#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_Chromosome_hg18	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_End_position_hg18	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_Start_position_hg18	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_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PLXDC2	84898	hgsc.bcm.edu	37	10	20568635	20568635	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:20568635C>T	ENST00000377252.4	+	14	2318	c.1477C>T	c.(1477-1479)Cgc>Tgc	p.R493C	PLXDC2_ENST00000377238.2_3'UTR|PLXDC2_ENST00000377242.3_Missense_Mutation_p.R444C	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	493					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.R493C(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(9)|ovary(2)|skin(3)|stomach(1)	34						GTTTCAGAGACGCCCAAGCAG	0.393																																																	1	Substitution - Missense(1)	stomach(1)	10											78.0	77.0	77.0					10																	20568635		2203	4300	6503	20608641	SO:0001583	missense	84898			AF378757	CCDS7132.1, CCDS60497.1	10p12.33	2006-04-12			ENSG00000120594	ENSG00000120594			21013	protein-coding gene	gene with protein product	"""tumor endothelial marker 7-related precursor"""	606827				11559528	Standard	NM_001282736		Approved	TEM7R, FLJ14623	uc001iqg.1	Q6UX71	OTTHUMG00000017781	ENST00000377252.4:c.1477C>T	10.37:g.20568635C>T	ENSP00000366460:p.Arg493Cys	Somatic		Capture	Illumina HiSeq	Phase_I	20608641	Q96E59|Q96PD9|Q96SU9	Missense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.460213	0.84317	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	T;T	0.56103	0.48;0.74	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.75496	0.3857	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.76836	-0.2812	10	0.87932	D	0	.	20.2406	0.98372	0.0:1.0:0.0:0.0	.	444;493	Q6UX71-2;Q6UX71	.;PXDC2_HUMAN	C	493;444;356;479	ENSP00000366460:R493C;ENSP00000366450:R444C	ENSP00000366446:R356C	R	+	1	0	PLXDC2	20608641	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.133000	0.77259	2.857000	0.98124	0.650000	0.86243	CGC		PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812	
ARHGAP21	57584	hgsc.bcm.edu	37	10	24909794	24909794	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:24909794T>C	ENST00000396432.2	-	9	1516	c.1030A>G	c.(1030-1032)Att>Gtt	p.I344V	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.I131V	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	343					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TTAAGTAAAATTCCAGAAGGT	0.423																																																	0			10											101.0	102.0	101.0					10																	24909794		2203	4300	6503	24949800	SO:0001583	missense	57584			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.1030A>G	10.37:g.24909794T>C	ENSP00000379709:p.Ile344Val	Somatic		Capture	Illumina HiSeq	Phase_I	24949800	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	3.444	-0.113424	0.06881	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.42131	2.94;3.02;0.98;0.99	5.6	0.35	0.16037	.	0.974264	0.08495	N	0.937347	T	0.22859	0.0552	N	0.17674	0.51	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.28004	-1.0057	10	0.12103	T	0.63	.	5.4131	0.16358	0.1193:0.2689:0.0:0.6118	.	334;343	F8W9U9;Q5T5U3	.;RHG21_HUMAN	V	344;333;131;334;344;179	ENSP00000379709:I344V;ENSP00000365604:I131V;ENSP00000365592:I334V;ENSP00000405018:I344V	ENSP00000365604:I131V	I	-	1	0	ARHGAP21	24949800	0.537000	0.26386	0.024000	0.17045	0.973000	0.67179	0.876000	0.28092	0.106000	0.17784	0.528000	0.53228	ATT		ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
PHYHIPL	84457	hgsc.bcm.edu	37	10	61004855	61004855	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:61004855A>G	ENST00000373880.4	+	5	899	c.635A>G	c.(634-636)gAt>gGt	p.D212G	PHYHIPL_ENST00000373878.3_Missense_Mutation_p.D186G	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	212						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						TCTGTCAAGGATAACAGTGGT	0.428																																																	0			10											70.0	64.0	66.0					10																	61004855		2203	4300	6503	60674861	SO:0001583	missense	84457			AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"""Fibronectin type III domain containing"""	29378	protein-coding gene	gene with protein product			"""phytanoyl-CoA hydroxylase interacting protein-like"""			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.635A>G	10.37:g.61004855A>G	ENSP00000362987:p.Asp212Gly	Somatic		Capture	Illumina HiSeq	Phase_I	60674861	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Missense_Mutation	SNP	ENST00000373880.4	37	CCDS7254.1	.	.	.	.	.	.	.	.	.	.	A	18.75	3.690835	0.68271	.	.	ENSG00000165443	ENST00000373880;ENST00000373878	T;T	0.42131	1.38;0.98	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.69196	0.3084	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.74850	-0.3524	10	0.87932	D	0	-15.652	16.1968	0.82036	1.0:0.0:0.0:0.0	.	186;212	Q96FC7-2;Q96FC7	.;PHIPL_HUMAN	G	212;186	ENSP00000362987:D212G;ENSP00000362985:D186G	ENSP00000362985:D186G	D	+	2	0	PHYHIPL	60674861	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	2.225000	0.72522	0.533000	0.62120	GAT		PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439	
PTEN	5728	hgsc.bcm.edu	37	10	89685281	89685281	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:89685281C>T	ENST00000371953.3	+	3	1533	c.176C>T	c.(175-177)tCa>tTa	p.S59L		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	59	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.S59*(4)|p.Y27fs*1(2)|p.R55fs*2(1)|p.S59L(1)|p.V54fs*29(1)|p.R55_L70>S(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TTTTTGGATTCAAAGCATAAA	0.254		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																													yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	59	Whole gene deletion(37)|Deletion - Frameshift(10)|Unknown(6)|Substitution - Nonsense(4)|Complex - deletion inframe(1)|Substitution - Missense(1)	prostate(16)|central_nervous_system(12)|lung(7)|skin(7)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|ovary(3)|urinary_tract(2)|breast(2)|soft_tissue(1)	10	GRCh37	CM043772	PTEN	M							31.0	33.0	33.0					10																	89685281		2182	4276	6458	89675261	SO:0001583	missense	5728	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.176C>T	10.37:g.89685281C>T	ENSP00000361021:p.Ser59Leu	Somatic		Capture	Illumina HiSeq	Phase_I	89675261	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.515368	0.64634	.	.	ENSG00000171862	ENST00000371953	D	0.98419	-4.92	5.46	5.46	0.80206	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.96719	0.8929	L	0.50993	1.605	0.80722	D	1	B	0.22346	0.068	B	0.24006	0.05	D	0.94948	0.8097	9	.	.	.	-6.4254	19.2989	0.94134	0.0:1.0:0.0:0.0	.	59	P60484	PTEN_HUMAN	L	59	ENSP00000361021:S59L	.	S	+	2	0	PTEN	89675261	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.244000	0.78228	2.563000	0.86464	0.655000	0.94253	TCA		PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
CH25H	9023	hgsc.bcm.edu	37	10	90966639	90966639	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:90966639C>T	ENST00000371852.2	-	1	432	c.411G>A	c.(409-411)atG>atA	p.M137I		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	137					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		CGAAGAACTCCATGTCGAAGA	0.632																																																	0			10											75.0	73.0	74.0					10																	90966639		2203	4300	6503	90956619	SO:0001583	missense	9023			AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.411G>A	10.37:g.90966639C>T	ENSP00000360918:p.Met137Ile	Somatic		Capture	Illumina HiSeq	Phase_I	90956619	B2RBY3	Missense_Mutation	SNP	ENST00000371852.2	37	CCDS7400.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.249706	0.22880	.	.	ENSG00000138135	ENST00000371852	D	0.83163	-1.69	5.3	0.197	0.15164	Fatty acid hydroxylase (1);	0.810877	0.11339	N	0.574289	T	0.54143	0.1840	N	0.01576	-0.805	0.22017	N	0.99941	B	0.06786	0.001	B	0.08055	0.003	T	0.43940	-0.9360	10	0.13470	T	0.59	-7.1466	6.2913	0.21061	0.2708:0.2328:0.4964:0.0	.	137	O95992	CH25H_HUMAN	I	137	ENSP00000360918:M137I	ENSP00000360918:M137I	M	-	3	0	CH25H	90956619	0.994000	0.37717	0.143000	0.22291	0.960000	0.62799	0.317000	0.19487	-0.143000	0.11334	-0.171000	0.13296	ATG		CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
AGL	178	hgsc.bcm.edu	37	1	100343239	100343239	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:100343239A>G	ENST00000294724.4	+	12	1944	c.1466A>G	c.(1465-1467)gAc>gGc	p.D489G	AGL_ENST00000361522.4_Missense_Mutation_p.D472G|AGL_ENST00000370163.3_Missense_Mutation_p.D489G|AGL_ENST00000361302.3_Missense_Mutation_p.D473G|AGL_ENST00000370161.2_Missense_Mutation_p.D473G|AGL_ENST00000370165.3_Missense_Mutation_p.D489G|AGL_ENST00000361915.3_Missense_Mutation_p.D489G	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	489					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TGCTGGGGAGACAGTGTTAAA	0.363																																																	0			1											102.0	99.0	100.0					1																	100343239		2203	4300	6503	100115827	SO:0001583	missense	178			BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.1466A>G	1.37:g.100343239A>G	ENSP00000294724:p.Asp489Gly	Somatic		Capture	Illumina HiSeq	Phase_I	100115827	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838082	0.91117	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	D;D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-3.12;-3.12;-3.12;-3.12	5.97	5.97	0.96955	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.96787	0.8951	M	0.92507	3.315	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97687	1.0176	10	0.87932	D	0	.	16.4608	0.84044	1.0:0.0:0.0:0.0	.	472;473;489	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	G	489;489;489;489;473;473;472	ENSP00000355106:D489G;ENSP00000359184:D489G;ENSP00000359182:D489G;ENSP00000294724:D489G;ENSP00000354971:D473G;ENSP00000359180:D473G;ENSP00000354635:D472G	ENSP00000294724:D489G	D	+	2	0	AGL	100115827	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.896000	0.92521	2.288000	0.76882	0.533000	0.62120	GAC		AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
CASP5	838	hgsc.bcm.edu	37	11	104869632	104869632	+	Missense_Mutation	SNP	G	G	T	rs531060230		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:104869632G>T	ENST00000260315.3	-	7	1075	c.1076C>A	c.(1075-1077)gCt>gAt	p.A359D	CASP5_ENST00000418434.1_Missense_Mutation_p.A217D|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000444749.2_Missense_Mutation_p.A301D|CASP5_ENST00000393141.2_Missense_Mutation_p.A372D|CASP5_ENST00000526056.1_Missense_Mutation_p.A372D|CASP5_ENST00000531367.1_Missense_Mutation_p.A217D			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	359					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		AGAACAGAAAGCAATGAAGTC	0.448																																																	0			11											143.0	133.0	136.0					11																	104869632		2202	4299	6501	104374842	SO:0001583	missense	838				CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.1076C>A	11.37:g.104869632G>T	ENSP00000260315:p.Ala359Asp	Somatic		Capture	Illumina HiSeq	Phase_I	104374842	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Missense_Mutation	SNP	ENST00000260315.3	37	CCDS8328.2	.	.	.	.	.	.	.	.	.	.	G	10.31	1.315384	0.23908	.	.	ENSG00000137757	ENST00000393141;ENST00000418434;ENST00000260315;ENST00000444749;ENST00000526056;ENST00000531367	T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99	3.66	1.73	0.24493	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase non-catalytic subunit p10 (1);Peptidase C14, caspase precursor p45, core (1);	0.288882	0.33110	N	0.005266	T	0.46229	0.1382	M	0.92555	3.32	0.58432	D	0.999999	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	D;D;D;D	0.79108	0.967;0.976;0.992;0.981	T	0.36187	-0.9758	10	0.87932	D	0	.	2.3071	0.04177	0.1113:0.1936:0.4962:0.1989	.	217;301;359;372	P51878-3;P51878-2;P51878;P51878-5	.;.;CASP5_HUMAN;.	D	372;217;359;301;372;217	ENSP00000376849:A372D;ENSP00000398130:A217D;ENSP00000260315:A359D;ENSP00000388365:A301D;ENSP00000436877:A372D;ENSP00000434471:A217D	ENSP00000260315:A359D	A	-	2	0	CASP5	104374842	0.131000	0.22433	0.895000	0.35142	0.022000	0.10575	1.481000	0.35476	0.330000	0.23485	-0.311000	0.09066	GCT		CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
ATM	472	hgsc.bcm.edu	37	11	108170479	108170479	+	Missense_Mutation	SNP	G	G	T	rs121434217		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:108170479G>T	ENST00000452508.2	+	35	5233	c.5044G>T	c.(5044-5046)Gat>Tat	p.D1682Y	ATM_ENST00000278616.4_Missense_Mutation_p.D1682Y			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1682			D -> H (in T-prolymphocytic leukemia). {ECO:0000269|PubMed:9288106}.		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.D1682Y(2)|p.D1682H(1)		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)	GGGTCCTATAGATTTCTCTAC	0.358			"""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"""	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	11											132.0	139.0	136.0					11																	108170479		2201	4298	6499	107675689	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.5044G>T	11.37:g.108170479G>T	ENSP00000388058:p.Asp1682Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	107675689	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805415	0.70682	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73047	-0.71;-0.71	5.2	4.28	0.50868	Armadillo-type fold (1);	0.044055	0.85682	D	0.000000	T	0.82029	0.4948	M	0.74258	2.255	0.46564	D	0.999107	D	0.89917	1.0	D	0.87578	0.998	T	0.83316	-0.0020	10	0.87932	D	0	.	10.8473	0.46751	0.1519:0.0:0.8481:0.0	.	1682	Q13315	ATM_HUMAN	Y	1682	ENSP00000278616:D1682Y;ENSP00000388058:D1682Y	ENSP00000278616:D1682Y	D	+	1	0	ATM	107675689	1.000000	0.71417	0.993000	0.49108	0.952000	0.60782	2.926000	0.48892	1.180000	0.42898	0.650000	0.86243	GAT		ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
ATM	472	hgsc.bcm.edu	37	11	108186757	108186757	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:108186757G>A	ENST00000452508.2	+	43	6304	c.6115G>A	c.(6115-6117)Gaa>Aaa	p.E2039K	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.E2039K			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2039	FAT. {ECO:0000255|PROSITE- ProRule:PRU00534}.				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.E2039K(1)		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)	ATATGAACACGAAGCAATGTG	0.398			"""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"""	1	Substitution - Missense(1)	large_intestine(1)	11											103.0	93.0	96.0					11																	108186757		2201	4298	6499	107691967	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.6115G>A	11.37:g.108186757G>A	ENSP00000388058:p.Glu2039Lys	Somatic		Capture	Illumina HiSeq	Phase_I	107691967	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819217	0.71028	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.02015	4.5;4.5	5.24	5.24	0.73138	PIK-related kinase (1);Armadillo-type fold (1);	0.213177	0.48767	D	0.000164	T	0.12987	0.0315	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.67548	0.952	T	0.00376	-1.1779	10	0.49607	T	0.09	.	17.0101	0.86404	0.0:0.0:1.0:0.0	.	2039	Q13315	ATM_HUMAN	K	2039	ENSP00000278616:E2039K;ENSP00000388058:E2039K	ENSP00000278616:E2039K	E	+	1	0	ATM	107691967	1.000000	0.71417	1.000000	0.80357	0.624000	0.37722	9.101000	0.94219	2.447000	0.82792	0.305000	0.20034	GAA		ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
KCNA2	3737	hgsc.bcm.edu	37	1	111146297	111146297	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:111146297C>T	ENST00000485317.1	-	3	1781	c.1108G>A	c.(1108-1110)Gtc>Atc	p.V370I	KCNA2_ENST00000440270.1_Missense_Mutation_p.V370I|KCNA2_ENST00000316361.4_Missense_Mutation_p.V370I|KCNA2_ENST00000369770.3_Intron|KCNA2_ENST00000525120.1_5'Flank			P16389	KCNA2_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 2	370					optic nerve structural organization (GO:0021633)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	juxtaparanode region of axon (GO:0044224)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		all_cancers(81;5.55e-06)|all_epithelial(167;1.87e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Colorectal(144;0.00878)|Lung(183;0.0234)|all cancers(265;0.0492)|Epithelial(280;0.0529)|COAD - Colon adenocarcinoma(174;0.131)|LUSC - Lung squamous cell carcinoma(189;0.133)|READ - Rectum adenocarcinoma(129;0.191)	Dalfampridine(DB06637)	GTCATGGAGACGACTGCCCAC	0.517																																					Pancreas(18;568 735 10587 23710 36357)												0			1											51.0	54.0	53.0					1																	111146297		2203	4300	6503	110947820	SO:0001583	missense	3737			L02752	CCDS827.1, CCDS55625.1	1p13	2012-07-05			ENSG00000177301	ENSG00000177301		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6220	protein-coding gene	gene with protein product		176262				16382104	Standard	NM_004974		Approved	Kv1.2, HK4	uc009wfw.3	P16389	OTTHUMG00000011567	ENST00000485317.1:c.1108G>A	1.37:g.111146297C>T	ENSP00000433109:p.Val370Ile	Somatic		Capture	Illumina HiSeq	Phase_I	110947820	Q86XG6	Missense_Mutation	SNP	ENST00000485317.1	37	CCDS827.1	.	.	.	.	.	.	.	.	.	.	C	19.30	3.800235	0.70567	.	.	ENSG00000177301	ENST00000485317;ENST00000440270;ENST00000316361	D;D;D	0.97620	-4.46;-4.46;-4.46	5.71	5.71	0.89125	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97436	0.9161	L	0.46741	1.465	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96260	0.9190	10	0.32370	T	0.25	.	19.857	0.96762	0.0:1.0:0.0:0.0	.	370	P16389	KCNA2_HUMAN	I	370	ENSP00000433109:V370I;ENSP00000415257:V370I;ENSP00000314520:V370I	ENSP00000314520:V370I	V	-	1	0	KCNA2	110947820	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.770000	0.85390	2.703000	0.92315	0.655000	0.94253	GTC		KCNA2-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128001.2	NM_004974	
UPK2	7379	hgsc.bcm.edu	37	11	118827131	118827131	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:118827131C>A	ENST00000264031.2	+	1	106	c.71C>A	c.(70-72)gCt>gAt	p.A24D	UPK2_ENST00000534788.1_Intron|RP11-158I9.7_ENST00000584831.1_RNA	NM_006760.3	NP_006751.1	O00526	UPK2_HUMAN	uroplakin 2	24					epithelial cell differentiation (GO:0030855)|membrane organization (GO:0061024)|multicellular organismal development (GO:0007275)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)				kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.122)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		TCCCCAGGGGCTGCAGGTCTC	0.637																																																	0			11											59.0	51.0	54.0					11																	118827131		2200	4295	6495	118332341	SO:0001583	missense	7379			Y13645	CCDS8404.1	11q23	2008-07-21				ENSG00000110375			12579	protein-coding gene	gene with protein product	"""uroplakin II"", ""uroplakin-2"""	611558				9515818, 9846985	Standard	NM_006760		Approved	UP2, UPII, MGC138598	uc001puh.3	O00526		ENST00000264031.2:c.71C>A	11.37:g.118827131C>A	ENSP00000264031:p.Ala24Asp	Somatic		Capture	Illumina HiSeq	Phase_I	118332341	B0YJ92|O00457|Q53YV0	Missense_Mutation	SNP	ENST00000264031.2	37	CCDS8404.1	.	.	.	.	.	.	.	.	.	.	C	8.795	0.931585	0.18131	.	.	ENSG00000110375	ENST00000264031	T	0.36878	1.23	5.22	3.38	0.38709	.	0.644480	0.14496	N	0.316013	T	0.37183	0.0994	L	0.54323	1.7	0.19775	N	0.999959	P	0.42456	0.78	B	0.43123	0.409	T	0.17899	-1.0354	10	0.66056	D	0.02	-0.8848	9.8206	0.40880	0.0:0.8851:0.0:0.1149	.	24	O00526	UPK2_HUMAN	D	24	ENSP00000264031:A24D	ENSP00000264031:A24D	A	+	2	0	UPK2	118332341	0.799000	0.28903	0.688000	0.30117	0.097000	0.18754	0.884000	0.28214	0.795000	0.33922	-1.073000	0.02249	GCT		UPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389311.1	NM_006760	
NTM	50863	hgsc.bcm.edu	37	11	132016335	132016335	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:132016335C>A	ENST00000374786.1	+	2	806	c.327C>A	c.(325-327)gaC>gaA	p.D109E	NTM_ENST00000374791.3_Missense_Mutation_p.D109E|NTM_ENST00000427481.2_Missense_Mutation_p.D100E|NTM_ENST00000539799.1_Missense_Mutation_p.D109E|NTM_ENST00000374784.1_Missense_Mutation_p.D109E|NTM_ENST00000425719.2_Missense_Mutation_p.D109E	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	109	Ig-like C2-type 1.				cell adhesion (GO:0007155)|neuron recognition (GO:0008038)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(30)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	56						ATGTGTATGACGAGGGCCCTT	0.577																																																	0			11											172.0	118.0	136.0					11																	132016335		2201	4297	6498	131521545	SO:0001583	missense	50863			AF126426	CCDS8491.1, CCDS41733.1, CCDS44777.1, CCDS44778.1	11q25	2013-01-11			ENSG00000182667	ENSG00000182667		"""Immunoglobulin superfamily / I-set domain containing"""	17941	protein-coding gene	gene with protein product	"""neurotrimin"", ""IgLON family member 2"""	607938				7891157	Standard	NM_001048209		Approved	HNT, NTRI, IGLON2	uc001qgq.3	Q9P121	OTTHUMG00000066364	ENST00000374786.1:c.327C>A	11.37:g.132016335C>A	ENSP00000363918:p.Asp109Glu	Somatic		Capture	Illumina HiSeq	Phase_I	131521545	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.139607	0.77775	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36;0.36;0.36	5.58	-3.24	0.05094	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.045498	0.85682	D	0.000000	T	0.69459	0.3113	M	0.90977	3.165	0.43021	D	0.994577	P;P;D;P;P;D	0.54047	0.933;0.539;0.964;0.539;0.935;0.964	P;P;P;P;P;P	0.61722	0.893;0.893;0.881;0.893;0.766;0.829	T	0.72360	-0.4317	10	0.87932	D	0	-30.9792	10.0169	0.42020	0.102:0.2652:0.0:0.6328	.	109;100;109;109;109;109	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	E	109;109;100;100;109;109;109	ENSP00000363923:D109E;ENSP00000437668:D109E;ENSP00000448104:D100E;ENSP00000416320:D100E;ENSP00000363918:D109E;ENSP00000396722:D109E;ENSP00000363916:D109E	ENSP00000363916:D109E	D	+	3	2	NTM	131521545	0.673000	0.27539	0.906000	0.35671	0.987000	0.75469	-0.050000	0.11904	-0.734000	0.04843	-0.137000	0.14449	GAC		NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522	
