#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
ASAP2	8853	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	9484692	9484692	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:9484692G>A	ENST00000281419.3	+	10	1221	c.881G>A	c.(880-882)aGc>aAc	p.S294N	ASAP2_ENST00000315273.4_Missense_Mutation_p.S294N	NM_003887.2	NP_003878.1	O43150	ASAP2_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 2	294					positive regulation of catalytic activity (GO:0043085)|regulation of ARF GTPase activity (GO:0032312)	Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|enzyme activator activity (GO:0008047)|zinc ion binding (GO:0008270)	p.S294N(2)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	36						ACAGCTTATAGCTTACATCAG	0.458																																																	2	Substitution - Missense(2)	kidney(1)|skin(1)											101.0	95.0	97.0					2																	9484692		2203	4300	6503	SO:0001583	missense	8853			AB007860	CCDS1661.1, CCDS46224.1	2p24	2013-01-10	2008-09-22	2008-09-22	ENSG00000151693	ENSG00000151693		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	2721	protein-coding gene	gene with protein product	"""centaurin, beta 3"""	603817	"""development and differentiation enhancing factor 2"""	DDEF2		10022920, 9455477	Standard	NM_003887		Approved	KIAA0400, PAP, SHAG1, CENTB3	uc002qzh.2	O43150	OTTHUMG00000117485	ENST00000281419.3:c.881G>A	2.37:g.9484692G>A	ENSP00000281419:p.Ser294Asn	Somatic		WXS	Illumina HiSeq	Phase_I	D6W4Y8	Missense_Mutation	SNP	ENST00000281419.3	37	CCDS1661.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095415	0.94197	.	.	ENSG00000151693	ENST00000281419;ENST00000315273	T;T	0.59772	0.25;0.24	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.73783	0.3631	L	0.58302	1.8	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.75484	0.986;0.968	T	0.72551	-0.4259	10	0.45353	T	0.12	.	19.408	0.94656	0.0:0.0:1.0:0.0	.	294;294	O43150-2;O43150	.;ASAP2_HUMAN	N	294	ENSP00000281419:S294N;ENSP00000316404:S294N	ENSP00000281419:S294N	S	+	2	0	ASAP2	9402143	1.000000	0.71417	0.996000	0.52242	0.962000	0.63368	6.727000	0.74764	2.643000	0.89663	0.650000	0.86243	AGC		0.458	ASAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000237522.1		NM_003887	
ATM	472	broad.mit.edu;ucsc.edu	37	11	108115600	108115600	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr11:108115600C>T	ENST00000452508.2	+	8	937	c.748C>T	c.(748-750)Cga>Tga	p.R250*	ATM_ENST00000278616.4_Nonsense_Mutation_p.R250*			Q13315	ATM_HUMAN	ATM serine/threonine kinase	250			R -> Q. {ECO:0000269|PubMed:17344846}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.R250*(4)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTTTCGAATTCGAGTGTGTGA	0.338			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	4	Substitution - Nonsense(4)	large_intestine(2)|kidney(2)	GRCh37	CM030188|CS991299	ATM	M|S							123.0	114.0	117.0					11																	108115600		2200	4298	6498	SO:0001587	stop_gained	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.748C>T	11.37:g.108115600C>T	ENSP00000388058:p.Arg250*	Somatic		WXS	Illumina GAIIx	Phase_I	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Nonsense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	C	38	6.953864	0.97960	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	.	.	.	5.33	3.43	0.39272	.	0.499073	0.19940	N	0.102677	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.6503	0.45645	0.1323:0.7986:0.0:0.0691	.	.	.	.	X	250	.	ENSP00000278616:R250X	R	+	1	2	ATM	107620810	1.000000	0.71417	0.203000	0.23512	0.947000	0.59692	2.176000	0.42500	0.725000	0.32318	0.650000	0.86243	CGA		0.338	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1		NM_000051	
ATM	472	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	108127062	108127062	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr11:108127062G>A	ENST00000452508.2	+	15	2434	c.2245G>A	c.(2245-2247)Gcc>Acc	p.A749T	ATM_ENST00000278616.4_Missense_Mutation_p.A749T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	749					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.A749T(2)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	ATTCCAGAAAGCCAAGGTAGG	0.348			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)																													yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	2	Substitution - Missense(2)	kidney(2)											85.0	85.0	85.0					11																	108127062		2201	4298	6499	SO:0001583	missense	472	Familial Cancer Database	AT, Louis-Bar syndrome	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2245G>A	11.37:g.108127062G>A	ENSP00000388058:p.Ala749Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.172729	0.78452	.	.	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74526	-0.85;-0.85;-0.85	5.45	5.45	0.79879	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.77552	0.4147	M	0.69823	2.125	0.47584	D	0.999469	P	0.49862	0.929	P	0.46389	0.515	T	0.74009	-0.3802	10	0.15952	T	0.53	.	19.6568	0.95845	0.0:0.0:1.0:0.0	.	749	Q13315	ATM_HUMAN	T	749	ENSP00000435747:A749T;ENSP00000278616:A749T;ENSP00000388058:A749T	ENSP00000278616:A749T	A	+	1	0	ATM	107632272	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.479000	0.81095	2.710000	0.92621	0.557000	0.71058	GCC		0.348	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1		NM_000051	
C17orf75	64149	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	30660439	30660439	+	Silent	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:30660439T>C	ENST00000577809.1	-	9	1021	c.972A>G	c.(970-972)ctA>ctG	p.L324L	C17orf75_ENST00000225805.4_Silent_p.L324L|RP11-227G15.3_ENST00000581915.1_RNA	NM_022344.3	NP_071739.2	Q9HAS0	NJMU_HUMAN	chromosome 17 open reading frame 75	324								p.L324L(1)		ovary(1)	1		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			TAATTACCTTTAGTTTAAAGT	0.373																																																	1	Substitution - coding silent(1)	kidney(1)											113.0	111.0	112.0					17																	30660439		1823	4076	5899	SO:0001819	synonymous_variant	64149			AB062437	CCDS58537.1	17q11.2	2013-01-21			ENSG00000108666	ENSG00000108666			30173	protein-coding gene	gene with protein product							Standard	NM_022344		Approved	NJMU-R1	uc002hhg.3	Q9HAS0		ENST00000577809.1:c.972A>G	17.37:g.30660439T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q7Z2H4	Silent	SNP	ENST00000577809.1	37	CCDS58537.1																																																																																				0.373	C17orf75-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447204.1		NM_022344	
C7orf13	129790	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	156432294	156432295	+	3'UTR	DNP	GA	GA	TT			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr7:156432294_156432295GA>TT	ENST00000333319.6	-	0	1053_1054				RNF32_ENST00000405335.1_5'Flank|RNF32_ENST00000311822.8_5'Flank|RNF32_ENST00000317955.5_5'Flank|RNF32_ENST00000432459.2_5'Flank			Q8NI28	CG013_HUMAN	chromosome 7 open reading frame 13							integral component of membrane (GO:0016021)											gggaagcaGCGAGCCAGAGTAT	0.53																																																	0																																										SO:0001624	3_prime_UTR_variant	129790					7q36.3	2013-01-15			ENSG00000244291	ENSG00000244291			17126	other	unknown		610242				11890671	Standard	NR_026865		Approved	MY040	uc003wmm.3	Q8NI28	OTTHUMG00000157237	ENST00000333319.6:c.649_649delinsTT	7.37:g.156432294_156432295delinsTT		Somatic		WXS	Illumina HiSeq	Phase_I		RNA	SNP	ENST00000333319.6	37																																																																																					0.530	C7orf13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000348106.1		NR_026865	
CACNA1G	8913	hgsc.bcm.edu	37	17	48692779	48692787	+	In_Frame_Del	DEL	ACTTGTGCA	ACTTGTGCA	-	rs200825775	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	ACTTGTGCA	ACTTGTGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:48692779_48692787delACTTGTGCA	ENST00000359106.5	+	27	4817_4825	c.4817_4825delACTTGTGCA	c.(4816-4827)cacttgtgcacc>ccc	p.1606_1609HLCT>P	CACNA1G_ENST00000502264.1_In_Frame_Del_p.1583_1586HLCT>P|CACNA1G_ENST00000510115.1_In_Frame_Del_p.1572_1575HLCT>P|CACNA1G_ENST00000360761.4_In_Frame_Del_p.1583_1586HLCT>P|CACNA1G_ENST00000510366.1_In_Frame_Del_p.1554_1557HLCT>P|CACNA1G_ENST00000515411.1_In_Frame_Del_p.1588_1591HLCT>P|CACNA1G_ENST00000514717.1_In_Frame_Del_p.1549_1552HLCT>P|CACNA1G_ENST00000354983.4_In_Frame_Del_p.1572_1575HLCT>P|CACNA1G_ENST00000512389.1_In_Frame_Del_p.1595_1598HLCT>P|CACNA1G_ENST00000513964.1_In_Frame_Del_p.1561_1564HLCT>P|CACNA1G_ENST00000442258.2_In_Frame_Del_p.1565_1568HLCT>P|CACNA1G_ENST00000507510.2_In_Frame_Del_p.1606_1609HLCT>P|CACNA1G_ENST00000505165.1_In_Frame_Del_p.1606_1609HLCT>P|CACNA1G_ENST00000429973.2_In_Frame_Del_p.1588_1591HLCT>P|CACNA1G_ENST00000515765.1_In_Frame_Del_p.1595_1598HLCT>P|CACNA1G_ENST00000515165.1_In_Frame_Del_p.1606_1609HLCT>P|CACNA1G_ENST00000507896.1_In_Frame_Del_p.1595_1598HLCT>P|CACNA1G_ENST00000352832.5_In_Frame_Del_p.1572_1575HLCT>P|CACNA1G_ENST00000358244.5_In_Frame_Del_p.1572_1575HLCT>P|CACNA1G_ENST00000514079.1_In_Frame_Del_p.1613_1616HLCT>P|CACNA1G_ENST00000507336.1_In_Frame_Del_p.1595_1598HLCT>P|CACNA1G_ENST00000507609.1_In_Frame_Del_p.1606_1609HLCT>P|CACNA1G_ENST00000514181.1_In_Frame_Del_p.1588_1591HLCT>P|CACNA1G_ENST00000513689.2_In_Frame_Del_p.1561_1564HLCT>P|CACNA1G_ENST00000503485.1_In_Frame_Del_p.1572_1575HLCT>P	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1606					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CTCGTCCACCACTTGTGCACCAGCCACTA	0.612																																																	0																																										SO:0001651	inframe_deletion	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4817_4825delACTTGTGCA	17.37:g.48692779_48692787delACTTGTGCA	ENSP00000352011:p.His1606_Thr1609delinsPro	Somatic		WXS	Illumina HiSeq	Phase_I	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	In_Frame_Del	DEL	ENST00000359106.5	37	CCDS45730.1																																																																																				0.612	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1		NM_018896	
CAPZA1	829	broad.mit.edu;ucsc.edu	37	1	113192053	113192053	+	Silent	SNP	A	A	T	rs371130747		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:113192053A>T	ENST00000263168.3	+	3	789	c.117A>T	c.(115-117)ctA>ctT	p.L39L	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	39					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)	p.L39L(1)		breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCGGCTACTACTTAATAATG	0.358																																																	1	Substitution - coding silent(1)	kidney(1)											112.0	107.0	109.0					1																	113192053		2203	4300	6503	SO:0001819	synonymous_variant	829			U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.117A>T	1.37:g.113192053A>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q53FQ6|Q6FHD5	Silent	SNP	ENST00000263168.3	37	CCDS30805.1																																																																																				0.358	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2		NM_006135	
CLMN	79789	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	95688029	95688029	+	Splice_Site	SNP	T	T	C	rs574353507		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr14:95688029T>C	ENST00000298912.4	-	4	436	c.323A>G	c.(322-324)aAt>aGt	p.N108S		NM_024734.3	NP_079010.2	Q96JQ2	CLMN_HUMAN	calmin (calponin-like, transmembrane)	108	Actin-binding.|CH 1. {ECO:0000255|PROSITE- ProRule:PRU00044}.				negative regulation of cell proliferation (GO:0008285)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)		p.N108S(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(17)|prostate(3)|skin(3)	44				Epithelial(152;0.193)		AACACTTACATTGCTATCTTC	0.423													T|||	1	0.000199681	0.0	0.0014	5008	,	,		21549	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											115.0	105.0	108.0					14																	95688029		2203	4300	6503	SO:0001630	splice_region_variant	79789			AB033014	CCDS9933.1	14q32.13	2012-10-02			ENSG00000165959	ENSG00000165959			19972	protein-coding gene	gene with protein product		611121				11386753	Standard	NM_024734		Approved	FLJ12383, KIAA1188, KIAA0500	uc001yef.2	Q96JQ2	OTTHUMG00000171629	ENST00000298912.4:c.324+1A>G	14.37:g.95688029T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2RAR7|Q9H713|Q9HA23|Q9HA57|Q9UFP4|Q9ULN2	Missense_Mutation	SNP	ENST00000298912.4	37	CCDS9933.1	.	.	.	.	.	.	.	.	.	.	T	18.54	3.645559	0.67358	.	.	ENSG00000165959	ENST00000298912;ENST00000555336;ENST00000555615	T;T;T	0.60171	0.21;0.21;0.21	5.19	4.04	0.47022	Calponin homology domain (5);	0.000000	0.44097	D	0.000484	T	0.63343	0.2503	L	0.37697	1.125	0.80722	D	1	D	0.67145	0.996	D	0.67103	0.949	T	0.61671	-0.7015	10	0.44086	T	0.13	.	11.2473	0.49004	0.0:0.0721:0.0:0.9279	.	108	Q96JQ2	CLMN_HUMAN	S	108;40;40	ENSP00000298912:N108S;ENSP00000451705:N40S;ENSP00000452525:N40S	ENSP00000298912:N108S	N	-	2	0	CLMN	94757782	1.000000	0.71417	0.990000	0.47175	0.983000	0.72400	5.551000	0.67274	0.915000	0.36847	0.459000	0.35465	AAT		0.423	CLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414518.2			Missense_Mutation
CLPTM1L	81037	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	1331925	1331925	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:1331925G>A	ENST00000320895.5	-	8	1222	c.965C>T	c.(964-966)tCc>tTc	p.S322F	CLPTM1L_ENST00000320927.6_Missense_Mutation_p.S322F|CLPTM1L_ENST00000507807.1_Missense_Mutation_p.S189F	NM_030782.3	NP_110409.2	Q96KA5	CLP1L_HUMAN	CLPTM1-like	322					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.S322F(1)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24	Lung NSC(6;5.78e-14)|all_lung(6;4.47e-13)|all_epithelial(6;4.47e-09)		Epithelial(17;0.00931)|OV - Ovarian serous cystadenocarcinoma(19;0.0116)|all cancers(22;0.0181)	KIRC - Kidney renal clear cell carcinoma(5;0.177)|Kidney(13;0.208)		TGCCTTGGTGGACATGCCGAT	0.552																																																	1	Substitution - Missense(1)	kidney(1)											125.0	117.0	120.0					5																	1331925		2203	4298	6501	SO:0001583	missense	81037			AK027306	CCDS3862.1	5p15.33	2008-02-05			ENSG00000049656	ENSG00000049656			24308	protein-coding gene	gene with protein product	"""cisplatin resistance related protein"""	612585				11162647	Standard	NM_030782		Approved	FLJ14400, CRR9	uc003jch.3	Q96KA5	OTTHUMG00000131015	ENST00000320895.5:c.965C>T	5.37:g.1331925G>A	ENSP00000313854:p.Ser322Phe	Somatic		WXS	Illumina HiSeq	Phase_I	D3DTC1|Q658W6|Q7LG29|Q96AZ0|Q9H3N4	Missense_Mutation	SNP	ENST00000320895.5	37	CCDS3862.1	.	.	.	.	.	.	.	.	.	.	g	21.6	4.170308	0.78452	.	.	ENSG00000049656	ENST00000320895;ENST00000507807;ENST00000320927	T;T;T	0.71579	-0.58;0.41;0.26	5.01	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.86690	0.5993	M	0.92219	3.285	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89304	0.3628	10	0.87932	D	0	-47.583	12.723	0.57152	0.0819:0.0:0.9181:0.0	.	322;189	Q96KA5;G5E9Z2	CLP1L_HUMAN;.	F	322;189;322	ENSP00000313854:S322F;ENSP00000423321:S189F;ENSP00000315196:S322F	ENSP00000313854:S322F	S	-	2	0	CLPTM1L	1384925	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.854000	0.92228	1.243000	0.43853	0.586000	0.80456	TCC		0.552	CLPTM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253649.2		NM_030782	
CNNM1	26507	broad.mit.edu;hgsc.bcm.edu	37	10	101151192	101151192	+	Splice_Site	SNP	A	A	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr10:101151192A>G	ENST00000356713.4	+	11	3065		c.e11-1		CNNM1_ENST00000446890.1_Splice_Site|CNNM1_ENST00000370534.4_Splice_Site|CNNM1_ENST00000370528.3_Splice_Site	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1						ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.?(2)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		TGTTTTTTTCAGGTGGCCAAA	0.438																																																	2	Unknown(2)	kidney(2)											78.0	70.0	73.0					10																	101151192		2203	4300	6503	SO:0001630	splice_region_variant	26507			AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.2777-1A>G	10.37:g.101151192A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Splice_Site	SNP	ENST00000356713.4	37	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	A	17.83	3.485894	0.63962	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534;ENST00000545665	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3709	0.83357	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNNM1	101141182	1.000000	0.71417	0.997000	0.53966	0.733000	0.41908	6.522000	0.73783	2.261000	0.74972	0.528000	0.53228	.		0.438	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2		NM_020348	Intron
CNOT6	57472	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	179994125	179994125	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:179994125T>C	ENST00000393356.1	+	10	1179	c.755T>C	c.(754-756)gTa>gCa	p.V252A	CNOT6_ENST00000261951.4_Missense_Mutation_p.V252A			Q9ULM6	CNOT6_HUMAN	CCR4-NOT transcription complex, subunit 6	252	Nuclease domain. {ECO:0000250}.				exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|gene silencing by miRNA (GO:0035195)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of ligand-dependent nuclear receptor transcription coactivator activity (GO:2000327)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	exoribonuclease activity (GO:0004532)|metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)|RNA binding (GO:0003723)	p.V252A(1)		central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|skin(1)	23	all_cancers(89;3.3e-05)|all_epithelial(37;7.38e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00543)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	OV - Ovarian serous cystadenocarcinoma(192;0.023)		TTTTTTCTGGTAGAGCTGAAA	0.363																																																	1	Substitution - Missense(1)	kidney(1)											127.0	124.0	125.0					5																	179994125		2203	4300	6503	SO:0001583	missense	57472			AB033020	CCDS4455.1	5q35.3	2014-06-17			ENSG00000113300	ENSG00000113300			14099	protein-coding gene	gene with protein product		608951				11889047	Standard	XM_005265953		Approved	CCR4, KIAA1194, Ccr4a	uc003mlx.3	Q9ULM6	OTTHUMG00000130935	ENST00000393356.1:c.755T>C	5.37:g.179994125T>C	ENSP00000377024:p.Val252Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A7MD46|D3DWR0	Missense_Mutation	SNP	ENST00000393356.1	37	CCDS4455.1	.	.	.	.	.	.	.	.	.	.	T	14.29	2.492308	0.44352	.	.	ENSG00000113300	ENST00000261951;ENST00000393356;ENST00000504343	T;T;T	0.78924	-1.22;-1.22;-1.22	5.36	5.36	0.76844	Endonuclease/exonuclease/phosphatase (2);	0.199295	0.44688	N	0.000427	T	0.58221	0.2107	N	0.14661	0.345	0.39721	D	0.971467	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.001	T	0.55328	-0.8158	9	.	.	.	-9.4813	8.2077	0.31465	0.0:0.1501:0.0:0.8499	.	156;252	D6R9H6;Q9ULM6	.;CNOT6_HUMAN	A	252;252;156	ENSP00000261951:V252A;ENSP00000377024:V252A;ENSP00000422087:V156A	.	V	+	2	0	CNOT6	179926731	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.620000	0.36976	2.173000	0.68751	0.533000	0.62120	GTA		0.363	CNOT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253532.1		NM_015455	
