocarcinoma(302;0.00114)		GGCTCAGTGAGGTCCAGCTGA	0.443								Base excision repair (BER), DNA glycosylases																																									1	Substitution - coding silent(1)	stomach(1)											124.0	116.0	118.0					12																	104376608		2203	4300	6503	SO:0001819	synonymous_variant	6996			U51166	CCDS9095.1	12q24.1	2014-05-14			ENSG00000139372	ENSG00000139372	3.2.2.29		11700	protein-coding gene	gene with protein product	"""G/T mismatch-specific thymine DNA glycosylase"""	601423				8662714, 9299239	Standard	NM_003211		Approved		uc001tkg.3	Q13569	OTTHUMG00000168418	ENST00000392872.3:c.510G>A	12.37:g.104376608G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IUZ6|Q8IZM3	Silent	SNP	ENST00000392872.3	37	CCDS9095.1																																																																																				0.443	TDG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399673.2			
TEX264	51368	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	51708346	51708346	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:51708346T>A	ENST00000415259.1	+	2	1107	c.26T>A	c.(25-27)cTg>cAg	p.L9Q	TEX264_ENST00000341333.5_Missense_Mutation_p.L9Q|TEX264_ENST00000416589.1_Missense_Mutation_p.L9Q|TEX264_ENST00000457573.1_Missense_Mutation_p.L9Q|TEX264_ENST00000395057.1_Missense_Mutation_p.L9Q			Q9Y6I9	TX264_HUMAN	testis expressed 264	9						extracellular vesicular exosome (GO:0070062)		p.L9Q(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	7				BRCA - Breast invasive adenocarcinoma(193;8.53e-05)|Kidney(197;0.000594)|KIRC - Kidney renal clear cell carcinoma(197;0.000759)		CTACTGGGCCTGATTGGGGGC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											77.0	78.0	78.0					3																	51708346		2203	4300	6503	SO:0001583	missense	51368			AF072733	CCDS2833.1, CCDS74945.1	3p21	2007-03-13	2007-03-13		ENSG00000164081	ENSG00000164081			30247	protein-coding gene	gene with protein product			"""testis expressed gene 264"", ""testis expressed sequence 264"""			12975309	Standard	NM_001243725		Approved	ZSIG11, FLJ13935	uc003dbm.4	Q9Y6I9	OTTHUMG00000156901	ENST00000415259.1:c.26T>A	3.37:g.51708346T>A	ENSP00000396628:p.Leu9Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B3KN87|Q9UKD7	Missense_Mutation	SNP	ENST00000415259.1	37	CCDS2833.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.592459	0.66219	.	.	ENSG00000164081	ENST00000419358;ENST00000457573;ENST00000341333;ENST00000412249;ENST00000425781;ENST00000415259;ENST00000395057;ENST00000416589;ENST00000457927;ENST00000444233	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	5.46	5.46	0.80206	.	0.075872	0.56097	D	0.000037	T	0.69780	0.3149	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.72918	-0.4146	10	0.72032	D	0.01	7.5028	14.7181	0.69286	0.0:0.0:0.0:1.0	.	9;9	Q53GI2;Q9Y6I9	.;TX264_HUMAN	Q	9	ENSP00000408186:L9Q;ENSP00000340969:L9Q;ENSP00000396628:L9Q;ENSP00000378497:L9Q;ENSP00000398802:L9Q	ENSP00000340969:L9Q	L	+	2	0	TEX264	51683386	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.249000	0.72427	2.084000	0.62774	0.454000	0.30748	CTG		0.607	TEX264-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346530.1		NM_015926	
NELFCD	51497	hgsc.bcm.edu;ucsc.edu	37	20	57567073	57567076	+	Splice_Site	DEL	TAGG	TAGG	-			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	TAGG	TAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr20:57567073_57567076delTAGG	ENST00000344018.3	+	10	1281_1283	c.1254_1256delTAGG	c.