SLC16A1	6566	hgsc.bcm.edu	37	1	113460045	113460045	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:113460045C>T	ENST00000538576.1	-	4	1814	c.983G>A	c.(982-984)cGa>cAa	p.R328Q	SLC16A1_ENST00000433570.4_Missense_Mutation_p.R328Q|SLC16A1_ENST00000369626.3_Missense_Mutation_p.R328Q	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	328					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	ATACTGAATTCGAGGTCTTAT	0.453																																																	0			1											61.0	50.0	54.0					1																	113460045		2203	4300	6503	113261568	SO:0001583	missense	6566			BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"""Solute carriers"""	10922	protein-coding gene	gene with protein product		600682	"""solute carrier family 16 (monocarboxylic acid transporters), member 1"", ""solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"""			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.983G>A	1.37:g.113460045C>T	ENSP00000441065:p.Arg328Gln	Somatic		Capture	Illumina HiSeq	Phase_I	113261568	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080583	0.76528	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570	T;T;T;T	0.59502	0.26;0.26;0.26;0.26	5.56	4.65	0.58169	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.053038	0.64402	D	0.000001	T	0.68137	0.2968	M	0.85630	2.765	0.42796	D	0.993912	D;D	0.71674	0.996;0.998	P;D	0.65773	0.87;0.938	T	0.74080	-0.3780	10	0.59425	D	0.04	.	10.4687	0.44624	0.0:0.8501:0.0:0.1499	.	328;328	Q49A45;P53985	.;MOT1_HUMAN	Q	328	ENSP00000358640:R328Q;ENSP00000441065:R328Q;ENSP00000416167:R328Q;ENSP00000445061:R328Q	ENSP00000358640:R328Q	R	-	2	0	SLC16A1	113261568	0.962000	0.33011	0.998000	0.56505	0.902000	0.53008	2.039000	0.41193	1.481000	0.48307	0.563000	0.77884	CGA		SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051	
LMO2	4005	hgsc.bcm.edu	37	11	33881081	33881081	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:33881081G>A	ENST00000395833.3	-	3	727	c.298C>T	c.(298-300)Cgg>Tgg	p.R100W	LMO2_ENST00000257818.2_Missense_Mutation_p.R169W	NM_001142315.1|NM_001142316.1	NP_001135787.1|NP_001135788.1	P25791	RBTN2_HUMAN	LIM domain only 2 (rhombotin-like 1)	100	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cellular response to thyroid hormone stimulus (GO:0097067)|embryonic hemopoiesis (GO:0035162)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|cofactor binding (GO:0048037)|E-box binding (GO:0070888)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|zinc ion binding (GO:0008270)			NS(1)|endometrium(2)|large_intestine(1)|lung(7)|prostate(1)|stomach(1)|urinary_tract(1)	14						GCACGAATCCGCTTGTCACAG	0.488			T	TRD@	T-ALL																																			Dom	yes		11	11p13	4005	LIM domain only 2 (rhombotin-like 1) (RBTN2)		L	0			11											98.0	89.0	92.0					11																	33881081		2202	4298	6500	33837657	SO:0001583	missense	4005			X61118	CCDS7888.2, CCDS44567.1	11p13	2008-07-18			ENSG00000135363	ENSG00000135363			6642	protein-coding gene	gene with protein product	"""T-cell translocation gene 2"", ""rhombotin-like 1"""	180385		RBTNL1		2034676	Standard	NM_005574		Approved	TTG2, RHOM2, RBTN2	uc010rem.2	P25791	OTTHUMG00000157176	ENST00000395833.3:c.298C>T	11.37:g.33881081G>A	ENSP00000379175:p.Arg100Trp	Somatic		Capture	Illumina HiSeq	Phase_I	33837657	Q9HD58	Missense_Mutation	SNP	ENST00000395833.3	37	CCDS44567.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479767	0.44044	.	.	ENSG00000135363	ENST00000395833;ENST00000257818	D;D	0.87103	-2.21;-2.21	5.29	4.38	0.52667	Zinc finger, LIM-type (5);	0.052193	0.85682	N	0.000000	D	0.91290	0.7254	L	0.54323	1.7	0.58432	D	0.999999	D;D	0.89917	0.997;1.0	D;D	0.68353	0.957;0.957	D	0.92114	0.5698	10	0.66056	D	0.02	.	15.813	0.78578	0.0:0.0:0.8628:0.1372	.	169;100	P25791-3;P25791	.;RBTN2_HUMAN	W	100;169	ENSP00000379175:R100W;ENSP00000257818:R169W	ENSP00000257818:R169W	R	-	1	2	LMO2	33837657	1.000000	0.71417	1.000000	0.80357	0.014000	0.08584	4.023000	0.57211	1.391000	0.46566	-0.196000	0.12772	CGG		LMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347777.1	NM_005574	
PLEKHO1	51177	hgsc.bcm.edu	37	1	150131472	150131472	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:150131472A>G	ENST00000369124.4	+	6	1262	c.984A>G	c.(982-984)ggA>ggG	p.G328G	PLEKHO1_ENST00000025469.6_Silent_p.G294G|PLEKHO1_ENST00000369126.1_Silent_p.G145G	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	328	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTTCAGGGACTGGGAGATG	0.642																																																	0			1											52.0	57.0	56.0					1																	150131472		2203	4300	6503	148398096	SO:0001819	synonymous_variant	51177			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"""Pleckstrin homology (PH) domain containing"""	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.984A>G	1.37:g.150131472A>G		Somatic		Capture	Illumina HiSeq	Phase_I	148398096	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Silent	SNP	ENST00000369124.4	37	CCDS945.1																																																																																				PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274	
LCE3A	353142	hgsc.bcm.edu	37	1	152595447	152595447	+	Missense_Mutation	SNP	G	G	A	rs375349290		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:152595447G>A	ENST00000335674.1	-	1	132	c.133C>T	c.(133-135)Cgc>Tgc	p.R45C		NM_178431.1	NP_848518.1	Q5TA76	LCE3A_HUMAN	late cornified envelope 3A	45					keratinization (GO:0031424)					endometrium(1)|lung(5)	6	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CAGCAGCTGCGCTCGGAGCTG	0.657																																																	0			1											47.0	50.0	49.0					1																	152595447		2203	4300	6503	150862071	SO:0001583	missense	353142				CCDS1017.1	1q21.3	2008-02-05			ENSG00000185962	ENSG00000185962		"""Late cornified envelopes"""	29461	protein-coding gene	gene with protein product		612613				11698679	Standard	NM_178431		Approved	LEP13	uc010pdt.2	Q5TA76	OTTHUMG00000012397	ENST00000335674.1:c.133C>T	1.37:g.152595447G>A	ENSP00000335006:p.Arg45Cys	Somatic		Capture	Illumina HiSeq	Phase_I	150862071		Missense_Mutation	SNP	ENST00000335674.1	37	CCDS1017.1	.	.	.	.	.	.	.	.	.	.	C	8.887	0.953125	0.18431	.	.	ENSG00000185962	ENST00000335674	T	0.03553	3.89	3.61	1.65	0.23941	.	.	.	.	.	T	0.00936	0.0031	.	.	.	0.09310	N	1	B	0.23058	0.079	B	0.10450	0.005	T	0.48031	-0.9070	8	0.56958	D	0.05	.	4.2341	0.10616	0.0:0.5864:0.1897:0.2239	.	45	Q5TA76	LCE3A_HUMAN	C	45	ENSP00000335006:R45C	ENSP00000335006:R45C	R	-	1	0	LCE3A	150862071	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.720000	0.04969	0.014000	0.14944	-0.786000	0.03341	CGC		LCE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034517.2	NM_178431	
SPRR3	6707	hgsc.bcm.edu	37	1	152975543	152975543	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:152975543T>C	ENST00000295367.4	+	2	89	c.47T>C	c.(46-48)cTt>cCt	p.L16P	SPRR3_ENST00000331860.3_Missense_Mutation_p.L16P|SPRR3_ENST00000542696.1_Missense_Mutation_p.L16P	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	16					epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCACCTCAGCTTCAACAGCAG	0.488																																																	0			1											86.0	82.0	84.0					1																	152975543		2203	4300	6503	151242167	SO:0001583	missense	6707			AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.47T>C	1.37:g.152975543T>C	ENSP00000295367:p.Leu16Pro	Somatic		Capture	Illumina HiSeq	Phase_I	151242167	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	.	.	.	.	.	.	.	.	.	.	T	9.780	1.175172	0.21704	.	.	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.17370	2.5;2.28;2.5;2.34	4.49	-1.91	0.07641	.	.	.	.	.	T	0.01627	0.0052	N	0.01800	-0.715	0.19300	N	0.999975	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.47381	-0.9122	9	0.29301	T	0.29	.	8.7832	0.34804	0.0:0.3031:0.0:0.6969	.	16;16	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	P	16	ENSP00000330391:L16P;ENSP00000402016:L16P;ENSP00000295367:L16P;ENSP00000441477:L16P	ENSP00000295367:L16P	L	+	2	0	SPRR3	151242167	0.000000	0.05858	0.001000	0.08648	0.867000	0.49689	-1.227000	0.02950	-0.229000	0.09854	-0.376000	0.06991	CTT		SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
LELP1	149018	hgsc.bcm.edu	37	1	153177339	153177339	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:153177339T>C	ENST00000368747.1	+	2	266	c.156T>C	c.(154-156)tgT>tgC	p.C52C		NM_001010857.1	NP_001010857.1	Q5T871	LELP1_HUMAN	late cornified envelope-like proline-rich 1	52	Cys/Pro-rich.									NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(9)|ovary(1)|pancreas(1)|prostate(1)	19	all_lung(78;3.51e-31)|Lung NSC(65;1.34e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			GGGAAAAGTGTCCAGCACCAC	0.562																																																	0			1											181.0	148.0	159.0					1																	153177339		2203	4300	6503	151443963	SO:0001819	synonymous_variant	149018				CCDS30869.1	1q21.3	2008-02-05			ENSG00000203784	ENSG00000203784			32046	protein-coding gene	gene with protein product		611042					Standard	NM_001010857		Approved		uc001fbl.4	Q5T871	OTTHUMG00000013935	ENST00000368747.1:c.156T>C	1.37:g.153177339T>C		Somatic		Capture	Illumina HiSeq	Phase_I	151443963	A1L4E1	Silent	SNP	ENST00000368747.1	37	CCDS30869.1																																																																																				LELP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039104.1	NM_001010857	
NES	10763	hgsc.bcm.edu	37	1	156640308	156640308	+	Silent	SNP	C	C	T	rs3748571	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:156640308C>T	ENST00000368223.3	-	4	3804	c.3672G>A	c.(3670-3672)acG>acA	p.T1224T		NM_006617.1	NP_006608.1	P48681	NEST_HUMAN	nestin	1224	Tail.				brain development (GO:0007420)|cell projection morphogenesis (GO:0048858)|central nervous system development (GO:0007417)|embryonic camera-type eye development (GO:0031076)|G2/M transition of mitotic cell cycle (GO:0000086)|negative regulation of catalytic activity (GO:0043086)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein binding (GO:0032091)|positive regulation of intermediate filament depolymerization (GO:0030844)|positive regulation of neural precursor cell proliferation (GO:2000179)|stem cell proliferation (GO:0072089)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	intermediate filament binding (GO:0019215)|structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(30)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(4)	64	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCGGGGTGTACGTTGGGCTGG	0.652													C|||	1123	0.224241	0.0159	0.2882	5008	,	,		17214	0.2946		0.3032	False		,,,				2504	0.3067																0			1						C		278,4128	154.8+/-188.1	8,262,1933	79.0	78.0	79.0		3672	-6.6	0.0	1	dbSNP_107	79	2455,6145	399.5+/-346.5	350,1755,2195	no	coding-synonymous	NES	NM_006617.1		358,2017,4128	TT,TC,CC		28.5465,6.3096,21.0134		1224/1622	156640308	2733,10273	2203	4300	6503	154906932	SO:0001819	synonymous_variant	10763			X65964	CCDS1151.1	1q23	2013-01-16			ENSG00000132688	ENSG00000132688		"""Intermediate filaments type IV"""	7756	protein-coding gene	gene with protein product		600915				1478958, 9104587	Standard	NM_006617		Approved	FLJ21841	uc001fpq.3	P48681	OTTHUMG00000034299	ENST00000368223.3:c.3672G>A	1.37:g.156640308C>T		Somatic		Capture	Illumina HiSeq	Phase_I	154906932	O00552|Q3LIF5|Q5SYZ6	Silent	SNP	ENST00000368223.3	37	CCDS1151.1																																																																																				NES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082844.2	NM_006617	
OR5D16	390144	hgsc.bcm.edu	37	11	55606641	55606641	+	Silent	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:55606641C>A	ENST00000378396.1	+	1	414	c.414C>A	c.(412-414)atC>atA	p.I138I		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	138						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|large_intestine(4)|lung(26)|ovary(5)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_epithelial(135;0.208)				CAGTTGCCATCTCCCAGAAAC	0.458																																																	0			11											121.0	110.0	113.0					11																	55606641		2201	4296	6497	55363217	SO:0001819	synonymous_variant	390144			AB065783	CCDS31512.1	11q11	2012-08-09			ENSG00000205029	ENSG00000205029		"""GPCR / Class A : Olfactory receptors"""	15283	protein-coding gene	gene with protein product							Standard	NM_001005496		Approved		uc010rio.2	Q8NGK9	OTTHUMG00000154233	ENST00000378396.1:c.414C>A	11.37:g.55606641C>A		Somatic		Capture	Illumina HiSeq	Phase_I	55363217	Q6IF65|Q96RB4	Silent	SNP	ENST00000378396.1	37	CCDS31512.1																																																																																				OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496	
SPTA1	6708	hgsc.bcm.edu	37	1	158582696	158582696	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:158582696C>T	ENST00000368147.4	-	51	7225	c.7045G>A	c.(7045-7047)Gaa>Aaa	p.E2349K	SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2349	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTGATGTTTTCTGACTCCTTG	0.473																																																	0			1											107.0	102.0	104.0					1																	158582696		1949	4148	6097	156849320	SO:0001583	missense	6708			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.7045G>A	1.37:g.158582696C>T	ENSP00000357129:p.Glu2349Lys	Somatic		Capture	Illumina HiSeq	Phase_I	156849320	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	35	5.461592	0.96240	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.22336	1.96;1.96	5.39	5.39	0.77823	EF-hand-like domain (1);	0.000000	0.32624	N	0.005851	T	0.39989	0.1099	M	0.71036	2.16	0.58432	D	0.999999	D	0.71674	0.998	D	0.74348	0.983	T	0.17837	-1.0356	10	0.72032	D	0.01	.	17.8981	0.88895	0.0:1.0:0.0:0.0	.	2349	P02549	SPTA1_HUMAN	K	2349;2346	ENSP00000357130:E2349K;ENSP00000357129:E2346K	ENSP00000357129:E2346K	E	-	1	0	SPTA1	156849320	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	6.962000	0.76048	2.795000	0.96236	0.655000	0.94253	GAA		SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SMPD1	6609	hgsc.bcm.edu	37	11	6411935	6411935	+	Missense_Mutation	SNP	T	T	C	rs550365194|rs550067660|rs1050228|rs71056748|rs558809956|rs3838786	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:6411935T>C	ENST00000342245.4	+	1	275	c.107T>C	c.(106-108)gTg>gCg	p.V36A	SMPD1_ENST00000299397.3_Missense_Mutation_p.V36A|SMPD1_ENST00000527275.1_Missense_Mutation_p.V36A|SMPD1_ENST00000533196.1_3'UTR|SMPD1_ENST00000356761.2_Missense_Mutation_p.V36A	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	36			V -> A (in dbSNP:rs1050228). {ECO:0000269|PubMed:1740330}.	Missing (in Ref. 4; CAA42584). {ECO:0000305}.	cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	ATGGGCctggtgctggcgctg	0.706													T|||	2811	0.561302	0.202	0.6729	5008	,	,		11441	0.8075		0.5905	False		,,,				2504	0.684																0			11						T	ALA/VAL,ALA/VAL	1052,3322		158,736,1293	14.0	16.0	15.0		107,107	0.7	0.0	11	dbSNP_86	15	4795,3693		1471,1853,920	no	missense,missense	SMPD1	NM_000543.4,NM_001007593.2	64,64	1629,2589,2213	CC,CT,TT		43.5085,24.0512,45.4595	benign,benign	36/632,36/631	6411935	5847,7015	2187	4244	6431	6368511	SO:0001583	missense	6609			AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.107T>C	11.37:g.6411935T>C	ENSP00000340409:p.Val36Ala	Somatic		Capture	Illumina HiSeq	Phase_I	6368511	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Missense_Mutation	SNP	ENST00000342245.4	37	CCDS44531.1	1284	0.5879120879120879	106	0.21544715447154472	226	0.6243093922651933	466	0.8146853146853147	486	0.6411609498680739	T	9.778	1.174552	0.21704	0.240512	0.564915	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	T;T;T;T	0.09350	2.99;2.99;3.0;3.0	4.16	0.672	0.17935	.	0.945921	0.08638	N	0.915970	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.12243	-1.0555	9	0.19590	T	0.45	.	7.0836	0.25245	0.0:0.3281:0.4874:0.1844	rs1050228;rs2450945;rs3190530;rs11544729;rs12417689;rs16912853	36;36	E9PKS3;G3XAB5	.;.	A	36	ENSP00000299397:V36A;ENSP00000349203:V36A;ENSP00000340409:V36A;ENSP00000435350:V36A	ENSP00000299397:V36A	V	+	2	0	SMPD1	6368511	0.001000	0.12720	0.010000	0.14722	0.010000	0.07245	0.500000	0.22562	0.243000	0.21327	-0.445000	0.05633	GTG		SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
SLC25A45	283130	hgsc.bcm.edu	37	11	65147382	65147382	+	Missense_Mutation	SNP	G	G	A	rs377005228		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:65147382G>A	ENST00000527174.1	-	3	164	c.109C>T	c.(109-111)Cgg>Tgg	p.R37W	SLC25A45_ENST00000360662.3_Intron|SLC25A45_ENST00000377152.2_5'UTR|SLC25A45_ENST00000526432.1_Missense_Mutation_p.R37W|SLC25A45_ENST00000534028.1_Intron|SLC25A45_ENST00000294187.6_5'UTR|SLC25A45_ENST00000398802.1_Missense_Mutation_p.R37W|SLC25A45_ENST00000417511.2_5'UTR			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	37					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						ACGATGCCCCGGTAGGTGGTC	0.627																																																	0			11						G	,TRP/ARG	0,4102		0,0,2051	61.0	68.0	66.0		,109	4.4	1.0	11		66	3,8393		0,3,4195	no	utr-5,missense	SLC25A45	NM_001077241.1,NM_182556.2	,101	0,3,6246	AA,AG,GG		0.0357,0.0,0.024	,probably-damaging	,37/289	65147382	3,12495	2051	4198	6249	64903958	SO:0001583	missense	283130			BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.109C>T	11.37:g.65147382G>A	ENSP00000435489:p.Arg37Trp	Somatic		Capture	Illumina HiSeq	Phase_I	64903958	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.896045	0.72639	0.0	3.57E-4	ENSG00000162241	ENST00000527174;ENST00000398802;ENST00000526432;ENST00000530936	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	4.38	4.38	0.52667	Mitochondrial carrier domain (2);	.	.	.	.	D	0.88687	0.6504	M	0.89904	3.07	0.80722	D	1	D;D	0.67145	0.996;0.995	P;P	0.55303	0.761;0.773	D	0.91161	0.4961	9	0.66056	D	0.02	.	14.4776	0.67557	0.0:0.0:1.0:0.0	.	37;37	E9PJQ3;Q8N413	.;S2545_HUMAN	W	37	ENSP00000435489:R37W;ENSP00000381782:R37W;ENSP00000435547:R37W;ENSP00000431642:R37W	ENSP00000381782:R37W	R	-	1	2	SLC25A45	64903958	1.000000	0.71417	1.000000	0.80357	0.734000	0.41952	5.116000	0.64661	2.251000	0.74343	0.561000	0.74099	CGG		SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556	
CPT1A	1374	hgsc.bcm.edu	37	11	68566756	68566756	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:68566756T>G	ENST00000265641.5	-	6	777	c.623A>C	c.(622-624)gAt>gCt	p.D208A	CPT1A_ENST00000538994.1_5'Flank|CPT1A_ENST00000539743.1_Missense_Mutation_p.D208A|CPT1A_ENST00000376618.2_Missense_Mutation_p.D208A|CPT1A_ENST00000540367.1_Missense_Mutation_p.D208A	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	208					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GACAGCAAAATCTTGAGCAAG	0.408																																																	0			11											100.0	98.0	99.0					11																	68566756		2200	4294	6494	68323332	SO:0001583	missense	1374			L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.623A>C	11.37:g.68566756T>G	ENSP00000265641:p.Asp208Ala	Somatic		Capture	Illumina HiSeq	Phase_I	68323332	Q8TCU0|Q9BWK0	Missense_Mutation	SNP	ENST00000265641.5	37	CCDS8185.1	.	.	.	.	.	.	.	.	.	.	t	16.42	3.118742	0.56505	.	.	ENSG00000110090	ENST00000540367;ENST00000376618;ENST00000265641;ENST00000538308;ENST00000539743	D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	D	0.90937	0.7151	M	0.66378	2.025	0.80722	D	1	B;P;P	0.48911	0.363;0.88;0.917	B;P;P	0.51945	0.196;0.685;0.557	D	0.91130	0.4937	10	0.49607	T	0.09	.	14.1003	0.65051	0.0:0.0:0.0:1.0	.	208;208;208	B2RAQ8;P50416;P50416-2	.;CPT1A_HUMAN;.	A	208	ENSP00000439084:D208A;ENSP00000365803:D208A;ENSP00000265641:D208A;ENSP00000446108:D208A	ENSP00000265641:D208A	D	-	2	0	CPT1A	68323332	1.000000	0.71417	0.364000	0.25888	0.075000	0.17131	7.636000	0.83301	1.742000	0.51746	0.379000	0.24179	GAT		CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	
PADI1	29943	hgsc.bcm.edu	37	1	17555207	17555207	+	Missense_Mutation	SNP	T	T	A	rs371985846		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:17555207T>A	ENST00000375471.4	+	7	832	c.740T>A	c.(739-741)aTc>aAc	p.I247N		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	247					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GAGCAGGAGATCAAGTTCTAT	0.572																																					Esophageal Squamous(80;414 1257 4580 27746 50832)												0			1											142.0	145.0	144.0					1																	17555207		2203	4300	6503	17427794	SO:0001583	missense	29943			AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.740T>A	1.37:g.17555207T>A	ENSP00000364620:p.Ile247Asn	Somatic		Capture	Illumina HiSeq	Phase_I	17427794	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	T	6.452	0.451601	0.12223	.	.	ENSG00000142623	ENST00000375471	T	0.14766	2.48	4.44	4.44	0.53790	Protein-arginine deiminase (PAD), central domain (2);	0.628414	0.16721	N	0.202243	T	0.17746	0.0426	L	0.50333	1.59	0.80722	D	1	P	0.50369	0.934	P	0.47206	0.541	T	0.02208	-1.1195	10	0.29301	T	0.29	-17.4383	11.6905	0.51512	0.0:0.0:0.0:1.0	.	247	Q9ULC6	PADI1_HUMAN	N	247	ENSP00000364620:I247N	ENSP00000364620:I247N	I	+	2	0	PADI1	17427794	0.002000	0.14202	0.473000	0.27253	0.046000	0.14306	0.370000	0.20433	1.859000	0.53934	0.459000	0.35465	ATC		PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
USP35	57558	hgsc.bcm.edu	37	11	77920855	77920855	+	Missense_Mutation	SNP	A	A	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:77920855A>C	ENST00000529308.1	+	10	2215	c.1954A>C	c.(1954-1956)Acc>Ccc	p.T652P	USP35_ENST00000530267.1_Missense_Mutation_p.T220P|USP35_ENST00000530535.1_3'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.T383P|USP35_ENST00000441408.2_Missense_Mutation_p.T238P	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	652	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			CACAGAGGACACCCCCCCCAC	0.607																																																	0			11											43.0	54.0	51.0					11																	77920855		1918	4119	6037	77598503	SO:0001583	missense	57558			AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.1954A>C	11.37:g.77920855A>C	ENSP00000431876:p.Thr652Pro	Somatic		Capture	Illumina HiSeq	Phase_I	77598503		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	.	.	.	.	.	.	.	.	.	.	a	6.235	0.411447	0.11812	.	.	ENSG00000118369	ENST00000530267;ENST00000529308;ENST00000441408;ENST00000526425	T;T;T;T	0.11712	3.27;3.51;2.75;3.41	4.86	0.734	0.18294	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.616023	0.14255	N	0.331177	T	0.03348	0.0097	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42275	-0.9461	10	0.30854	T	0.27	-8.4612	4.9036	0.13788	0.4292:0.1497:0.421:0.0	.	652;238	Q9P2H5;E7EWV7	UBP35_HUMAN;.	P	220;652;238;383	ENSP00000435468:T220P;ENSP00000431876:T652P;ENSP00000400825:T238P;ENSP00000434942:T383P	ENSP00000400825:T238P	T	+	1	0	USP35	77598503	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.290000	0.18975	0.014000	0.14944	-1.111000	0.02071	ACC		USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