CRB1	23418	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	197404477	197404477	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:197404477C>A	ENST00000367400.3	+	9	3619	c.3484C>A	c.(3484-3486)Cat>Aat	p.H1162N	CRB1_ENST00000538660.1_Intron|CRB1_ENST00000367399.2_Missense_Mutation_p.H1050N|CRB1_ENST00000367397.1_Missense_Mutation_p.H543N|CRB1_ENST00000535699.1_Missense_Mutation_p.H1138N|RP11-75C23.1_ENST00000422250.1_RNA|CRB1_ENST00000544212.1_Missense_Mutation_p.H643N	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	1162	EGF-like 15. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H1162N(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						TAGCTCTTATCATTGCTCCTG	0.463																																																	1	Substitution - Missense(1)	kidney(1)											126.0	101.0	109.0					1																	197404477		2203	4300	6503	SO:0001583	missense	23418				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.3484C>A	1.37:g.197404477C>A	ENSP00000356370:p.His1162Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	C	9.852	1.193993	0.22037	.	.	ENSG00000134376	ENST00000535699;ENST00000367400;ENST00000367399;ENST00000544212;ENST00000367397;ENST00000367401	D;D;D;D;D	0.92199	-2.99;-2.99;-2.99;-2.22;-2.22	5.7	3.65	0.41850	EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	D	0.84129	0.5404	N	0.20574	0.59	0.09310	N	1	P;P;B;P	0.41848	0.646;0.763;0.114;0.485	B;B;B;B	0.37550	0.213;0.21;0.032;0.253	T	0.73199	-0.4058	9	0.23891	T	0.37	.	11.7122	0.51630	0.2258:0.6503:0.1239:0.0	.	1138;1050;811;1162	F5H0L2;P82279-3;P82279-4;P82279	.;.;.;CRUM1_HUMAN	N	1138;1162;1050;643;543;811	ENSP00000438786:H1138N;ENSP00000356370:H1162N;ENSP00000356369:H1050N;ENSP00000444556:H643N;ENSP00000356367:H543N	ENSP00000356367:H543N	H	+	1	0	CRB1	195671100	0.011000	0.17503	0.229000	0.23960	0.258000	0.26162	0.984000	0.29565	1.353000	0.45828	0.650000	0.86243	CAT		0.463	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2		NM_201253	
CRYBB1	1414	hgsc.bcm.edu	37	22	27012238	27012239	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr22:27012238_27012239insC	ENST00000215939.2	-	2	175_176	c.45_46insG	c.(43-48)gtgaacfs	p.N16fs		NM_001887.3	NP_001878.1	P53674	CRBB1_HUMAN	crystallin, beta B1	16	N-terminal arm.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			breast(1)|endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(3)|skin(2)|urinary_tract(4)	31						GGCCCTGGGTTCACCGCCACTG	0.629																																																	0																																										SO:0001589	frameshift_variant	1414				CCDS13840.1	22q12.1	2008-06-10			ENSG00000100122	ENSG00000100122			2397	protein-coding gene	gene with protein product		600929				8575764, 12360425	Standard	NM_001887		Approved		uc003acy.1	P53674	OTTHUMG00000150980	ENST00000215939.2:c.46dupG	22.37:g.27012239_27012239dupC	ENSP00000215939:p.Asn16fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000215939.2	37	CCDS13840.1																																																																																				0.629	CRYBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320767.1		NM_001887	
CTSA	5476	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	44521907	44521907	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr20:44521907T>C	ENST00000372459.2	+	6	842	c.649T>C	c.(649-651)Tcc>Ccc	p.S217P	CTSA_ENST00000354880.5_Missense_Mutation_p.S218P|CTSA_ENST00000191018.5_Missense_Mutation_p.S217P|RP3-337O18.9_ENST00000607703.1_RNA|NEURL2_ENST00000372518.4_5'Flank|CTSA_ENST00000372484.3_Missense_Mutation_p.S235P			P10619	PPGB_HUMAN	cathepsin A	217					glycosphingolipid metabolic process (GO:0006687)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|enzyme activator activity (GO:0008047)|serine-type carboxypeptidase activity (GO:0004185)	p.S235P(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				GAATGACAACTCCCTGGTCTA	0.557																																																	1	Substitution - Missense(1)	kidney(1)											144.0	122.0	130.0					20																	44521907		2203	4300	6503	SO:0001583	missense	5476			M22960	CCDS13385.2, CCDS46609.1, CCDS54467.1	20q13.12	2012-02-10	2006-12-05	2006-12-05	ENSG00000064601	ENSG00000064601	3.4.16.5	"""Cathepsins"""	9251	protein-coding gene	gene with protein product	"""carboxypeptidase C"", ""lysosomal protective protein"", ""carboxypeptidase-L"", ""carboxypeptidase Y-like kininase"", ""deamidase"", ""lysosomal carboxypeptidase A"", ""urinary kininase"""	613111	"""protective protein for beta-galactosidase (galactosialidosis)"""	GSL, PPGB		2071143	Standard	NM_000308		Approved		uc002xqh.3	P10619	OTTHUMG00000033078	ENST00000372459.2:c.649T>C	20.37:g.44521907T>C	ENSP00000361537:p.Ser217Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B2R798|Q561W6|Q5JZH1|Q96KJ2|Q9BR08|Q9BW68	Missense_Mutation	SNP	ENST00000372459.2	37	CCDS46609.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.455699	0.84209	.	.	ENSG00000064601	ENST00000354880;ENST00000372484;ENST00000191018;ENST00000419493;ENST00000372459	D;D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24;-3.24	5.21	4.04	0.47022	.	0.161093	0.56097	D	0.000021	D	0.96734	0.8934	M	0.90198	3.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.91635	0.998;0.999;0.962	D	0.96671	0.9496	10	0.56958	D	0.05	-13.3163	10.9715	0.47442	0.1398:0.0:0.0:0.8602	.	217;217;234	B4E324;P10619;Q59EV6	.;PPGB_HUMAN;.	P	218;235;217;200;217	ENSP00000346952:S218P;ENSP00000361562:S235P;ENSP00000191018:S217P;ENSP00000408533:S200P;ENSP00000361537:S217P	ENSP00000191018:S217P	S	+	1	0	CTSA	43955314	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.214000	0.72200	1.970000	0.57323	0.533000	0.62120	TCC		0.557	CTSA-012	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000471297.2		NM_000308	
PGS1	9489	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	76421493	76421493	+	IGR	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:76421493T>C	ENST00000262764.6	+	0	2201				DNAH17_ENST00000389840.5_Missense_Mutation_p.K4382E|DNAH17_ENST00000586052.1_5'UTR|AC061992.1_ENST00000600087.1_5'Flank|DNAH17_ENST00000585328.1_Missense_Mutation_p.K4354E	NM_024419.3	NP_077733.3	Q32NB8	PGPS1_HUMAN	phosphatidylglycerophosphate synthase 1						cardiolipin biosynthetic process (GO:0032049)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity (GO:0008444)	p.K4354E(1)		cervix(2)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	10			BRCA - Breast invasive adenocarcinoma(99;0.00144)|OV - Ovarian serous cystadenocarcinoma(97;0.031)			TCTCGGTTTTTCTTGGTCACC	0.567																																					Esophageal Squamous(45;182 1126 10685 43198)												1	Substitution - Missense(1)	kidney(1)											126.0	123.0	124.0					17																	76421493		2203	4300	6503	SO:0001628	intergenic_variant	8632				CCDS42391.1	17q25.3	2006-02-09							30029	protein-coding gene	gene with protein product		614942				9880566	Standard	XR_243691		Approved	DKFZP762M186	uc002jvm.3	Q32NB8			17.37:g.76421493T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZA32|Q8IYK9|Q8TA85|Q96A75|Q9H7G9|Q9NPW7	Missense_Mutation	SNP	ENST00000262764.6	37	CCDS42391.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.761507	0.89932	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.09630	2.96	4.85	4.85	0.62838	.	0.302640	0.27961	N	0.017158	T	0.33059	0.0850	M	0.73598	2.24	0.48830	D	0.999716	D	0.76494	0.999	D	0.76071	0.987	T	0.08166	-1.0735	10	0.72032	D	0.01	.	14.6095	0.68507	0.0:0.0:0.0:1.0	.	4354	E7EUM8	.	E	4354;4382	ENSP00000374490:K4382E	ENSP00000300671:K4354E	K	-	1	0	DNAH17	73933088	1.000000	0.71417	0.993000	0.49108	0.792000	0.44763	7.765000	0.85310	2.027000	0.59764	0.482000	0.46254	AAA		0.567	PGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437301.1		NM_024419	
DNAH3	55567	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	21136611	21136611	+	Nonsense_Mutation	SNP	G	G	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr16:21136611G>C	ENST00000261383.3	-	9	1288	c.1289C>G	c.(1288-1290)tCa>tGa	p.S430*	CTC-508F8.1_ENST00000575612.1_RNA|DNAH3_ENST00000415178.1_Nonsense_Mutation_p.S430*	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	430	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.S430*(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GTTTCGACTTGAGTCATAGTT	0.483																																																	2	Substitution - Nonsense(2)	kidney(2)											120.0	118.0	119.0					16																	21136611		2201	4300	6501	SO:0001587	stop_gained	55567			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.1289C>G	16.37:g.21136611G>C	ENSP00000261383:p.Ser430*	Somatic		WXS	Illumina HiSeq	Phase_I	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Nonsense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.154022	0.78114	.	.	ENSG00000158486	ENST00000261383;ENST00000415178;ENST00000396036	.	.	.	5.75	5.75	0.90469	.	0.813239	0.11189	N	0.590121	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	18.7237	0.91705	0.0:0.0:1.0:0.0	.	.	.	.	X	430;430;401	.	ENSP00000261383:S430X	S	-	2	0	DNAH3	21044112	1.000000	0.71417	0.151000	0.22473	0.029000	0.11900	4.532000	0.60608	2.725000	0.93324	0.655000	0.94253	TCA		0.483	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1		NM_017539	
DNAJC1	64215	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	22193512	22193512	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr10:22193512delT	ENST00000376980.3	-	7	1049	c.759delA	c.(757-759)aaafs	p.K253fs		NM_022365.3	NP_071760.2	Q96KC8	DNJC1_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 1	253					negative regulation of proteolysis (GO:0045861)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)|regulation of protein secretion (GO:0050708)|regulation of translation (GO:0006417)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(13)|skin(2)|upper_aerodigestive_tract(2)	21		Breast(68;0.00869)|Prostate(175;0.0181)|Lung SC(717;0.0262)				ATCTTGTTTCTTTATATTTAG	0.279																																																	0													109.0	95.0	100.0					10																	22193512		2201	4295	6496	SO:0001589	frameshift_variant	64215			AK026062	CCDS7136.1	10p11.23	2011-09-02			ENSG00000136770	ENSG00000136770		"""Heat shock proteins / DNAJ (HSP40)"""	20090	protein-coding gene	gene with protein product		611207					Standard	NM_022365		Approved	DNAJL1, ERdj1, MTJ1	uc001irc.3	Q96KC8	OTTHUMG00000017800	ENST00000376980.3:c.759delA	10.37:g.22193512delT	ENSP00000366179:p.Lys253fs	Somatic		WXS	Illumina HiSeq	Phase_I	B0YIZ8|Q5VX89|Q9H6B8	Frame_Shift_Del	DEL	ENST00000376980.3	37	CCDS7136.1																																																																																				0.279	DNAJC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047149.1		NM_022365	
DOK7	285489	broad.mit.edu;ucsc.edu	37	4	3478155	3478155	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr4:3478155T>G	ENST00000340083.5	+	4	483	c.418T>G	c.(418-420)Ttg>Gtg	p.L140V	DOK7_ENST00000389653.2_Missense_Mutation_p.L140V|DOK7_ENST00000507039.1_Missense_Mutation_p.L140V	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7	140	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)	p.L140V(1)		kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TGTCCTCGTCTTGGCCAGGGA	0.647																																																	1	Substitution - Missense(1)	kidney(1)											93.0	78.0	83.0					4																	3478155		2203	4299	6502	SO:0001583	missense	285489			AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.418T>G	4.37:g.3478155T>G	ENSP00000344432:p.Leu140Val	Somatic		WXS	Illumina GAIIx	Phase_I	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Missense_Mutation	SNP	ENST00000340083.5	37	CCDS3370.2	.	.	.	.	.	.	.	.	.	.	T	14.25	2.478206	0.44044	.	.	ENSG00000175920	ENST00000389653;ENST00000507039;ENST00000340083	D;D;D	0.91124	-2.79;-2.79;-2.79	4.42	0.878	0.19150	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (2);	0.296706	0.26496	N	0.024054	D	0.83041	0.5168	L	0.41356	1.27	0.31151	N	0.705441	B	0.06786	0.001	B	0.12156	0.007	T	0.73325	-0.4018	10	0.34782	T	0.22	-12.0487	6.6704	0.23066	0.0:0.5497:0.2011:0.2492	.	140	Q18PE1	DOK7_HUMAN	V	140	ENSP00000374304:L140V;ENSP00000423614:L140V;ENSP00000344432:L140V	ENSP00000344432:L140V	L	+	1	2	DOK7	3447953	0.086000	0.21541	0.560000	0.28344	0.985000	0.73830	0.248000	0.18198	0.099000	0.17552	0.402000	0.26972	TTG		0.647	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1		NM_173660	
DPP4	1803	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	162902066	162902066	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:162902066A>C	ENST00000360534.3	-	5	902	c.342T>G	c.(340-342)atT>atG	p.I114M		NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	114					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.I114M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	ATTCTAAGAGAATAAACTGCC	0.303																																																	1	Substitution - Missense(1)	kidney(1)											79.0	83.0	82.0					2																	162902066		2203	4299	6502	SO:0001583	missense	1803			M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.342T>G	2.37:g.162902066A>C	ENSP00000353731:p.Ile114Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q53TN1	Missense_Mutation	SNP	ENST00000360534.3	37	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	A	13.33	2.204370	0.38905	.	.	ENSG00000197635	ENST00000360534	D	0.96587	-4.06	4.15	2.89	0.33648	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.580057	0.18526	N	0.138639	D	0.96349	0.8809	L	0.55103	1.725	0.24889	N	0.992178	B	0.25521	0.128	P	0.48873	0.593	D	0.92492	0.6001	10	0.72032	D	0.01	2.9651	8.0895	0.30793	0.8194:0.0:0.0:0.1806	.	114	P27487	DPP4_HUMAN	M	114	ENSP00000353731:I114M	ENSP00000353731:I114M	I	-	3	3	DPP4	162610312	0.997000	0.39634	0.987000	0.45799	0.939000	0.58152	1.125000	0.31332	1.888000	0.54679	0.379000	0.24179	ATT		0.303	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			
EPB41L4B	54566	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	112005948	112005948	+	Silent	SNP	A	A	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr9:112005948A>G	ENST00000374566.3	-	15	1876	c.1359T>C	c.(1357-1359)ccT>ccC	p.P453P	EPB41L4B_ENST00000374557.4_Silent_p.P453P	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	453					actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)	p.P453P(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GATGGATATTAGGATGATATT	0.453																																																	2	Substitution - coding silent(2)	kidney(2)											92.0	96.0	95.0					9																	112005948		1905	4124	6029	SO:0001819	synonymous_variant	54566			AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1359T>C	9.37:g.112005948A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	37	CCDS43859.1																																																																																				0.453	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1		NM_018424	
ERAL1	26284	broad.mit.edu;ucsc.edu	37	17	27182269	27182269	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:27182269T>C	ENST00000254928.5	+	1	314	c.217T>C	c.(217-219)Ttc>Ctc	p.F73L	ERAL1_ENST00000578001.1_3'UTR|FAM222B_ENST00000583953.1_5'Flank	NM_005702.2	NP_005693.1	O75616	ERAL1_HUMAN	Era-like 12S mitochondrial rRNA chaperone 1	73					ribosomal small subunit assembly (GO:0000028)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)	p.F73L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	11	all_cancers(5;2.12e-15)|all_epithelial(6;3.44e-19)|Lung NSC(42;0.01)		Epithelial(11;1.12e-05)|all cancers(11;5.32e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000272)|OV - Ovarian serous cystadenocarcinoma(11;0.105)			CCTGGACCACTTCCTCGGATT	0.627																																																	1	Substitution - Missense(1)	kidney(1)											43.0	44.0	44.0					17																	27182269		2203	4300	6503	SO:0001583	missense	26284			AF082657	CCDS11244.1	17q11.2	2013-05-22	2013-05-22		ENSG00000132591	ENSG00000132591			3424	protein-coding gene	gene with protein product		607435	"""Era (E. coli G-protein homolog)-like 1"", ""Era G-protein-like 1 (E. coli)"""			10945472, 20604745	Standard	NM_005702		Approved	HERA-B	uc002hcy.1	O75616	OTTHUMG00000132675	ENST00000254928.5:c.217T>C	17.37:g.27182269T>C	ENSP00000254928:p.Phe73Leu	Somatic		WXS	Illumina GAIIx	Phase_I	B3KN21|C9JEC6|O75617|Q8WUY4|Q96LE2|Q96TC0	Missense_Mutation	SNP	ENST00000254928.5	37	CCDS11244.1	.	.	.	.	.	.	.	.	.	.	T	10.28	1.306837	0.23821	.	.	ENSG00000132591	ENST00000254928	.	.	.	5.25	3.0	0.34707	.	0.252133	0.37304	N	0.002142	T	0.21550	0.0519	L	0.29908	0.895	0.25115	N	0.990682	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.31138	-0.9954	9	0.02654	T	1	-15.4598	4.3953	0.11360	0.1786:0.0929:0.0:0.7285	.	73;73	O75616;O75616-2	ERAL1_HUMAN;.	L	73	.	ENSP00000254928:F73L	F	+	1	0	ERAL1	24206395	0.856000	0.29760	0.937000	0.37676	0.073000	0.16967	0.745000	0.26259	0.426000	0.26116	-0.411000	0.06167	TTC		0.627	ERAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255937.2			