(1252-1257)attagg>atg	p.IR418fs	NELFCD_ENST00000479207.1_3'UTR|NELFCD_ENST00000602795.1_Splice_Site_p.IR427fs			Q8IXH7	NELFD_HUMAN	negative elongation factor complex member C/D	418					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	membrane (GO:0016020)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)											ATCAGTGTATTAGGTAAGCAAAAC	0.407																																																	0																																										SO:0001630	splice_region_variant	51497			AF161479	CCDS13473.1, CCDS13473.2	20q13	2013-01-31	2013-01-31	2013-01-31	ENSG00000101158	ENSG00000101158			15934	protein-coding gene	gene with protein product	"""trihydrophobin 1"""	605297	"""TH1-like (Drosophila homolog)"", ""TH1-like (Drosophila)"""	TH1L		11030415, 11042152	Standard	NM_198976		Approved	HSPC130, TH1, NELF-C, NELF-D	uc002yag.4	Q8IXH7	OTTHUMG00000032861	ENST00000344018.3:c.1256+1TAGG>-	20.37:g.57567073_57567076delTAGG		Somatic		WXS	Illumina HiSeq	Phase_I	B4DE06|Q9BYL2|Q9H405|Q9H888|Q9H8T3|Q9NVX5|Q9P029|Q9UGN1|Q9UGN2|Q9UGN3	Frame_Shift_Del	DEL	ENST00000344018.3	37																																																																																					0.407	NELFCD-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_198976	Frame_Shift_Del
THAP6	152815	hgsc.bcm.edu;ucsc.edu	37	4	76440718	76440721	+	Frame_Shift_Del	DEL	AGTT	AGTT	-			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	AGTT	AGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr4:76440718_76440721delAGTT	ENST00000311638.3	+	2	124_127	c.56_59delAGTT	c.(55-60)aagttafs	p.KL19fs	THAP6_ENST00000380837.3_Frame_Shift_Del_p.KL19fs|THAP6_ENST00000514480.1_Frame_Shift_Del_p.KL19fs|THAP6_ENST00000507885.1_Intron|RCHY1_ENST00000514021.1_5'Flank|THAP6_ENST00000507557.1_Intron|THAP6_ENST00000502620.1_Intron|THAP6_ENST00000507556.1_Frame_Shift_Del_p.KL19fs|RCHY1_ENST00000380840.2_5'Flank|THAP6_ENST00000508105.1_Intron|RCHY1_ENST00000513257.1_5'Flank|RCHY1_ENST00000324439.5_5'Flank|RCHY1_ENST00000512706.1_5'Flank|RCHY1_ENST00000451788.1_5'Flank|THAP6_ENST00000504190.1_Intron	NM_144721.4	NP_653322.1	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	19						microtubule cytoskeleton (GO:0015630)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(5)	5			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			CCAAATTCGAAGTTAAAAGGACTG	0.358																																																	0																																										SO:0001589	frameshift_variant	152815			BC022989	CCDS3568.1	4q21.21	2013-01-25			ENSG00000174796	ENSG00000174796		"""THAP (C2CH-type zinc finger) domain containing"""	23189	protein-coding gene	gene with protein product		612535				12575992	Standard	NM_144721		Approved	MGC30052	uc003him.3	Q8TBB0	OTTHUMG00000130108	ENST00000311638.3:c.56_59delAGTT	4.37:g.76440718_76440721delAGTT	ENSP00000309007:p.Lys19fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4E146|Q5HYJ7|Q5JPC6	Frame_Shift_Del	DEL	ENST00000311638.3	37	CCDS3568.1																																																																																				0.358	THAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252414.1		NM_144721	
THUMPD2	80745	hgsc.bcm.edu;ucsc.edu	37	2	39993264	39993264	+	Intron	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr2:39993264A>G	ENST00000505747.1	-	5	778				THUMPD2_ENST00000260619.6_Intron|THUMPD2_ENST00000454352.2_Intron|THUMPD2_ENST00000403537.3_5'Flank	NM_025264.4	NP_079540.2	Q9BTF0	THUM2_HUMAN	THUMP domain containing 2								methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	17		all_hematologic(82;0.248)				AAGAACAAACACAGAAGTTAG	0.323																																																	0													86.0	87.0	87.0					2																	39993264		2203	4300	6503	SO:0001627	intron_variant	80745			AF380576	CCDS1805.1, CCDS1805.2	2p22.2	2004-06-04	2004-06-04	2004-06-04	ENSG00000138050	ENSG00000138050			14890	protein-coding gene	gene with protein product		611751	"""chromosome 2 open reading frame 8"""	C2orf8		12063391	Standard	NM_025264		Approved	MGC2454	uc002rru.2	Q9BTF0	OTTHUMG00000102149	ENST00000505747.1:c.751-15T>C	2.37:g.39993264A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7I7|Q53TT8|Q53TV0	RNA	SNP	ENST00000505747.1	37	CCDS1805.2																																																																																				0.323	THUMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219991.2		NM_025264	