SLC36A4	120103	hgsc.bcm.edu	37	11	92895991	92895991	+	Silent	SNP	C	C	T	rs34525400	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr11:92895991C>T	ENST00000326402.4	-	9	1048	c.918G>A	c.(916-918)gcG>gcA	p.A306A	SLC36A4_ENST00000529184.1_Silent_p.A171A	NM_152313.2	NP_689526.2	Q6YBV0	S36A4_HUMAN	solute carrier family 36 (proton/amino acid symporter), member 4	306					L-alanine transport (GO:0015808)|proline transport (GO:0015824)|tryptophan transport (GO:0015827)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	25		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				CAATATTCAACGCTTGAGGGA	0.323													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		15291	0.0		0.0	False		,,,				2504	0.0																0			11						C		99,4303	78.3+/-116.7	1,97,2103	92.0	90.0	91.0		918	-2.9	0.2	11	dbSNP_126	91	0,8596		0,0,4298	no	coding-synonymous	SLC36A4	NM_152313.2		1,97,6401	TT,TC,CC		0.0,2.249,0.7617		306/505	92895991	99,12899	2201	4298	6499	92535639	SO:0001819	synonymous_variant	120103			AY162216	CCDS8291.1, CCDS66202.1	11q21	2013-05-22			ENSG00000180773	ENSG00000180773		"""Solute carriers"""	19660	protein-coding gene	gene with protein product		613760					Standard	XM_005273758		Approved	PAT4, FLJ38932	uc001pdn.3	Q6YBV0	OTTHUMG00000167368	ENST00000326402.4:c.918G>A	11.37:g.92895991C>T		Somatic		Capture	Illumina HiSeq	Phase_I	92535639	Q86X30|Q8IVM5|Q8N8S6	Silent	SNP	ENST00000326402.4	37	CCDS8291.1																																																																																				SLC36A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394329.2		
AKR7A2	8574	hgsc.bcm.edu	37	1	19633531	19633531	+	Silent	SNP	G	G	A	rs2231202	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:19633531G>A	ENST00000235835.3	-	5	774	c.753C>T	c.(751-753)ttC>ttT	p.F251F	RNU6-1099P_ENST00000363533.1_RNA	NM_003689.3	NP_003680.2	O43488	ARK72_HUMAN	aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)	251					carbohydrate metabolic process (GO:0005975)|cellular aldehyde metabolic process (GO:0006081)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|electron carrier activity (GO:0009055)|phenanthrene-9,10-epoxide hydrolase activity (GO:0019119)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00461)|BRCA - Breast invasive adenocarcinoma(304;1.83e-05)|Kidney(64;0.000167)|GBM - Glioblastoma multiforme(114;0.00115)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TATTCCCAAAGAAGCGGCCCA	0.602													G|||	6	0.00119808	0.0038	0.0014	5008	,	,		13940	0.0		0.0	False		,,,				2504	0.0																0			1						G		17,4389	24.3+/-50.5	0,17,2186	100.0	108.0	105.0		753	4.3	1.0	1	dbSNP_98	105	0,8600		0,0,4300	no	coding-synonymous	AKR7A2	NM_003689.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		251/360	19633531	17,12989	2203	4300	6503	19506118	SO:0001819	synonymous_variant	8574			AF026947	CCDS194.1	1p36.13	2010-09-30			ENSG00000053371	ENSG00000053371		"""Aldo-keto reductases"""	389	protein-coding gene	gene with protein product		603418				9576847	Standard	NM_003689		Approved	AFAR	uc001bbw.3	O43488	OTTHUMG00000002522	ENST00000235835.3:c.753C>T	1.37:g.19633531G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19506118	O75749|Q5TG63	Silent	SNP	ENST00000235835.3	37	CCDS194.1																																																																																				AKR7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007165.2	NM_003689	
RITA1	84934	hgsc.bcm.edu	37	12	113629545	113629545	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:113629545C>T	ENST00000548278.1	+	4	1425	c.733C>T	c.(733-735)Cgc>Tgc	p.R245C	C12orf52_ENST00000552495.1_Missense_Mutation_p.R269C|RP11-545P7.4_ENST00000552525.1_RNA|C12orf52_ENST00000549621.1_Missense_Mutation_p.R245C	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		245	Interaction with tubulin.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)			large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						TTCCAGGGCTCGCTCAGTTAG	0.587																																																	0			12											57.0	56.0	56.0					12																	113629545		2203	4300	6503	112113928	SO:0001583	missense	84934																														ENST00000548278.1:c.733C>T	12.37:g.113629545C>T	ENSP00000449841:p.Arg245Cys	Somatic		Capture	Illumina HiSeq	Phase_I	112113928	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	37	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	C	3.887	-0.024704	0.07589	.	.	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000266813	T;T;T	0.33654	1.42;1.42;1.4	4.89	-1.67	0.08238	.	0.498586	0.17804	N	0.161448	T	0.17874	0.0429	N	0.19112	0.55	0.09310	N	0.999992	B;B	0.14438	0.01;0.005	B;B	0.06405	0.002;0.002	T	0.10086	-1.0645	10	0.35671	T	0.21	0.4668	5.5682	0.17182	0.0:0.3153:0.4226:0.2621	.	269;245	F8VRG5;Q96K30	.;RITA_HUMAN	C	245;245;269;245;242	ENSP00000448289:R245C;ENSP00000449841:R245C;ENSP00000448680:R269C	ENSP00000266813:R242C	R	+	1	0	C12orf52	112113928	0.089000	0.21612	0.002000	0.10522	0.061000	0.15899	0.392000	0.20801	-0.563000	0.06078	-0.165000	0.13383	CGC		C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1		
DCP1B	196513	hgsc.bcm.edu	37	12	2062353	2062353	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:2062353G>C	ENST00000280665.6	-	7	832	c.753C>G	c.(751-753)caC>caG	p.H251Q	DCP1B_ENST00000540622.1_Missense_Mutation_p.H125Q|DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_Missense_Mutation_p.H149Q	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	251				H -> HQ (in Ref. 1; AAN62764, 2; BAB71118 and 4; AAH15368/AAH43437). {ECO:0000305}.	exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			gctgctgctgGTGGAGAGTCT	0.552																																																	0			12											36.0	42.0	40.0					12																	2062353		2203	4300	6503	1932614	SO:0001583	missense	196513			AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"""DCP1 decapping enzyme homolog B (S. cerevisiae)"""			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.753C>G	12.37:g.2062353G>C	ENSP00000280665:p.His251Gln	Somatic		Capture	Illumina HiSeq	Phase_I	1932614	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Missense_Mutation	SNP	ENST00000280665.6	37	CCDS31727.1	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.346987	0.01266	.	.	ENSG00000151065	ENST00000280665;ENST00000397173;ENST00000540622	T;T;T	0.17054	2.32;2.31;2.3	4.5	0.369	0.16151	.	1.548950	0.03620	N	0.236163	T	0.16769	0.0403	L	0.36672	1.1	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.41822	-0.9487	10	0.12766	T	0.61	0.002	15.1763	0.72913	0.0:0.5449:0.4551:0.0	.	149;251	B4DRD1;Q8IZD4	.;DCP1B_HUMAN	Q	251;149;125	ENSP00000280665:H251Q;ENSP00000380358:H149Q;ENSP00000444374:H125Q	ENSP00000280665:H251Q	H	-	3	2	DCP1B	1932614	0.003000	0.15002	0.000000	0.03702	0.002000	0.02628	-0.086000	0.11233	-0.095000	0.12351	-0.835000	0.03068	CAC		DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640	
KRAS	3845	hgsc.bcm.edu	37	12	25378647	25378647	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:25378647T>A	ENST00000256078.4	-	4	414	c.351A>T	c.(349-351)aaA>aaT	p.K117N	KRAS_ENST00000311936.3_Missense_Mutation_p.K117N|KRAS_ENST00000557334.1_Intron|AC087239.1_ENST00000594112.1_5'Flank	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	117			K -> N (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.K117N(9)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCAAATCACATTTATTTCCTA	0.358		119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)			Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	9	Substitution - Missense(9)	large_intestine(8)|haematopoietic_and_lymphoid_tissue(1)	12											164.0	149.0	154.0					12																	25378647		2202	4299	6501	25269914	SO:0001583	missense	3845	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.351A>T	12.37:g.25378647T>A	ENSP00000256078:p.Lys117Asn	Somatic		Capture	Illumina HiSeq	Phase_I	25269914	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.959738	0.74016	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.94650	-3.48;-2.31	5.52	0.583	0.17417	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.98448	0.9483	H	0.99940	5	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.976;0.998	D	0.96017	0.9006	10	0.72032	D	0.01	.	9.1263	0.36816	0.0:0.4112:0.0:0.5888	.	117;117	P01116-2;P01116	.;RASK_HUMAN	N	117	ENSP00000308495:K117N;ENSP00000256078:K117N	ENSP00000256078:K117N	K	-	3	2	KRAS	25269914	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.664000	0.25068	0.131000	0.18576	0.477000	0.44152	AAA		KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
WDR66	144406	hgsc.bcm.edu	37	12	122359392	122359392	+	Missense_Mutation	SNP	G	G	A	rs114531812		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:122359392G>A	ENST00000288912.4	+	2	1035	c.181G>A	c.(181-183)Gaa>Aaa	p.E61K	WDR66_ENST00000397454.2_Missense_Mutation_p.E61K	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	61	Glu-rich.		E -> G (in dbSNP:rs12824001).				calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		gggcgaggaggaaggggagga	0.468																																					Esophageal Squamous(85;849 1794 49757 52143)												0			12											51.0	54.0	53.0					12																	122359392		1941	4124	6065	120843775	SO:0001583	missense	144406			AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.181G>A	12.37:g.122359392G>A	ENSP00000288912:p.Glu61Lys	Somatic		Capture	Illumina HiSeq	Phase_I	120843775	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	G	12.11	1.839198	0.32513	.	.	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.12984	2.69;2.63	2.92	-1.07	0.09968	.	.	.	.	.	T	0.07593	0.0191	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35025	-0.9805	9	0.42905	T	0.14	.	3.4144	0.07371	0.3738:0.2278:0.3984:0.0	.	61	Q8TBY9	WDR66_HUMAN	K	61	ENSP00000288912:E61K;ENSP00000380595:E61K	ENSP00000288912:E61K	E	+	1	0	WDR66	120843775	0.000000	0.05858	0.000000	0.03702	0.263000	0.26337	-0.063000	0.11655	-0.231000	0.09825	0.313000	0.20887	GAA		WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
ACTN2	88	hgsc.bcm.edu	37	1	236924324	236924324	+	Missense_Mutation	SNP	G	G	A	rs145450474		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:236924324G>A	ENST00000366578.4	+	20	2543	c.2377G>A	c.(2377-2379)Gaa>Aaa	p.E793K	ACTN2_ENST00000546208.1_Missense_Mutation_p.E287K|ACTN2_ENST00000542672.1_Missense_Mutation_p.E793K	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	793	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			GGGTGAAGCCGAATTTGCCCG	0.512																																																	0			1						G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	179.0	145.0	156.0		2377	5.8	1.0	1	dbSNP_134	156	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACTN2	NM_001103.2	56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	possibly-damaging	793/895	236924324	2,13004	2203	4300	6503	234990947	SO:0001583	missense	88			BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.2377G>A	1.37:g.236924324G>A	ENSP00000355537:p.Glu793Lys	Somatic		Capture	Illumina HiSeq	Phase_I	234990947	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Missense_Mutation	SNP	ENST00000366578.4	37	CCDS1613.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851598	0.97023	2.27E-4	1.16E-4	ENSG00000077522	ENST00000542672;ENST00000366578;ENST00000546208;ENST00000545611	D;D;D	0.84223	-1.82;-1.82;-1.82	5.78	5.78	0.91487	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.94430	0.8208	M	0.91354	3.2	0.80722	D	1	D;P;D;D	0.89917	1.0;0.727;1.0;0.978	D;B;D;D	0.87578	0.998;0.256;0.998;0.921	D	0.94925	0.8077	10	0.87932	D	0	.	20.0197	0.97489	0.0:0.0:1.0:0.0	.	578;793;563;793	B7Z4K1;B2RCS5;Q59FD9;P35609	.;.;.;ACTN2_HUMAN	K	793;793;287;562	ENSP00000443495:E793K;ENSP00000355537:E793K;ENSP00000438384:E287K	ENSP00000355537:E793K	E	+	1	0	ACTN2	234990947	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	9.831000	0.99420	2.718000	0.92993	0.655000	0.94253	GAA		ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
RYR2	6262	hgsc.bcm.edu	37	1	237666672	237666672	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:237666672T>C	ENST00000366574.2	+	22	2797	c.2480T>C	c.(2479-2481)cTg>cCg	p.L827P	RYR2_ENST00000542537.1_Missense_Mutation_p.L811P|RYR2_ENST00000360064.6_Missense_Mutation_p.L825P	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	827					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			GAAGCTGTTCTGCCAAAAGAA	0.488																																																	0			1											89.0	90.0	90.0					1																	237666672		1942	4137	6079	235733295	SO:0001583	missense	6262			X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.2480T>C	1.37:g.237666672T>C	ENSP00000355533:p.Leu827Pro	Somatic		Capture	Illumina HiSeq	Phase_I	235733295	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614381	0.87359	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97186	-4.28;-4.25;-4.27	5.86	5.86	0.93980	.	0.000000	0.48767	D	0.000171	D	0.98388	0.9464	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99187	1.0869	10	0.59425	D	0.04	.	16.5602	0.84551	0.0:0.0:0.0:1.0	.	827	Q92736	RYR2_HUMAN	P	827;825;811	ENSP00000355533:L827P;ENSP00000353174:L825P;ENSP00000443798:L811P	ENSP00000353174:L825P	L	+	2	0	RYR2	235733295	0.998000	0.40836	0.997000	0.53966	0.968000	0.65278	7.990000	0.88215	2.367000	0.80283	0.528000	0.53228	CTG		RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
WDR64	128025	hgsc.bcm.edu	37	1	241886616	241886616	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:241886616C>T	ENST00000366552.2	+	9	1249	c.1042C>T	c.(1042-1044)Cgg>Tgg	p.R348W	WDR64_ENST00000437684.2_Missense_Mutation_p.R348W	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	348										breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(17)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	Ovarian(103;0.103)	all_cancers(173;0.0121)	OV - Ovarian serous cystadenocarcinoma(106;0.0116)			TAAGGTCATCCGGTTGTGGCA	0.443																																																	0			1											108.0	100.0	103.0					1																	241886616		2203	4300	6503	239953239	SO:0001583	missense	128025			AK057540		1q43	2013-01-09			ENSG00000162843	ENSG00000162843		"""WD repeat domain containing"""	26570	protein-coding gene	gene with protein product							Standard	NM_144625		Approved	FLJ32978	uc001hzg.2	B1ANS9	OTTHUMG00000039705	ENST00000366552.2:c.1042C>T	1.37:g.241886616C>T	ENSP00000355510:p.Arg348Trp	Somatic		Capture	Illumina HiSeq	Phase_I	239953239	B1ANT0|Q7Z573|Q96LY9	Missense_Mutation	SNP	ENST00000366552.2	37		.	.	.	.	.	.	.	.	.	.	C	14.83	2.653764	0.47362	.	.	ENSG00000162843	ENST00000366552;ENST00000437684;ENST00000414635	T;T;T	0.43688	1.97;0.94;4.85	4.7	3.71	0.42584	.	0.133058	0.33553	N	0.004794	T	0.61489	0.2351	M	0.73598	2.24	0.36875	D	0.889129	D	0.89917	1.0	D	0.91635	0.999	T	0.70428	-0.4874	10	0.87932	D	0	-10.0835	11.161	0.48516	0.1839:0.8161:0.0:0.0	.	68	D1MPS4	.	W	348;348;119	ENSP00000355510:R348W;ENSP00000402446:R348W;ENSP00000406656:R119W	ENSP00000355510:R348W	R	+	1	2	WDR64	239953239	1.000000	0.71417	0.833000	0.33012	0.363000	0.29612	2.807000	0.47955	2.308000	0.77769	0.563000	0.77884	CGG		WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625	
KRT4	3851	hgsc.bcm.edu	37	12	53207603	53207603	+	Silent	SNP	A	A	G	rs7135148		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:53207603A>G	ENST00000551956.1	-	1	732	c.240T>C	c.(238-240)ttT>ttC	p.F80F	KRT4_ENST00000293774.4_Silent_p.F154F|KRT4_ENST00000458244.2_Silent_p.F60F			P19013	K2C4_HUMAN	keratin 4	80	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CACCAGTGCCAAAGCCTCCAG	0.602																																					Pancreas(190;284 2995 41444 45903)												0			12											82.0	99.0	94.0					12																	53207603		2119	4253	6372	51493870	SO:0001819	synonymous_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240T>C	12.37:g.53207603A>G		Somatic		Capture	Illumina HiSeq	Phase_I	51493870	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																				KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
KRT4	3851	hgsc.bcm.edu	37	12	53207606	53207606	+	Silent	SNP	G	G	A	rs79164931		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:53207606G>A	ENST00000551956.1	-	1	729	c.237C>T	c.(235-237)ggC>ggT	p.G79G	KRT4_ENST00000293774.4_Silent_p.G153G|KRT4_ENST00000458244.2_Silent_p.G59G			P19013	K2C4_HUMAN	keratin 4	79	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CAGTGCCAAAGCCTCCAGCAC	0.597																																					Pancreas(190;284 2995 41444 45903)												0			12											85.0	102.0	96.0					12																	53207606		2113	4248	6361	51493873	SO:0001819	synonymous_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.237C>T	12.37:g.53207606G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51493873	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Silent	SNP	ENST00000551956.1	37	CCDS41787.2																																																																																				KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
PAFAH2	5051	hgsc.bcm.edu	37	1	26303229	26303229	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:26303229T>C	ENST00000374282.3	-	8	881	c.702A>G	c.(700-702)ggA>ggG	p.G234G	PAFAH2_ENST00000374284.1_Silent_p.G234G	NM_000437.3	NP_000428.2	Q99487	PAFA2_HUMAN	platelet-activating factor acetylhydrolase 2, 40kDa	234					lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)	1-alkyl-2-acetylglycerophosphocholine esterase activity (GO:0003847)|phospholipid binding (GO:0005543)			NS(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|urinary_tract(1)	9		Colorectal(325;3.47e-05)|Lung NSC(340;6.23e-05)|all_lung(284;9.48e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.84e-25)|Colorectal(126;3.57e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00155)|GBM - Glioblastoma multiforme(114;0.00717)|READ - Rectum adenocarcinoma(331;0.0649)		CAAATGAATGTCCCATCACAG	0.493																																																	0			1											94.0	80.0	85.0					1																	26303229		2203	4300	6503	26175816	SO:0001819	synonymous_variant	5051			D87845	CCDS270.1	1p34.3	2008-09-19	2002-08-29		ENSG00000158006	ENSG00000158006			8579	protein-coding gene	gene with protein product		602344	"""platelet-activating factor acetylhydrolase 2 (40kD)"""			8955149, 9494101	Standard	NM_000437		Approved	HSD-PLA2	uc001bld.4	Q99487	OTTHUMG00000007437	ENST00000374282.3:c.702A>G	1.37:g.26303229T>C		Somatic		Capture	Illumina HiSeq	Phase_I	26175816	D3DPK1|O15458|Q5SY02	Silent	SNP	ENST00000374282.3	37	CCDS270.1																																																																																				PAFAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019544.1	NM_000437	
NALCN	259232	hgsc.bcm.edu	37	13	101717772	101717772	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:101717772A>G	ENST00000251127.6	-	40	4669	c.4588T>C	c.(4588-4590)Ttc>Ctc	p.F1530L		NM_052867.2	NP_443099.1	Q8IZF0	NALCN_HUMAN	sodium leak channel, non-selective	1530					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|membrane depolarization during action potential (GO:0086010)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium channel activity (GO:0005272)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|autonomic_ganglia(2)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(33)|liver(2)|lung(81)|ovary(8)|pancreas(3)|prostate(5)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	177	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)					ACATCATGGAAGGTGACGTCG	0.552																																																	0			13											154.0	125.0	135.0					13																	101717772		2203	4300	6503	100515773	SO:0001583	missense	259232			AY141972	CCDS9498.1	13q32.3	2012-02-21	2007-04-26	2007-04-26	ENSG00000102452	ENSG00000102452		"""Ion channels / Sodium leak channels, non-selective"""	19082	protein-coding gene	gene with protein product		611549	"""voltage gated channel like 1"""	VGCNL1		17448995	Standard	XM_006719943		Approved	bA430M15.1, CanIon	uc001vox.1	Q8IZF0	OTTHUMG00000017295	ENST00000251127.6:c.4588T>C	13.37:g.101717772A>G	ENSP00000251127:p.Phe1530Leu	Somatic		Capture	Illumina HiSeq	Phase_I	100515773	Q6P2S6|Q6ZMI7|Q8IZZ1|Q8TAH1	Missense_Mutation	SNP	ENST00000251127.6	37	CCDS9498.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.918562	0.92249	.	.	ENSG00000102452	ENST00000251127	D	0.98684	-5.07	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.98745	0.9578	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99892	1.1137	10	0.59425	D	0.04	.	15.9883	0.80179	1.0:0.0:0.0:0.0	.	1530	Q8IZF0	NALCN_HUMAN	L	1530	ENSP00000251127:F1530L	ENSP00000251127:F1530L	F	-	1	0	NALCN	100515773	1.000000	0.71417	0.977000	0.42913	0.829000	0.46940	8.956000	0.93066	2.172000	0.68678	0.533000	0.62120	TTC		NALCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045663.2	NM_052867	