F5	2153	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	169528479	169528479	+	Silent	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:169528479T>C	ENST00000367797.3	-	5	843	c.642A>G	c.(640-642)ctA>ctG	p.L214L	F5_ENST00000367796.3_Silent_p.L214L|F5_ENST00000546081.1_Silent_p.L77L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	214	F5/8 type A 1.|Plastocyanin-like 2.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)	p.L214L(1)		NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	ACACAGCAAATAGTAGCACGA	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											175.0	133.0	147.0					1																	169528479		2203	4300	6503	SO:0001819	synonymous_variant	2153			M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.642A>G	1.37:g.169528479T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Silent	SNP	ENST00000367797.3	37	CCDS1281.1																																																																																				0.453	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1		NM_000130	
GMFB	2764	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	54948128	54948128	+	Splice_Site	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr14:54948128G>A	ENST00000358056.3	-	4	467	c.199C>T	c.(199-201)Cgc>Tgc	p.R67C	GMFB_ENST00000553566.1_5'UTR|GMFB_ENST00000554908.1_3'UTR	NM_004124.2	NP_004115.1	P60983	GMFB_HUMAN	glia maturation factor, beta	67	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of protein kinase activity (GO:0006469)|nervous system development (GO:0007399)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)|signal transducer activity (GO:0004871)	p.R67C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)	8						AAAGGATATCGAGGTTGTCGT	0.363																																																	1	Substitution - Missense(1)	kidney(1)											115.0	111.0	112.0					14																	54948128		2203	4300	6503	SO:0001630	splice_region_variant	2764			M86492	CCDS9718.1	14q22.2	2010-07-06			ENSG00000197045	ENSG00000197045			4373	protein-coding gene	gene with protein product		601713				1712830	Standard	NM_004124		Approved	GMF	uc021rtf.1	P60983	OTTHUMG00000140307	ENST00000358056.3:c.200+1C>T	14.37:g.54948128G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2R499|P17774|Q9BS35	Missense_Mutation	SNP	ENST00000358056.3	37	CCDS9718.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.0|29.0	4.971635|4.971635	0.92919|0.92919	.|.	.|.	ENSG00000197045|ENSG00000197045	ENST00000358056|ENST00000354747;ENST00000553333	T|.	0.37584|.	1.19|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.060297|0.060297	0.64402|0.64402	D|D	0.000005|0.000005	T|.	0.79667|.	0.4485|.	M|M	0.93978|0.93978	3.48|3.48	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.79371|.	-0.1831|.	8|.	0.87932|0.02654	D|T	0|1	1.2545|1.2545	14.3343|14.3343	0.66578|0.66578	0.0:0.0:0.8517:0.1483|0.0:0.0:0.8517:0.1483	.|.	.|.	.|.	.|.	C|X	67|67;79	ENSP00000350757:R67C|.	ENSP00000350757:R67C|ENSP00000346789:R67X	R|R	-|-	1|1	0|2	GMFB|GMFB	54017878|54017878	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	6.594000|6.594000	0.74104|0.74104	2.672000|2.672000	0.90937|0.90937	0.585000|0.585000	0.79938|0.79938	CGC|CGA		0.363	GMFB-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276903.2		NM_004124	Missense_Mutation
GPR124	25960	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	37688398	37688398	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr8:37688398C>T	ENST00000412232.2	+	7	902	c.889C>T	c.(889-891)Ctc>Ttc	p.L297F	GPR124_ENST00000315215.7_Missense_Mutation_p.L297F	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	297	Ig-like.				central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.L290F(1)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GGCGGGCATCCTCCTGGCCGA	0.647																																																	1	Substitution - Missense(1)	kidney(1)											55.0	41.0	46.0					8																	37688398		2196	4289	6485	SO:0001583	missense	25960			AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.889C>T	8.37:g.37688398C>T	ENSP00000406367:p.Leu297Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	37	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	C	3.319	-0.139224	0.06669	.	.	ENSG00000020181	ENST00000416514;ENST00000315215;ENST00000412232	T;T	0.57907	0.37;0.53	5.02	2.95	0.34219	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.504894	0.20519	N	0.090723	T	0.20129	0.0484	N	0.01874	-0.695	0.25546	N	0.987132	B;B	0.22276	0.067;0.012	B;B	0.24541	0.054;0.009	T	0.27054	-1.0085	10	0.07482	T	0.82	-18.2695	6.6814	0.23123	0.4381:0.4373:0.1246:0.0	.	297;297	Q96PE1-2;Q96PE1	.;GP124_HUMAN	F	290;297;297	ENSP00000323508:L297F;ENSP00000406367:L297F	ENSP00000323508:L297F	L	+	1	0	GPR124	37807556	0.955000	0.32602	0.997000	0.53966	0.754000	0.42855	1.833000	0.39161	1.076000	0.40961	0.655000	0.94253	CTC		0.647	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			
HIST1H1A	3024	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	26017495	26017495	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr6:26017495C>A	ENST00000244573.3	-	1	545	c.466G>T	c.(466-468)Gct>Tct	p.A156S		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	156					nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)	p.A156S(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						GGCTTTTTAGCCTTTTTCGGA	0.463																																																	1	Substitution - Missense(1)	kidney(1)											163.0	173.0	169.0					6																	26017495		2203	4300	6503	SO:0001583	missense	3024			AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"""Histones / Replication-dependent"""	4715	protein-coding gene	gene with protein product		142709	"""H1 histone family, member 1"", ""histone 1, H1a"""	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.466G>T	6.37:g.26017495C>A	ENSP00000244573:p.Ala156Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	7.105	0.574920	0.13623	.	.	ENSG00000124610	ENST00000244573	T	0.17854	2.25	4.31	1.46	0.22682	.	0.344359	0.29080	N	0.013217	T	0.04003	0.0112	L	0.36672	1.1	0.33357	D	0.571839	P	0.35745	0.518	B	0.30401	0.115	T	0.33803	-0.9854	10	0.52906	T	0.07	-5.0413	6.0122	0.19582	0.0:0.5237:0.3057:0.1706	.	156	Q02539	H11_HUMAN	S	156	ENSP00000244573:A156S	ENSP00000244573:A156S	A	-	1	0	HIST1H1A	26125474	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.843000	0.27640	0.147000	0.19030	0.609000	0.83330	GCT		0.463	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1		NM_005325	
IVL	3713	hgsc.bcm.edu;ucsc.edu	37	1	152882534	152882545	+	In_Frame_Del	DEL	GCAGCAACAGCA	GCAGCAACAGCA	-	rs149812110|rs201279635|rs386635518	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	GCAGCAACAGCA	GCAGCAACAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:152882534_152882545delGCAGCAACAGCA	ENST00000368764.3	+	2	325_336	c.261_272delGCAGCAACAGCA	c.(259-273)ctgcagcaacagcac>ctc	p.QQQH88del	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	88					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			agcaggagctgcagcaacagcactgggaacag	0.495																																																	0																																										SO:0001651	inframe_deletion	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.261_272delGCAGCAACAGCA	1.37:g.152882534_152882545delGCAGCAACAGCA	ENSP00000357753:p.Gln88_His91del	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T7P4	In_Frame_Del	DEL	ENST00000368764.3	37	CCDS1030.1																																																																																				0.495	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1		NM_005547	
IVL	3713	hgsc.bcm.edu;ucsc.edu	37	1	152882546	152882547	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:152882546_152882547insT	ENST00000368764.3	+	2	337_338	c.273_274insT	c.(274-276)tggfs	p.W92fs	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	92					isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			agcaacagcactgggaacagca	0.495																																																	0																																										SO:0001589	frameshift_variant	3713			BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.274dupT	1.37:g.152882547_152882547dupT	ENSP00000357753:p.Trp92fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T7P4	Frame_Shift_Ins	INS	ENST00000368764.3	37	CCDS1030.1																																																																																				0.495	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1		NM_005547	
KCNK10	54207	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	88658594	88658594	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr14:88658594G>A	ENST00000340700.5	-	5	1278	c.827C>T	c.(826-828)aCg>aTg	p.T276M	KCNK10_ENST00000319231.5_Missense_Mutation_p.T281M|KCNK10_ENST00000312350.5_Missense_Mutation_p.T281M	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	276					signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.T281M(2)|p.T276M(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	47						AAAGCCCACCGTGGTCAGAGT	0.537																																																	3	Substitution - Missense(3)	kidney(3)											102.0	111.0	108.0					14																	88658594		2203	4300	6503	SO:0001583	missense	54207			AF279890	CCDS9880.1, CCDS9881.1, CCDS9882.1	14q31	2014-06-12						"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6273	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 97"""	605873				10880510, 16382106	Standard	NM_021161		Approved	K2p10.1, TREK-2, TREK2, PPP1R97	uc001xwn.3	P57789		ENST00000340700.5:c.827C>T	14.37:g.88658594G>A	ENSP00000343104:p.Thr276Met	Somatic		WXS	Illumina HiSeq	Phase_I	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	37	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	G	32	5.107577	0.94292	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231	T;T;T	0.70282	-0.47;-0.47;-0.47	5.89	5.89	0.94794	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	D	0.92093	0.7494	H	0.99379	4.54	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.94948	0.8097	10	0.87932	D	0	.	20.248	0.98401	0.0:0.0:1.0:0.0	.	276;281;281	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	M	276;281;281	ENSP00000343104:T276M;ENSP00000310568:T281M;ENSP00000312811:T281M	ENSP00000310568:T281M	T	-	2	0	KCNK10	87728347	1.000000	0.71417	0.968000	0.41197	0.997000	0.91878	9.869000	0.99810	2.790000	0.95986	0.655000	0.94253	ACG		0.537	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1		NM_021161	
CFAP74	85452	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	1888064	1888064	+	IGR	SNP	T	T	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:1888064T>G								TMEM52 (37352 upstream) : C1orf222 (31498 downstream)														p.K671Q(1)									CTCACTAATTTCAGGGCAGAC	0.572																																																	1	Substitution - Missense(1)	kidney(1)											55.0	60.0	58.0					1																	1888064		2080	4230	6310	SO:0001628	intergenic_variant	85452																															1.37:g.1888064T>G		Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	T	14.61	2.587086	0.46110	.	.	ENSG00000142609	ENST00000270720;ENST00000461752	.	.	.	4.34	4.34	0.51931	.	1.157120	0.06411	N	0.720613	T	0.71879	0.3392	M	0.65975	2.015	0.34855	D	0.74205	D;D	0.67145	0.996;0.993	D;P	0.63793	0.918;0.857	T	0.63409	-0.6644	9	0.27785	T	0.31	-3.3053	10.2207	0.43194	0.0:0.0:0.0:1.0	.	671;671	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	Q	671;118	.	ENSP00000270720:K671Q	K	-	1	0	C1orf222	1877924	0.003000	0.15002	0.002000	0.10522	0.003000	0.03518	1.340000	0.33896	1.746000	0.51805	0.533000	0.62120	AAA	0	0.572									
MAP3K2	10746	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	128066283	128066283	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:128066283delG	ENST00000409947.1	-	16	1794	c.1512delC	c.(1510-1512)gccfs	p.A504fs	MAP3K2_ENST00000344908.5_Frame_Shift_Del_p.A504fs			Q9Y2U5	M3K2_HUMAN	mitogen-activated protein kinase kinase kinase 2	504	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPK activity (GO:0000187)|cellular response to mechanical stimulus (GO:0071260)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|large_intestine(1)|lung(3)|ovary(2)	7	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0706)	Bosutinib(DB06616)	GCCGTTTGCTGGCCCCAAAAT	0.468																																																	0													127.0	128.0	127.0					2																	128066283		1946	4154	6100	SO:0001589	frameshift_variant	10746			AF111105	CCDS46404.1	2q21.1	2011-06-09			ENSG00000169967	ENSG00000169967		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6854	protein-coding gene	gene with protein product	"""MAP/ERK kinase kinase 2"""	609487		MEKK2		8621389, 10085062	Standard	NM_006609		Approved	MEKK2B	uc002toj.2	Q9Y2U5	OTTHUMG00000153397	ENST00000409947.1:c.1512delC	2.37:g.128066283delG	ENSP00000387246:p.Ala504fs	Somatic		WXS	Illumina HiSeq	Phase_I	B9EG87|Q53QL9|Q53S75|Q59GZ6|Q8NC32|Q9NYK3	Frame_Shift_Del	DEL	ENST00000409947.1	37	CCDS46404.1																																																																																				0.468	MAP3K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331014.1		NM_006609	
KIF1A	547	broad.mit.edu;ucsc.edu	37	2	241662861	241662861	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:241662861C>T	ENST00000320389.7	-	40	4288	c.4130G>A	c.(4129-4131)tGg>tAg	p.W1377*	KIF1A_ENST00000498729.2_Nonsense_Mutation_p.W1478*	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1377					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.W1377*(1)		NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		CTCCAGCTCCCACTGGTGGTC	0.627																																																	1	Substitution - Nonsense(1)	kidney(1)											19.0	23.0	22.0					2																	241662861		2006	4098	6104	SO:0001587	stop_gained	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.4130G>A	2.37:g.241662861C>T	ENSP00000322791:p.Trp1377*	Somatic		WXS	Illumina GAIIx	Phase_I	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Nonsense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	45|45	12.019250|12.019250	0.99627|0.99627	.|.	.|.	ENSG00000130294|ENSG00000130294	ENST00000431776|ENST00000320389;ENST00000498729;ENST00000373308	.|.	.|.	.|.	3.33|3.33	3.33|3.33	0.38152|0.38152	.|.	.|0.000000	.|0.85682	.|U	.|0.000000	T|.	0.44244|.	0.1284|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.46624|.	-0.9178|.	3|.	.|0.10111	.|T	.|0.7	.|.	14.6499|14.6499	0.68789|0.68789	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	R|X	310|1377;1478;1486	.|.	.|ENSP00000322791:W1377X	G|W	-|-	1|2	0|0	KIF1A|KIF1A	241311534|241311534	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	7.567000|7.567000	0.82357|0.82357	1.403000|1.403000	0.46800|0.46800	0.491000|0.491000	0.48974|0.48974	GGG|TGG		0.627	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3		NM_138483	
MAPK14	1432	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	36043701	36043701	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr6:36043701C>A	ENST00000229794.4	+	7	960	c.572C>A	c.(571-573)cCt>cAt	p.P191H	MAPK14_ENST00000229795.3_Missense_Mutation_p.P191H|MAPK14_ENST00000310795.4_Missense_Mutation_p.P191H|MAPK14_ENST00000468133.1_Missense_Mutation_p.P114H	NM_139012.2|NM_139014.2	NP_620581.1|NP_620583.1	Q16539	MK14_HUMAN	mitogen-activated protein kinase 14	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cartilage condensation (GO:0001502)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|cellular component movement (GO:0006928)|cellular response to ionizing radiation (GO:0071479)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chemotaxis (GO:0006935)|chondrocyte differentiation (GO:0002062)|DNA damage checkpoint (GO:0000077)|fatty acid oxidation (GO:0019395)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myoblast differentiation involved in skeletal muscle regeneration (GO:0014835)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|neurotrophin TRK receptor signaling pathway (GO:0048011)|osteoclast differentiation (GO:0030316)|p38MAPK cascade (GO:0038066)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myoblast fusion (GO:1901741)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to muramyl dipeptide (GO:0032495)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|signal transduction in response to DNA damage (GO:0042770)|skeletal muscle tissue development (GO:0007519)|stress-activated MAPK cascade (GO:0051403)|stress-induced premature senescence (GO:0090400)|striated muscle cell differentiation (GO:0051146)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|MAP kinase kinase activity (GO:0004708)|NFAT protein binding (GO:0051525)|protein serine/threonine kinase activity (GO:0004674)	p.P191H(2)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|stomach(1)	16						TACAGGGCTCCTGAGATCATG	0.468																																					Pancreas(20;8 363 26997 32430 36377 43317 49243 50560 51947)|Colon(176;951 1093 20177 30266 32328 34418 35271 44052 51610)												2	Substitution - Missense(2)	kidney(2)											134.0	121.0	125.0					6																	36043701		2203	4300	6503	SO:0001583	missense	1432			L35263	CCDS4815.1, CCDS4816.1, CCDS4817.1	6p21.3-p21.2	2011-06-09			ENSG00000112062	ENSG00000112062		"""Mitogen-activated protein kinase cascade / Kinases"""	6876	protein-coding gene	gene with protein product	"""p38 MAP kinase"""	600289		CSPB1, CSBP1, CSBP2		7997261	Standard	NM_139012		Approved	PRKM14, p38, Mxi2, PRKM15	uc003olq.3	Q16539	OTTHUMG00000159806	ENST00000229794.4:c.572C>A	6.37:g.36043701C>A	ENSP00000229794:p.Pro191His	Somatic		WXS	Illumina HiSeq	Phase_I	A6ZJ92|A8K6P4|B0LPH0|B5TY32|O60776|Q13083|Q14084|Q8TDX0	Missense_Mutation	SNP	ENST00000229794.4	37	CCDS4816.1	.	.	.	.	.	.	.	.	.	.	C	33	5.251993	0.95336	.	.	ENSG00000112062	ENST00000229795;ENST00000229794;ENST00000468133;ENST00000310795;ENST00000472333	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.97	5.97	0.96955	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90672	0.7074	H	0.99689	4.705	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	D	0.94125	0.7383	10	0.87932	D	0	-8.2201	20.4388	0.99107	0.0:1.0:0.0:0.0	.	191;191;191;191;191	B5TY32;Q16539-4;Q16539;Q16539-2;Q16539-3	.;.;MK14_HUMAN;.;.	H	191;191;114;191;114	ENSP00000229795:P191H;ENSP00000229794:P191H;ENSP00000419837:P114H;ENSP00000308669:P191H;ENSP00000419141:P114H	ENSP00000229794:P191H	P	+	2	0	MAPK14	36151679	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	CCT		0.468	MAPK14-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357450.1		NM_001315	