EMC3	55831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10005822	10005822	+	Silent	SNP	T	T	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:10005822T>C	ENST00000245046.2	-	8	1175	c.717A>G	c.(715-717)gaA>gaG	p.E239E	RP11-1020A11.2_ENST00000602436.1_RNA	NM_018447.2	NP_060917.1	Q9P0I2	EMC3_HUMAN	ER membrane protein complex subunit 3	239						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)		p.E239E(1)									CCATGAGCTCTTCTTCGACAT	0.483																																																	1	Substitution - coding silent(1)	kidney(1)											134.0	124.0	128.0					3																	10005822		2203	4300	6503	SO:0001819	synonymous_variant	0			AF157321	CCDS2594.1	3p25.3	2012-05-23	2012-05-23	2012-05-23	ENSG00000125037	ENSG00000125037			23999	protein-coding gene	gene with protein product			"""transmembrane protein 111"""	TMEM111		19797678, 22119785	Standard	NM_018447		Approved		uc003bun.3	Q9P0I2	OTTHUMG00000128652	ENST00000245046.2:c.717A>G	3.37:g.10005822T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2R4Z9|Q53GH8|Q6ZMC2	Silent	SNP	ENST00000245046.2	37	CCDS2594.1																																																																																				0.483	EMC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250532.1		NM_018447	
TOPBP1	11073	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	133362056	133362056	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr3:133362056A>T	ENST00000260810.5	-	12	2140	c.2009T>A	c.(2008-2010)cTc>cAc	p.L670H	TOPBP1_ENST00000511439.1_5'Flank	NM_007027.3	NP_008958.2	Q92547	TOPB1_HUMAN	topoisomerase (DNA) II binding protein 1	670	BRCT 5. {ECO:0000255|PROSITE- ProRule:PRU00033}.				cellular response to DNA damage stimulus (GO:0006974)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|response to ionizing radiation (GO:0010212)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)	p.L583H(1)|p.L670H(1)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(5)|lung(14)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	40						TGCTCCAAGGAGGTTTGCTAG	0.353								Other conserved DNA damage response genes																													Ovarian(21;193 658 4424 15423 17362)												2	Substitution - Missense(2)	kidney(2)											100.0	98.0	99.0					3																	133362056		1853	4097	5950	SO:0001583	missense	11073			AB019397	CCDS46919.1	3q22.1	2004-06-21			ENSG00000163781	ENSG00000163781			17008	protein-coding gene	gene with protein product		607760				9461304, 9039502	Standard	NM_007027		Approved	KIAA0259, TOP2BP1	uc003eps.3	Q92547	OTTHUMG00000159773	ENST00000260810.5:c.2009T>A	3.37:g.133362056A>T	ENSP00000260810:p.Leu670His	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7W8|Q7LGC1|Q9UEB9	Missense_Mutation	SNP	ENST00000260810.5	37	CCDS46919.1	.	.	.	.	.	.	.	.	.	.	A	1.347	-0.592379	0.03799	.	.	ENSG00000163781	ENST00000260810	D	0.83163	-1.69	5.86	-11.7	0.00046	BRCT (4);	1.195780	0.05699	N	0.593773	T	0.62454	0.2429	N	0.16037	0.36	0.09310	N	1	B	0.09022	0.002	B	0.12156	0.007	T	0.49322	-0.8952	10	0.12430	T	0.62	.	11.1492	0.48449	0.5466:0.0762:0.0:0.3772	.	670	Q92547	TOPB1_HUMAN	H	670	ENSP00000260810:L670H	ENSP00000260810:L670H	L	-	2	0	TOPBP1	134844746	0.004000	0.15560	0.004000	0.12327	0.295000	0.27426	0.019000	0.13444	-3.387000	0.00174	-1.236000	0.01555	CTC		0.353	TOPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357254.1		NM_007027	
TSC22D4	81628	broad.mit.edu;ucsc.edu	37	7	100065183	100065183	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr7:100065183G>T	ENST00000300181.2	-	4	1724	c.970C>A	c.(970-972)Caa>Aaa	p.Q324K	TSC22D4_ENST00000496728.1_5'UTR|TSC22D4_ENST00000393991.1_Missense_Mutation_p.Q85K	NM_030935.3	NP_112197.1	Q9Y3Q8	T22D4_HUMAN	TSC22 domain family, member 4	324					negative regulation of transcription, DNA-templated (GO:0045892)|response to osmotic stress (GO:0006970)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q324K(1)		breast(2)|kidney(1)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(1)	8	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ACCATGGCTTGCTCGATTTTG	0.577																																																	1	Substitution - Missense(1)	kidney(1)											148.0	138.0	141.0					7																	100065183		2203	4300	6503	SO:0001583	missense	81628			BC010406	CCDS5695.1	7p21-p15	2010-04-30			ENSG00000166925	ENSG00000166925			21696	protein-coding gene	gene with protein product		611914					Standard	NM_030935		Approved	THG-1, TILZ2	uc003uva.3	Q9Y3Q8	OTTHUMG00000150233	ENST00000300181.2:c.970C>A	7.37:g.100065183G>T	ENSP00000300181:p.Gln324Lys	Somatic		WXS	Illumina GAIIx	Phase_I	A4D2C3|A8MWR6|D6W5V9	Missense_Mutation	SNP	ENST00000300181.2	37	CCDS5695.