SPOCD1	90853	hgsc.bcm.edu	37	1	32262288	32262288	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:32262288T>C	ENST00000360482.2	-	10	2303	c.2174A>G	c.(2173-2175)aAg>aGg	p.K725R	SPOCD1_ENST00000373648.2_3'UTR|SPOCD1_ENST00000533231.1_Missense_Mutation_p.K725R|SPOCD1_ENST00000257100.3_Missense_Mutation_p.K218R	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	725	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				negative regulation of phosphatase activity (GO:0010923)|transcription, DNA-templated (GO:0006351)					NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|liver(1)|lung(7)|ovary(6)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	37		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)|Ovarian(437;0.199)		STAD - Stomach adenocarcinoma(196;0.18)		GCACGGCTCCTTCTGTTGCTG	0.567																																																	0			1											145.0	137.0	140.0					1																	32262288		2203	4300	6503	32034875	SO:0001583	missense	90853			AK058077	CCDS347.1, CCDS60066.1, CCDS72748.1	1p35.1	2014-06-13			ENSG00000134668	ENSG00000134668			26338	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 146"""					12477932	Standard	NM_144569		Approved	FLJ25348, PPP1R146	uc001bts.1	Q6ZMY3	OTTHUMG00000003879	ENST00000360482.2:c.2174A>G	1.37:g.32262288T>C	ENSP00000353670:p.Lys725Arg	Somatic		Capture	Illumina HiSeq	Phase_I	32034875	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.	.	.	.	.	.	.	.	.	.	T	8.531	0.870903	0.17322	.	.	ENSG00000134668	ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231	T;T;T;T	0.45276	0.9;1.92;0.93;1.91	4.34	1.64	0.23874	Transcription elongation factor S-II, central domain (1);	.	.	.	.	T	0.15869	0.0382	N	0.05078	-0.115	0.80722	D	1	B;B;B;B	0.22746	0.039;0.074;0.007;0.044	B;B;B;B	0.25140	0.01;0.058;0.006;0.036	T	0.14254	-1.0479	9	0.05959	T	0.93	-11.2123	4.7501	0.13056	0.0:0.3215:0.0:0.6785	.	69;725;162;725	Q6ZMY3-4;Q6ZMY3-2;E9PPM7;Q6ZMY3	.;.;.;SPOC1_HUMAN	R	218;725;123;162;725	ENSP00000257100:K218R;ENSP00000353670:K725R;ENSP00000399778:K162R;ENSP00000435851:K725R	ENSP00000257100:K218R	K	-	2	0	SPOCD1	32034875	0.988000	0.35896	0.996000	0.52242	0.808000	0.45660	0.107000	0.15375	0.644000	0.30656	0.379000	0.24179	AAG		SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569	
PARP4	143	hgsc.bcm.edu	37	13	25052321	25052321	+	Silent	SNP	A	A	G	rs149727830		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:25052321A>G	ENST00000381989.3	-	13	1647	c.1542T>C	c.(1540-1542)caT>caC	p.H514H		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	514	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		AGTCCTTCTCATGTAAGTCCA	0.473																																																	0			13											113.0	91.0	98.0					13																	25052321		2203	4300	6503	23950321	SO:0001819	synonymous_variant	143			AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.1542T>C	13.37:g.25052321A>G		Somatic		Capture	Illumina HiSeq	Phase_I	23950321	O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	CCDS9307.1																																																																																				PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
MTIF3	219402	hgsc.bcm.edu	37	13	28009776	28009776	+	3'UTR	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:28009776G>A	ENST00000405591.2	-	0	1068				MTIF3_ENST00000431572.2_3'UTR|MTIF3_ENST00000461838.1_5'Flank|GTF3A_ENST00000470606.1_3'UTR|GTF3A_ENST00000381140.4_3'UTR	NM_001166261.1|NM_001166262.1	NP_001159733.1|NP_001159734.1	Q9H2K0	IF3M_HUMAN	mitochondrial translational initiation factor 3						formation of translation initiation complex (GO:0001732)|regulation of translational initiation (GO:0006446)|ribosome disassembly (GO:0032790)	mitochondrion (GO:0005739)	ribosomal small subunit binding (GO:0043024)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	7		Lung SC(185;0.0161)	Colorectal(13;0.00042)|READ - Rectum adenocarcinoma(15;0.105)	all cancers(112;0.108)|OV - Ovarian serous cystadenocarcinoma(117;0.157)		ACCAAGGAGCGAGCTTTCTCT	0.418																																																	0			13											104.0	106.0	105.0					13																	28009776		2203	4300	6503	26907776	SO:0001624	3_prime_UTR_variant	219402			BC046166	CCDS9322.1	13q12.2	2007-05-03			ENSG00000122033	ENSG00000122033			29788	protein-coding gene	gene with protein product						12095986	Standard	NM_152912		Approved	IF-3mt, IF3(mt)	uc001uri.3	Q9H2K0	OTTHUMG00000016633	ENST00000405591.2:c.*36C>T	13.37:g.28009776G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26907776	Q05BL8|Q5W0V0|Q86X68	Splice_Site	SNP	ENST00000405591.2	37	CCDS9322.1																																																																																				MTIF3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044301.2	NM_152912	
ELF1	1997	hgsc.bcm.edu	37	13	41515327	41515327	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:41515327G>A	ENST00000239882.3	-	8	1300	c.986C>T	c.(985-987)tCg>tTg	p.S329L	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Missense_Mutation_p.S305L	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	329					cell differentiation (GO:0030154)|negative regulation of T cell receptor signaling pathway (GO:0050860)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine production (GO:0001817)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37		Lung NSC(96;8.3e-05)|Prostate(109;0.0233)|Breast(139;0.0296)|Lung SC(185;0.0367)		all cancers(112;1.87e-08)|Epithelial(112;8.45e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000202)|GBM - Glioblastoma multiforme(144;0.00266)|BRCA - Breast invasive adenocarcinoma(63;0.072)		AGATACTCTCGACCGGCTGGT	0.428																																																	0			13											118.0	126.0	123.0					13																	41515327		2203	4300	6503	40413327	SO:0001583	missense	84337			M82882	CCDS9374.1	13q13	2008-07-18			ENSG00000120690	ENSG00000120690			3316	protein-coding gene	gene with protein product		189973				1545787	Standard	NM_001145353		Approved		uc001uxs.3	P32519	OTTHUMG00000016783	ENST00000239882.3:c.986C>T	13.37:g.41515327G>A	ENSP00000239882:p.Ser329Leu	Somatic		Capture	Illumina HiSeq	Phase_I	40413327	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Missense_Mutation	SNP	ENST00000239882.3	37	CCDS9374.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167161	0.38217	.	.	ENSG00000120690	ENST00000442101;ENST00000379498;ENST00000239882	T;T	0.54479	0.57;0.57	5.47	5.47	0.80525	.	0.214873	0.41605	D	0.000847	T	0.40067	0.1102	L	0.34521	1.04	0.52099	D	0.999949	P;P	0.43750	0.669;0.816	B;B	0.27380	0.057;0.079	T	0.49551	-0.8928	10	0.62326	D	0.03	.	19.6893	0.95993	0.0:0.0:1.0:0.0	.	305;329	E9PDQ9;P32519	.;ELF1_HUMAN	L	305;71;329	ENSP00000405580:S305L;ENSP00000239882:S329L	ENSP00000239882:S329L	S	-	2	0	ELF1	40413327	1.000000	0.71417	0.726000	0.30738	0.026000	0.11368	6.515000	0.73751	2.729000	0.93468	0.655000	0.94253	TCG		ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373	
C1orf94	84970	hgsc.bcm.edu	37	1	34666527	34666527	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:34666527T>C	ENST00000488417.1	+	3	1284	c.1164T>C	c.(1162-1164)tgT>tgC	p.C388C	C1orf94_ENST00000373374.3_Silent_p.C198C	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	388										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				AACCTACATGTCCAGCCGAGA	0.607																																																	0			1											55.0	55.0	55.0					1																	34666527		2203	4300	6503	34439114	SO:0001819	synonymous_variant	84970			AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.1164T>C	1.37:g.34666527T>C		Somatic		Capture	Illumina HiSeq	Phase_I	34439114	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Silent	SNP	ENST00000488417.1	37	CCDS44108.1																																																																																				C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
ALG11	440138	hgsc.bcm.edu	37	13	52586597	52586597	+	Splice_Site	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:52586597A>G	ENST00000521508.1	+	1	48	c.43A>G	c.(43-45)Agg>Ggg	p.R15G	ATP7B_ENST00000400366.3_5'Flank|ATP7B_ENST00000448424.2_5'Flank|ATP7B_ENST00000344297.5_5'Flank|ATP7B_ENST00000242839.4_5'Flank|ATP7B_ENST00000400370.3_5'Flank|ATP7B_ENST00000418097.2_5'Flank|ALG11_ENST00000523764.1_Splice_Site_p.R15G	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	15					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		CAAGTTGTTGAGGTGAGCAGC	0.562																																																	0			13											95.0	87.0	89.0					13																	52586597		2203	4300	6503	51484598	SO:0001630	splice_region_variant	440138			AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.44+1A>G	13.37:g.52586597A>G		Somatic		Capture	Illumina HiSeq	Phase_I	51484598	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	37	CCDS31977.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.313977	0.23908	.	.	ENSG00000253710	ENST00000523764;ENST00000521508	T;T	0.78126	0.77;-1.15	5.1	3.89	0.44902	.	0.000000	0.85682	U	0.000000	T	0.77061	0.4075	M	0.79123	2.44	0.53005	D	0.999964	P	0.46706	0.883	B	0.42827	0.399	T	0.78013	-0.2370	10	0.72032	D	0.01	.	8.8967	0.35470	0.7294:0.2706:0.0:0.0	.	15	Q2TAA5	ALG11_HUMAN	G	15	ENSP00000429497:R15G;ENSP00000430236:R15G	ENSP00000430236:R15G	R	+	1	2	ALG11	51484598	1.000000	0.71417	0.994000	0.49952	0.245000	0.25701	2.461000	0.45040	0.984000	0.38629	0.482000	0.46254	AGG		ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	Missense_Mutation
CLSPN	63967	hgsc.bcm.edu	37	1	36213602	36213602	+	Missense_Mutation	SNP	C	C	G	rs561888056		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:36213602C>G	ENST00000318121.3	-	14	2590	c.2533G>C	c.(2533-2535)Gcc>Ccc	p.A845P	CLSPN_ENST00000251195.5_Missense_Mutation_p.A845P|CLSPN_ENST00000520551.1_Missense_Mutation_p.A792P|CLSPN_ENST00000373220.3_Missense_Mutation_p.A781P	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	845					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				TCTGGGGAGGCGTTATACAGA	0.448																																																	0			1											224.0	234.0	231.0					1																	36213602		2203	4300	6503	35986189	SO:0001583	missense	63967			AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.2533G>C	1.37:g.36213602C>G	ENSP00000312995:p.Ala845Pro	Somatic		Capture	Illumina HiSeq	Phase_I	35986189	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	.	.	.	.	.	.	.	.	.	.	C	14.79	2.640477	0.47153	.	.	ENSG00000092853	ENST00000251195;ENST00000318121;ENST00000373220;ENST00000520551	T;T;T;T	0.31769	1.48;1.5;1.6;1.59	5.69	4.78	0.61160	.	0.053886	0.85682	D	0.000000	T	0.51398	0.1672	L	0.60455	1.87	0.52099	D	0.99994	D;P	0.89917	1.0;0.837	D;B	0.79784	0.993;0.353	T	0.52675	-0.8544	10	0.54805	T	0.06	-2.2542	14.8584	0.70359	0.0:0.9309:0.0:0.0691	.	781;845	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	P	845;845;781;792	ENSP00000251195:A845P;ENSP00000312995:A845P;ENSP00000362317:A781P;ENSP00000428848:A792P	ENSP00000251195:A845P	A	-	1	0	CLSPN	35986189	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.011000	0.40922	1.409000	0.46915	0.563000	0.77884	GCC		CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
COMMD6	170622	hgsc.bcm.edu	37	13	76111932	76111932	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr13:76111932A>G	ENST00000377615.3	-	2	174	c.10T>C	c.(10-12)Tcc>Ccc	p.S4P	COMMD6_ENST00000406936.3_Missense_Mutation_p.S4P|COMMD6_ENST00000377619.5_5'Flank|COMMD6_ENST00000460675.1_Intron|COMMD6_ENST00000355801.4_Missense_Mutation_p.S4P			Q7Z4G1	COMD6_HUMAN	COMM domain containing 6	4					negative regulation of NF-kappaB transcription factor activity (GO:0032088)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			breast(1)|lung(1)|urinary_tract(1)	3		Breast(118;0.0979)|Prostate(6;0.122)		GBM - Glioblastoma multiforme(99;0.0104)		GGCTCGCTGGACGCCTCCATG	0.632																																																	0			13											73.0	74.0	74.0					13																	76111932		2203	4300	6503	75009933	SO:0001583	missense	170622			AY542161	CCDS9451.1, CCDS9452.1	13q22	2004-02-18			ENSG00000188243	ENSG00000188243			24015	protein-coding gene	gene with protein product		612377				15799966	Standard	NM_203497		Approved	Acrg	uc001vjn.1	Q7Z4G1	OTTHUMG00000017089	ENST00000377615.3:c.10T>C	13.37:g.76111932A>G	ENSP00000366841:p.Ser4Pro	Somatic		Capture	Illumina HiSeq	Phase_I	75009933	A6NF28|B7ZLN0|Q5TBK4	Missense_Mutation	SNP	ENST00000377615.3	37	CCDS9451.1	.	.	.	.	.	.	.	.	.	.	a	10.52	1.373613	0.24857	.	.	ENSG00000188243	ENST00000406936;ENST00000377615;ENST00000355801	T;T;T	0.48201	0.86;0.86;0.82	4.52	-4.63	0.03359	.	0.970579	0.08519	N	0.933780	T	0.25938	0.0632	.	.	.	0.09310	N	1	B;P	0.35982	0.072;0.531	B;B	0.31812	0.018;0.136	T	0.17258	-1.0375	9	0.48119	T	0.1	.	2.4675	0.04556	0.2416:0.1375:0.0846:0.5362	.	4;4	Q7Z4G1;Q7Z4G1-2	COMD6_HUMAN;.	P	4	ENSP00000385660:S4P;ENSP00000366841:S4P;ENSP00000348054:S4P	ENSP00000348054:S4P	S	-	1	0	COMMD6	75009933	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.282000	0.08445	-0.626000	0.05596	-3.262000	0.00049	TCC		COMMD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045288.4	XM_085023	
MACF1	23499	hgsc.bcm.edu	37	1	39913186	39913186	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:39913186A>G	ENST00000372915.3	+	80	19472	c.19385A>G	c.(19384-19386)gAg>gGg	p.E6462G	MACF1_ENST00000545844.1_Missense_Mutation_p.E4504G|MACF1_ENST00000567887.1_Missense_Mutation_p.E6600G|MACF1_ENST00000539005.1_Missense_Mutation_p.E4374G|MACF1_ENST00000361689.2_Missense_Mutation_p.E4504G|MACF1_ENST00000564288.1_Missense_Mutation_p.E6563G|MACF1_ENST00000317713.7_Missense_Mutation_p.E4504G|MACF1_ENST00000289893.4_Missense_Mutation_p.E5006G			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6462			E -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACTCTAGCAGAGCAGAGTTTA	0.408																																																	0			1											95.0	96.0	96.0					1																	39913186		2203	4300	6503	39685773	SO:0001583	missense	23499			AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.19385A>G	1.37:g.39913186A>G	ENSP00000362006:p.Glu6462Gly	Somatic		Capture	Illumina HiSeq	Phase_I	39685773	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	A	28.2	4.903802	0.92035	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	6.07	6.07	0.98685	.	0.000000	0.64402	D	0.000005	T	0.74574	0.3734	M	0.88450	2.955	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	T	0.79787	-0.1656	10	0.87932	D	0	.	16.6277	0.84984	1.0:0.0:0.0:0.0	.	6462;4504	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	G	4504;6462;4504;4504;4374;5006	ENSP00000439537:E4504G;ENSP00000362006:E6462G;ENSP00000354573:E4504G;ENSP00000313438:E4504G;ENSP00000444364:E4374G;ENSP00000289893:E5006G	ENSP00000289893:E5006G	E	+	2	0	MACF1	39685773	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.330000	0.79161	0.528000	0.53228	GAG		MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
HPCAL4	51440	hgsc.bcm.edu	37	1	40149642	40149642	+	Silent	SNP	G	G	T	rs784634	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:40149642G>T	ENST00000372844.3	-	3	736	c.345C>A	c.(343-345)cgC>cgA	p.R115R		NM_001282396.1|NM_001282397.1|NM_016257.2	NP_001269325.1|NP_001269326.1|NP_057341.1	Q9UM19	HPCL4_HUMAN	hippocalcin like 4	115	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				central nervous system development (GO:0007417)|signal transduction (GO:0007165)	intracellular (GO:0005622)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|lung(5)|stomach(1)	8	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GGCGCGTGATGCGCCCGTCGC	0.692													G|||	4288	0.85623	0.9191	0.8256	5008	,	,		12058	0.8165		0.825	False		,,,				2504	0.8661																0			1						G		3857,547	762.6+/-413.1	1694,469,39	40.0	42.0	41.0		345	3.5	1.0	1	dbSNP_86	41	6936,1664	729.4+/-406.7	2788,1360,152	no	coding-synonymous	HPCAL4	NM_016257.2		4482,1829,191	TT,TG,GG		19.3488,12.4205,17.0025		115/192	40149642	10793,2211	2202	4300	6502	39922229	SO:0001819	synonymous_variant	51440			AB001105	CCDS441.1, CCDS72761.1	1p34.2	2013-01-10			ENSG00000116983	ENSG00000116983		"""EF-hand domain containing"""	18212	protein-coding gene	gene with protein product						10520747	Standard	NM_016257		Approved	HLP4, DKFZp761G122	uc001cdr.3	Q9UM19	OTTHUMG00000009246	ENST00000372844.3:c.345C>A	1.37:g.40149642G>T		Somatic		Capture	Illumina HiSeq	Phase_I	39922229	B2R5U2|D3DPU1|Q5TG97|Q8N611	Silent	SNP	ENST00000372844.3	37	CCDS441.1																																																																																				HPCAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025640.1	NM_016257	
RTL1	388015	hgsc.bcm.edu	37	14	101350472	101350472	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:101350472T>C	ENST00000534062.1	-	1	712	c.654A>G	c.(652-654)gtA>gtG	p.V218V	MIR136_ENST00000385207.1_RNA|MIR432_ENST00000606207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	218					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GTTGGCAGAGTACGATGAACT	0.493																																																	0			14											133.0	109.0	116.0					14																	101350472		692	1591	2283	100420225	SO:0001819	synonymous_variant	388015				CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.654A>G	14.37:g.101350472T>C		Somatic		Capture	Illumina HiSeq	Phase_I	100420225	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																				RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
SLFNL1	200172	hgsc.bcm.edu	37	1	41481845	41481845	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:41481845T>C	ENST00000359345.1	-	4	3733	c.1157A>G	c.(1156-1158)gAg>gGg	p.E386G	SLFNL1_ENST00000302946.8_Missense_Mutation_p.E386G|SLFNL1_ENST00000372611.1_Missense_Mutation_p.E327G|SLFNL1_ENST00000439569.2_Missense_Mutation_p.E386G|SLFNL1_ENST00000372613.2_Missense_Mutation_p.E338G|SLFNL1_ENST00000397197.2_Missense_Mutation_p.E338G	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	386							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				CTGCTCCTTCTCCATCATCAG	0.642																																																	0			1											93.0	84.0	87.0					1																	41481845		2203	4300	6503	41254432	SO:0001583	missense	200172			BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1157A>G	1.37:g.41481845T>C	ENSP00000352299:p.Glu386Gly	Somatic		Capture	Illumina HiSeq	Phase_I	41254432	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.239922	0.58995	.	.	ENSG00000171790	ENST00000302946;ENST00000372613;ENST00000372611;ENST00000359345;ENST00000439569;ENST00000397197	T;T;T;T;T;T	0.37915	1.37;1.17;1.5;1.37;1.37;1.17	5.25	5.25	0.73442	.	0.000000	0.49916	D	0.000130	T	0.47728	0.1461	L	0.34521	1.04	0.36682	D	0.879113	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.994;0.996	T	0.57974	-0.7718	10	0.87932	D	0	-35.3513	11.5599	0.50769	0.0:0.0:0.0:1.0	.	338;327;386	Q499Z3-3;Q499Z3-2;Q499Z3	.;.;SLNL1_HUMAN	G	386;338;327;386;386;338	ENSP00000304401:E386G;ENSP00000361696:E338G;ENSP00000361694:E327G;ENSP00000352299:E386G;ENSP00000398938:E386G;ENSP00000380381:E338G	ENSP00000304401:E386G	E	-	2	0	SLFNL1	41254432	1.000000	0.71417	0.925000	0.36789	0.373000	0.29922	4.572000	0.60886	1.991000	0.58162	0.459000	0.35465	GAG		SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
DLGAP5	9787	hgsc.bcm.edu	37	14	55636179	55636179	+	Nonsense_Mutation	SNP	G	G	A	rs565083852		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:55636179G>A	ENST00000247191.2	-	12	1702	c.1486C>T	c.(1486-1488)Cga>Tga	p.R496*	DLGAP5_ENST00000395425.2_Nonsense_Mutation_p.R496*	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	496					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TTTATACCTCGTTTATATTCA	0.363													G|||	1	0.000199681	0.0	0.0	5008	,	,		16074	0.001		0.0	False		,,,				2504	0.0																0			14											116.0	105.0	109.0					14																	55636179		2203	4300	6503	54705932	SO:0001587	stop_gained	9787			D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1486C>T	14.37:g.55636179G>A	ENSP00000247191:p.Arg496*	Somatic		Capture	Illumina HiSeq	Phase_I	54705932	A8MTM6|B4DRM8|Q86T11|Q8NG58	Nonsense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531200	0.85706	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	.	.	.	5.85	2.93	0.34026	.	0.242538	0.42420	D	0.000720	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.1119	0.42568	0.1297:0.1155:0.7548:0.0	.	.	.	.	X	496	.	ENSP00000247191:R496X	R	-	1	2	DLGAP5	54705932	0.996000	0.38824	0.101000	0.21167	0.009000	0.06853	2.861000	0.48380	0.897000	0.36392	-0.140000	0.14226	CGA		DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
PPP1R36	145376	hgsc.bcm.edu	37	14	65054959	65054959	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:65054959T>C	ENST00000298705.1	+	11	1124	c.1028T>C	c.(1027-1029)tTc>tCc	p.F343S	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	343					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GACGTCAGATTCCCAGCCGAG	0.488																																																	0			14											98.0	95.0	96.0					14																	65054959		2203	4300	6503	64124712	SO:0001583	missense	145376				CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.1028T>C	14.37:g.65054959T>C	ENSP00000298705:p.Phe343Ser	Somatic		Capture	Illumina HiSeq	Phase_I	64124712	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	T	10.25	1.298445	0.23650	.	.	ENSG00000165807	ENST00000298705	T	0.31247	1.5	5.03	-2.4	0.06583	.	1.132860	0.06558	N	0.746156	T	0.19644	0.0472	L	0.47716	1.5	0.09310	N	1	B	0.29805	0.257	B	0.24155	0.051	T	0.23868	-1.0176	10	0.24483	T	0.36	3.0E-4	1.588	0.02648	0.469:0.0903:0.1464:0.2943	.	343	Q96LQ0	PPR36_HUMAN	S	343	ENSP00000298705:F343S	ENSP00000298705:F343S	F	+	2	0	C14orf50	64124712	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.544000	0.06077	-0.187000	0.10516	-0.258000	0.10820	TTC		PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