MARCH6	10299	broad.mit.edu;ucsc.edu	37	5	10407230	10407230	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:10407230T>C	ENST00000274140.5	+	17	1601	c.1469T>C	c.(1468-1470)aTt>aCt	p.I490T	MARCH6_ENST00000510792.1_Missense_Mutation_p.I188T|MARCH6_ENST00000503788.1_Missense_Mutation_p.I385T|MARCH6_ENST00000449913.2_Missense_Mutation_p.I442T	NM_005885.3	NP_005876.2	O60337	MARH6_HUMAN	membrane-associated ring finger (C3HC4) 6, E3 ubiquitin protein ligase	490					protein K48-linked ubiquitination (GO:0070936)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	enzyme binding (GO:0019899)|ligase activity (GO:0016874)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.I490T(1)		breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(35)|ovary(1)|urinary_tract(3)	54						TTTGGCTCCATTGTCCTCCTG	0.418																																																	1	Substitution - Missense(1)	kidney(1)											358.0	320.0	333.0					5																	10407230		2203	4300	6503	SO:0001583	missense	10299			AB011169	CCDS34135.1, CCDS59487.1, CCDS59488.1	5p15.2	2013-01-09	2012-02-23		ENSG00000145495	ENSG00000145495		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	30550	protein-coding gene	gene with protein product		613297	"""membrane-associated ring finger (C3HC4) 6"""			14722266	Standard	NM_001270660		Approved	TEB4, MARCH-VI, RNF176	uc003jet.2	O60337	OTTHUMG00000162027	ENST00000274140.5:c.1469T>C	5.37:g.10407230T>C	ENSP00000274140:p.Ile490Thr	Somatic		WXS	Illumina GAIIx	Phase_I	A5PKZ4|B4DKJ2|B4DT33|D3DTC8|O14670|Q86X77	Missense_Mutation	SNP	ENST00000274140.5	37	CCDS34135.1	.	.	.	.	.	.	.	.	.	.	T	7.917	0.737787	0.15574	.	.	ENSG00000145495	ENST00000449913;ENST00000503788;ENST00000274140;ENST00000510792	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.16385	0.0394	N	0.03948	-0.315	0.80722	D	1	B;B;B;B	0.20887	0.012;0.017;0.049;0.006	B;B;B;B	0.20184	0.028;0.007;0.023;0.006	T	0.13229	-1.0517	10	0.22706	T	0.39	-27.5156	16.3245	0.82970	0.0:0.0:0.0:1.0	.	385;442;70;490	B4DKJ2;B4DT33;B2RBJ1;O60337	.;.;.;MARH6_HUMAN	T	442;385;490;188	ENSP00000414643:I442T;ENSP00000425930:I385T;ENSP00000274140:I490T;ENSP00000424512:I188T	ENSP00000274140:I490T	I	+	2	0	MARCH6	10460230	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.629000	0.83207	2.254000	0.74563	0.460000	0.39030	ATT		0.418	MARCH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366919.2		NM_005885	
MFAP4	4239	hgsc.bcm.edu;ucsc.edu	37	17	19288733	19288734	+	Frame_Shift_Del	DEL	AA	AA	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:19288733_19288734delAA	ENST00000299610.4	-	4	358_359	c.274_275delTT	c.(274-276)ttcfs	p.F93fs	MFAP4_ENST00000395592.2_Frame_Shift_Del_p.F117fs|MFAP4_ENST00000574313.2_5'Flank|MFAP4_ENST00000497081.2_Frame_Shift_Del_p.F118fs	NM_002404.2	NP_002395.1	P55083	MFAP4_HUMAN	microfibrillar-associated protein 4	93	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|cellular response to UV-B (GO:0071493)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|regulation of collagen metabolic process (GO:0010712)|UV protection (GO:0009650)	elastic fiber (GO:0071953)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)				large_intestine(1)|lung(6)|prostate(2)|upper_aerodigestive_tract(1)	10	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					GCCGCGGAAGAAACTTACTGAG	0.574																																																	0																																										SO:0001589	frameshift_variant	4239			L38486	CCDS11208.1, CCDS56023.1	17p11.2	2013-02-06			ENSG00000166482	ENSG00000166482		"""Fibrinogen C domain containing"""	7035	protein-coding gene	gene with protein product	"""microfibril-associated glycoprotein 4"""	600596				7633408	Standard	NM_001198695		Approved		uc002gvs.3	P55083	OTTHUMG00000059585	ENST00000299610.4:c.274_275delTT	17.37:g.19288733_19288734delAA	ENSP00000299610:p.Phe93fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8KAJ1|A8MVM2|B4E317|Q6P680	Frame_Shift_Del	DEL	ENST00000299610.4	37	CCDS11208.1																																																																																				0.574	MFAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132493.2		NM_002404	
SLIT2	9353	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	20529994	20529994	+	Intron	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr4:20529994C>T	ENST00000504154.1	+	16	1714				SLIT2_ENST00000273739.5_Intron|SLIT2_ENST00000503823.1_Intron|SLIT2_ENST00000503837.1_Intron|MIR218-1_ENST00000384999.1_RNA	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)						apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TGGAACGTCACGCAGCTTTCT	0.413																																																	0													144.0	123.0	129.0					4																	20529994		1568	3582	5150	SO:0001627	intron_variant	407000			AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1463-578C>T	4.37:g.20529994C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	RNA	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																				0.413	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			
MKI67	4288	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	129906122	129906122	+	Missense_Mutation	SNP	C	C	T	rs201476882		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr10:129906122C>T	ENST00000368654.3	-	13	4357	c.3982G>A	c.(3982-3984)Ggc>Agc	p.G1328S	MKI67_ENST00000368653.3_Missense_Mutation_p.G968S	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1328	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.G1328S(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTCTTGCTGCCGGTTAAGTTC	0.502													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18289	0.0		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)											177.0	177.0	177.0					10																	129906122		2203	4300	6503	SO:0001583	missense	4288			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.3982G>A	10.37:g.129906122C>T	ENSP00000357643:p.Gly1328Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.46	1.645411	0.29246	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.03065	4.06;4.06	4.23	2.34	0.29019	.	0.603419	0.13829	N	0.359869	T	0.07098	0.0180	L	0.54323	1.7	0.09310	N	1	D;D;B	0.71674	0.998;0.998;0.02	P;P;B	0.53649	0.731;0.731;0.027	T	0.25363	-1.0134	10	0.11794	T	0.64	.	8.4218	0.32705	0.0:0.7374:0.0:0.2626	.	1327;968;1328	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	S	1328;968;1327	ENSP00000357643:G1328S;ENSP00000357642:G968S	ENSP00000357642:G968S	G	-	1	0	MKI67	129796112	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.139000	0.10358	0.341000	0.23771	0.561000	0.74099	GGC		0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1		NM_002417	
MUC16	94025	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	9000513	9000513	+	Missense_Mutation	SNP	G	G	C	rs541610415	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:9000513G>C	ENST00000397910.4	-	54	40674	c.40471C>G	c.(40471-40473)Cgg>Ggg	p.R13491G	MUC16_ENST00000380951.5_Missense_Mutation_p.R132G	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13493	SEA 10. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.R13491G(1)|p.R176G(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TCCTCATACCGCAGGTTAGTG	0.473																																																	2	Substitution - Missense(2)	kidney(2)											185.0	155.0	164.0					19																	9000513		1960	4141	6101	SO:0001583	missense	94025			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.40471C>G	19.37:g.9000513G>C	ENSP00000381008:p.Arg13491Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	7.085|7.085	0.571076|0.571076	0.13623|0.13623	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.28666	.|1.6;1.6	2.9|2.9	-3.02|-3.02	0.05446|0.05446	.|SEA (3);	.|.	.|.	.|.	.|.	T|T	0.27098|0.27098	0.0664|0.0664	N|N	0.22421|0.22421	0.69|0.69	.|.	.|.	.|.	.|B;D	.|0.60575	.|0.0;0.988	.|B;D	.|0.74674	.|0.001;0.984	T|T	0.28808|0.28808	-1.0032|-1.0032	4|8	.|0.17369	.|T	.|0.5	0.5079|0.5079	0.6463|0.6463	0.00819|0.00819	0.2477:0.1863:0.3758:0.1902|0.2477:0.1863:0.3758:0.1902	.|.	.|21136;13491	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	W|G	330|13491;132	.|ENSP00000381008:R13491G;ENSP00000370338:R132G	.|ENSP00000370338:R132G	C|R	-|-	3|1	2|2	MUC16|MUC16	8861513|8861513	0.004000|0.004000	0.15560|0.15560	0.001000|0.001000	0.08648|0.08648	0.001000|0.001000	0.01503|0.01503	-0.202000|-0.202000	0.09451|0.09451	-0.609000|-0.609000	0.05724|0.05724	-0.727000|-0.727000	0.03589|0.03589	TGC|CGG		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1		NM_024690	
MUC4	4585	hgsc.bcm.edu	37	3	195506281	195506282	+	Missense_Mutation	DNP	AA	AA	GC	rs199896027|rs201679145	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:195506281_195506282AA>GC	ENST00000463781.3	-	2	12628_12629	c.12169_12170TT>GC	c.(12169-12171)TTa>GCa	p.L4057A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L4057A|MUC4_ENST00000346145.4_Intron	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)			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)		ACCTGTGGATAATGAGGAAGCA	0.574																																																	0																																										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.12169_12170delinsGC	3.37:g.195506281_195506282delinsGC	ENSP00000417498:p.Leu4057Ala	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																				0.574	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYH2	4620	broad.mit.edu;hgsc.bcm.edu	37	17	10429940	10429940	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:10429940C>T	ENST00000245503.5	-	30	4547	c.4163G>A	c.(4162-4164)cGc>cAc	p.R1388H	MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.R1388H	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1388					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|plasma membrane repair (GO:0001778)|response to activity (GO:0014823)	A band (GO:0031672)|actomyosin contractile ring (GO:0005826)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|protein complex (GO:0043234)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)	p.R1388H(2)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(99)|ovary(6)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(4)	176						CTCCTCTGTGCGCTGGATGGC	0.512																																																	2	Substitution - Missense(2)	ovary(1)|kidney(1)											175.0	162.0	166.0					17																	10429940		2203	4300	6503	SO:0001583	missense	4620				CCDS11156.1	17p13.1	2014-02-04	2006-09-29		ENSG00000125414	ENSG00000125414		"""Myosins / Myosin superfamily : Class II"""	7572	protein-coding gene	gene with protein product		160740	"""myosin, heavy polypeptide 2, skeletal muscle, adult"", ""inclusion body myopathy 3, autosomal dominant"""	IBM3		7545970, 11889243	Standard	NM_001100112		Approved	MYH2A, MYHSA2, MyHC-IIa, MYHas8, MyHC-2A	uc010coi.3	Q9UKX2	OTTHUMG00000130363	ENST00000245503.5:c.4163G>A	17.37:g.10429940C>T	ENSP00000245503:p.Arg1388His	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	35	5.504663	0.96371	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	T;T	0.80480	-1.38;-1.38	5.2	5.2	0.72013	Myosin tail (1);	0.000000	0.40144	U	0.001162	D	0.91402	0.7287	M	0.89030	3	0.58432	D	0.999997	D	0.89917	1.0	D	0.74023	0.982	D	0.92664	0.6144	10	0.87932	D	0	.	18.9148	0.92501	0.0:1.0:0.0:0.0	.	1388	Q9UKX2	MYH2_HUMAN	H	1388	ENSP00000245503:R1388H;ENSP00000380367:R1388H	ENSP00000245503:R1388H	R	-	2	0	MYH2	10370665	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.651000	0.83577	2.703000	0.92315	0.655000	0.94253	CGC		0.512	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3		NM_017534	
NFATC3	4775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	68160480	68160480	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr16:68160480delA	ENST00000346183.3	+	3	1392	c.1368delA	c.(1366-1368)gtafs	p.V456fs	NFATC3_ENST00000329524.4_Frame_Shift_Del_p.V456fs|NFATC3_ENST00000349223.5_Frame_Shift_Del_p.V456fs|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Frame_Shift_Del_p.V456fs	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	456	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GAGGGGCAGTAAAAGCATCTA	0.423																																																	0													90.0	84.0	86.0					16																	68160480		2198	4300	6498	SO:0001589	frameshift_variant	4775			L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1368delA	16.37:g.68160480delA	ENSP00000300659:p.Val456fs	Somatic		WXS	Illumina HiSeq	Phase_I	O75211|Q14516|Q99840|Q99841|Q99842	Frame_Shift_Del	DEL	ENST00000346183.3	37	CCDS10860.1																																																																																				0.423	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2		NM_004555	
NPAT	4863	hgsc.bcm.edu;ucsc.edu	37	11	108056204	108056205	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr11:108056204_108056205insT	ENST00000278612.8	-	9	848_849	c.743_744insA	c.(742-744)aatfs	p.N248fs	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	248	Interaction with MIZF.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		TTTCTCGTGCATTTTCAATAAC	0.282																																																	0																																										SO:0001589	frameshift_variant	4863			X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.744dupA	11.37:g.108056208_108056208dupT	ENSP00000278612:p.Asn248fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Frame_Shift_Ins	INS	ENST00000278612.8	37	CCDS41710.1																																																																																				0.282	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2		NM_002519	
TENM3	55714	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	183714853	183714853	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr4:183714853A>G	ENST00000511685.1	+	26	7151	c.7028A>G	c.(7027-7029)tAt>tGt	p.Y2343C	TENM3_ENST00000406950.2_Missense_Mutation_p.Y2343C			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2343					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.Y2343C(1)									GGTGGCCTGTATGACCCACTC	0.403																																																	1	Substitution - Missense(1)	kidney(1)											126.0	124.0	125.0					4																	183714853		1867	4094	5961	SO:0001583	missense	0			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7028A>G	4.37:g.183714853A>G	ENSP00000424226:p.Tyr2343Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.231330	0.58777	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.88046	-2.33;-2.33	5.17	5.17	0.71159	Rhs repeat-associated core (1);	.	.	.	.	D	0.93752	0.8003	M	0.84433	2.695	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.94642	0.7831	9	0.72032	D	0.01	.	15.1922	0.73053	1.0:0.0:0.0:0.0	.	2343	Q9P273	TEN3_HUMAN	C	2343	ENSP00000424226:Y2343C;ENSP00000385276:Y2343C	ENSP00000385276:Y2343C	Y	+	2	0	ODZ3	183951847	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.107000	0.94261	2.168000	0.68352	0.533000	0.62120	TAT		0.403	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			
OR5AR1	219493	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	56431824	56431824	+	Silent	SNP	C	C	A	rs144241394		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr11:56431824C>A	ENST00000302969.2	+	1	687	c.663C>A	c.(661-663)atC>atA	p.I221I		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I221I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						ATACCTTTATCCTTGTTGCAA	0.483																																																	1	Substitution - coding silent(1)	kidney(1)											163.0	139.0	147.0					11																	56431824		2201	4296	6497	SO:0001819	synonymous_variant	219493			AB065740	CCDS31535.1	11q11	2013-10-10	2013-10-10		ENSG00000172459	ENSG00000172459		"""GPCR / Class A : Olfactory receptors"""	15260	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AR, member 1"""				Standard	NM_001004730		Approved		uc010rjm.2	Q8NGP9	OTTHUMG00000154213	ENST00000302969.2:c.663C>A	11.37:g.56431824C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6IF61	Silent	SNP	ENST00000302969.2	37	CCDS31535.1																																																																																				0.483	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1		NM_001004730	
PBRM1	55193	hgsc.bcm.edu	37	3	52678784	52678784	+	Frame_Shift_Del	DEL	T	T	-	rs369874660		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:52678784delT	ENST00000296302.7	-	8	836	c.835delA	c.(835-837)atafs	p.I279fs	PBRM1_ENST00000409114.3_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.I279fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.I279fs			Q86U86	PB1_HUMAN	polybromo 1	279					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.I279fs*4(7)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		atataaaatatttttttaatt	0.358			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	7	Deletion - Frameshift(7)	kidney(7)											41.0	41.0	41.0					3																	52678784		2200	4299	6499	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.835delA	3.37:g.52678784delT	ENSP00000296302:p.Ile279fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.358	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCYOX1	51449	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	70502693	70502693	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:70502693G>T	ENST00000433351.2	+	5	782	c.754G>T	c.(754-756)Ggt>Tgt	p.G252C	PCYOX1_ENST00000545138.1_Missense_Mutation_p.G174C|PCYOX1_ENST00000264441.5_Missense_Mutation_p.G252C|PCYOX1_ENST00000505044.2_Missense_Mutation_p.G175C	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	252					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)	p.G252C(1)		breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						GGCAGTAGAAGGTGGCAATAA	0.433																																																	1	Substitution - Missense(1)	kidney(1)											127.0	112.0	117.0					2																	70502693		2203	4300	6503	SO:0001583	missense	51449			AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.754G>T	2.37:g.70502693G>T	ENSP00000387654:p.Gly252Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Missense_Mutation	SNP	ENST00000433351.2	37	CCDS1902.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.890593	0.91889	.	.	ENSG00000116005	ENST00000505044;ENST00000414812;ENST00000433351;ENST00000264441;ENST00000545138	T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01	5.43	5.43	0.79202	Prenylcysteine lyase (1);	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.77579	-0.2535	10	0.87932	D	0	-16.2952	17.9695	0.89108	0.0:0.0:1.0:0.0	.	234;252	B7Z8A2;Q9UHG3	.;PCYOX_HUMAN	C	175;175;252;252;174	ENSP00000441566:G175C;ENSP00000413178:G175C;ENSP00000387654:G252C;ENSP00000264441:G252C;ENSP00000439916:G174C	ENSP00000264441:G252C	G	+	1	0	PCYOX1	70356197	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.174000	0.94824	2.824000	0.97209	0.655000	0.94253	GGT		0.433	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3		NM_016297	