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.65|16.65	3.182568|3.182568	0.57800|0.57800	.|.	.|.	ENSG00000166925|ENSG00000166925	ENST00000300181;ENST00000393991|ENST00000423266;ENST00000456330	.|.	.|.	.|.	4.51|4.51	4.51|4.51	0.55191|0.55191	.|.	0.161948|.	0.28647|.	N|.	0.014604|.	T|T	0.50394|0.50394	0.1613|0.1613	N|N	0.19112|0.19112	0.55|0.55	0.54753|0.54753	D|D	0.999988|0.999988	B|.	0.17038|.	0.02|.	B|.	0.19946|.	0.027|.	T|T	0.46105|0.46105	-0.9215|-0.9215	9|5	0.66056|.	D|.	0.02|.	-2.6902|-2.6902	15.0806|15.0806	0.72110|0.72110	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	324|.	Q9Y3Q8|.	T22D4_HUMAN|.	K|R	324;85|139;141	.|.	ENSP00000300181:Q324K|.	Q|S	-|-	1|3	0|2	TSC22D4|TSC22D4	99903119|99903119	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	7.224000|7.224000	0.78042|0.78042	2.199000|2.199000	0.70637|0.70637	0.650000|0.650000	0.86243|0.86243	CAA|AGC		0.577	TSC22D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316970.1		NM_030935	
WDR35	57539	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	20153652	20153652	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr2:20153652T>C	ENST00000345530.3	-	13	1491	c.1376A>G	c.(1375-1377)aAg>aGg	p.K459R	WDR35_ENST00000281405.4_Missense_Mutation_p.K448R|WDR35_ENST00000416055.2_Missense_Mutation_p.K24R	NM_001006657.1	NP_001006658.1	Q9P2L0	WDR35_HUMAN	WD repeat domain 35	459					cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)		p.K459R(1)		breast(1)|endometrium(5)|kidney(8)|large_intestine(8)|lung(16)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGCTGTGAGCTTCTTTGCCAC	0.373																																																	1	Substitution - Missense(1)	kidney(1)											224.0	210.0	215.0					2																	20153652		2203	4300	6503	SO:0001583	missense	57539			AB037757	CCDS1695.1, CCDS33152.1	2p24.3	2014-02-21			ENSG00000118965	ENSG00000118965		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	29250	protein-coding gene	gene with protein product		613602				10718198	Standard	NM_001006657		Approved	MGC33196, KIAA1336, IFT121, IFTA1	uc002rdi.3	Q9P2L0	OTTHUMG00000090737	ENST00000345530.3:c.1376A>G	2.37:g.20153652T>C	ENSP00000314444:p.Lys459Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B3KVI5|Q4ZG01|Q8NE11	Missense_Mutation	SNP	ENST00000345530.3	37	CCDS33152.1	.	.	.	.	.	.	.	.	.	.	T	17.28	3.348409	0.61183	.	.	ENSG00000118965	ENST00000345530;ENST00000281405;ENST00000416055	D;D;D	0.91237	-2.81;-2.81;-2.81	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.92919	0.7747	L	0.52905	1.665	0.80722	D	1	B;D;B;P	0.71674	0.196;0.998;0.029;0.532	B;D;B;B	0.67231	0.118;0.95;0.009;0.175	D	0.90855	0.4734	10	0.19590	T	0.45	-21.546	15.0583	0.71933	0.0:0.0:0.0:1.0	.	459;448;459;24	F8WB94;Q9P2L0-2;Q9P2L0;B3KR94	.;.;WDR35_HUMAN;.	R	459;448;24	ENSP00000314444:K459R;ENSP00000281405:K448R;ENSP00000399159:K24R	ENSP00000281405:K448R	K	-	2	0	WDR35	20017133	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.005000	0.70716	2.158000	0.67659	0.459000	0.35465	AAG		0.373	WDR35-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000207472.2		NM_020779	
WASH2P	375260	broad.mit.edu	37	2	114356198	114356198	+	RNA	SNP	G	G	A	rs200217121	byFrequency	TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr2:114356198G>A	ENST00000538033.2	+	0	2378							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CTCTGGGAAAGGACCTGGGGC	0.622													.|||	268	0.0535144	0.0446	0.0303	5008	,	,		29876	0.0883		0.0547	False		,,,				2504	0.045																0																																												375260					2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114356198G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000538033.2	37																																																																																					0.622	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1		NM_198943	