SRSF5	6430	hgsc.bcm.edu	37	14	70234923	70234923	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr14:70234923A>G	ENST00000553521.1	+	3	1503	c.50A>G	c.(49-51)gAg>gGg	p.E17G	SRSF5_ENST00000394366.2_Missense_Mutation_p.E17G|SRSF5_ENST00000553635.1_Missense_Mutation_p.E17G|SRSF5_ENST00000554021.1_Missense_Mutation_p.E17G|SRSF5_ENST00000555349.1_Missense_Mutation_p.E17G|SRSF5_ENST00000451983.2_Missense_Mutation_p.E17G|SRSF5_ENST00000557154.1_Missense_Mutation_p.E17G|SRSF5_ENST00000556587.1_3'UTR|SRSF5_ENST00000553548.1_Missense_Mutation_p.E17G			Q13243	SRSF5_HUMAN	serine/arginine-rich splicing factor 5	17	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of cell cycle (GO:0051726)|response to wounding (GO:0009611)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(1)|liver(1)	2						GCGGCCAGGGAGAAGGACGTG	0.428																																																	0			14											157.0	170.0	165.0					14																	70234923		2203	4300	6503	69304676	SO:0001583	missense	0			AF020307	CCDS32109.1	14q24	2013-02-12	2010-06-22	2010-06-22	ENSG00000100650	ENSG00000100650		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10787	protein-coding gene	gene with protein product	"""SR splicing factor 5"""	600914	"""splicing factor, arginine/serine-rich 5"""	SFRS5		7686911, 20516191	Standard	XM_005267998		Approved	SRP40, HRS	uc001xlp.3	Q13243		ENST00000553521.1:c.50A>G	14.37:g.70234923A>G	ENSP00000452123:p.Glu17Gly	Somatic		Capture	Illumina HiSeq	Phase_I	69304676	O14797|Q16662|Q49AD6|Q6FGE0	Missense_Mutation	SNP	ENST00000553521.1	37	CCDS32109.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.757652	0.89843	.	.	ENSG00000100650	ENST00000553521;ENST00000394366;ENST00000553548;ENST00000553369;ENST00000557154;ENST00000451983;ENST00000553635;ENST00000555349;ENST00000554021	T;T;T;T;T;T;T;T;T	0.80214	1.91;1.91;-1.35;-1.35;1.91;-1.35;1.91;-1.35;-1.35	5.86	5.86	0.93980	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.89473	0.6725	M	0.73430	2.235	0.80722	D	1	P;P;D	0.89917	0.531;0.73;1.0	P;P;D	0.87578	0.614;0.652;0.998	D	0.90582	0.4530	10	0.87932	D	0	.	16.2453	0.82441	1.0:0.0:0.0:0.0	.	17;17;17	Q13243-3;Q6FGE0;Q13243	.;.;SRSF5_HUMAN	G	17	ENSP00000452123:E17G;ENSP00000377892:E17G;ENSP00000452400:E17G;ENSP00000452449:E17G;ENSP00000451088:E17G;ENSP00000402734:E17G;ENSP00000451391:E17G;ENSP00000452090:E17G;ENSP00000450918:E17G	ENSP00000377892:E17G	E	+	2	0	SRSF5	69304676	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.306000	0.78905	2.241000	0.73720	0.533000	0.62120	GAG		SRSF5-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412456.1	NM_001039465	
MGA	23269	hgsc.bcm.edu	37	15	42041775	42041775	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:42041775G>A	ENST00000570161.1	+	16	5970	c.5970G>A	c.(5968-5970)acG>acA	p.T1990T	MGA_ENST00000389936.4_Silent_p.T1951T|MGA_ENST00000219905.7_Silent_p.T1990T|MGA_ENST00000566586.1_Silent_p.T1781T|MGA_ENST00000545763.1_Silent_p.T1781T			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	AGCAAGAAACGAAGAAGGTTC	0.413																																																	0			15											67.0	66.0	66.0					15																	42041775		1850	4090	5940	39829067	SO:0001819	synonymous_variant	23269			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.5970G>A	15.37:g.42041775G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39829067	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																				MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
ICE2	79664	hgsc.bcm.edu	37	15	60720652	60720652	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:60720652T>C	ENST00000261520.4	-	15	3030	c.2796A>G	c.(2794-2796)tcA>tcG	p.S932S	NARG2_ENST00000439632.1_Silent_p.S795S	NM_024611.4	NP_078887.2												p.S932S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						TGGTATCCAGTGATTTCGGTG	0.373																																																	1	Substitution - coding silent(1)	lung(1)	15											136.0	129.0	132.0					15																	60720652		2203	4300	6503	58507944	SO:0001819	synonymous_variant	79664																														ENST00000261520.4:c.2796A>G	15.37:g.60720652T>C		Somatic		Capture	Illumina HiSeq	Phase_I	58507944		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																				NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1		
IGDCC3	9543	hgsc.bcm.edu	37	15	65623923	65623923	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:65623923G>T	ENST00000327987.4	-	8	1474	c.1223C>A	c.(1222-1224)tCa>tAa	p.S408*	IGDCC3_ENST00000559231.1_5'UTR	NM_004884.3	NP_004875.2	Q8IVU1	IGDC3_HUMAN	immunoglobulin superfamily, DCC subclass, member 3	408	Ig-like C2-type 4.				neuromuscular process controlling balance (GO:0050885)	integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(9)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GGCCTGTGATGAGCCCGCACT	0.612																																																	0			15											42.0	41.0	41.0					15																	65623923		2201	4299	6500	63410976	SO:0001587	stop_gained	9543			AF063936	CCDS10205.1	15q22.3-q23	2013-02-11	2009-01-08	2009-01-08	ENSG00000174498	ENSG00000174498		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9700	protein-coding gene	gene with protein product		604184	"""putative neuronal cell adhesion molecule"""	PUNC		9922388	Standard	NM_004884		Approved	HsT18880	uc002aos.2	Q8IVU1	OTTHUMG00000133137	ENST00000327987.4:c.1223C>A	15.37:g.65623923G>T	ENSP00000332773:p.Ser408*	Somatic		Capture	Illumina HiSeq	Phase_I	63410976	O95215	Nonsense_Mutation	SNP	ENST00000327987.4	37	CCDS10205.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.679380	0.88542	.	.	ENSG00000174498	ENST00000327987;ENST00000443278	.	.	.	4.92	4.92	0.64577	.	0.063209	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.8131	18.1374	0.89624	0.0:0.0:1.0:0.0	.	.	.	.	X	408;271	.	ENSP00000332773:S408X	S	-	2	0	IGDCC3	63410976	1.000000	0.71417	0.888000	0.34837	0.235000	0.25334	7.831000	0.86748	2.241000	0.73720	0.655000	0.94253	TCA		IGDCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256826.1	NM_004884	
NR2E3	10002	hgsc.bcm.edu	37	15	72105929	72105929	+	RNA	SNP	C	C	A	rs139176226|rs11351249|rs398027866		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:72105929C>A	ENST00000398840.2	+	0	1138							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						TGGCGGTGGACCCCCACGGAG	0.607																																																	0			15											6.0	5.0	5.0					15																	72105929		1758	3851	5609	69892983			10002				CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"""Nuclear hormone receptors"""	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72105929C>A		Somatic		Capture	Illumina HiSeq	Phase_I	69892983	B6ZGU0|Q9UHM4	Missense_Mutation	SNP	ENST00000398840.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.549|1.549	-0.539623|-0.539623	0.04053|0.04053	.|.	.|.	ENSG00000031544|ENSG00000031544	ENST00000326995;ENST00000398840|ENST00000326995;ENST00000398840	.|.	.|.	.|.	.|.	.|.	.|.	.|Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	.|0.597438	.|0.17891	.|N	.|0.158507	.|T	.|0.74824	.|0.3767	M|M	0.88570|0.88570	2.965|2.965	.|.	.|.	.|.	.|D	.|0.67145	.|0.996	.|D	.|0.73380	.|0.98	.|T	.|0.78897	.|-0.2023	.|6	.|0.87932	.|D	.|0	.|.	.|.	.|.	.|.	.|.	.|316	.|Q9Y5X4	.|NR2E3_HUMAN	.|E	-1|228;316	.|.	.|ENSP00000317199:D228E	.|D	+|+	.|3	.|2	NR2E3|NR2E3	69892983|69892983	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.857000|0.857000	0.48899|0.48899	0.000000|0.000000	0.12993|0.12993	0.000000|0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	.|GAC		NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249	
CRABP1	1381	hgsc.bcm.edu	37	15	78640277	78640277	+	Silent	SNP	C	C	T	rs201099878		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:78640277C>T	ENST00000299529.6	+	4	477	c.372C>T	c.(370-372)ggC>ggT	p.G124G		NM_004378.2	NP_004369.1	P29762	RABP1_HUMAN	cellular retinoic acid binding protein 1	124					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoic acid binding (GO:0001972)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			breast(1)|lung(4)|skin(1)	6					Alitretinoin(DB00523)|Tretinoin(DB00755)	AGACGTTTGGCGCCGATGACG	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		18987	0.0		0.001	False		,,,				2504	0.0				Ovarian(146;578 3231 38536)												0			15											165.0	147.0	153.0					15																	78640277		2196	4293	6489	76427332	SO:0001819	synonymous_variant	1381				CCDS10301.1	15q24	2013-03-01	2001-11-28		ENSG00000166426	ENSG00000166426		"""Fatty acid binding protein family"""	2338	protein-coding gene	gene with protein product		180230	"""cellular retinoic acid-binding protein 1"""	RBP5		9154115	Standard	NM_004378		Approved	CRABP, CRABP-I, CRABPI	uc002bdp.2	P29762	OTTHUMG00000143862	ENST00000299529.6:c.372C>T	15.37:g.78640277C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76427332	Q6IAY7|Q8WTV5	Silent	SNP	ENST00000299529.6	37	CCDS10301.1																																																																																				CRABP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290110.2	NM_004378	
TMED3	23423	hgsc.bcm.edu	37	15	79614396	79614396	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:79614396A>G	ENST00000299705.5	+	3	682	c.494A>G	c.(493-495)gAg>gGg	p.E165G	TMED3_ENST00000536821.1_Intron|TMED3_ENST00000558562.1_3'UTR|TMED3_ENST00000424155.2_Intron	NM_007364.2	NP_031390.1	Q9Y3Q3	TMED3_HUMAN	transmembrane emp24 protein transport domain containing 3	165					protein transport (GO:0015031)	COPI vesicle coat (GO:0030126)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)|ovary(1)|skin(1)	9						CGGCTGCGGGAGGCCCAGGAC	0.582																																																	0			15											72.0	69.0	70.0					15																	79614396		2196	4293	6489	77401451	SO:0001583	missense	23423			BC022232	CCDS10310.1, CCDS73768.1	15q24-q25	2011-02-09	2005-08-26	2005-01-07	ENSG00000166557	ENSG00000166557			28889	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 22"", ""transmembrane emp24 domain containing 3"""	C15orf22		12975309	Standard	XM_005254263		Approved	p24B	uc002beu.3	Q9Y3Q3	OTTHUMG00000144170	ENST00000299705.5:c.494A>G	15.37:g.79614396A>G	ENSP00000299705:p.Glu165Gly	Somatic		Capture	Illumina HiSeq	Phase_I	77401451	A8K069|B4DN05|Q2T9F8	Missense_Mutation	SNP	ENST00000299705.5	37	CCDS10310.1	.	.	.	.	.	.	.	.	.	.	A	28.7	4.944788	0.92593	.	.	ENSG00000166557	ENST00000299705	T	0.28454	1.61	4.86	4.86	0.63082	GOLD (1);	0.062952	0.64402	D	0.000007	T	0.66809	0.2827	H	0.96518	3.835	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.77520	-0.2557	10	0.87932	D	0	-31.98	12.4554	0.55702	1.0:0.0:0.0:0.0	.	165	Q9Y3Q3	TMED3_HUMAN	G	165	ENSP00000299705:E165G	ENSP00000299705:E165G	E	+	2	0	TMED3	77401451	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.813000	0.75231	2.029000	0.59856	0.482000	0.46254	GAG		TMED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291369.1	NM_007364	
MEF2A	4205	hgsc.bcm.edu	37	15	100252738	100252738	+	Missense_Mutation	SNP	A	A	C	rs560400205|rs201861701	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr15:100252738A>C	ENST00000557785.1	+	11	1605	c.1256A>C	c.(1255-1257)cAg>cCg	p.Q419P	MEF2A_ENST00000453228.2_Missense_Mutation_p.Q419P|MEF2A_ENST00000557942.1_Missense_Mutation_p.Q427P|MEF2A_ENST00000449277.2_Missense_Mutation_p.Q351P|MEF2A_ENST00000338042.6_Missense_Mutation_p.Q428P|MEF2A_ENST00000558812.1_Missense_Mutation_p.Q359P|MEF2A_ENST00000354410.5_Missense_Mutation_p.Q421P	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	429					apoptotic process (GO:0006915)|cardiac conduction (GO:0061337)|cellular response to calcium ion (GO:0071277)|dendrite morphogenesis (GO:0048813)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|mitochondrial genome maintenance (GO:0000002)|mitochondrion distribution (GO:0048311)|muscle cell differentiation (GO:0042692)|muscle organ development (GO:0007517)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|ventricular cardiac myofibril assembly (GO:0055005)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|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)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)			endometrium(2)|large_intestine(2)|lung(7)|ovary(1)	12	Lung NSC(78;0.00335)|all_lung(78;0.00659)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00085)			cagcagcagcagcagcCGCCG	0.637																																																	0			15																																								98070261	SO:0001583	missense	4205				CCDS45362.1, CCDS45363.1, CCDS53978.1, CCDS58401.1	15q26	2008-02-05	2007-04-24			ENSG00000068305		"""Myocyte enhancer factors"""	6993	protein-coding gene	gene with protein product		600660				1516833	Standard	NM_005587		Approved	RSRFC4, RSRFC9	uc002bvf.3	Q02078		ENST00000557785.1:c.1256A>C	15.37:g.100252738A>C	ENSP00000453441:p.Gln419Pro	Somatic		Capture	Illumina HiSeq	Phase_I	98070261	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Missense_Mutation	SNP	ENST00000557785.1	37	CCDS53978.1	.	.	.	.	.	.	.	.	.	.	a	0	-2.790689	0.00077	.	.	ENSG00000068305	ENST00000453228;ENST00000354410;ENST00000338042;ENST00000449277	T;T;T	0.07800	3.16;3.16;3.16	0.337	0.337	0.15966	.	.	.	.	.	T	0.08802	0.0218	N	0.08118	0	0.18873	N	0.999989	B;B;B;D;B;D	0.53462	0.0;0.0;0.0;0.96;0.001;0.96	B;B;B;D;B;D	0.64237	0.0;0.0;0.0;0.923;0.0;0.923	T	0.40776	-0.9545	8	0.23891	T	0.37	.	.	.	.	.	429;359;340;419;421;427	Q02078;B4DFQ7;Q7Z6C9;Q02078-6;Q02078-5;Q02078-2	MEF2A_HUMAN;.;.;.;.;.	P	419;421;428;359	ENSP00000404110:Q419P;ENSP00000346389:Q421P;ENSP00000337202:Q428P	ENSP00000337202:Q428P	Q	+	2	0	MEF2A	98070261	0.962000	0.33011	0.021000	0.16686	0.081000	0.17604	-0.272000	0.08560	0.353000	0.24079	0.342000	0.21767	CAG		MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1		
CLEC16A	23274	hgsc.bcm.edu	37	16	11214599	11214599	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:11214599G>A	ENST00000409790.1	+	20	2474	c.2244G>A	c.(2242-2244)gtG>gtA	p.V748V	CLEC16A_ENST00000409552.3_Silent_p.V730V|CLEC16A_ENST00000465491.1_3'UTR	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GCTGGGGAGTGGTCAAGTTTG	0.532																																																	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	16											110.0	113.0	112.0					16																	11214599		2062	4203	6265	11122100	SO:0001819	synonymous_variant	23274			AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2244G>A	16.37:g.11214599G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11122100		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																				CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
COG7	91949	hgsc.bcm.edu	37	16	23436075	23436075	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:23436075T>G	ENST00000307149.5	-	7	1189	c.1004A>C	c.(1003-1005)cAc>cCc	p.H335P		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	335					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		TTTACGTAGGTGGGGGAGCAG	0.567																																																	0			16											99.0	106.0	104.0					16																	23436075		2197	4300	6497	23343576	SO:0001583	missense	91949			AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1004A>C	16.37:g.23436075T>G	ENSP00000305442:p.His335Pro	Somatic		Capture	Illumina HiSeq	Phase_I	23343576	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	.	.	.	.	.	.	.	.	.	.	T	9.838	1.190124	0.21954	.	.	ENSG00000168434	ENST00000307149	T	0.42513	0.97	5.31	3.07	0.35406	.	0.398252	0.32343	N	0.006238	T	0.26159	0.0638	N	0.22421	0.69	0.37382	D	0.912064	B	0.02656	0.0	B	0.01281	0.0	T	0.09314	-1.0680	10	0.30078	T	0.28	-14.5543	8.7063	0.34356	0.0:0.1543:0.0:0.8457	.	335	P83436	COG7_HUMAN	P	335	ENSP00000305442:H335P	ENSP00000305442:H335P	H	-	2	0	COG7	23343576	1.000000	0.71417	0.020000	0.16555	0.469000	0.32828	3.263000	0.51546	0.356000	0.24157	0.482000	0.46254	CAC		COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
ITGAL	3683	hgsc.bcm.edu	37	16	30507513	30507513	+	Silent	SNP	C	C	T	rs148420170	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:30507513C>T	ENST00000356798.6	+	14	1779	c.1599C>T	c.(1597-1599)ggC>ggT	p.G533G	ITGAL_ENST00000358164.5_Silent_p.G450G|ITGAL_ENST00000433423.2_Intron|RP11-297C4.1_ENST00000563751.1_RNA|ITGAL_ENST00000568012.1_3'UTR	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	533					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	ACATCAACGGCGATGGGCTGG	0.622													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		15652	0.0		0.0	False		,,,				2504	0.0				NSCLC(110;1462 1641 3311 33990 49495)												0			16						C	,	6,4388	11.4+/-27.6	0,6,2191	88.0	97.0	94.0		1350,1599	2.8	0.9	16	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	0,7,6490	TT,TC,CC		0.0116,0.1365,0.0539	,	450/1087,533/1171	30507513	7,12987	2197	4300	6497	30415014	SO:0001819	synonymous_variant	3683				CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.1599C>T	16.37:g.30507513C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30415014	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																				ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
BCKDK	10295	hgsc.bcm.edu	37	16	31121793	31121793	+	Silent	SNP	G	G	A	rs14235	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:31121793G>A	ENST00000394951.1	+	8	1238	c.615G>A	c.(613-615)acG>acA	p.T205T	BCKDK_ENST00000219794.6_Silent_p.T205T|BCKDK_ENST00000394950.3_Silent_p.T205T|BCKDK_ENST00000287507.3_Silent_p.T205T|AC135050.1_ENST00000517000.2_RNA			O14874	BCKD_HUMAN	branched chain ketoacid dehydrogenase kinase	205	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				branched-chain amino acid catabolic process (GO:0009083)|cellular amino acid catabolic process (GO:0009063)|phosphorylation (GO:0016310)|protein phosphorylation (GO:0006468)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrion (GO:0005739)	[3-methyl-2-oxobutanoate dehydrogenase (acetyl-transferring)] kinase activity (GO:0047323)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|stomach(1)	2						TGTTGGCCACGCATCACCTGG	0.567													G|||	1799	0.359225	0.0893	0.3833	5008	,	,		18067	0.8849		0.3817	False		,,,				2504	0.1421																0			16						G	,	592,3802	255.8+/-260.9	44,504,1649	62.0	63.0	63.0		615,615	-9.0	0.9	16	dbSNP_52	63	3344,5256	492.2+/-373.3	638,2068,1594	no	coding-synonymous,coding-synonymous	BCKDK	NM_001122957.1,NM_005881.2	,	682,2572,3243	AA,AG,GG		38.8837,13.4729,30.2909	,	205/366,205/413	31121793	3936,9058	2197	4300	6497	31029294	SO:0001819	synonymous_variant	10295			AF026548	CCDS10705.1, CCDS45467.1, CCDS61917.1	16p11.2	2008-05-14			ENSG00000103507	ENSG00000103507			16902	protein-coding gene	gene with protein product		614901				1889817	Standard	NM_005881		Approved		uc002eaw.5	O14874	OTTHUMG00000047356	ENST00000394951.1:c.615G>A	16.37:g.31121793G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31029294	A8MY43|Q6FGL4|Q96G95|Q96IN5	Silent	SNP	ENST00000394951.1	37	CCDS10705.1																																																																																				BCKDK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108514.1	NM_005881	
MMP2	4313	hgsc.bcm.edu	37	16	55539301	55539301	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:55539301A>G	ENST00000219070.4	+	13	2439	c.1930A>G	c.(1930-1932)Agt>Ggt	p.S644G	MMP2_ENST00000437642.2_Missense_Mutation_p.S594G|MMP2_ENST00000543485.1_Missense_Mutation_p.S568G|MMP2_ENST00000570308.1_Missense_Mutation_p.S568G	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	644	Required for inhibitor TIMP2 binding.		S -> I (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	GGAGAACCAAAGTCTGAAGAG	0.537																																																	0			16											168.0	163.0	165.0					16																	55539301		2198	4300	6498	54096802	SO:0001583	missense	4313				CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"""matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)"", ""matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"""	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.1930A>G	16.37:g.55539301A>G	ENSP00000219070:p.Ser644Gly	Somatic		Capture	Illumina HiSeq	Phase_I	54096802	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906323	0.52333	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.02606	4.23;4.23;4.23	5.38	5.38	0.77491	Hemopexin/matrixin (2);	0.163087	0.64402	D	0.000002	T	0.04907	0.0132	L	0.42245	1.32	0.80722	D	1	P;P	0.43169	0.8;0.647	B;B	0.43950	0.437;0.122	T	0.54846	-0.8232	10	0.32370	T	0.25	.	14.3832	0.66926	1.0:0.0:0.0:0.0	.	594;644	E9PE45;P08253	.;MMP2_HUMAN	G	644;568;594	ENSP00000219070:S644G;ENSP00000444143:S568G;ENSP00000394237:S594G	ENSP00000219070:S644G	S	+	1	0	MMP2	54096802	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.196000	0.89725	2.050000	0.60909	0.460000	0.39030	AGT		MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3		
CES5A	221223	hgsc.bcm.edu	37	16	55890317	55890317	+	Missense_Mutation	SNP	A	A	G	rs199767426		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:55890317A>G	ENST00000290567.9	-	9	1218	c.1097T>C	c.(1096-1098)cTt>cCt	p.L366P	CES5A_ENST00000521992.1_Missense_Mutation_p.L395P|CES5A_ENST00000518005.1_Missense_Mutation_p.L260P|CES5A_ENST00000319165.9_Missense_Mutation_p.L366P|CES5A_ENST00000520435.1_Missense_Mutation_p.L336P|CES5A_ENST00000541580.1_5'UTR	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	366						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						ATGGAGGGCAAGGGACTTGTT	0.527																																																	0			16											149.0	125.0	133.0					16																	55890317		2198	4300	6498	54447818	SO:0001583	missense	0			AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1097T>C	16.37:g.55890317A>G	ENSP00000290567:p.Leu366Pro	Somatic		Capture	Illumina HiSeq	Phase_I	54447818	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	11.51	1.659670	0.29515	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	3.18	2.09	0.27110	Carboxylesterase, type B (1);	1.293400	0.05941	N	0.636938	T	0.69260	0.3091	L	0.41906	1.305	0.26833	N	0.968533	D;D	0.58970	0.984;0.966	P;P	0.60541	0.876;0.735	T	0.54549	-0.8277	10	0.32370	T	0.25	.	4.5993	0.12345	0.8456:0.0:0.1544:0.0	.	366;366	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	P	395;366;260;366;336;146	ENSP00000428864:L395P;ENSP00000324271:L366P;ENSP00000428571:L260P;ENSP00000290567:L366P;ENSP00000428887:L336P	ENSP00000290567:L366P	L	-	2	0	CES5A	54447818	0.000000	0.05858	0.214000	0.23707	0.118000	0.20060	0.801000	0.27055	0.633000	0.30452	0.369000	0.22263	CTT		CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