PGAP1	80055	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	197777686	197777686	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:197777686T>G	ENST00000354764.4	-	4	683	c.569A>C	c.(568-570)aAg>aCg	p.K190T	PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409475.1_Missense_Mutation_p.K190T|PGAP1_ENST00000409188.1_Missense_Mutation_p.K148T	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	190					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)	p.K190T(1)		breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						CAGATCATGCTTAAAATTTTT	0.378																																																	1	Substitution - Missense(1)	kidney(1)											107.0	103.0	104.0					2																	197777686		2203	4300	6503	SO:0001583	missense	80055				CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.569A>C	2.37:g.197777686T>G	ENSP00000346809:p.Lys190Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	T	18.35	3.603880	0.66445	.	.	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.85773	-2.03;-2.03;-2.03	5.25	4.07	0.47477	.	0.100034	0.64402	D	0.000002	T	0.76227	0.3958	N	0.17474	0.49	0.36810	D	0.885832	P;D;B	0.56035	0.837;0.974;0.103	P;P;B	0.48189	0.551;0.57;0.062	T	0.74166	-0.3753	10	0.10902	T	0.67	-15.116	12.4003	0.55410	0.0:0.0:0.1407:0.8593	.	148;190;190	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	T	190;190;148	ENSP00000346809:K190T;ENSP00000387028:K190T;ENSP00000386802:K148T	ENSP00000346809:K190T	K	-	2	0	PGAP1	197485931	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.352000	0.66028	0.999000	0.39023	0.529000	0.55759	AAG		0.378	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5		NM_024989	
PIM3	415116	hgsc.bcm.edu;ucsc.edu	37	22	50356427	50356428	+	Frame_Shift_Ins	INS	-	-	C	rs139618660		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr22:50356427_50356428insC	ENST00000360612.4	+	5	1142_1143	c.707_708insC	c.(706-711)tacgatfs	p.D237fs		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	237	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		GTGCTTCTCTACGATATGGTGT	0.668																																																	0																																										SO:0001589	frameshift_variant	415116			BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.708dupC	22.37:g.50356428_50356428dupC	ENSP00000353824:p.Asp237fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Frame_Shift_Ins	INS	ENST00000360612.4	37	CCDS33678.1																																																																																				0.668	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1		NM_001001852	
PKD1L3	342372	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	71967417	71967417	+	RNA	SNP	A	A	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr16:71967417A>G	ENST00000534738.1	-	0	4827				RP11-498D10.6_ENST00000573861.1_RNA			Q7Z443	PK1L3_HUMAN	polycystic kidney disease 1-like 3						cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|neuropeptide signaling pathway (GO:0007218)|sensory perception of sour taste (GO:0050915)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)	p.L1609P(1)		autonomic_ganglia(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|lung(3)|skin(2)	22						TCCAAACAGCAGGTTAAACTG	0.483																																																	1	Substitution - Missense(1)	kidney(1)											71.0	59.0	63.0					16																	71967417		692	1591	2283			342372			AY164485	CCDS73912.1	16q22.2	2008-02-05				ENSG00000277481			21716	protein-coding gene	gene with protein product		607895				12782129	Standard	NM_181536		Approved		uc010vmm.2	Q7Z443			16.37:g.71967417A>G		Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000534738.1	37																																																																																					0.483	PKD1L3-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000387876.1		NM_181536	
PLIN4	729359	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	4510945	4510945	+	Missense_Mutation	SNP	T	T	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:4510945T>A	ENST00000301286.3	-	3	2984	c.2985A>T	c.(2983-2985)aaA>aaT	p.K995N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	995						cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.K995N(1)|p.K923N(1)		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						GGACGGCCCCTTTGGCCATGC	0.627																																																	2	Substitution - Missense(2)	kidney(2)											47.0	50.0	49.0					19																	4510945		1994	4157	6151	SO:0001583	missense	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.2985A>T	19.37:g.4510945T>A	ENSP00000301286:p.Lys995Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.003617	0.35320	.	.	ENSG00000167676	ENST00000301286	T	0.06449	3.3	4.9	-0.109	0.13584	.	0.155567	0.29572	N	0.011780	T	0.13884	0.0336	L	0.59436	1.845	0.27177	N	0.96077	D	0.62365	0.991	P	0.61477	0.889	T	0.03933	-1.0991	10	0.54805	T	0.06	-0.3272	7.8921	0.29684	0.0:0.3545:0.0:0.6455	.	995	Q96Q06	PLIN4_HUMAN	N	995	ENSP00000301286:K995N	ENSP00000301286:K995N	K	-	3	2	PLIN4	4461945	0.000000	0.05858	0.373000	0.26003	0.039000	0.13416	-1.363000	0.02592	-0.365000	0.08076	0.418000	0.28097	AAA		0.627	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1		XM_170901	
PLXNA4	91584	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	131866156	131866156	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr7:131866156G>A	ENST00000359827.3	-	18	4438	c.3476C>T	c.(3475-3477)aCg>aTg	p.T1159M	PLXNA4_ENST00000321063.4_Missense_Mutation_p.T1159M			Q9HCM2	PLXA4_HUMAN	plexin A4	1159	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.T1159M(2)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						GATGATGGGCGTGCCAGGCTT	0.582																																																	2	Substitution - Missense(2)	kidney(2)											158.0	165.0	162.0					7																	131866156		1952	4140	6092	SO:0001583	missense	91584			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3476C>T	7.37:g.131866156G>A	ENSP00000352882:p.Thr1159Met	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053605	0.75960	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.65732	-0.17;-0.17	5.1	5.1	0.69264	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	2.295700	0.01679	N	0.026049	T	0.70413	0.3221	L	0.36672	1.1	0.47994	D	0.999563	D	0.56521	0.976	P	0.52793	0.709	T	0.56950	-0.7894	10	0.62326	D	0.03	.	15.1678	0.72842	0.0:0.1515:0.8485:0.0	.	1159	Q9HCM2	PLXA4_HUMAN	M	1159	ENSP00000323194:T1159M;ENSP00000352882:T1159M	ENSP00000323194:T1159M	T	-	2	0	PLXNA4	131516696	1.000000	0.71417	0.938000	0.37757	0.978000	0.69477	6.290000	0.72712	2.381000	0.81170	0.561000	0.74099	ACG		0.582	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2		NM_181775	
PMEPA1	56937	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	56227136	56227136	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr20:56227136C>G	ENST00000341744.3	-	4	1156	c.837G>C	c.(835-837)aaG>aaC	p.K279N	PMEPA1_ENST00000265626.4_Missense_Mutation_p.K229N|PMEPA1_ENST00000347215.4_Missense_Mutation_p.K244N|PMEPA1_ENST00000395814.1_Missense_Mutation_p.K229N|PMEPA1_ENST00000395816.3_Missense_Mutation_p.K229N	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	279					androgen receptor signaling pathway (GO:0030521)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	R-SMAD binding (GO:0070412)|WW domain binding (GO:0050699)	p.K279N(1)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|prostate(1)	16						TCTGTTTATCCTTCTCTTTGC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											27.0	31.0	29.0					20																	56227136		2195	4287	6482	SO:0001583	missense	56937			AF224278	CCDS13462.1, CCDS13463.1, CCDS13464.1	20q13.31-q13.33	2008-04-03	2008-04-03	2008-04-03	ENSG00000124225	ENSG00000124225			14107	protein-coding gene	gene with protein product	"""solid tumor-associated 1"""	606564	"""transmembrane, prostate androgen induced RNA"""	TMEPAI		10873380	Standard	NM_020182		Approved	STAG1	uc002xyq.4	Q969W9	OTTHUMG00000032831	ENST00000341744.3:c.837G>C	20.37:g.56227136C>G	ENSP00000345826:p.Lys279Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Missense_Mutation	SNP	ENST00000341744.3	37	CCDS13463.1	.	.	.	.	.	.	.	.	.	.	C	12.82	2.051447	0.36181	.	.	ENSG00000124225	ENST00000341744;ENST00000347215;ENST00000395816;ENST00000265626;ENST00000395814	T;T;T;T;T	0.53423	0.62;0.64;0.65;0.65;0.65	5.17	2.99	0.34606	.	0.074774	0.53938	D	0.000042	T	0.61527	0.2354	M	0.73962	2.25	0.46298	D	0.998975	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.62487	-0.6844	10	0.87932	D	0	-28.3745	4.2191	0.10549	0.0:0.4971:0.0:0.5029	.	244;279	Q5JY37;Q969W9	.;PMEPA_HUMAN	N	279;244;229;229;229	ENSP00000345826:K279N;ENSP00000344014:K244N;ENSP00000379161:K229N;ENSP00000265626:K229N;ENSP00000379159:K229N	ENSP00000265626:K229N	K	-	3	2	PMEPA1	55660542	1.000000	0.71417	0.979000	0.43373	0.039000	0.13416	1.756000	0.38390	1.168000	0.42723	-0.157000	0.13467	AAG		0.622	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2		NM_020182	
PRAME	23532	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	22893221	22893221	+	Silent	SNP	A	A	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr22:22893221A>C	ENST00000398741.1	-	4	618	c.312T>G	c.(310-312)ctT>ctG	p.L104L	PRAME_ENST00000405655.3_Silent_p.L104L|PRAME_ENST00000406503.1_Silent_p.L104L|PRAME_ENST00000539862.1_Silent_p.L88L|PRAME_ENST00000424204.2_Silent_p.L88L|PRAME_ENST00000485532.1_5'UTR|PRAME_ENST00000398743.2_Silent_p.L104L|PRAME_ENST00000543184.1_Silent_p.L104L|PRAME_ENST00000402697.1_Silent_p.L104L	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	104					apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|regulation of growth (GO:0040008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|plasma membrane (GO:0005886)	retinoic acid receptor binding (GO:0042974)	p.L104L(1)		autonomic_ganglia(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)|all_lung(157;4.03e-05)		READ - Rectum adenocarcinoma(21;0.0649)		GGAGCACATCAAGTCCATCAA	0.597																																					Melanoma(73;1707 1838 15168 27201)												1	Substitution - coding silent(1)	kidney(1)											138.0	113.0	121.0					22																	22893221		2203	4300	6503	SO:0001819	synonymous_variant	23532			U65011	CCDS13801.1	22q11.22	2013-01-17			ENSG00000185686	ENSG00000185686		"""-"""	9336	protein-coding gene	gene with protein product	"""cancer/testis antigen 130"""	606021		MAPE		9047241, 10591208	Standard	XM_006725402		Approved	CT130	uc002zwj.3	P78395	OTTHUMG00000151172	ENST00000398741.1:c.312T>G	22.37:g.22893221A>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2R6Y7|O43481|Q8IXN8	Silent	SNP	ENST00000398741.1	37	CCDS13801.1	.	.	.	.	.	.	.	.	.	.	a	0.178	-1.064809	0.01934	.	.	ENSG00000185686	ENST00000438888	.	.	.	3.46	-6.92	0.01644	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999966	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9186	0.41450	0.5203:0.3773:0.1024:0.0	.	.	.	.	G	128	.	.	X	-	1	0	PRAME	21223221	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.792000	0.00766	-3.481000	0.00155	-1.046000	0.02355	TGA		0.597	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1		NM_206953	
PRUNE2	158471	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	79325303	79325303	+	Silent	SNP	G	G	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr9:79325303G>T	ENST00000376718.3	-	8	2010	c.1887C>A	c.(1885-1887)ctC>ctA	p.L629L	PRUNE2_ENST00000428286.1_Silent_p.L270L	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	629					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.L629L(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTTCTGTATAGAGTGAGGCTG	0.493																																																	1	Substitution - coding silent(1)	kidney(1)											111.0	100.0	103.0					9																	79325303		1568	3582	5150	SO:0001819	synonymous_variant	158471			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.1887C>A	9.37:g.79325303G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1																																																																																				0.493	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2		NM_138818	
PTPRZ1	5803	broad.mit.edu;hgsc.bcm.edu	37	7	121637955	121637955	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr7:121637955C>G	ENST00000393386.2	+	10	1546	c.1135C>G	c.(1135-1137)Cta>Gta	p.L379V	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.L379V	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	379	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.L379V(2)		NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CAATAATTTGCTACCCAATAT	0.348																																																	2	Substitution - Missense(2)	kidney(2)											77.0	74.0	75.0					7																	121637955		2203	4300	6503	SO:0001583	missense	5803			M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.1135C>G	7.37:g.121637955C>G	ENSP00000377047:p.Leu379Val	Somatic		WXS	Illumina HiSeq	Phase_I	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	C	9.251	1.040858	0.19669	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.57107	0.42;0.42	5.51	3.68	0.42216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.380794	0.22351	N	0.061204	T	0.34019	0.0883	N	0.12182	0.205	0.27806	N	0.942324	B;P	0.38110	0.013;0.618	B;B	0.42138	0.016;0.377	T	0.14392	-1.0474	10	0.41790	T	0.15	.	5.124	0.14875	0.2669:0.5345:0.129:0.0695	.	379;379	C9JFM0;P23471	.;PTPRZ_HUMAN	V	379	ENSP00000377047:L379V;ENSP00000410000:L379V	ENSP00000377047:L379V	L	+	1	2	PTPRZ1	121425191	0.931000	0.31567	0.999000	0.59377	0.982000	0.71751	0.052000	0.14163	0.663000	0.31027	0.585000	0.79938	CTA		0.348	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1		NM_002851	
RGS7	6000	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	240969479	240969479	+	Silent	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:240969479G>A	ENST00000407727.1	-	14	1229	c.1230C>T	c.(1228-1230)aaC>aaT	p.N410N	RGS7_ENST00000348120.2_Silent_p.N357N|RGS7_ENST00000446183.2_Silent_p.N326N|RGS7_ENST00000366563.1_Silent_p.N410N|RGS7_ENST00000366562.4_Silent_p.N410N|RGS7_ENST00000366564.1_Silent_p.N410N|RGS7_ENST00000331110.7_Silent_p.N384N|RGS7_ENST00000366565.1_Silent_p.N410N|RGS7_ENST00000401882.1_Silent_p.N357N			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	410	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite terminus (GO:0044292)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta-subunit binding (GO:0031681)|GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)	p.N410N(2)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(51)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	76		all_cancers(173;0.0131)	OV - Ovarian serous cystadenocarcinoma(106;0.027)			GTTCCTTCACGTTCTGTGTGG	0.483																																																	2	Substitution - coding silent(2)	kidney(2)											206.0	175.0	185.0					1																	240969479		2203	4300	6503	SO:0001819	synonymous_variant	6000			BC022009	CCDS31071.1, CCDS60457.1, CCDS60458.1, CCDS60459.1	1q43	2008-02-05	2007-08-14		ENSG00000182901	ENSG00000182901		"""Regulators of G-protein signaling"""	10003	protein-coding gene	gene with protein product		602517	"""regulator of G-protein signalling 7"""			8548815	Standard	XM_005273218		Approved		uc001hyv.2	P49802	OTTHUMG00000040107	ENST00000407727.1:c.1230C>T	1.37:g.240969479G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Silent	SNP	ENST00000407727.1	37																																																																																					0.483	RGS7-204	KNOWN	basic	protein_coding	protein_coding			NM_002924	
RMND5A	64795	broad.mit.edu;hgsc.bcm.edu	37	2	86980658	86980658	+	Silent	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:86980658C>T	ENST00000283632.4	+	4	993	c.498C>T	c.(496-498)gtC>gtT	p.V166V		NM_022780.3	NP_073617.1	Q9H871	RMD5A_HUMAN	required for meiotic nuclear division 5 homolog A (S. cerevisiae)	166	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.							p.V166V(1)		kidney(1)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	17						CATTAAAGGTCAGAGTTCTGA	0.373																																																	1	Substitution - coding silent(1)	kidney(1)											129.0	128.0	128.0					2																	86980658		2203	4300	6503	SO:0001819	synonymous_variant	64795			BC012165	CCDS1991.1	2p11.2	2012-07-20			ENSG00000153561	ENSG00000153561			25850	protein-coding gene	gene with protein product	"""GID complex subunit 2 homolog A"""					12477932	Standard	NM_022780		Approved	FLJ13910, RMD5, GID2, GID2A	uc002srs.4	Q9H871	OTTHUMG00000130262	ENST00000283632.4:c.498C>T	2.37:g.86980658C>T		Somatic		WXS	Illumina HiSeq	Phase_I	D6W5M6|Q6NTF0|Q9H6W5|Q9H9H2	Silent	SNP	ENST00000283632.4	37	CCDS1991.1																																																																																				0.373	RMND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252591.2		NM_022780	