ZFHX3	463	hgsc.bcm.edu	37	16	72992626	72992626	+	Silent	SNP	C	C	T			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr16:72992626C>T	ENST00000268489.5	-	2	2091	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	473	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctcctcctcctccgcctctt	0.577																																																	0													41.0	44.0	43.0					16																	72992626		2198	4300	6498	SO:0001819	synonymous_variant	463			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1419G>A	16.37:g.72992626C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																				0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1		NM_006885	
ZIK1	284307	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	58101848	58101848	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr19:58101848A>C	ENST00000597850.1	+	4	884	c.669A>C	c.(667-669)aaA>aaC	p.K223N	ZIK1_ENST00000536878.2_Missense_Mutation_p.K210N|ZIK1_ENST00000307468.4_3'UTR|ZIK1_ENST00000599456.1_Missense_Mutation_p.K168N	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K223N(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CCAGGCACAAACACACTCCTG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											65.0	64.0	64.0					19																	58101848		2203	4300	6503	SO:0001583	missense	284307			AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"""Zinc fingers, C2H2-type"", ""-"""	33104	protein-coding gene	gene with protein product			"""zinc finger protein interacting with K protein 1 homolog (mouse)"""				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.669A>C	19.37:g.58101848A>C	ENSP00000472867:p.Lys223Asn	Somatic		WXS	Illumina HiSeq	Phase_I	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	37	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	A	9.452	1.090947	0.20471	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.30448	1.53	3.58	-1.44	0.08856	.	.	.	.	.	T	0.13457	0.0326	N	0.20445	0.575	0.09310	N	1	B;B	0.29162	0.235;0.124	B;B	0.22386	0.039;0.022	T	0.20505	-1.0273	9	0.30078	T	0.28	.	1.0814	0.01644	0.402:0.1546:0.2926:0.1508	.	210;223	F5H435;Q3SY52	.;ZIK1_HUMAN	N	210;204;223	ENSP00000438487:K210N	ENSP00000303820:K223N	K	+	3	2	ZIK1	62793660	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.556000	0.00924	-0.526000	0.06383	0.528000	0.53228	AAA		0.463	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1		NM_001010879	
ZNF879	345462	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	178459395	178459395	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4163-01A-02D-1386-10	TCGA-BP-4163-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c16047c-68f3-4023-bc90-6d54cad76b07	96e16b66-2582-47e7-a107-858bf7cbf242	g.chr5:178459395A>G	ENST00000444149.2	+	5	634	c.446A>G	c.(445-447)tAc>tGc	p.Y149C		NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	149					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Y149C(1)		endometrium(3)|kidney(2)|pancreas(1)|stomach(1)	7						AAAAAAGTCTACATGAAGGAG	0.353																																																	1	Substitution - Missense(1)	kidney(1)											97.0	80.0	85.0					5																	178459395		692	1591	2283	SO:0001583	missense	345462			AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.446A>G	5.37:g.178459395A>G	ENSP00000414887:p.Tyr149Cys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	.	.	.	.	.	.	.	.	.	.	A	3.473	-0.107490	0.06924	.	.	ENSG00000234284	ENST00000444149	T	0.06449	3.3	4.59	-1.11	0.09840	.	.	.	.	.	T	0.02767	0.0083	N	0.05510	-0.035	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44298	-0.9337	9	0.36615	T	0.2	-0.8871	2.8161	0.05456	0.4185:0.0:0.2624:0.3191	.	149	B4DU55	ZN879_HUMAN	C	149	ENSP00000414887:Y149C	ENSP00000414887:Y149C	Y	+	2	0	ZNF879	178392001	0.000000	0.05858	0.000000	0.03702	0.556000	0.35491	0.356000	0.20181	0.031000	0.15407	0.482000	0.46254	TAC		0.353	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1		NM_001136116	