DPEP2	64174	hgsc.bcm.edu	37	16	68021778	68021778	+	Silent	SNP	G	G	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:68021778G>T	ENST00000572888.1	-	9	1833	c.1183C>A	c.(1183-1185)Cgg>Agg	p.R395R	DPEP2_ENST00000412757.2_Silent_p.R395R|DPEP2_ENST00000393847.1_Silent_p.R395R			Q9H4A9	DPEP2_HUMAN	dipeptidase 2	395					arachidonic acid metabolic process (GO:0019369)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	dipeptidase activity (GO:0016805)|dipeptidyl-peptidase activity (GO:0008239)|metal ion binding (GO:0046872)|metalloexopeptidase activity (GO:0008235)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0489)|all cancers(182;0.239)		CTGAAGACCCGCAGCAGGTTT	0.567																																																	0			16											129.0	129.0	129.0					16																	68021778		2198	4300	6498	66579279	SO:0001819	synonymous_variant	64174			AJ295149	CCDS10857.1	16q22.1	2011-07-22			ENSG00000167261	ENSG00000167261	3.4.13.19		23028	protein-coding gene	gene with protein product		609925					Standard	NM_022355		Approved		uc002eve.4	Q9H4A9	OTTHUMG00000137542	ENST00000572888.1:c.1183C>A	16.37:g.68021778G>T		Somatic		Capture	Illumina HiSeq	Phase_I	66579279	B2RCF8|Q6UX92|Q8TC95	Silent	SNP	ENST00000572888.1	37	CCDS10857.1																																																																																				DPEP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437026.1	NM_022355	
HYDIN	54768	hgsc.bcm.edu	37	16	70841910	70841910	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:70841910T>C	ENST00000393567.2	-	86	15089	c.14939A>G	c.(14938-14940)cAg>cGg	p.Q4980R		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4980					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				AGTGCCTCCCTGGCCTCCTGG	0.532																																																	0			16											61.0	63.0	62.0					16																	70841910		1982	4150	6132	69399411	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.14939A>G	16.37:g.70841910T>C	ENSP00000377197:p.Gln4980Arg	Somatic		Capture	Illumina HiSeq	Phase_I	69399411	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.444244	0.63067	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00882	5.58	5.91	5.91	0.95273	.	0.339335	0.16344	U	0.218528	T	0.03011	0.0089	M	0.75447	2.3	0.80722	D	1	P	0.47762	0.9	P	0.52454	0.699	T	0.63888	-0.6535	10	0.17369	T	0.5	.	11.9385	0.52886	0.1301:0.0:0.0:0.8699	.	4979	F8WD23	.	R	4980;4979	ENSP00000377197:Q4980R	ENSP00000313052:Q4979R	Q	-	2	0	HYDIN	69399411	0.892000	0.30473	0.997000	0.53966	0.593000	0.36681	1.145000	0.31577	2.254000	0.74563	0.533000	0.62120	CAG		HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
IST1	9798	hgsc.bcm.edu	37	16	71956517	71956517	+	Silent	SNP	C	C	A	rs549750934|rs372825060	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:71956517C>A	ENST00000378799.6	+	7	1049	c.693C>A	c.(691-693)ccC>ccA	p.P231P	IST1_ENST00000606369.1_Silent_p.P83P|IST1_ENST00000378798.5_Silent_p.P231P|RP11-498D10.5_ENST00000567146.1_RNA|IST1_ENST00000535424.1_Silent_p.P244P|IST1_ENST00000538565.1_3'UTR|IST1_ENST00000538850.1_Silent_p.P83P|IST1_ENST00000544564.1_Silent_p.P231P|IST1_ENST00000329908.8_Silent_p.P231P|IST1_ENST00000541571.2_Silent_p.P231P			P53990	IST1_HUMAN	increased sodium tolerance 1 homolog (yeast)	229	Interaction with VPS37B.|Interaction with VTA1.				abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of proteolysis (GO:0045862)|protein localization (GO:0008104)|viral capsid secondary envelopment (GO:0046745)|viral release from host cell (GO:0019076)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Flemming body (GO:0090543)|midbody (GO:0030496)	MIT domain binding (GO:0090541)|protein complex binding (GO:0032403)|protein domain specific binding (GO:0019904)										tgccaatgcccatgcccatgc	0.498																																																	0			16											102.0	70.0	81.0					16																	71956517		2198	4300	6498	70514018	SO:0001819	synonymous_variant	9798			BC004359	CCDS10905.1, CCDS59271.1, CCDS59272.1, CCDS59273.1, CCDS59274.1	16q22.2	2011-08-18	2011-08-18	2011-08-18	ENSG00000182149	ENSG00000182149			28977	protein-coding gene	gene with protein product			"""KIAA0174"""	KIAA0174		8724849, 19129480	Standard	NM_001270975		Approved		uc002fbm.2	P53990	OTTHUMG00000137597	ENST00000378799.6:c.693C>A	16.37:g.71956517C>A		Somatic		Capture	Illumina HiSeq	Phase_I	70514018	A8KAH5|J3QLU7|Q3SYM4|Q9BQ81|Q9BWN2	Silent	SNP	ENST00000378799.6	37	CCDS59272.1	.	.	.	.	.	.	.	.	.	.	C	7.943	0.743115	0.15642	.	.	ENSG00000182149	ENST00000541848	.	.	.	5.54	-4.88	0.03113	.	0.046113	0.85682	D	0.000000	T	0.58750	0.2144	.	.	.	0.58432	D	0.999993	.	.	.	.	.	.	T	0.60454	-0.7260	6	0.62326	D	0.03	-2.7071	8.7497	0.34609	0.1145:0.2195:0.0:0.666	.	.	.	.	Q	118	.	ENSP00000437499:P118Q	P	+	2	0	KIAA0174	70514018	0.000000	0.05858	0.488000	0.27440	0.917000	0.54804	-3.886000	0.00342	-0.979000	0.03529	-0.122000	0.15005	CCA		IST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269005.2	NM_014761	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77334230	77334230	+	Silent	SNP	T	T	G	rs201338151	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:77334230T>G	ENST00000282849.5	-	17	3022	c.2604A>C	c.(2602-2604)ccA>ccC	p.P868P		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	868	Spacer.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						TTGTGGCTGGTGGAGTTCCAT	0.458																																																	0			16											145.0	122.0	130.0					16																	77334230		2198	4300	6498	75891731	SO:0001819	synonymous_variant	170692			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2604A>C	16.37:g.77334230T>G		Somatic		Capture	Illumina HiSeq	Phase_I	75891731	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																				ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
CDH13	1012	hgsc.bcm.edu	37	16	83711906	83711906	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr16:83711906T>C	ENST00000566620.1	+	10	1668	c.1378T>C	c.(1378-1380)Tcc>Ccc	p.S460P	CDH13_ENST00000428848.3_Missense_Mutation_p.S421P|CDH13_ENST00000268613.10_Missense_Mutation_p.S507P	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	460	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		CGGCCCCAGCTCCACAGCCAC	0.562																																																	0			16											83.0	90.0	88.0					16																	83711906		2096	4215	6311	82269407	SO:0001583	missense	1012			U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1378T>C	16.37:g.83711906T>C	ENSP00000454435:p.Ser460Pro	Somatic		Capture	Illumina HiSeq	Phase_I	82269407	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.393670	0.83011	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000540531	T	0.55760	0.5	4.81	4.81	0.61882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74092	0.3671	M	0.84773	2.715	0.80722	D	1	P;P;D	0.76494	0.908;0.722;0.999	P;P;D	0.81914	0.737;0.519;0.995	T	0.78914	-0.2016	9	0.66056	D	0.02	.	13.5579	0.61770	0.0:0.0:0.0:1.0	.	421;507;460	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	P	507;460;421;162;150	ENSP00000268613:S507P	ENSP00000268613:S507P	S	+	1	0	CDH13	82269407	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.387000	0.79785	1.809000	0.52856	0.482000	0.46254	TCC		CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
INPP5K	51763	hgsc.bcm.edu	37	17	1416807	1416807	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:1416807G>A	ENST00000421807.2	-	3	589	c.201C>T	c.(199-201)gcC>gcT	p.A67A	INPP5K_ENST00000397335.3_Intron|INPP5K_ENST00000406424.4_5'UTR|INPP5K_ENST00000320345.6_5'UTR|INPP5K_ENST00000542125.1_Silent_p.A67A	NM_016532.3	NP_057616.2	Q9BT40	INP5K_HUMAN	inositol polyphosphate-5-phosphatase K	67	Catalytic. {ECO:0000255}.				actin cytoskeleton organization (GO:0030036)|cellular response to cAMP (GO:0071320)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to hormone stimulus (GO:0032870)|cellular response to insulin stimulus (GO:0032869)|cellular response to tumor necrosis factor (GO:0071356)|dephosphorylation (GO:0016311)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|in utero embryonic development (GO:0001701)|inositol phosphate dephosphorylation (GO:0046855)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of dephosphorylation (GO:0035305)|negative regulation of glucose transport (GO:0010829)|negative regulation of glycogen (starch) synthase activity (GO:2000466)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of renal water transport (GO:2001153)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|protein targeting to plasma membrane (GO:0072661)|regulation of glycogen biosynthetic process (GO:0005979)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	inositol bisphosphate phosphatase activity (GO:0016312)|inositol trisphosphate phosphatase activity (GO:0046030)|inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity (GO:0052659)|inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|inositol-polyphosphate 5-phosphatase activity (GO:0004445)|lipid phosphatase activity (GO:0042577)|phosphatidylinositol phosphate 5-phosphatase activity (GO:0034595)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)|phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:0034485)|vasopressin receptor activity (GO:0005000)			endometrium(1)|large_intestine(7)|lung(3)|skin(1)	12						AGTCATTAAAGGCAGCATCGG	0.512																																																	0			17											212.0	193.0	200.0					17																	1416807		2203	4300	6503	1363557	SO:0001819	synonymous_variant	51763				CCDS11004.1, CCDS11005.1	17p13.3	2008-09-09			ENSG00000132376	ENSG00000132376			33882	protein-coding gene	gene with protein product	"""skeletal muscle and kidney enriched inositol phosphatase"""	607875				10753883, 12536145	Standard	NM_016532		Approved	SKIP	uc002fsr.3	Q9BT40	OTTHUMG00000150648	ENST00000421807.2:c.201C>T	17.37:g.1416807G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1363557	B2R6I2|B2R750|D3DTH8|Q15733|Q9NPJ5|Q9P2R5	Silent	SNP	ENST00000421807.2	37	CCDS11004.1																																																																																				INPP5K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319381.4		
LLGL1	3996	hgsc.bcm.edu	37	17	18137141	18137141	+	Missense_Mutation	SNP	A	A	G	rs2290505	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:18137141A>G	ENST00000316843.4	+	5	538	c.442A>G	c.(442-444)Agc>Ggc	p.S148G		NM_004140.3	NP_004131	Q15334	L2GL1_HUMAN	lethal giant larvae homolog 1 (Drosophila)	148			S -> G (in dbSNP:rs2290505). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7542763, ECO:0000269|PubMed:8565641}.		axonogenesis (GO:0007409)|cortical actin cytoskeleton organization (GO:0030866)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|maintenance of apical/basal cell polarity (GO:0035090)|positive regulation of Rab GTPase activity (GO:0032851)|protein complex assembly (GO:0006461)	cell projection (GO:0042995)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome membrane (GO:0031901)|Golgi cis cisterna (GO:0000137)|myelin sheath abaxonal region (GO:0035748)|trans-Golgi network membrane (GO:0032588)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)|structural molecule activity (GO:0005198)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_neural(463;0.228)					GGTGGCTGCCAGCGACATAGC	0.632													G|||	3918	0.782348	0.848	0.7493	5008	,	,		11652	0.6786		0.7614	False		,,,				2504	0.8456																0			17						G	GLY/SER	3690,716	298.1+/-285.1	1556,578,69	89.0	80.0	83.0		442	2.6	0.0	17	dbSNP_100	83	6459,2141	365.6+/-334.0	2422,1615,263	yes	missense	LLGL1	NM_004140.3	56	3978,2193,332	GG,GA,AA		24.8953,16.2506,21.9668	benign	148/1065	18137141	10149,2857	2203	4300	6503	18077866	SO:0001583	missense	3996				CCDS32586.1	17p11.2	2013-01-10	2001-11-28		ENSG00000131899	ENSG00000131899		"""WD repeat domain containing"""	6628	protein-coding gene	gene with protein product		600966	"""lethal giant larvae (Drosophila) homolog 1"""	DLG4, LLGL, HUGL, HUGL-1		7542763, 8565641	Standard	XM_005256643		Approved		uc002gsp.3	Q15334	OTTHUMG00000059396	ENST00000316843.4:c.442A>G	17.37:g.18137141A>G	ENSP00000321537:p.Ser148Gly	Somatic		Capture	Illumina HiSeq	Phase_I	18077866	A7MBM7|O00188|Q58F11|Q86UK6	Missense_Mutation	SNP	ENST00000316843.4	37	CCDS32586.1	1650	0.7554945054945055	406	0.8252032520325203	274	0.7569060773480663	402	0.7027972027972028	568	0.7493403693931399	G	0.008	-1.867144	0.00547	0.837494	0.751047	ENSG00000131899	ENST00000316843	T	0.05139	3.49	5.87	2.63	0.31362	WD40 repeat-like-containing domain (1);	0.357650	0.36444	N	0.002589	T	0.00012	0.0000	N	0.11341	0.13	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07673	-1.0760	9	0.16896	T	0.51	-8.2838	7.0524	0.25081	0.2156:0.0:0.6055:0.1788	rs2290505;rs58954283;rs2290505	148	Q15334	L2GL1_HUMAN	G	148	ENSP00000321537:S148G	ENSP00000321537:S148G	S	+	1	0	LLGL1	18077866	0.002000	0.14202	0.001000	0.08648	0.033000	0.12548	-0.023000	0.12456	0.428000	0.26173	-0.748000	0.03510	AGC		LLGL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132067.3		
KCNJ12	3768	hgsc.bcm.edu	37	17	21319767	21319767	+	Silent	SNP	C	C	T	rs1612176	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:21319767C>T	ENST00000583088.1	+	3	2008	c.1113C>T	c.(1111-1113)agC>agT	p.S371S	KCNJ12_ENST00000331718.5_Silent_p.S371S	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	371				S -> R (in Ref. 2; AAC50615). {ECO:0000305}.	muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGCTGCCCAGCGCCAACTCCT	0.607										Prostate(3;0.18)																																							0			17																																								21260360	SO:0001819	synonymous_variant	3768			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1113C>T	17.37:g.21319767C>T		Somatic		Capture	Illumina HiSeq	Phase_I	21260360	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
KLHL11	55175	hgsc.bcm.edu	37	17	40011144	40011144	+	Silent	SNP	T	T	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:40011144T>G	ENST00000319121.3	-	2	1035	c.975A>C	c.(973-975)gcA>gcC	p.A325A		NM_018143.1	NP_060613.1	Q9NVR0	KLH11_HUMAN	kelch-like family member 11	325										NS(2)|breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17		Breast(137;0.00156)				GTCTCTCCACTGCGTCAGCGA	0.483																																																	0			17											105.0	95.0	98.0					17																	40011144		2203	4300	6503	37264670	SO:0001819	synonymous_variant	55175				CCDS11411.1	17q21	2013-01-30	2013-01-30		ENSG00000178502	ENSG00000178502		"""Kelch-like"", ""BTB/POZ domain containing"""	19008	protein-coding gene	gene with protein product			"""kelch-like 11 (Drosophila)"""				Standard	NM_018143		Approved	FLJ10572	uc002hyf.1	Q9NVR0	OTTHUMG00000133506	ENST00000319121.3:c.975A>C	17.37:g.40011144T>G		Somatic		Capture	Illumina HiSeq	Phase_I	37264670		Silent	SNP	ENST00000319121.3	37	CCDS11411.1																																																																																				KLHL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257464.2	NM_018143	
KAT7	11143	hgsc.bcm.edu	37	17	47869354	47869354	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:47869354G>A	ENST00000259021.4	+	2	402	c.122G>A	c.(121-123)cGa>cAa	p.R41Q	KAT7_ENST00000510819.1_Missense_Mutation_p.R41Q|KAT7_ENST00000509773.1_Missense_Mutation_p.R41Q|KAT7_ENST00000435742.2_5'UTR|KAT7_ENST00000454930.2_Missense_Mutation_p.R41Q|KAT7_ENST00000424009.2_Missense_Mutation_p.R41Q|KAT7_ENST00000503935.2_5'UTR	NM_007067.4	NP_008998.1	O95251	KAT7_HUMAN	K(lysine) acetyltransferase 7	41	Ser-rich.			Missing (in Ref. 5; BAG57945). {ECO:0000305}.|R -> Q (in Ref. 5; BAG57346). {ECO:0000305}.	chromatin organization (GO:0006325)|DNA replication (GO:0006260)|histone H3 acetylation (GO:0043966)|histone H4-K12 acetylation (GO:0043983)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										CGATCTGCTCGAGTCACCCGC	0.498																																																	0			17											108.0	99.0	102.0					17																	47869354		2203	4300	6503	45224353	SO:0001583	missense	11143			AF074606	CCDS11554.1, CCDS56035.1, CCDS56036.1, CCDS56037.1, CCDS56038.1	17q21.32	2013-01-10	2011-07-21	2011-07-21	ENSG00000136504	ENSG00000136504	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	17016	protein-coding gene	gene with protein product	"""histone acetyltransferase binding to ORC1"""	609880	"""MYST histone acetyltransferase 2"""	MYST2		10438470, 10930412	Standard	NM_001199155		Approved	HBOA, HBO1, ZC2HC7	uc002ipm.3	O95251	OTTHUMG00000161770	ENST00000259021.4:c.122G>A	17.37:g.47869354G>A	ENSP00000259021:p.Arg41Gln	Somatic		Capture	Illumina HiSeq	Phase_I	45224353	B3KN74|B4DF85|B4DFB4|B4DFE0|B4DGY4|E7ER15|G5E9K7	Missense_Mutation	SNP	ENST00000259021.4	37	CCDS11554.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542729	0.85917	.	.	ENSG00000136504	ENST00000259021;ENST00000454930;ENST00000509773;ENST00000510819;ENST00000424009	.	.	.	5.82	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	L	0.48642	1.525	0.80722	D	1	B;B;B;D;D	0.76494	0.147;0.079;0.079;0.999;0.999	B;B;B;D;D	0.72625	0.006;0.003;0.003;0.978;0.975	T	0.68550	-0.5379	9	0.42905	T	0.14	-8.7342	14.3568	0.66742	0.0715:0.0:0.9285:0.0	.	41;41;41;41;41	B4DFE0;B4DFB4;E7ER15;O95251;G5E9K7	.;.;.;KAT7_HUMAN;.	Q	41	.	ENSP00000259021:R41Q	R	+	2	0	KAT7	45224353	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	9.448000	0.97600	1.475000	0.48197	0.650000	0.86243	CGA		KAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366032.1	NM_007067	
MED13	9969	hgsc.bcm.edu	37	17	60060307	60060307	+	Silent	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:60060307C>A	ENST00000397786.2	-	16	3133	c.3057G>T	c.(3055-3057)cgG>cgT	p.R1019R		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1019					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CACGAGGAGTCCGAGGAGTCC	0.517																																																	0			17											66.0	68.0	67.0					17																	60060307		1920	4130	6050	57415089	SO:0001819	synonymous_variant	9969			AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.3057G>T	17.37:g.60060307C>A		Somatic		Capture	Illumina HiSeq	Phase_I	57415089	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																				MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
PRKCA	5578	hgsc.bcm.edu	37	17	64800031	64800031	+	Missense_Mutation	SNP	G	G	A	rs140466753		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:64800031G>A	ENST00000413366.3	+	17	1921	c.1895G>A	c.(1894-1896)cGa>cAa	p.R632Q		NM_002737.2	NP_002728	P17252	KPCA_HUMAN	protein kinase C, alpha	632	AGC-kinase C-terminal.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|chondrocyte differentiation (GO:0002062)|desmosome assembly (GO:0002159)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|histone H3-T6 phosphorylation (GO:0035408)|inactivation of MAPK activity (GO:0000188)|induction of positive chemotaxis (GO:0050930)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|mRNA metabolic process (GO:0016071)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of glucose import (GO:0046325)|negative regulation of insulin receptor signaling pathway (GO:0046627)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|peptidyl-serine autophosphorylation (GO:0036289)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of dense core granule biogenesis (GO:2000707)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of protein phosphorylation (GO:0001934)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of muscle contraction (GO:0006937)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of platelet aggregation (GO:0090330)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|regulation of the force of heart contraction (GO:0002026)|response to interleukin-1 (GO:0070555)|rhodopsin mediated signaling pathway (GO:0016056)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|enzyme binding (GO:0019899)|histone kinase activity (H3-T6 specific) (GO:0035403)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	38			BRCA - Breast invasive adenocarcinoma(6;4.68e-09)		Ingenol Mebutate(DB05013)|Phosphatidylserine(DB00144)|Tamoxifen(DB00675)|Vitamin E(DB00163)	TTCTTCACACGAGGACAGCCC	0.473																																																	0			17						G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	147.0	125.0	132.0		1895	4.6	0.9	17	dbSNP_134	132	0,8600		0,0,4300	no	missense	PRKCA	NM_002737.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	632/673	64800031	1,13005	2203	4300	6503	62230493	SO:0001583	missense	5578				CCDS11664.1	17q22-q24	2009-07-10				ENSG00000154229	2.7.11.1		9393	protein-coding gene	gene with protein product		176960		PKCA			Standard	NM_002737		Approved		uc002jfp.1	P17252		ENST00000413366.3:c.1895G>A	17.37:g.64800031G>A	ENSP00000408695:p.Arg632Gln	Somatic		Capture	Illumina HiSeq	Phase_I	62230493	B5BU22|Q15137|Q32M72|Q96RE4	Missense_Mutation	SNP	ENST00000413366.3	37	CCDS11664.1	.	.	.	.	.	.	.	.	.	.	G	12.09	1.834989	0.32421	2.27E-4	0.0	ENSG00000154229	ENST00000413366	T	0.57436	0.4	5.57	4.6	0.57074	Protein kinase, C-terminal (1);AGC-kinase, C-terminal (2);	0.000000	0.64402	D	0.000001	T	0.48352	0.1495	L	0.52011	1.625	0.52099	D	0.999944	B	0.19583	0.037	B	0.14023	0.01	T	0.46965	-0.9153	10	0.56958	D	0.05	.	14.3942	0.67001	0.0707:0.0:0.9293:0.0	.	632	P17252	KPCA_HUMAN	Q	632	ENSP00000408695:R632Q	ENSP00000408695:R632Q	R	+	2	0	PRKCA	62230493	1.000000	0.71417	0.940000	0.37924	0.307000	0.27823	9.414000	0.97362	1.363000	0.46019	-0.136000	0.14681	CGA		PRKCA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446976.1		