RP1	6101	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	55540593	55540593	+	Missense_Mutation	SNP	T	T	G	rs557457666		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr8:55540593T>G	ENST00000220676.1	+	4	4299	c.4151T>G	c.(4150-4152)tTt>tGt	p.F1384C		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1384					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)	p.F1384C(1)		NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			AAAAATGGATTTAATACATTG	0.328																																					Colon(91;1014 1389 7634 14542 40420)												1	Substitution - Missense(1)	kidney(1)											52.0	57.0	56.0					8																	55540593		2201	4300	6501	SO:0001583	missense	6101			AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.4151T>G	8.37:g.55540593T>G	ENSP00000220676:p.Phe1384Cys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	T	2.901	-0.227558	0.06022	.	.	ENSG00000104237	ENST00000220676	T	0.21191	2.02	5.52	-1.12	0.09808	.	1.641830	0.03423	N	0.206583	T	0.15435	0.0372	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.35574	-0.9783	10	0.72032	D	0.01	.	6.4223	0.21750	0.0:0.3907:0.2626:0.3468	.	1384	P56715	RP1_HUMAN	C	1384	ENSP00000220676:F1384C	ENSP00000220676:F1384C	F	+	2	0	RP1	55703146	0.000000	0.05858	0.001000	0.08648	0.315000	0.28087	-0.195000	0.09546	-0.440000	0.07211	-0.274000	0.10170	TTT		0.328	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2		NM_006269	
SI	6476	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	164754179	164754179	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:164754179T>G	ENST00000264382.3	-	22	2575	c.2513A>C	c.(2512-2514)aAa>aCa	p.K838T		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	838	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)	p.K838T(1)		NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	AGACTTACCTTTAGTTTCTCC	0.338										HNSCC(35;0.089)																																							1	Substitution - Missense(1)	kidney(1)											110.0	113.0	112.0					3																	164754179		2203	4299	6502	SO:0001583	missense	6476			X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2513A>C	3.37:g.164754179T>G	ENSP00000264382:p.Lys838Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	8.726	0.915438	0.17907	.	.	ENSG00000090402	ENST00000264382	D	0.88509	-2.39	4.52	-6.69	0.01772	.	0.237557	0.43110	N	0.000608	T	0.78020	0.4218	L	0.55103	1.725	0.21802	N	0.999537	B	0.09022	0.002	B	0.09377	0.004	T	0.62282	-0.6887	10	0.23302	T	0.38	.	3.6385	0.08158	0.3167:0.071:0.4303:0.182	.	838	P14410	SUIS_HUMAN	T	838	ENSP00000264382:K838T	ENSP00000264382:K838T	K	-	2	0	SI	166236873	0.143000	0.22626	0.044000	0.18714	0.837000	0.47467	-0.144000	0.10280	-1.239000	0.02532	-0.321000	0.08615	AAA		0.338	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1		NM_001041	
SIRPB1	10326	broad.mit.edu;hgsc.bcm.edu	37	20	1552666	1552666	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr20:1552666C>T	ENST00000381605.4	-	3	515	c.451G>A	c.(451-453)Gtg>Atg	p.V151M	RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	151	Ig-like C1-type 1.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V151M(1)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						CCCGATACCACGGGGGCAGAG	0.527																																																	1	Substitution - Missense(1)	kidney(1)											84.0	80.0	81.0					20																	1552666		2203	4300	6503	SO:0001583	missense	10326			Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.451G>A	20.37:g.1552666C>T	ENSP00000371018:p.Val151Met	Somatic		WXS	Illumina HiSeq	Phase_I	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	5.492	0.275773	0.10403	.	.	ENSG00000101307	ENST00000381605	T	0.00642	6.02	2.51	-2.16	0.07080	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.579431	0.15277	N	0.270921	T	0.00356	0.0011	N	0.25201	0.72	0.09310	N	1	P	0.43542	0.81	B	0.24974	0.057	T	0.52238	-0.8602	10	0.36615	T	0.2	.	2.5645	0.04779	0.2266:0.3141:0.0:0.4592	.	151	O00241	SIRB1_HUMAN	M	151	ENSP00000371018:V151M	ENSP00000371018:V151M	V	-	1	0	SIRPB1	1500666	0.000000	0.05858	0.005000	0.12908	0.025000	0.11179	-3.630000	0.00409	-0.355000	0.08199	0.462000	0.41574	GTG		0.527	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2		NM_006065	
SIRT1	23411	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	69651246	69651247	+	Missense_Mutation	DNP	TC	TC	AT			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr10:69651246_69651247TC>AT	ENST00000212015.6	+	4	929_930	c.876_877TC>AT	c.(874-879)gaTCct>gaATct	p.292_293DP>ES	SIRT1_ENST00000406900.1_5'UTR|SIRT1_ENST00000497639.1_3'UTR|SIRT1_ENST00000432464.1_5'UTR	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	292	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.|Interaction with CCAR2.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.P293S(1)|p.D292E(1)		central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						ATCTTCCAGATCCTCAAGCGAT	0.406																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	23411			AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	Exception_encountered	10.37:g.69651246_69651247delinsAT	ENSP00000212015:p.D292_P293delinsES	Somatic		WXS	Illumina HiSeq	Phase_I	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1																																																																																				0.406	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			
SPAG17	200162	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	118584465	118584465	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:118584465delT	ENST00000336338.5	-	21	3080	c.3015delA	c.(3013-3015)gaafs	p.E1006fs		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1006						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		GGGGGGACTCTTCTGTTACTT	0.383																																																	0													331.0	329.0	330.0					1																	118584465		2203	4300	6503	SO:0001589	frameshift_variant	200162				CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.3015delA	1.37:g.118584465delT	ENSP00000337804:p.Glu1006fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NAZ1|Q9NT21	Frame_Shift_Del	DEL	ENST00000336338.5	37	CCDS899.1																																																																																				0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1		NM_206996	
SREK1	140890	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	65455077	65455077	+	5'UTR	SNP	C	C	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:65455077C>G	ENST00000380918.3	+	0	638				SREK1_ENST00000334121.6_Missense_Mutation_p.S109C|SREK1_ENST00000284041.3_3'UTR	NM_139168.3	NP_631907.1	Q8WXA9	SREK1_HUMAN	splicing regulatory glutamine/lysine-rich protein 1						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S109C(1)		breast(1)|kidney(3)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)	9						AAAGCCCTCTCTTTATTGGCT	0.428																																					GBM(10;31 347 27684 38976 41583)												1	Substitution - Missense(1)	kidney(1)											82.0	85.0	84.0					5																	65455077		2203	4300	6503	SO:0001623	5_prime_UTR_variant	140890			AF459094	CCDS3991.1, CCDS43323.1, CCDS75253.1	5q11.2-q12.1	2013-02-12	2010-09-08	2010-09-08	ENSG00000153914	ENSG00000153914		"""RNA binding motif (RRM) containing"""	17882	protein-coding gene	gene with protein product	"""serine-arginine-rich splicing regulatory protein 508"""	609268	"""splicing factor, arginine/serine-rich 12"""	SFRS12		12043562	Standard	NM_001077199		Approved	DKFZp564B176, SRrp86, SRrp508	uc003jun.4	Q8WXA9	OTTHUMG00000097809	ENST00000380918.3:c.-23C>G	5.37:g.65455077C>G		Somatic		WXS	Illumina HiSeq	Phase_I	A4FTW3|Q2M1J0|Q86X37	Missense_Mutation	SNP	ENST00000380918.3	37	CCDS3991.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812963	0.50527	.	.	ENSG00000153914	ENST00000334121;ENST00000537482	T	0.50277	0.75	5.73	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	L	0.60455	1.87	0.80722	D	1	D	0.69078	0.997	P	0.58873	0.847	T	0.64685	-0.6349	10	0.66056	D	0.02	.	14.7007	0.69154	0.0:0.9303:0.0:0.0697	.	109	Q8WXA9-2	.	C	109	ENSP00000334538:S109C	ENSP00000334538:S109C	S	+	2	0	SREK1	65490833	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	7.818000	0.86416	1.421000	0.47157	-0.229000	0.12294	TCT		0.428	SREK1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381118.1		NM_001077199	
SUPT3H	8464	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	44921067	44921067	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr6:44921067G>C	ENST00000371459.1	-	9	946	c.781C>G	c.(781-783)Cag>Gag	p.Q261E	SUPT3H_ENST00000371461.2_Missense_Mutation_p.Q272E|SUPT3H_ENST00000371460.1_Missense_Mutation_p.Q272E|SUPT3H_ENST00000306867.5_Missense_Mutation_p.Q261E|SUPT3H_ENST00000371458.1_Missense_Mutation_p.Q44E	NM_001261823.1|NM_003599.3	NP_001248752.1|NP_003590.1	O75486	SUPT3_HUMAN	suppressor of Ty 3 homolog (S. cerevisiae)	343					chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	transcription coactivator activity (GO:0003713)	p.Q272E(1)|p.Q261E(1)		breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)	12						TTGTGATACTGAATGAAGGTT	0.393																																																	2	Substitution - Missense(2)	kidney(2)											100.0	95.0	97.0					6																	44921067		2203	4300	6503	SO:0001583	missense	8464			AF069734	CCDS34465.1, CCDS34466.1, CCDS75464.1	6p21.1-p12.3	2008-05-15	2001-11-28		ENSG00000196284	ENSG00000196284			11466	protein-coding gene	gene with protein product		602947	"""suppressor of Ty (S.cerevisiae) 3 homolog"""			9674425, 9726987	Standard	NM_003599		Approved	SPT3, SPT3L	uc003oxp.4	O75486	OTTHUMG00000014773	ENST00000371459.1:c.781C>G	6.37:g.44921067G>C	ENSP00000360514:p.Gln261Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKG9|B2R9Q5|O76066|Q5TAV9|Q86VN7	Missense_Mutation	SNP	ENST00000371459.1	37	CCDS34465.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032438	0.54790	.	.	ENSG00000196284	ENST00000371460;ENST00000371459;ENST00000371458;ENST00000306867;ENST00000371461	T;T;T;T;T	0.42513	0.99;1.01;0.97;1.01;0.99	6.04	6.04	0.98038	.	0.178915	0.51477	D	0.000088	T	0.20981	0.0505	L	0.35414	1.06	0.51233	D	0.999914	P;D	0.54207	0.774;0.965	P;B	0.44946	0.465;0.322	T	0.06607	-1.0817	10	0.02654	T	1	.	18.7754	0.91910	0.0:0.0:1.0:0.0	.	272;343	O75486-3;O75486	.;SUPT3_HUMAN	E	272;261;44;261;272	ENSP00000360515:Q272E;ENSP00000360514:Q261E;ENSP00000360513:Q44E;ENSP00000306718:Q261E;ENSP00000360516:Q272E	ENSP00000306718:Q261E	Q	-	1	0	SUPT3H	45029045	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.409000	0.90223	2.873000	0.98535	0.563000	0.77884	CAG		0.393	SUPT3H-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106911.2		NM_181356	
SUPT5H	6829	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	39965287	39965287	+	Nonsense_Mutation	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:39965287C>T	ENST00000599117.1	+	29	3320	c.2953C>T	c.(2953-2955)Cag>Tag	p.Q985*	SUPT5H_ENST00000402194.2_Nonsense_Mutation_p.Q981*|SUPT5H_ENST00000598725.1_Nonsense_Mutation_p.Q985*|SUPT5H_ENST00000359191.6_Nonsense_Mutation_p.Q981*|SUPT5H_ENST00000432763.2_Nonsense_Mutation_p.Q985*			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	985					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.Q985*(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CACTGACATTCAGGTGAAGGT	0.612																																																	1	Substitution - Nonsense(1)	kidney(1)											71.0	58.0	62.0					19																	39965287		2203	4300	6503	SO:0001587	stop_gained	6829			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2953C>T	19.37:g.39965287C>T	ENSP00000470252:p.Gln985*	Somatic		WXS	Illumina HiSeq	Phase_I	O43279|Q59G52|Q99639	Nonsense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	C	41	8.701800	0.98920	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.45	4.45	0.53987	.	0.140552	0.49305	D	0.000146	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.6887	16.0174	0.80450	0.0:1.0:0.0:0.0	.	.	.	.	X	985;981;963;985	.	.	Q	+	1	0	SUPT5H	44657127	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.567000	0.53813	2.293000	0.77203	0.462000	0.41574	CAG		0.612	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1		NM_003169	
TAS2R39	259285	hgsc.bcm.edu;ucsc.edu	37	7	142881197	142881197	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr7:142881197delC	ENST00000446620.1	+	1	686	c.686delC	c.(685-687)accfs	p.T229fs		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	229					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					CTGACAGCCACCCTGCTGATC	0.502																																																	0													135.0	125.0	128.0					7																	142881197		1993	4155	6148	SO:0001589	frameshift_variant	259285			AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.686delC	7.37:g.142881197delC	ENSP00000405095:p.Thr229fs	Somatic		WXS	Illumina HiSeq	Phase_I	A4FUI7|Q3ZCN6|Q645W4	Frame_Shift_Del	DEL	ENST00000446620.1	37	CCDS47729.1																																																																																				0.502	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2		NM_176881	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244067	11244068	+	Frame_Shift_Ins	INS	-	-	TT	rs201300744	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr12:11244067_11244068insTT	ENST00000531678.1	-	1	844_845	c.761_762insAA	c.(760-762)agtfs	p.S254fs	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	254					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TGTTTTCCAGACTTCCAAAACT	0.396																																																	0																																										SO:0001589	frameshift_variant	259289			AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.761_762insAA	12.37:g.11244067_11244068insTT	ENSP00000431719:p.Ser254fs	Somatic		WXS	Illumina HiSeq	Phase_I	P59546|Q645X4	Frame_Shift_Ins	INS	ENST00000531678.1	37	CCDS53749.1																																																																																				0.396	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1		NM_176884	
TAS2R43	259289	hgsc.bcm.edu	37	12	11244071	11244072	+	Frame_Shift_Del	DEL	CC	CC	-	rs202114077|rs200981579	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr12:11244071_11244072delCC	ENST00000531678.1	-	1	840_841	c.757_758delGG	c.(757-759)ggafs	p.G253fs	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	253					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TTCCAGACTTCCAAAACTCCAA	0.401																																																	0										209,3737		84,41,1848						-5.1	0.0			127	837,6533		316,205,3164	no	frameshift	TAS2R43	NM_176884.2		400,246,5012	A1A1,A1R,RR		11.3569,5.2965,9.2435				1046,10270				SO:0001589	frameshift_variant	259289			AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.757_758delGG	12.37:g.11244071_11244072delCC	ENSP00000431719:p.Gly253fs	Somatic		WXS	Illumina HiSeq	Phase_I	P59546|Q645X4	Frame_Shift_Del	DEL	ENST00000531678.1	37	CCDS53749.1																																																																																				0.401	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1		NM_176884	
TCHH	7062	broad.mit.edu;ucsc.edu	37	1	152083904	152083904	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr1:152083904T>C	ENST00000368804.1	-	2	1788	c.1789A>G	c.(1789-1791)Agg>Ggg	p.R597G		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	597	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.R597G(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCTCGAGCCTCTCTTCCTGC	0.682																																																	1	Substitution - Missense(1)	kidney(1)											42.0	48.0	46.0					1																	152083904		1964	4133	6097	SO:0001583	missense	7062			L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1789A>G	1.37:g.152083904T>C	ENSP00000357794:p.Arg597Gly	Somatic		WXS	Illumina GAIIx	Phase_I	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	t	6.852	0.526490	0.13066	.	.	ENSG00000159450	ENST00000368804	T	0.05258	3.47	2.39	-4.77	0.03219	.	.	.	.	.	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	B	0.29212	0.237	B	0.28305	0.088	T	0.47548	-0.9109	9	0.23302	T	0.38	.	4.7817	0.13206	0.0:0.2627:0.3912:0.3461	.	597	Q07283	TRHY_HUMAN	G	597	ENSP00000357794:R597G	ENSP00000357794:R597G	R	-	1	2	TCHH	150350528	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-2.154000	0.01285	-0.609000	0.05724	0.157000	0.16456	AGG		0.682	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2		NM_007113	
TGFBI	7045	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	135382106	135382107	+	Silent	DNP	GC	GC	AT			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:135382106_135382107GC>AT	ENST00000442011.2	+	4	542_543	c.381_382GC>AT	c.(379-384)aaGCtg>aaATtg	p.127_128KL>KL	TGFBI_ENST00000305126.8_Silent_p.127_128KL>KL|TGFBI_ENST00000504185.1_3'UTR	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	127	FAS1 1. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)	p.L128L(1)|p.K127K(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			GCACGGAGAAGCTGAGGCCTGA	0.619																																																	2	Substitution - coding silent(2)	kidney(2)																																								SO:0001819	synonymous_variant	7045			M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	Exception_encountered	5.37:g.135382106_135382107delinsAT		Somatic		WXS	Illumina HiSeq	Phase_I	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Silent	SNP	ENST00000442011.2	37	CCDS47266.1																																																																																				0.619	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			
TLE3	7090	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	70351055	70351055	+	Missense_Mutation	SNP	A	A	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr15:70351055A>T	ENST00000558939.1	-	11	2242	c.865T>A	c.(865-867)Tcg>Acg	p.S289T	TLE3_ENST00000560939.1_Missense_Mutation_p.S294T|TLE3_ENST00000557907.1_Missense_Mutation_p.S289T|TLE3_ENST00000442299.2_Missense_Mutation_p.S289T|TLE3_ENST00000559048.1_Missense_Mutation_p.S294T|TLE3_ENST00000557997.1_Missense_Mutation_p.S289T|TLE3_ENST00000440567.3_Missense_Mutation_p.S282T|TLE3_ENST00000539550.1_Missense_Mutation_p.S233T|TLE3_ENST00000558379.1_Missense_Mutation_p.S289T|TLE3_ENST00000559191.1_Intron|TLE3_ENST00000560589.1_Missense_Mutation_p.S233T|TLE3_ENST00000558201.1_Missense_Mutation_p.S295T|TLE3_ENST00000559929.1_Missense_Mutation_p.S299T|TLE3_ENST00000317509.8_Missense_Mutation_p.S289T|TLE3_ENST00000451782.2_Missense_Mutation_p.S289T	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	289	Pro/Ser-rich.				Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S289T(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GAGGCCACCGAGGCAGGGCTG	0.632																																																	1	Substitution - Missense(1)	kidney(1)											28.0	31.0	30.0					15																	70351055		1926	4120	6046	SO:0001583	missense	7090			M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.865T>A	15.37:g.70351055A>T	ENSP00000452871:p.Ser289Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.982772	0.74474	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.55930	0.72;0.73;0.82;0.74;0.49	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.79693	2.465	0.80722	D	1	P;B;P;B;P;B;P;D	0.55800	0.904;0.083;0.69;0.047;0.552;0.117;0.57;0.973	P;B;B;B;B;B;P;P	0.57720	0.812;0.033;0.248;0.023;0.209;0.42;0.543;0.826	T	0.73372	-0.4003	10	0.51188	T	0.08	-1.8949	15.6681	0.77247	1.0:0.0:0.0:0.0	.	282;289;289;289;289;289;294;233	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	T	289;289;289;282;233	ENSP00000390007:S289T;ENSP00000394717:S289T;ENSP00000319233:S289T;ENSP00000415057:S282T;ENSP00000442594:S233T	ENSP00000319233:S289T	S	-	1	0	TLE3	68138109	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	9.028000	0.93712	2.288000	0.76882	0.533000	0.62120	TCG		0.632	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1		NM_005078	