SDK2	54549	hgsc.bcm.edu	37	17	71382658	71382658	+	Missense_Mutation	SNP	C	C	T	rs368464336		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:71382658C>T	ENST00000392650.3	-	31	4424	c.4424G>A	c.(4423-4425)cGa>cAa	p.R1475Q	SDK2_ENST00000388726.3_Missense_Mutation_p.R1475Q	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	1475	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(15)|lung(31)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	86						CGCCTTCACTCGGAACTTGTA	0.587																																																	0			17						C	GLN/ARG	0,4390		0,0,2195	65.0	48.0	54.0		4424	4.1	1.0	17		54	1,8549		0,1,4274	no	missense	SDK2	NM_001144952.1	43	0,1,6469	TT,TC,CC		0.0117,0.0,0.0077	probably-damaging	1475/2173	71382658	1,12939	2195	4275	6470	68894253	SO:0001583	missense	54549			AB040947	CCDS45769.1	17q21.31	2013-02-11	2011-12-09		ENSG00000069188	ENSG00000069188		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19308	protein-coding gene	gene with protein product		607217	"""sidekick homolog 2 (chicken)"""			12230981, 15213259	Standard	NM_001144952		Approved	FLJ10832, KIAA1514	uc010dfm.3	Q58EX2	OTTHUMG00000152726	ENST00000392650.3:c.4424G>A	17.37:g.71382658C>T	ENSP00000376421:p.Arg1475Gln	Somatic		Capture	Illumina HiSeq	Phase_I	68894253	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.020236	0.75275	0.0	1.17E-4	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893	T;T;T	0.59772	0.24;0.24;0.24	5.08	4.12	0.48240	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77143	0.4087	M	0.85542	2.76	0.50171	D	0.999855	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.80469	-0.1369	10	0.62326	D	0.03	.	13.1413	0.59436	0.0:0.9216:0.0:0.0784	.	1475;1475;1475	Q58EX2-2;Q58EX2;Q58EX2-3	.;SDK2_HUMAN;.	Q	1099;1475;1475;651;1475	ENSP00000376421:R1475Q;ENSP00000373378:R1475Q;ENSP00000407098:R651Q	ENSP00000324967:R1475Q	R	-	2	0	SDK2	68894253	1.000000	0.71417	0.996000	0.52242	0.314000	0.28054	7.742000	0.85008	1.154000	0.42482	-0.192000	0.12808	CGA		SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064	
TP53	7157	hgsc.bcm.edu	37	17	7577080	7577080	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577080T>C	ENST00000269305.4	-	8	1047	c.858A>G	c.(856-858)gaA>gaG	p.E286E	TP53_ENST00000455263.2_Silent_p.E286E|TP53_ENST00000420246.2_Silent_p.E286E|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Silent_p.E286E|TP53_ENST00000445888.2_Silent_p.E286E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	286	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		E -> A (in LFS; germline mutation and in sporadic cancers; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:11023613, ECO:0000269|PubMed:8316628}.|E -> L (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|E -> Q (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:8829627}.|E -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.0?(8)|p.?(2)|p.E286D(2)|p.E286fs*17(2)|p.E286E(2)|p.R283fs*16(2)|p.R282_E287delRRTEEE(1)|p.L265_K305del41(1)|p.T284fs*57(1)|p.T284_G293del10(1)|p.E285_L289delEEENL(1)|p.R283fs*56(1)|p.E285fs*13(1)|p.V272_K292del21(1)|p.E285_N288delEEEN(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GGAGATTCTCTTCCTCTGTGC	0.567		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	27	Whole gene deletion(8)|Deletion - Frameshift(7)|Deletion - In frame(6)|Unknown(2)|Substitution - Missense(2)|Substitution - coding silent(2)	liver(5)|bone(4)|upper_aerodigestive_tract(3)|large_intestine(3)|breast(3)|stomach(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|urinary_tract(2)|pancreas(1)	17											96.0	82.0	87.0					17																	7577080		2203	4300	6503	7517805	SO:0001819	synonymous_variant	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.858A>G	17.37:g.7577080T>C		Somatic		Capture	Illumina HiSeq	Phase_I	7517805	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	37	CCDS11118.1																																																																																				TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7577153	7577153	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577153C>A	ENST00000269305.4	-	8	974	c.785G>T	c.(784-786)gGt>gTt	p.G262V	TP53_ENST00000455263.2_Missense_Mutation_p.G262V|TP53_ENST00000420246.2_Missense_Mutation_p.G262V|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Missense_Mutation_p.G262V|TP53_ENST00000445888.2_Missense_Mutation_p.G262V	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	262	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		G -> C (in a sporadic cancer; somatic mutation).|G -> D (in sporadic cancers; somatic mutation).|G -> H (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|G -> S (in sporadic cancers; somatic mutation).|G -> V (in sporadic cancers; somatic mutation). {ECO:0000269|Ref.23}.|GN -> PD (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.G262V(19)|p.0?(8)|p.G262D(4)|p.?(3)|p.G262_F270delGNLLGRNSF(2)|p.G262fs*83(2)|p.G262_S269delGNLLGRNS(2)|p.G262del(2)|p.G262H(1)|p.E258fs*71(1)|p.S261_L264>R(1)|p.G262fs*2(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAGTAGATTACCACTACTCAG	0.517		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	46	Substitution - Missense(24)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(4)|Unknown(3)|Complex - deletion inframe(1)	lung(8)|large_intestine(5)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(5)|ovary(5)|upper_aerodigestive_tract(4)|bone(4)|endometrium(2)|urinary_tract(2)|pancreas(2)|eye(1)|liver(1)|breast(1)|stomach(1)	17											40.0	37.0	38.0					17																	7577153		2203	4299	6502	7517878	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.785G>T	17.37:g.7577153C>A	ENSP00000269305:p.Gly262Val	Somatic		Capture	Illumina HiSeq	Phase_I	7517878	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565296	0.86439	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99957	-9.0;-9.0;-9.0;-9.0;-9.0;-9.0	5.03	5.03	0.67393	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99955	0.9981	M	0.90977	3.165	0.80722	D	1	D;P;D;D	0.89917	1.0;0.819;0.999;1.0	D;P;D;D	0.83275	0.996;0.537;0.996;0.992	D	0.95599	0.8661	10	0.87932	D	0	-15.6281	15.9038	0.79403	0.0:1.0:0.0:0.0	.	262;262;262;262	P04637-2;P04637-3;P04637;Q1MSW8	.;.;P53_HUMAN;.	V	262;262;262;262;262;251;130	ENSP00000352610:G262V;ENSP00000269305:G262V;ENSP00000398846:G262V;ENSP00000391127:G262V;ENSP00000391478:G262V;ENSP00000425104:G130V	ENSP00000269305:G262V	G	-	2	0	TP53	7517878	1.000000	0.71417	0.951000	0.38953	0.085000	0.17905	7.572000	0.82409	2.619000	0.88677	0.462000	0.41574	GGT		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7577571	7577571	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577571A>G	ENST00000269305.4	-	7	899	c.710T>C	c.(709-711)aTg>aCg	p.M237T	TP53_ENST00000455263.2_Missense_Mutation_p.M237T|TP53_ENST00000420246.2_Missense_Mutation_p.M237T|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Missense_Mutation_p.M237T|TP53_ENST00000359597.4_Missense_Mutation_p.M237T|TP53_ENST00000445888.2_Missense_Mutation_p.M237T	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	237	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		M -> I (in LFS; germline mutation and in sporadic cancers; somatic mutation).|M -> K (in sporadic cancers; somatic mutation).|M -> L (in sporadic cancers; somatic mutation).|M -> R (in sporadic cancers; somatic mutation).|M -> T (in sporadic cancers; somatic mutation).|M -> V (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.M237K(11)|p.0?(8)|p.?(5)|p.M237_N239delMCN(4)|p.M237R(3)|p.M237T(2)|p.M237fs*10(2)|p.Y236_M237delYM(1)|p.H233fs*6(1)|p.M144K(1)|p.M144_N146delMCN(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.H233_C242del10(1)|p.M237fs*1(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACTGTTACACATGTAGTTGTA	0.572		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	43	Substitution - Missense(17)|Whole gene deletion(8)|Deletion - In frame(8)|Deletion - Frameshift(5)|Unknown(5)	ovary(6)|biliary_tract(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(4)|endometrium(4)|bone(4)|upper_aerodigestive_tract(3)|lung(3)|breast(3)|central_nervous_system(2)|pancreas(2)|stomach(1)|urinary_tract(1)|prostate(1)	17											130.0	102.0	111.0					17																	7577571		2203	4300	6503	7518296	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.710T>C	17.37:g.7577571A>G	ENSP00000269305:p.Met237Thr	Somatic		Capture	Illumina HiSeq	Phase_I	7518296	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.930451	0.73327	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99815	-6.9;-6.9;-6.9;-6.9;-6.9;-6.9;-6.9;-6.9	4.09	4.09	0.47781	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	M	0.86953	2.85	0.58432	D	0.999997	D;P;D;D;D;D	0.89917	1.0;0.647;1.0;1.0;0.999;1.0	D;B;D;D;D;D	0.97110	1.0;0.408;1.0;1.0;1.0;1.0	D	0.96910	0.9666	10	0.87932	D	0	-32.6033	11.6823	0.51466	1.0:0.0:0.0:0.0	.	237;237;144;237;237;237	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	T	237;237;237;237;237;237;226;144;105;144	ENSP00000410739:M237T;ENSP00000352610:M237T;ENSP00000269305:M237T;ENSP00000398846:M237T;ENSP00000391127:M237T;ENSP00000391478:M237T;ENSP00000425104:M105T;ENSP00000423862:M144T	ENSP00000269305:M237T	M	-	2	0	TP53	7518296	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.021000	0.93673	2.074000	0.62210	0.379000	0.24179	ATG		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
TP53	7157	hgsc.bcm.edu	37	17	7577574	7577574	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:7577574T>C	ENST00000269305.4	-	7	896	c.707A>G	c.(706-708)tAc>tGc	p.Y236C	TP53_ENST00000455263.2_Missense_Mutation_p.Y236C|TP53_ENST00000420246.2_Missense_Mutation_p.Y236C|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000413465.2_Missense_Mutation_p.Y236C|TP53_ENST00000359597.4_Missense_Mutation_p.Y236C|TP53_ENST00000445888.2_Missense_Mutation_p.Y236C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	236	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation).|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|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)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y236C(61)|p.0?(8)|p.?(5)|p.Y143C(5)|p.Y236del(4)|p.Y236S(3)|p.Y236_M237delYM(1)|p.I232_Y236delIHYNY(1)|p.H233fs*6(1)|p.Y236_M243delYMCNSSCM(1)|p.V225fs*23(1)|p.Y236fs*4(1)|p.H233_C242del10(1)|p.N235_Y236delNY(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GTTACACATGTAGTTGTAGTG	0.572		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											Pancreas(47;798 1329 9957 10801)		yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	94	Substitution - Missense(69)|Deletion - In frame(9)|Whole gene deletion(8)|Unknown(5)|Deletion - Frameshift(2)|Insertion - Frameshift(1)	breast(13)|ovary(13)|lung(9)|haematopoietic_and_lymphoid_tissue(7)|biliary_tract(6)|stomach(6)|oesophagus(6)|upper_aerodigestive_tract(5)|central_nervous_system(5)|urinary_tract(5)|pancreas(5)|prostate(4)|bone(4)|liver(2)|large_intestine(2)|soft_tissue(1)|endometrium(1)	17	GRCh37	CM004907	TP53	M							126.0	100.0	109.0					17																	7577574		2203	4300	6503	7518299	SO:0001583	missense	7157	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.707A>G	17.37:g.7577574T>C	ENSP00000269305:p.Tyr236Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7518299	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	16.62	3.173261	0.57584	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99801	-6.81;-6.81;-6.81;-6.81;-6.81;-6.81;-6.81;-6.81	4.09	0.528	0.17089	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.335105	0.32884	N	0.005532	D	0.99582	0.9849	M	0.74258	2.255	0.44570	D	0.997534	D;D;D;D;D;D	0.89917	0.998;0.982;1.0;0.998;0.999;1.0	D;P;D;D;D;D	0.81914	0.974;0.898;0.99;0.985;0.992;0.995	D	0.99253	1.0888	10	0.87932	D	0	-12.7522	10.2884	0.43581	0.222:0.0:0.0:0.778	.	236;236;143;236;236;236	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	C	236;236;236;236;236;236;225;143;104;143	ENSP00000410739:Y236C;ENSP00000352610:Y236C;ENSP00000269305:Y236C;ENSP00000398846:Y236C;ENSP00000391127:Y236C;ENSP00000391478:Y236C;ENSP00000425104:Y104C;ENSP00000423862:Y143C	ENSP00000269305:Y236C	Y	-	2	0	TP53	7518299	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	1.502000	0.35704	0.034000	0.15491	0.379000	0.24179	TAC		TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
ITGB4	3691	hgsc.bcm.edu	37	17	73747128	73747128	+	Silent	SNP	G	G	A	rs61735289	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr17:73747128G>A	ENST00000200181.3	+	30	3916	c.3729G>A	c.(3727-3729)ccG>ccA	p.P1243P	ITGB4_ENST00000339591.3_Silent_p.P1243P|ITGB4_ENST00000450894.3_Silent_p.P1243P|ITGB4_ENST00000449880.2_Silent_p.P1243P|ITGB4_ENST00000579662.1_Silent_p.P1243P	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1243	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			GGGCTGAGCCGGCTGAGACCA	0.597													G|||	76	0.0151757	0.0015	0.0173	5008	,	,		22177	0.0		0.0348	False		,,,				2504	0.0276																0			17						G	,,	30,4376	35.2+/-66.4	0,30,2173	92.0	85.0	88.0		3729,3729,3729	-10.7	0.0	17	dbSNP_129	88	323,8277	114.2+/-174.2	6,311,3983	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,,	6,341,6156	AA,AG,GG		3.7558,0.6809,2.7141	,,	1243/1823,1243/1806,1243/1753	73747128	353,12653	2203	4300	6503	71258723	SO:0001819	synonymous_variant	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3729G>A	17.37:g.73747128G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71258723	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																				ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
AK5	26289	hgsc.bcm.edu	37	1	77752792	77752792	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:77752792G>A	ENST00000354567.2	+	2	490	c.227G>A	c.(226-228)cGg>cAg	p.R76Q	AK5_ENST00000344720.5_Missense_Mutation_p.R50Q|AK5_ENST00000317704.4_3'UTR	NM_174858.2	NP_777283.1	Q9Y6K8	KAD5_HUMAN	adenylate kinase 5	76					ADP biosynthetic process (GO:0006172)|ATP metabolic process (GO:0046034)|dADP biosynthetic process (GO:0006173)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|pyrimidine ribonucleotide biosynthetic process (GO:0009220)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule organizing center (GO:0005815)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside kinase activity (GO:0019206)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|prostate(1)|skin(2)|stomach(1)	40						GGACAGTCACGGAGATCCTTT	0.368																																																	0			1											71.0	70.0	70.0					1																	77752792		2203	4300	6503	77525380	SO:0001583	missense	26289			AF062595	CCDS675.1, CCDS676.1	1p31	2008-02-05			ENSG00000154027	ENSG00000154027		"""Adenylate kinases"""	365	protein-coding gene	gene with protein product		608009				10215863	Standard	NM_012093		Approved		uc001dhn.3	Q9Y6K8	OTTHUMG00000009796	ENST00000354567.2:c.227G>A	1.37:g.77752792G>A	ENSP00000346577:p.Arg76Gln	Somatic		Capture	Illumina HiSeq	Phase_I	77525380	Q5U622|Q6FH66|Q7Z4T5|Q86YS0|Q8N464|Q96EC9	Missense_Mutation	SNP	ENST00000354567.2	37	CCDS675.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939429	0.92526	.	.	ENSG00000154027	ENST00000354567;ENST00000344720;ENST00000478407	T;T;D	0.83914	-0.62;-0.67;-1.78	5.59	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.78748	0.4332	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;0.957	P;B	0.59546	0.859;0.223	T	0.78033	-0.2362	10	0.38643	T	0.18	-0.7307	14.2613	0.66088	0.0717:0.0:0.9283:0.0	.	76;76	Q9Y6K8;Q8N291	KAD5_HUMAN;.	Q	76;50;50	ENSP00000346577:R76Q;ENSP00000341430:R50Q;ENSP00000434409:R50Q	ENSP00000341430:R50Q	R	+	2	0	AK5	77525380	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.583000	0.82559	2.809000	0.96659	0.650000	0.86243	CGG		AK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026993.4	NM_174858	
COL24A1	255631	hgsc.bcm.edu	37	1	86252103	86252103	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:86252103A>G	ENST00000370571.2	-	48	4359	c.3993T>C	c.(3991-3993)gcT>gcC	p.A1331A	COL24A1_ENST00000436319.1_Silent_p.A1331A	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1331	Collagen-like 15.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		GAGGACCTGGAGCCCCAGCAA	0.463																																																	0			1											88.0	91.0	90.0					1																	86252103		1835	4083	5918	86024691	SO:0001819	synonymous_variant	255631			AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3993T>C	1.37:g.86252103A>G		Somatic		Capture	Illumina HiSeq	Phase_I	86024691	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																				COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
ATP9B	374868	hgsc.bcm.edu	37	18	77063654	77063654	+	Missense_Mutation	SNP	G	G	A	rs201117656		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr18:77063654G>A	ENST00000426216.2	+	14	1479	c.1462G>A	c.(1462-1464)Gtg>Atg	p.V488M	ATP9B_ENST00000307671.7_Missense_Mutation_p.V488M	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	488					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CCTGGGCACCGTGTCCTATGG	0.552													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17828	0.0		0.0	False		,,,				2504	0.0																0			18											90.0	80.0	83.0					18																	77063654		2203	4300	6503	75164642	SO:0001583	missense	374868			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1462G>A	18.37:g.77063654G>A	ENSP00000398076:p.Val488Met	Somatic		Capture	Illumina HiSeq	Phase_I	75164642	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	19.34	3.808632	0.70797	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	T;T	0.65364	-0.15;-0.15	4.94	4.94	0.65067	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.063082	0.64402	D	0.000007	T	0.78059	0.4224	M	0.71581	2.175	0.80722	D	1	D;D	0.60575	0.988;0.985	D;D	0.66847	0.947;0.911	T	0.79455	-0.1796	10	0.52906	T	0.07	.	18.5557	0.91083	0.0:0.0:1.0:0.0	.	488;488	O43861;O43861-2	ATP9B_HUMAN;.	M	488	ENSP00000398076:V488M;ENSP00000304500:V488M	ENSP00000304500:V488M	V	+	1	0	ATP9B	75164642	1.000000	0.71417	0.637000	0.29366	0.564000	0.35744	9.057000	0.93889	2.435000	0.82474	0.655000	0.94253	GTG		ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
MRPL4	51073	hgsc.bcm.edu	37	19	10363280	10363280	+	Missense_Mutation	SNP	C	C	T	rs45520838	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:10363280C>T	ENST00000253099.6	+	3	465	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000307422.5_Missense_Mutation_p.R60C|MRPL4_ENST00000393733.2_Missense_Mutation_p.R60C|MRPL4_ENST00000590669.1_Missense_Mutation_p.R60C|MRPL4_ENST00000588502.1_Missense_Mutation_p.R59C	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	60					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		CACTCATCGACGCCCAGTGCA	0.682													C|||	9	0.00179712	0.0	0.0029	5008	,	,		16320	0.0		0.006	False		,,,				2504	0.001																0			19						C	CYS/ARG,CYS/ARG,CYS/ARG	3,4403		0,3,2200	37.0	41.0	39.0		178,178,178	1.4	0.0	19	dbSNP_127	39	44,8556		0,44,4256	yes	missense,missense,missense	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	180,180,180	0,47,6456	TT,TC,CC		0.5116,0.0681,0.3614	probably-damaging,probably-damaging,probably-damaging	60/312,60/312,60/264	10363280	47,12959	2203	4300	6503	10224280	SO:0001583	missense	51073			AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.178C>T	19.37:g.10363280C>T	ENSP00000253099:p.Arg60Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10224280	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.21	3.572904	0.65765	6.81E-4	0.005116	ENSG00000105364	ENST00000253099;ENST00000307422;ENST00000393733	.	.	.	4.89	1.37	0.22104	.	0.341831	0.30118	N	0.010366	T	0.31575	0.0801	L	0.47716	1.5	0.09310	N	1	D;D	0.71674	0.998;0.989	P;P	0.59825	0.864;0.613	T	0.08513	-1.0718	9	0.59425	D	0.04	-19.6719	3.669	0.08266	0.3659:0.443:0.0:0.1911	rs45520838	60;60	Q9BYD3-2;Q9BYD3	.;RM04_HUMAN	C	60	.	ENSP00000253099:R60C	R	+	1	0	MRPL4	10224280	0.177000	0.23109	0.014000	0.15608	0.044000	0.14063	0.602000	0.24134	0.650000	0.30769	-0.320000	0.08662	CGC		MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1		
FDX1L	112812	hgsc.bcm.edu	37	19	10421229	10421229	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:10421229G>A	ENST00000393708.3	-	5	503	c.485C>T	c.(484-486)gCg>gTg	p.A162V	FDX1L_ENST00000541276.1_3'UTR|FDX1L_ENST00000492239.1_5'UTR|FDX1L_ENST00000494368.1_Missense_Mutation_p.A27V|CTD-2369P2.10_ENST00000452032.2_3'UTR|ZGLP1_ENST00000403903.3_5'Flank|ZGLP1_ENST00000403352.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	162	2Fe-2S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00465}.				oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)			NS(2)|endometrium(1)|large_intestine(1)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(20;9.5e-10)|Epithelial(33;2.11e-06)|all cancers(31;5.06e-06)			GGTGAATTCCGCTCCTTCCAG	0.592																																																	0			19											127.0	102.0	111.0					19																	10421229		2203	4300	6503	10282229	SO:0001583	missense	112812			AK097022	CCDS32905.1	19p13.2	2012-10-09			ENSG00000267673	ENSG00000267673			30546	protein-coding gene	gene with protein product		614585				12477932	Standard	NM_001031734		Approved	MGC19604	uc002mny.1	Q6P4F2	OTTHUMG00000141299	ENST00000393708.3:c.485C>T	19.37:g.10421229G>A	ENSP00000377311:p.Ala162Val	Somatic		Capture	Illumina HiSeq	Phase_I	10282229	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	37	CCDS32905.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534889	0.27475	.	.	ENSG00000167807	ENST00000393708	.	.	.	4.25	2.02	0.26589	Beta-grasp fold, ferredoxin-type (1);Ferredoxin (2);	0.350657	0.29544	N	0.011852	T	0.16300	0.0392	N	0.05158	-0.105	0.20489	N	0.999894	B	0.15141	0.012	B	0.09377	0.004	T	0.16837	-1.0389	9	0.41790	T	0.15	-2.5169	8.0535	0.30591	0.2087:0.0:0.7913:0.0	.	162	Q6P4F2	ADXL_HUMAN	V	162	.	ENSP00000377311:A162V	A	-	2	0	FDX1L	10282229	0.982000	0.34865	0.756000	0.31282	0.964000	0.63967	2.177000	0.42509	0.738000	0.32606	0.555000	0.69702	GCG		FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2		
MOB3A	126308	hgsc.bcm.edu	37	19	2078488	2078488	+	Silent	SNP	T	T	C	rs2074894	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:2078488T>C	ENST00000357066.3	-	3	451	c.72A>G	c.(70-72)ccA>ccG	p.P24P	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.P24P	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	24						intracellular (GO:0005622)	metal ion binding (GO:0046872)										GCTGGGTGCCTGGCTCAAACT	0.627													C|||	1973	0.39397	0.6528	0.2507	5008	,	,		16431	0.1835		0.329	False		,,,				2504	0.4294																0			19						C		2793,1613	497.7+/-363.9	887,1019,297	55.0	57.0	56.0		72	-8.5	0.0	19	dbSNP_96	56	2932,5668	665.8+/-402.3	506,1920,1874	no	coding-synonymous	MOB3A	NM_130807.2		1393,2939,2171	CC,CT,TT		34.093,36.6092,44.0181		24/218	2078488	5725,7281	2203	4300	6503	2029488	SO:0001819	synonymous_variant	126308			AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.72A>G	19.37:g.2078488T>C		Somatic		Capture	Illumina HiSeq	Phase_I	2029488	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																				MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