TMC1	117531	hgsc.bcm.edu;ucsc.edu	37	9	75309453	75309471	+	Splice_Site	DEL	GTTTAGGTGAAGAGGAAGA	GTTTAGGTGAAGAGGAAGA	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	GTTTAGGTGAAGAGGAAGA	GTTTAGGTGAAGAGGAAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr9:75309453_75309471delGTTTAGGTGAAGAGGAAGA	ENST00000297784.5	+	7	604_617	c.64_77delGTTTAGGTGAAGAGGAAGA	c.(64-78)gtttaggtgaagagg>g	p.V*VKR22fs	TMC1_ENST00000340019.3_Splice_Site_p.V*VKR22fs|TMC1_ENST00000396237.3_Splice_Site_p.V*VKR22fs	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	22	Arg/Asp/Glu/Lys-rich (highly charged).				auditory receptor cell development (GO:0060117)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(21)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	36						CAAGTGCTATGTTTAGGTGAAGAGGAAGAGGAGGTGGAA	0.42																																					Pancreas(75;173 1345 14232 34245 43413)												0																																										SO:0001630	splice_region_variant	117531			AF417578	CCDS6643.1	9q21	2014-01-28			ENSG00000165091	ENSG00000165091			16513	protein-coding gene	gene with protein product		606706	"""transmembrane, cochlear expressed, 1"""	DFNA36, DFNB7, DFNB11		11850618, 11850623	Standard	NM_138691		Approved		uc004aiz.1	Q8TDI8	OTTHUMG00000020014	ENST00000297784.5:c.65-1GTTTAGGTGAAGAGGAAGA>-	9.37:g.75309453_75309471delGTTTAGGTGAAGAGGAAGA		Somatic		WXS	Illumina HiSeq	Phase_I	A8MVZ2|B1AM91	In_Frame_Del	DEL	ENST00000297784.5	37	CCDS6643.1																																																																																				0.420	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			Frame_Shift_Del
TOP1	7150	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	39741521	39741521	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr20:39741521A>G	ENST00000361337.2	+	14	1658	c.1408A>G	c.(1408-1410)Atg>Gtg	p.M470V	RP1-1J6.2_ENST00000454626.1_RNA	NM_003286.2	NP_003277.1	P11387	TOP1_HUMAN	topoisomerase (DNA) I	470					chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|DNA topological change (GO:0006265)|embryonic cleavage (GO:0040016)|phosphorylation (GO:0016310)|programmed cell death (GO:0012501)|response to drug (GO:0042493)|viral process (GO:0016032)	cytoplasmic mRNA processing body (GO:0000932)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|replication fork protection complex (GO:0031298)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|poly(A) RNA binding (GO:0044822)	p.M470V(1)		breast(5)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	37		Myeloproliferative disorder(115;0.00878)			Irinotecan(DB00762)|Lucanthone(DB04967)|Sodium stibogluconate(DB05630)|Topotecan(DB01030)	GTCCAAAGAGATGAAAGTCCG	0.498			T	NUP98	AML*																																			Dom	yes		20	20q12-q13.1	7150	topoisomerase (DNA) I		L	1	Substitution - Missense(1)	kidney(1)											95.0	85.0	88.0					20																	39741521		2203	4300	6503	SO:0001583	missense	7150				CCDS13312.1	20q12-q13.1	1990-06-22			ENSG00000198900	ENSG00000198900	5.99.1.2		11986	protein-coding gene	gene with protein product		126420					Standard	NM_003286		Approved		uc010ggd.1	P11387	OTTHUMG00000033057	ENST00000361337.2:c.1408A>G	20.37:g.39741521A>G	ENSP00000354522:p.Met470Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8KA78|E1P5W3|O43256|Q12855|Q12856|Q15610|Q5TFY3|Q9UJN0	Missense_Mutation	SNP	ENST00000361337.2	37	CCDS13312.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.602994	0.87157	.	.	ENSG00000198900	ENST00000361337	T	0.41400	1.0	5.6	5.6	0.85130	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha-helical subdomain, eukaryotic-type (1);	0.000000	0.85682	D	0.000000	T	0.50650	0.1628	M	0.82323	2.585	0.80722	D	1	P	0.44090	0.826	B	0.40677	0.337	T	0.60475	-0.7256	10	0.59425	D	0.04	-20.135	15.7928	0.78380	1.0:0.0:0.0:0.0	.	470	P11387	TOP1_HUMAN	V	470	ENSP00000354522:M470V	ENSP00000354522:M470V	M	+	1	0	TOP1	39174935	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.339000	0.96797	2.128000	0.65567	0.528000	0.53228	ATG		0.498	TOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080397.2			
UNC45B	146862	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	33477188	33477188	+	Silent	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:33477188G>A	ENST00000268876.5	+	4	424	c.327G>A	c.(325-327)cgG>cgA	p.R109R	UNC45B_ENST00000394570.2_Silent_p.R109R|UNC45B_ENST00000378449.1_Silent_p.R109R|UNC45B_ENST00000433649.1_Silent_p.R109R|UNC45B_ENST00000591048.1_Silent_p.R109R	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	109					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.R109R(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TCGAGCCACGGAACCAGAACT	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											99.0	84.0	89.0					17																	33477188		2203	4300	6503	SO:0001819	synonymous_variant	146862			AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.327G>A	17.37:g.33477188G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																				0.602	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2		NM_173167	
UNC80	285175	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	210640619	210640619	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr2:210640619G>C	ENST00000439458.1	+	3	228	c.148G>C	c.(148-150)Gag>Cag	p.E50Q	UNC80_ENST00000478701.1_3'UTR|UNC80_ENST00000272845.6_Missense_Mutation_p.E50Q	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	50					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.E50Q(4)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						ACAGTCCTTTGAGCGAGTGTT	0.408																																																	4	Substitution - Missense(4)	breast(2)|kidney(2)											90.0	90.0	90.0					2																	210640619		2203	4300	6503	SO:0001583	missense	285175			AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.148G>C	2.37:g.210640619G>C	ENSP00000391088:p.Glu50Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	37	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.894942	0.91962	.	.	ENSG00000144406	ENST00000439458;ENST00000281753;ENST00000272845	T;T	0.51574	0.7;0.71	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.69691	0.3139	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	0.989;1.0	D;D	0.85130	0.979;0.997	T	0.71699	-0.4514	10	0.87932	D	0	.	18.7669	0.91876	0.0:0.0:1.0:0.0	.	50;50	Q8N2C7;Q8N2C7-3	UNC80_HUMAN;.	Q	50	ENSP00000391088:E50Q;ENSP00000272845:E50Q	ENSP00000272845:E50Q	E	+	1	0	UNC80	210348864	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.330000	0.96422	2.763000	0.94921	0.650000	0.86243	GAG		0.408	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_182587	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10191558	10191558	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:10191558T>C	ENST00000256474.2	+	3	1391	c.551T>C	c.(550-552)cTc>cCc	p.L184P	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Missense_Mutation_p.L143P	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	184			L -> P (in VHLD; type I). {ECO:0000269|PubMed:8956040, ECO:0000269|PubMed:9829911}.|L -> R (in VHLD; type I). {ECO:0000269|PubMed:8956040}.		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.L184P(6)|p.L184R(1)|p.Y185fs*14(1)|p.S183*(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GTCAGGTCGCTCTACGAAGAT	0.517		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	9	Substitution - Missense(7)|Deletion - Frameshift(2)	kidney(9)	GRCh37	CM042503|CM941389|CM961440	VHL	M							83.0	75.0	78.0					3																	10191558		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.551T>C	3.37:g.10191558T>C	ENSP00000256474:p.Leu184Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	16.14	3.039597	0.55003	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	D;D	0.99879	-7.44;-7.44	4.97	4.97	0.65823	von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);von Hippel-Lindau disease tumor suppressor, alpha domain (1);	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96159	0.9114	10	0.87932	D	0	0.329	12.9354	0.58311	0.0:0.0:0.0:1.0	.	143;184	P40337-2;P40337	.;VHL_HUMAN	P	184;143;102	ENSP00000256474:L184P;ENSP00000344757:L143P	ENSP00000256474:L184P	L	+	2	0	VHL	10166558	0.992000	0.36948	0.737000	0.30932	0.208000	0.24298	5.765000	0.68834	2.209000	0.71365	0.533000	0.62120	CTC		0.517	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
WDR25	79446	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	100934461	100934461	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr14:100934461G>A	ENST00000335290.6	+	3	1152	c.926G>A	c.(925-927)aGt>aAt	p.S309N	WDR25_ENST00000402312.3_Missense_Mutation_p.S309N|WDR25_ENST00000554998.1_Missense_Mutation_p.S309N|WDR25_ENST00000542471.2_Missense_Mutation_p.S52N	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	309								p.S309N(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CGCATCCTCAGTGGTGGCTTT	0.642																																																	1	Substitution - Missense(1)	kidney(1)											136.0	126.0	129.0					14																	100934461		2203	4300	6503	SO:0001583	missense	79446			BC007953	CCDS32157.1	14q32.32	2013-01-09				ENSG00000176473		"""WD repeat domain containing"""	21064	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 67"""	C14orf67		15587985	Standard	NM_001161476		Approved	MGC4645	uc001yhn.3	Q64LD2		ENST00000335290.6:c.926G>A	14.37:g.100934461G>A	ENSP00000334148:p.Ser309Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.031117	0.75504	.	.	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	4.85	4.85	0.62838	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.168845	0.34986	N	0.003530	D	0.87341	0.6153	H	0.94964	3.605	0.26641	N	0.972289	P;D	0.76494	0.952;0.999	P;D	0.70487	0.724;0.969	T	0.82566	-0.0393	10	0.87932	D	0	-13.8988	13.5345	0.61641	0.0:0.1576:0.8424:0.0	.	52;309	Q64LD2-2;Q64LD2	.;WDR25_HUMAN	N	309;309;309;52	ENSP00000450661:S309N;ENSP00000385540:S309N;ENSP00000334148:S309N;ENSP00000441903:S52N	ENSP00000334148:S309N	S	+	2	0	WDR25	100004214	1.000000	0.71417	0.958000	0.39756	0.963000	0.63663	4.240000	0.58701	2.416000	0.81992	0.555000	0.69702	AGT		0.642	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1		NM_024515	
XIRP1	165904	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	39227553	39227553	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:39227553delG	ENST00000340369.3	-	2	3612	c.3384delC	c.(3382-3384)cccfs	p.P1128fs	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1128					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GCAGCCCTCTGGGTAGTGCTT	0.597																																																	0													66.0	71.0	69.0					3																	39227553		2203	4300	6503	SO:0001589	frameshift_variant	165904			AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.3384delC	3.37:g.39227553delG	ENSP00000343140:p.Pro1128fs	Somatic		WXS	Illumina HiSeq	Phase_I	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Frame_Shift_Del	DEL	ENST00000340369.3	37	CCDS2683.1																																																																																				0.597	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1		XM_093522	
ZNF845	91664	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	53856702	53856702	+	Missense_Mutation	SNP	G	G	A	rs200114728	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:53856702G>A	ENST00000595091.1	+	5	2993	c.2774G>A	c.(2773-2775)cGt>cAt	p.R925H	ZNF845_ENST00000458035.1_Missense_Mutation_p.R925H			Q96IR2	ZN845_HUMAN	zinc finger protein 845	925					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.R925H(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						AAAACCTTCCGTCACAATTCA	0.363													.|||	267	0.0533147	0.0484	0.0562	5008	,	,		21751	0.0466		0.0915	False		,,,				2504	0.0256																3	Substitution - Missense(3)	kidney(3)											33.0	30.0	31.0					19																	53856702		692	1591	2283	SO:0001583	missense	91664			BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2774G>A	19.37:g.53856702G>A	ENSP00000470005:p.Arg925His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	G	5.812	0.334080	0.11013	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.36157	1.27	2.0	-4.0	0.04057	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.42585	0.1209	L	0.58302	1.8	0.09310	N	1	D	0.55800	0.973	P	0.53760	0.734	T	0.43925	-0.9361	9	0.51188	T	0.08	.	10.7803	0.46374	0.0:0.6804:0.1821:0.1375	.	925	Q96IR2	ZN845_HUMAN	H	925;841	ENSP00000388311:R925H	ENSP00000412086:R841H	R	+	2	0	ZNF845	58548514	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-7.662000	0.00032	-1.603000	0.01597	-0.499000	0.04595	CGT		0.363	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1		XM_039908	
ZNF845	91664	broad.mit.edu;hgsc.bcm.edu	37	19	53856730	53856730	+	Silent	SNP	G	G	A	rs201351032	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:53856730G>A	ENST00000595091.1	+	5	3021	c.2802G>A	c.(2800-2802)aaG>aaA	p.K934K	ZNF845_ENST00000458035.1_Silent_p.K934K			Q96IR2	ZN845_HUMAN	zinc finger protein 845	934					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.K934K(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						TAATTCATAAGACAATTCATA	0.368													.|||	271	0.0541134	0.0507	0.0576	5008	,	,		22260	0.0456		0.0924	False		,,,				2504	0.0256																3	Substitution - coding silent(3)	kidney(3)																																								SO:0001819	synonymous_variant	91664			BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.2802G>A	19.37:g.53856730G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																				0.368	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1		XM_039908	
AGGF1	55109	broad.mit.edu	37	5	76348572	76348572	+	Silent	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:76348572T>C	ENST00000312916.7	+	9	1789	c.1407T>C	c.(1405-1407)taT>taC	p.Y469Y		NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	469	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|RNA processing (GO:0006396)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	nucleic acid binding (GO:0003676)	p.Y469Y(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(2)	20		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Ovarian(174;0.0129)|Prostate(461;0.11)		OV - Ovarian serous cystadenocarcinoma(54;4.51e-51)|Epithelial(54;2.2e-45)|all cancers(79;6.68e-41)		TACAAAGTTATGTCCTTGTGG	0.299																																																	1	Substitution - coding silent(1)	kidney(1)											93.0	90.0	91.0					5																	76348572		2203	4300	6503	SO:0001819	synonymous_variant	55109			AK001145	CCDS4035.1	5q13.3	2013-10-11			ENSG00000164252	ENSG00000164252		"""G patch domain containing"""	24684	protein-coding gene	gene with protein product		608464				18564129, 17103452	Standard	NM_018046		Approved	VG5Q, HSU84971, FLJ10283, GPATC7, GPATCH7	uc003ket.3	Q8N302	OTTHUMG00000102132	ENST00000312916.7:c.1407T>C	5.37:g.76348572T>C		Somatic		WXS	Illumina GAIIx	Phase_I	O00581|Q53YS3|Q9BU84|Q9NW66	Silent	SNP	ENST00000312916.7	37	CCDS4035.1																																																																																				0.299	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2		NM_018046	
ALDH3A1	218	broad.mit.edu	37	17	19641666	19641666	+	Silent	SNP	C	C	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr17:19641666C>T	ENST00000457500.2	-	9	1646	c.1317G>A	c.(1315-1317)ctG>ctA	p.L439L	ALDH3A1_ENST00000395555.3_Silent_p.L375L|ALDH3A1_ENST00000225740.6_Silent_p.L439L|ALDH3A1_ENST00000494157.2_Silent_p.L366L|ALDH3A1_ENST00000444455.1_Silent_p.L439L|RP11-311F12.2_ENST00000580884.1_RNA	NM_001135168.1	NP_001128640.1	P30838	AL3A1_HUMAN	aldehyde dehydrogenase 3 family, member A1	439					aging (GO:0007568)|cellular aldehyde metabolic process (GO:0006081)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|alcohol dehydrogenase (NADP+) activity (GO:0008106)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)	p.L439L(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(1)	13	all_cancers(12;4.01e-05)|all_epithelial(12;0.00301)|Breast(13;0.186)			Colorectal(15;0.0829)		ATCTGACCTTCAGGCCTTCAT	0.632																																																	1	Substitution - coding silent(1)	kidney(1)											66.0	71.0	69.0					17																	19641666		2203	4300	6503	SO:0001819	synonymous_variant	218			M74542	CCDS11212.1	17p11.2	2010-05-07	2010-05-07		ENSG00000108602	ENSG00000108602	1.2.1.5	"""Aldehyde dehydrogenases"""	405	protein-coding gene	gene with protein product	"""aldehyde dehydrogenase, dimeric NADP-preferring"""	100660		ALDH3		7774944, 1737758	Standard	NM_000691		Approved		uc010cqu.3	P30838	OTTHUMG00000059469	ENST00000457500.2:c.1317G>A	17.37:g.19641666C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A8K828|Q9BT37	Silent	SNP	ENST00000457500.2	37	CCDS11212.1																																																																																				0.632	ALDH3A1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132265.4		NM_000691	
CCDC102A	92922	broad.mit.edu	37	16	57552045	57552047	+	In_Frame_Del	DEL	GCC	GCC	-	rs201936316		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	GCC	GCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr16:57552045_57552047delGCC	ENST00000258214.2	-	6	1427_1429	c.1181_1183delGGC	c.(1180-1185)cggcaa>caa	p.R394del		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	394										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						CTGGCTGTTTGCCGCCGCCGCCG	0.68																																																	0																																										SO:0001651	inframe_deletion	92922			BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.1181_1183delGGC	16.37:g.57552054_57552056delGCC	ENSP00000258214:p.Arg394del	Somatic		WXS	Illumina GAIIx	Phase_I	Q9BT74	In_Frame_Del	DEL	ENST00000258214.2	37	CCDS10784.1																																																																																				0.680	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1		NM_033212	
CRAMP1L	57585	broad.mit.edu	37	16	1706867	1706867	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr16:1706867delG	ENST00000397412.3	+	10	2208	c.2109delG	c.(2107-2109)ctgfs	p.L703fs	CRAMP1L_ENST00000436138.3_Frame_Shift_Del_p.L700fs|CRAMP1L_ENST00000293925.5_Frame_Shift_Del_p.L703fs|LA16c-431H6.6_ENST00000454337.1_3'UTR|CRAMP1L_ENST00000262317.4_Frame_Shift_Del_p.L81fs			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	703						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						AGCTGCAGCTGGAGTACGACT	0.677																																																	0													4.0	5.0	4.0					16																	1706867		1840	3916	5756	SO:0001589	frameshift_variant	57585			AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.2109delG	16.37:g.1706867delG	ENSP00000380559:p.Leu703fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Frame_Shift_Del	DEL	ENST00000397412.3	37	CCDS10440.2																																																																																				0.677	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			
PHF2P2	100873793	broad.mit.edu	37	13	19625310	19625310	+	IGR	SNP	G	G	A	rs564022919		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr13:19625310G>A								RP11-301J16.7 (22469 upstream) : RNA5SP24 (37316 downstream)																							CCTTGAGCACGTGGTACCAGG	0.607													g|||	1	0.000199681	0.0	0.0	5008	,	,		19375	0.0		0.0	False		,,,				2504	0.001																0																																										SO:0001628	intergenic_variant	0																															13.37:g.19625310G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.607									
FAM46A	55603	broad.mit.edu	37	6	82461713	82461713	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr6:82461713delC	ENST00000320172.6	-	2	460	c.146delG	c.(145-147)ggtfs	p.G50fs	FAM46A_ENST00000369754.3_Frame_Shift_Del_p.G69fs|FAM46A_ENST00000369756.3_Frame_Shift_Del_p.G131fs	NM_017633.2	NP_060103.2	Q96IP4	FA46A_HUMAN	family with sequence similarity 46, member A	50					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)		poly(A) RNA binding (GO:0044822)	p.G49D(1)		endometrium(2)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	12		all_cancers(76;6.74e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000282)|all_epithelial(107;0.0104)		BRCA - Breast invasive adenocarcinoma(397;0.0428)		GCAATGCCCACCGAAgctgcc	0.672																																																	1	Substitution - Missense(1)	skin(1)											18.0	18.0	18.0					6																	82461713		2173	4262	6435	SO:0001589	frameshift_variant	55603			AF350451	CCDS34489.1	6q14	2008-07-03	2004-08-19	2004-08-26	ENSG00000112773	ENSG00000112773			18345	protein-coding gene	gene with protein product		611357	"""chromosome 6 open reading frame 37"""	C6orf37		12054608, 17803723	Standard	NM_017633		Approved	FLJ20037	uc003pjg.3	Q96IP4	OTTHUMG00000015097	ENST00000320172.6:c.146delG	6.37:g.82461713delC	ENSP00000318298:p.Gly50fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8K7U4|Q5TF86|Q8NFZ9|Q9BW32|Q9NXV5	Frame_Shift_Del	DEL	ENST00000320172.6	37	CCDS34489.1																																																																																				0.672	FAM46A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041331.1			
RP3-470B24.5	0	broad.mit.edu	37	6	168377135	168377135	+	lincRNA	SNP	T	T	C	rs372663828		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr6:168377135T>C	ENST00000538528.1	-	0	484																											CTGCAGTGTGTTGGGAGGAGG	0.622																																																	0													5.0	7.0	6.0					6																	168377135		670	1551	2221			100128124																															6.37:g.168377135T>C		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000538528.1	37																																																																																					0.622	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA				
ALG1L	200810	broad.mit.edu	37	3	125647387	125647387	+	IGR	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:125647387G>A	ENST00000340333.3	-	0	805				FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like								transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						ACCAGAAACTGTTTCCCTATG	0.502																																																	0																																										SO:0001628	intergenic_variant	0			BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588		3.37:g.125647387G>A		Somatic		WXS	Illumina GAIIx	Phase_I	D3DNA5	RNA	SNP	ENST00000340333.3	37	CCDS33840.1																																																																																				0.502	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1		NM_001015050	
ALG1L	200810	broad.mit.edu	37	3	125647396	125647396	+	IGR	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:125647396T>C	ENST00000340333.3	-	0	805				FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like								transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						TGTTTCCCTATGAAGAGCACT	0.502																																																	0																																										SO:0001628	intergenic_variant	0			BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588		3.37:g.125647396T>C		Somatic		WXS	Illumina GAIIx	Phase_I	D3DNA5	RNA	SNP	ENST00000340333.3	37	CCDS33840.1																																																																																				0.502	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1		NM_001015050	
PROB1	389333	broad.mit.edu	37	5	138728573	138728574	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:138728573_138728574delAT	ENST00000434752.2	-	1	2311_2312	c.2197_2198delAT	c.(2197-2199)atcfs	p.I733fs	MZB1_ENST00000412103.2_5'Flank|MZB1_ENST00000302125.8_5'Flank|MZB1_ENST00000457570.2_5'Flank	NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1	733	Pro-rich.																AGGCAGGCGGATCTCTGTGCGC	0.703																																																	0																																										SO:0001589	frameshift_variant	0			AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31		ENST00000434752.2:c.2197_2198delAT	5.37:g.138728573_138728574delAT	ENSP00000416033:p.Ile733fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4E007	Frame_Shift_Del	DEL	ENST00000434752.2	37	CCDS54909.1																																																																																				0.703	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1		NM_001161546	
PROB1	389333	broad.mit.edu	37	5	138728579	138728579	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:138728579delG	ENST00000434752.2	-	1	2306	c.2192delC	c.(2191-2193)acafs	p.T731fs	MZB1_ENST00000412103.2_5'Flank|MZB1_ENST00000302125.8_5'Flank|MZB1_ENST00000457570.2_5'Flank	NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1	731	Pro-rich.																GCGGATCTCTGTGCGCTTGAA	0.697																																																	0													12.0	21.0	18.0					5																	138728579		689	1585	2274	SO:0001589	frameshift_variant	0			AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31		ENST00000434752.2:c.2192delC	5.37:g.138728579delG	ENSP00000416033:p.Thr731fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4E007	Frame_Shift_Del	DEL	ENST00000434752.2	37	CCDS54909.1																																																																																				0.697	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1		NM_001161546	
PROB1	389333	broad.mit.edu	37	5	138728583	138728584	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr5:138728583_138728584insT	ENST00000434752.2	-	1	2301_2302	c.2187_2188insA	c.(2185-2190)aagcgcfs	p.R730fs	MZB1_ENST00000412103.2_5'Flank|MZB1_ENST00000302125.8_5'Flank|MZB1_ENST00000457570.2_5'Flank	NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1	730	Pro-rich.																ATCTCTGTGCGCTTGAAGGGCT	0.698																																																	0																																										SO:0001589	frameshift_variant	0			AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31		ENST00000434752.2:c.2187_2188insA	5.37:g.138728583_138728584insT	ENSP00000416033:p.Arg730fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4E007	Frame_Shift_Ins	INS	ENST00000434752.2	37	CCDS54909.1																																																																																				0.698	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1		NM_001161546	
LOC441666	441666	broad.mit.edu	37	10	42833429	42833429	+	RNA	SNP	A	A	G	rs201623926		TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr10:42833429A>G	ENST00000609841.1	-	0	474					NR_024380.1																						TCTTCTCCTAAGTCTATTTGA	0.333																																																	0																																												441666																															10.37:g.42833429A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000609841.1	37																																																																																					0.333	RP11-313J2.1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000472483.1			
Unknown	0	broad.mit.edu	37	9	66499770	66499770	+	IGR	SNP	G	G	T	rs75046133	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr9:66499770G>T								RP11-262H14.1 (30460 upstream) : RP11-262H14.7 (17435 downstream)																							CAACCTGGTGGCCATCGTGGT	0.582													g|||	500	0.0998403	0.0983	0.1614	5008	,	,		41958	0.0585		0.1342	False		,,,				2504	0.0654																0																																										SO:0001628	intergenic_variant	0																															9.37:g.66499770G>T		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP		37																																																																																				0	0.582									
FAM86C2P	645332	broad.mit.edu	37	11	67560717	67560717	+	RNA	SNP	G	G	A			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr11:67560717G>A	ENST00000528089.1	-	0	1033							A6NEL3	F86C2_HUMAN	family with sequence similarity 86, member C2, pseudogene									p.N119N(1)									TAGGGAAACAGTTTCTGGTCA	0.512																																																	1	Substitution - coding silent(1)	kidney(1)																																										0					11q13.2	2011-07-07			ENSG00000160172	ENSG00000160172			42392	pseudogene	pseudogene							Standard	NR_024249		Approved		uc001omt.4	A6NEL3	OTTHUMG00000167222		11.37:g.67560717G>A		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000528089.1	37																																																																																					0.512	FAM86C2P-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000393796.1			
MUC4	4585	broad.mit.edu	37	3	195509939	195509939	+	Missense_Mutation	SNP	G	G	T	rs202039836	byFrequency	TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr3:195509939G>T	ENST00000463781.3	-	2	8971	c.8512C>A	c.(8512-8514)Cct>Act	p.P2838T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2838T|MUC4_ENST00000346145.4_Intron	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.P2838T(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GCTGAGGAAGGGATGGTGACA	0.592													.|||	318	0.0634984	0.0045	0.0432	5008	,	,		7871	0.0417		0.1521	False		,,,				2504	0.089																3	Substitution - Missense(3)	kidney(3)											102.0	63.0	75.0					3																	195509939		690	1569	2259	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.8512C>A	3.37:g.195509939G>T	ENSP00000417498:p.Pro2838Thr	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	3.466	-0.108992	0.06924	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	.	.	.	.	T	0.10551	0.0258	N	0.08118	0	0.09310	N	1	P	0.38110	0.618	B	0.28638	0.092	T	0.19386	-1.0307	7	.	.	.	.	4.5444	0.12074	0.0:0.4166:0.5833:0.0	.	2710	E7ESK3	.	T	2838	ENSP00000417498:P2838T;ENSP00000420243:P2838T	.	P	-	1	0	MUC4	196994718	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.690000	0.00392	-0.000000	0.14550	0.000000	0.15137	CCT		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
RRBP1	6238	broad.mit.edu	37	20	17640580	17640580	+	Silent	SNP	T	T	G			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr20:17640580T>G	ENST00000377813.1	-	3	876	c.573A>C	c.(571-573)acA>acC	p.T191T	RRBP1_ENST00000246043.4_Silent_p.T191T|RRBP1_ENST00000360807.4_Intron|RRBP1_ENST00000455029.2_Intron|RRBP1_ENST00000377807.2_Intron			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	191					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						CAGTGGCTGGTGTGTTGCCCT	0.572																																																	0													21.0	18.0	19.0					20																	17640580		2201	4298	6499	SO:0001819	synonymous_variant	6238			AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.573A>C	20.37:g.17640580T>G		Somatic		WXS	Illumina GAIIx	Phase_I	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Silent	SNP	ENST00000377813.1	37																																																																																					0.572	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1		NM_001042576	
TMEM229A	730130	broad.mit.edu	37	7	123672832	123672832	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr7:123672832G>T	ENST00000455783.1	-	1	691	c.226C>A	c.(226-228)Cgc>Agc	p.R76S	RP5-921G16.1_ENST00000484322.1_RNA	NM_001136002.1	NP_001129474.1	B2RXF0	T229A_HUMAN	transmembrane protein 229A	76						host cell nucleus (GO:0042025)|integral component of membrane (GO:0016021)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R76S(2)		endometrium(3)|kidney(3)	6						CGGGCGAAGCGCCGGGCCGAG	0.677																																																	2	Substitution - Missense(2)	kidney(2)											33.0	40.0	38.0					7																	123672832		692	1591	2283	SO:0001583	missense	730130			BC157828	CCDS47694.1	7q31.32	2009-09-22			ENSG00000234224	ENSG00000234224			37279	protein-coding gene	gene with protein product							Standard	NM_001136002		Approved		uc011kob.2	B2RXF0	OTTHUMG00000154762	ENST00000455783.1:c.226C>A	7.37:g.123672832G>T	ENSP00000395244:p.Arg76Ser	Somatic		WXS	Illumina GAIIx	Phase_I	A4D0X6	Missense_Mutation	SNP	ENST00000455783.1	37	CCDS47694.1	.	.	.	.	.	.	.	.	.	.	G	1.160	-0.644224	0.03531	.	.	ENSG00000234224	ENST00000455783	.	.	.	3.48	-2.02	0.07388	.	.	.	.	.	T	0.17408	0.0418	N	0.19112	0.55	0.19775	N	0.99995	B	0.13594	0.008	B	0.06405	0.002	T	0.20538	-1.0272	8	0.42905	T	0.14	.	0.8973	0.01266	0.1393:0.2533:0.2809:0.3265	.	76	B2RXF0	T229A_HUMAN	S	76	.	ENSP00000395244:R76S	R	-	1	0	TMEM229A	123460068	0.756000	0.28383	0.773000	0.31616	0.133000	0.20885	0.462000	0.21956	-0.360000	0.08138	-1.512000	0.00943	CGC		0.677	TMEM229A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336960.3		NM_001136002	
LINC00933	100506874	broad.mit.edu	37	15	85121557	85121557	+	RNA	DEL	A	A	-			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr15:85121557delA	ENST00000557887.1	+	0	757					NR_038273.1|NR_038274.1				long intergenic non-protein coding RNA 933																		TTCTTGCCTTAAAAAAAAAAA	0.279																																																	0																																												0					15q25.2	2013-05-29			ENSG00000259728	ENSG00000259728		"""Long non-coding RNAs"""	48625	non-coding RNA	RNA, long non-coding							Standard	NR_038273		Approved				OTTHUMG00000172445		15.37:g.85121557delA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000557887.1	37																																																																																					0.279	LINC00933-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000418591.1			
UQCRFS1	7386	broad.mit.edu	37	19	29699033	29699033	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5703-01A-11D-1534-10	TCGA-B0-5703-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	963400a2-d939-41a5-8c42-9fc3a04b8362	56994dd1-cfd6-4939-8c18-bbc52a633306	g.chr19:29699033T>C	ENST00000304863.4	-	2	669	c.247A>G	c.(247-249)Atc>Gtc	p.I83V		NM_006003.2	NP_005994.2	P47985	UCRI_HUMAN	ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1	83					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)	p.I83V(4)		endometrium(4)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Breast(6;0.0545)|Esophageal squamous(110;0.239)		Lung(7;0.092)			GGCACCTTGATGTCTGTGTGG	0.423																																																	4	Substitution - Missense(4)	endometrium(2)|kidney(2)											53.0	59.0	57.0					19																	29699033		2203	4299	6502	SO:0001583	missense	7386			BC010035	CCDS12415.1	19q12	2011-07-04			ENSG00000169021	ENSG00000169021	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12587	protein-coding gene	gene with protein product	"""cytochrome b-c1 complex subunit 5"""	191327				8088805	Standard	NM_006003		Approved	RIS1, RIP1, UQCR5, RISP	uc002nsd.2	P47985		ENST00000304863.4:c.247A>G	19.37:g.29699033T>C	ENSP00000306397:p.Ile83Val	Somatic		WXS	Illumina GAIIx	Phase_I	A8K519|Q6NVX5|Q9UPH2	Missense_Mutation	SNP	ENST00000304863.4	37	CCDS12415.1	.	.	.	.	.	.	.	.	.	.	t	0.014	-1.596233	0.00857	.	.	ENSG00000169021	ENST00000304863	T	0.42131	0.98	5.42	-4.98	0.03019	Ubiquinol cytochrome reductase, transmembrane domain (3);	0.618499	0.17385	N	0.176150	T	0.22360	0.0539	N	0.16862	0.45	0.20764	N	0.999851	B	0.02656	0.0	B	0.14578	0.011	T	0.23976	-1.0173	10	0.08837	T	0.75	.	17.2071	0.86921	0.0:0.6778:0.0:0.3222	.	83	P47985	UCRI_HUMAN	V	83	ENSP00000306397:I83V	ENSP00000306397:I83V	I	-	1	0	UQCRFS1	34390873	0.987000	0.35691	0.084000	0.20598	0.009000	0.06853	0.184000	0.16939	-1.243000	0.02519	-3.117000	0.00062	ATC		0.423	UQCRFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458563.1		NM_006003	