ACP5	54	hgsc.bcm.edu	37	19	11687604	11687604	+	Missense_Mutation	SNP	C	C	T	rs148219285		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:11687604C>T	ENST00000592828.1	-	5	718	c.316G>A	c.(316-318)Gtg>Atg	p.V106M	ACP5_ENST00000412435.2_Missense_Mutation_p.V106M|ACP5_ENST00000433365.2_Missense_Mutation_p.V106M|ACP5_ENST00000218758.5_Missense_Mutation_p.V106M|ACP5_ENST00000590420.1_Intron	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	106					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						CCGGCTAGCACGTACCAGGGC	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		19155	0.001		0.0	False		,,,				2504	0.0																0			19						C	MET/VAL,MET/VAL,MET/VAL,MET/VAL	0,4406		0,0,2203	171.0	157.0	162.0		316,316,316,316	3.8	1.0	19	dbSNP_134	162	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	21,21,21,21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign	106/326,106/326,106/326,106/326	11687604	3,13003	2203	4300	6503	11548604	SO:0001583	missense	54			X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"""tartrate-resistant acid phosphatase"""	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.316G>A	19.37:g.11687604C>T	ENSP00000468767:p.Val106Met	Somatic		Capture	Illumina HiSeq	Phase_I	11548604	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Missense_Mutation	SNP	ENST00000592828.1	37	CCDS12265.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	13.64	2.298854	0.40694	0.0	3.49E-4	ENSG00000102575	ENST00000218758;ENST00000412435;ENST00000433365	D;D;D	0.85629	-2.01;-2.01;-2.01	4.87	3.82	0.43975	Metallophosphoesterase domain (1);	0.060473	0.64402	D	0.000003	D	0.82508	0.5052	L	0.49571	1.57	0.80722	D	1	D	0.55800	0.973	P	0.48227	0.571	T	0.80984	-0.1138	10	0.51188	T	0.08	-18.9338	7.8633	0.29522	0.0:0.7462:0.1652:0.0886	.	106	P13686	PPA5_HUMAN	M	106	ENSP00000218758:V106M;ENSP00000392374:V106M;ENSP00000413456:V106M	ENSP00000218758:V106M	V	-	1	0	ACP5	11548604	0.937000	0.31787	0.991000	0.47740	0.007000	0.05969	1.984000	0.40658	1.021000	0.39600	-0.175000	0.13238	GTG		ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1		
ZNF43	7594	hgsc.bcm.edu	37	19	21992107	21992108	+	Missense_Mutation	DNP	GC	GC	AA	rs201159112		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G|C	G|C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:21992107_21992108GC>AA	ENST00000354959.4	-	4	900_901	c.731_732GC>TT	c.(730-732)cGC>cTT	p.R244L	ZNF43_ENST00000595461.1_Missense_Mutation_p.R238L|ZNF43_ENST00000598381.1_Missense_Mutation_p.R238L|ZNF43_ENST00000594012.1_Missense_Mutation_p.R238L	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	244			R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GTGTAGTAAGGCGTGAGGACCA	0.347																																																	0			19																																								21783947|21783948	SO:0001583	missense	7594			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.731_732delinsAA	19.37:g.21992107_21992108delinsAA	ENSP00000347045:p.Arg244Leu	Somatic		Capture	Illumina HiSeq	Phase_I	21783947|21783948	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent|Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2																																																																																				ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
FCGBP	8857	hgsc.bcm.edu	37	19	40420087	40420087	+	Silent	SNP	G	G	A	rs12460562	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:40420087G>A	ENST00000221347.6	-	6	2914	c.2907C>T	c.(2905-2907)gcC>gcT	p.A969A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	969	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			TGCGCACGACGGCATCCCTGC	0.597													G|||	694	0.138578	0.0129	0.3329	5008	,	,		20473	0.0417		0.1998	False		,,,				2504	0.2076																0			19						G		208,4198	126.6+/-163.6	7,194,2002	62.0	58.0	60.0		2907	-9.7	0.0	19	dbSNP_120	60	1795,6805	321.8+/-315.3	192,1411,2697	no	coding-synonymous	FCGBP	NM_003890.2		199,1605,4699	AA,AG,GG		20.8721,4.7208,15.4006		969/5406	40420087	2003,11003	2203	4300	6503	45111927	SO:0001819	synonymous_variant	8857			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.2907C>T	19.37:g.40420087G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45111927	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
CYP2S1	29785	hgsc.bcm.edu	37	19	41709382	41709382	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:41709382A>G	ENST00000310054.4	+	7	1220	c.1004A>G	c.(1003-1005)gAg>gGg	p.E335G	CYP2S1_ENST00000542619.1_Missense_Mutation_p.E60G	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	335					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						CTGAATCGGGAGCTGGGGGCT	0.667																																																	0			19											32.0	31.0	31.0					19																	41709382		2202	4300	6502	46401222	SO:0001583	missense	29785			AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"""Cytochrome P450s"""	15654	protein-coding gene	gene with protein product		611529	"""cytochrome P450, subfamily IIS, polypeptide 1"""			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.1004A>G	19.37:g.41709382A>G	ENSP00000308032:p.Glu335Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46401222	Q9BZ66	Missense_Mutation	SNP	ENST00000310054.4	37	CCDS12573.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.989338	0.53934	.	.	ENSG00000167600	ENST00000301173;ENST00000310054;ENST00000542619	T;T	0.68181	-0.31;-0.31	5.02	3.93	0.45458	.	0.420777	0.22160	N	0.063798	T	0.73225	0.3560	L	0.55481	1.735	0.29838	N	0.829493	B;D	0.71674	0.093;0.998	B;D	0.67382	0.102;0.951	T	0.69544	-0.5117	10	0.87932	D	0	.	7.343	0.26648	0.6839:0.0:0.0:0.3161	.	60;335	B4DJI0;Q96SQ9	.;CP2S1_HUMAN	G	335;335;60	ENSP00000308032:E335G;ENSP00000445299:E60G	ENSP00000301173:E335G	E	+	2	0	CYP2S1	46401222	0.999000	0.42202	0.998000	0.56505	0.721000	0.41392	1.901000	0.39838	1.896000	0.54893	0.449000	0.29647	GAG		CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1		
HAS1	3036	hgsc.bcm.edu	37	19	52217338	52217338	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:52217338C>T	ENST00000222115.1	-	5	1113	c.1079G>A	c.(1078-1080)cGc>cAc	p.R360H	HAS1_ENST00000540069.2_Missense_Mutation_p.R359H|HAS1_ENST00000601714.1_Missense_Mutation_p.R367H|HAS1_ENST00000594621.1_Silent_p.P189P	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	360					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		TGAGTAGCAGCGGGACCTGGA	0.632																																					NSCLC(132;636 2450 45807 47979)												0			19											30.0	20.0	23.0					19																	52217338		2202	4297	6499	56909150	SO:0001583	missense	3036			U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1079G>A	19.37:g.52217338C>T	ENSP00000222115:p.Arg360His	Somatic		Capture	Illumina HiSeq	Phase_I	56909150	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	2.471|2.471	-0.321898|-0.321898	0.05386|0.05386	.|.	.|.	ENSG00000105509|ENSG00000105509	ENST00000376737|ENST00000540069;ENST00000222115	.|T;T	.|0.43294	.|0.95;0.95	2.98|2.98	2.98|2.98	0.34508|0.34508	.|.	.|0.159749	.|0.38111	.|U	.|0.001811	T|T	0.30727|0.30727	0.0774|0.0774	M|M	0.63428|0.63428	1.95|1.95	0.26810|0.26810	N|N	0.969013|0.969013	.|P;P;P	.|0.36048	.|0.478;0.534;0.534	.|B;B;B	.|0.31547	.|0.052;0.132;0.132	T|T	0.09400|0.09400	-1.0676|-1.0676	6|10	0.56958|0.15499	D|T	0.05|0.54	.|.	6.0486|6.0486	0.19773|0.19773	0.0:0.8529:0.0:0.1471|0.0:0.8529:0.0:0.1471	.|.	.|359;360;359	.|G3V1S7;Q92839;Q8IYH3	.|.;HAS1_HUMAN;.	T|H	173|359;360	.|ENSP00000445021:R359H;ENSP00000222115:R360H	ENSP00000365927:A173T|ENSP00000222115:R360H	A|R	-|-	1|2	0|0	HAS1|HAS1	56909150|56909150	0.614000|0.614000	0.27017|0.27017	0.893000|0.893000	0.35052|0.35052	0.020000|0.020000	0.10135|0.10135	1.058000|1.058000	0.30504|0.30504	1.693000|1.693000	0.51124|0.51124	0.174000|0.174000	0.16983|0.16983	GCT|CGC		HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
ZNF329	79673	hgsc.bcm.edu	37	19	58639353	58639353	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:58639353G>A	ENST00000598312.1	-	4	1751	c.1518C>T	c.(1516-1518)agC>agT	p.S506S	ZNF329_ENST00000358067.4_Silent_p.S506S	NM_024620.3	NP_078896.3	Q86UD4	ZN329_HUMAN	zinc finger protein 329	506					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|large_intestine(10)|lung(5)|skin(3)|urinary_tract(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.029)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.017)|Lung(386;0.216)		GACCCTCCCTGCTATGGAGTC	0.512																																																	0			19											134.0	129.0	131.0					19																	58639353		2203	4300	6503	63331165	SO:0001819	synonymous_variant	79673			AK022648	CCDS12972.1	19q13.43	2013-01-08				ENSG00000181894		"""Zinc fingers, C2H2-type"""	14209	protein-coding gene	gene with protein product							Standard	XM_006723381		Approved	FLJ12586	uc002qrn.3	Q86UD4		ENST00000598312.1:c.1518C>T	19.37:g.58639353G>A		Somatic		Capture	Illumina HiSeq	Phase_I	63331165	B3KR32|Q9H9R7	Silent	SNP	ENST00000598312.1	37	CCDS12972.1																																																																																				ZNF329-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466724.1	NM_024620	
CST9	128822	hgsc.bcm.edu	37	20	23586266	23586266	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:23586266T>C	ENST00000376971.3	-	1	247	c.236A>G	c.(235-237)gAg>gGg	p.E79G		NM_001008693.2	NP_001008693.2	Q5W186	CST9_HUMAN	cystatin 9 (testatin)	79						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			central_nervous_system(2)|large_intestine(4)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Colorectal(13;0.0993)					CATGCTATCCTCCCTCCATGA	0.532																																																	0			20											249.0	179.0	203.0					20																	23586266		2203	4300	6503	23534266	SO:0001583	missense	128822			AF494536	CCDS33450.1	20p11.21	2012-08-14			ENSG00000173335	ENSG00000173335			13261	protein-coding gene	gene with protein product						20565543	Standard	NM_001008693		Approved	CLM, CTES7A	uc002wtl.3	Q5W186	OTTHUMG00000032076	ENST00000376971.3:c.236A>G	20.37:g.23586266T>C	ENSP00000366170:p.Glu79Gly	Somatic		Capture	Illumina HiSeq	Phase_I	23534266	B2RP76|Q8TD53	Missense_Mutation	SNP	ENST00000376971.3	37	CCDS33450.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022710	0.35701	.	.	ENSG00000173335	ENST00000376971	T	0.22134	1.97	2.85	1.68	0.24146	Proteinase inhibitor I25, cystatin (1);	.	.	.	.	T	0.35158	0.0922	L	0.55213	1.73	0.09310	N	1	D	0.89917	1.0	D	0.77004	0.989	T	0.09335	-1.0679	9	0.87932	D	0	.	4.925	0.13889	0.2874:0.0:0.0:0.7126	.	79	Q5W186	CST9_HUMAN	G	79	ENSP00000366170:E79G	ENSP00000366170:E79G	E	-	2	0	CST9	23534266	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.669000	0.25142	0.469000	0.27268	0.482000	0.46254	GAG		CST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078341.1	NM_001008693.1	
TP53INP2	58476	hgsc.bcm.edu	37	20	33296656	33296656	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:33296656T>C	ENST00000374810.3	+	3	502	c.113T>C	c.(112-114)aTt>aCt	p.I38T	TP53INP2_ENST00000374809.2_Missense_Mutation_p.I38T|NCOA6_ENST00000593786.1_Intron	NM_021202.1	NP_067025.1	Q8IXH6	T53I2_HUMAN	tumor protein p53 inducible nuclear protein 2	38					autophagic vacuole assembly (GO:0000045)|osteoblast differentiation (GO:0001649)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(1)|urinary_tract(1)	2						TGGCTCATCATTGACCTGCCG	0.662																																																	0			20											43.0	42.0	42.0					20																	33296656		2202	4300	6502	32760317	SO:0001583	missense	58476			AL109824	CCDS13240.1	20q11.22	2010-01-05	2004-06-18	2004-06-18	ENSG00000078804	ENSG00000078804			16104	protein-coding gene	gene with protein product	"""diabetes and obesity regulated"""		"""chromosome 20 open reading frame 110"""	C20orf110		12477932	Standard	NM_021202		Approved	FLJ21759, FLJ23500, DKFZp434B2411, DKFZp434O0827, dJ1181N3.1, PINH, DOR	uc002xau.1	Q8IXH6	OTTHUMG00000032310	ENST00000374810.3:c.113T>C	20.37:g.33296656T>C	ENSP00000363943:p.Ile38Thr	Somatic		Capture	Illumina HiSeq	Phase_I	32760317	A8K8S8|E1P5P6|Q5JX64|Q8IYL5|Q9NU00	Missense_Mutation	SNP	ENST00000374810.3	37	CCDS13240.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.151371	0.78001	.	.	ENSG00000078804	ENST00000374810;ENST00000374809;ENST00000451665;ENST00000414082	T;T;T;T	0.52754	0.65;0.65;1.48;0.65	4.74	4.74	0.60224	.	0.063894	0.64402	D	0.000009	T	0.61590	0.2359	L	0.52573	1.65	0.80722	D	1	D	0.76494	0.999	D	0.69479	0.964	T	0.65520	-0.6148	10	0.87932	D	0	-7.3787	14.1776	0.65552	0.0:0.0:0.0:1.0	.	38	Q8IXH6	T53I2_HUMAN	T	38	ENSP00000363943:I38T;ENSP00000363942:I38T;ENSP00000395784:I38T;ENSP00000404410:I38T	ENSP00000363942:I38T	I	+	2	0	TP53INP2	32760317	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.082000	0.71318	1.894000	0.54839	0.454000	0.30748	ATT		TP53INP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078807.2	NM_021202	
PHF20	51230	hgsc.bcm.edu	37	20	34459662	34459662	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:34459662A>G	ENST00000374012.3	+	9	1322	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	PHF20_ENST00000439301.1_3'UTR|PHF20_ENST00000481202.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	398					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(5)|endometrium(1)|kidney(7)|large_intestine(6)|lung(11)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(12;0.00631)|all_lung(11;0.0145)					GCAGGCTTGGAGTTGAACTGC	0.483																																																	0			20											122.0	122.0	122.0					20																	34459662		2203	4300	6503	33923076	SO:0001583	missense	51230			AL109965	CCDS13268.1	20q11.22-q11.23	2013-01-28	2004-12-01	2004-12-01	ENSG00000025293	ENSG00000025293		"""Tudor domain containing"", ""Zinc fingers, PHD-type"""	16098	protein-coding gene	gene with protein product	"""tudor domain containing 20A"""	610335	"""chromosome 20 open reading frame 104"""	C20orf104			Standard	NM_016436		Approved	dJ1121G12.1, TDRD20A	uc002xek.1	Q9BVI0	OTTHUMG00000032367	ENST00000374012.3:c.1193A>G	20.37:g.34459662A>G	ENSP00000363124:p.Glu398Gly	Somatic		Capture	Illumina HiSeq	Phase_I	33923076	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	A	11.48	1.651858	0.29336	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.46819	1.42;0.86;0.86	5.56	3.29	0.37713	.	0.499842	0.21368	N	0.075696	T	0.23688	0.0573	N	0.08118	0	0.58432	D	0.999994	B;B	0.25667	0.131;0.003	B;B	0.22386	0.039;0.001	T	0.05649	-1.0872	10	0.48119	T	0.1	.	5.1478	0.14994	0.7244:0.1839:0.0916:0.0	.	398;398	Q9BVI0;Q66K49	PHF20_HUMAN;.	G	398	ENSP00000363124:E398G;ENSP00000341900:E398G;ENSP00000363112:E398G	ENSP00000341900:E398G	E	+	2	0	PHF20	33923076	0.956000	0.32656	0.990000	0.47175	0.752000	0.42762	1.482000	0.35486	0.916000	0.36871	0.482000	0.46254	GAG		PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436	
HNF4A	3172	hgsc.bcm.edu	37	20	43034729	43034729	+	Silent	SNP	C	C	T	rs570058788		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:43034729C>T	ENST00000316099.4	+	2	236	c.147C>T	c.(145-147)aaC>aaT	p.N49N	HNF4A_ENST00000609795.1_Silent_p.N27N|HNF4A_ENST00000316673.4_Silent_p.N27N|HNF4A_ENST00000443598.2_Silent_p.N49N|MIR3646_ENST00000578301.1_RNA|HNF4A_ENST00000415691.2_Silent_p.N49N|HNF4A_ENST00000457232.1_Silent_p.N27N	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	49					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CCAACCTCAACGCGCCCAACA	0.627																																					Colon(79;2 1269 8820 14841 52347)												0			20											143.0	142.0	142.0					20																	43034729		2203	4300	6503	42468143	SO:0001819	synonymous_variant	3172			X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"""Nuclear hormone receptors"""	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.147C>T	20.37:g.43034729C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42468143	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Silent	SNP	ENST00000316099.4	37	CCDS13330.1																																																																																				HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3		
PAXBP1	94104	hgsc.bcm.edu	37	21	34121003	34121003	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:34121003A>G	ENST00000331923.4	-	11	1919	c.1730T>C	c.(1729-1731)aTt>aCt	p.I577T	PAXBP1_ENST00000290178.4_Missense_Mutation_p.I577T	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	577					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TTCTTTTGAAATTCGATCTAA	0.328																																																	0			21											40.0	42.0	41.0					21																	34121003		2202	4300	6502	33042874	SO:0001583	missense	0			AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.1730T>C	21.37:g.34121003A>G	ENSP00000328992:p.Ile577Thr	Somatic		Capture	Illumina HiSeq	Phase_I	33042874	D3DSE7|Q96DU8|Q9NYQ0	Missense_Mutation	SNP	ENST00000331923.4	37	CCDS13619.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.082603	0.76528	.	.	ENSG00000159086	ENST00000331923;ENST00000290178	T;T	0.37411	1.64;1.2	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.58352	0.2116	M	0.70275	2.135	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.997	D;D;P	0.66084	0.937;0.941;0.879	T	0.61441	-0.7062	10	0.59425	D	0.04	-19.3128	15.5492	0.76133	1.0:0.0:0.0:0.0	.	577;577;86	Q9Y5B6-2;Q9Y5B6;B3KSC0	.;GCFC1_HUMAN;.	T	577	ENSP00000328992:I577T;ENSP00000290178:I577T	ENSP00000290178:I577T	I	-	2	0	GCFC1	33042874	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.962000	0.93254	2.154000	0.67381	0.455000	0.32223	ATT		PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	
CBS	875	hgsc.bcm.edu	37	21	44478973	44478973	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:44478973G>A	ENST00000398165.3	-	14	1588	c.1329C>T	c.(1327-1329)ttC>ttT	p.F443F	CBS_ENST00000352178.5_Silent_p.F443F|CBS_ENST00000398168.1_Silent_p.F443F|CBS_ENST00000359624.3_Silent_p.F443F|CBS_ENST00000398158.1_Silent_p.F443F|CBS_ENST00000544202.1_Silent_p.F355F	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	443	CBS. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cellular nitrogen compound metabolic process (GO:0034641)|cysteine biosynthetic process from serine (GO:0006535)|cysteine biosynthetic process via cystathionine (GO:0019343)|homocysteine catabolic process (GO:0043418)|homocysteine metabolic process (GO:0050667)|hydrogen sulfide biosynthetic process (GO:0070814)|L-cysteine catabolic process (GO:0019448)|L-serine catabolic process (GO:0006565)|L-serine metabolic process (GO:0006563)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|transsulfuration (GO:0019346)	cytosol (GO:0005829)|nucleus (GO:0005634)	adenyl nucleotide binding (GO:0030554)|cystathionine beta-synthase activity (GO:0004122)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|modified amino acid binding (GO:0072341)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(8)	17					L-Cysteine(DB00151)|L-Serine(DB00133)|S-Adenosylmethionine(DB00118)	GCGCCTGGTCGAAGCCCTTCT	0.662																																																	0			21											37.0	35.0	36.0					21																	44478973		2178	4275	6453	43352042	SO:0001819	synonymous_variant	875			L14577	CCDS13693.1	21q22.3	2014-09-17			ENSG00000160200	ENSG00000160200	4.2.1.22		1550	protein-coding gene	gene with protein product		613381				9790750	Standard	NM_000071		Approved	HIP4	uc002zcv.2	P35520	OTTHUMG00000086834	ENST00000398165.3:c.1329C>T	21.37:g.44478973G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43352042	B2R993|D3DSK4|Q99425|Q9BWC5	Silent	SNP	ENST00000398165.3	37	CCDS13693.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.962|9.962	1.222963|1.222963	0.22457|0.22457	.|.	.|.	ENSG00000160200|ENSG00000160200	ENST00000451248|ENST00000458223;ENST00000430013	.|.	.|.	.|.	4.71|4.71	-1.92|-1.92	0.07618|0.07618	.|.	.|.	.|.	.|.	.|.	.|T	.|0.55226	.|0.1907	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.50759	.|-0.8790	.|4	.|.	.|.	.|.	-27.3713|-27.3713	10.1165|10.1165	0.42593|0.42593	0.4423:0.0:0.5577:0.0|0.4423:0.0:0.5577:0.0	.|.	.|.	.|.	.|.	X|L	27|31;97	.|.	.|.	R|S	-|-	1|2	2|0	CBS|CBS	43352042|43352042	0.833000|0.833000	0.29383|0.29383	0.989000|0.989000	0.46669|0.46669	0.882000|0.882000	0.50991|0.50991	-0.118000|-0.118000	0.10692|0.10692	-0.440000|-0.440000	0.07211|0.07211	-0.259000|-0.259000	0.10710|0.10710	CGA|TCG		CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057593	46057593	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:46057593T>C	ENST00000380095.1	+	1	321	c.259T>C	c.(259-261)Tcc>Ccc	p.S87P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	87	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						TTGCTGCACCTCCTCCCcctg	0.642																																																	0			21											121.0	115.0	117.0					21																	46057593		2203	4300	6503	44882021	SO:0001583	missense	353333			AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.259T>C	21.37:g.46057593T>C	ENSP00000369438:p.Ser87Pro	Somatic		Capture	Illumina HiSeq	Phase_I	44882021		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	t	1.645	-0.515362	0.04200	.	.	ENSG00000221859	ENST00000380095	T	0.01304	5.03	3.33	-0.376	0.12505	.	.	.	.	.	T	0.01189	0.0039	L	0.39326	1.205	0.09310	N	1	B	0.15719	0.014	B	0.12837	0.008	T	0.49234	-0.8961	9	0.14252	T	0.57	.	2.6435	0.04978	0.2295:0.3936:0.0:0.377	.	87	P60014	KR10A_HUMAN	P	87	ENSP00000369438:S87P	ENSP00000369438:S87P	S	+	1	0	KRTAP10-10	44882021	0.000000	0.05858	0.380000	0.26093	0.077000	0.17291	-0.131000	0.10482	0.302000	0.22762	0.383000	0.25322	TCC		KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
COL6A1	1291	hgsc.bcm.edu	37	21	47418339	47418339	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:47418339G>A	ENST00000361866.3	+	24	1717	c.1603G>A	c.(1603-1605)Ggg>Agg	p.G535R		NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	535	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GGGCGCTCCCGGGATAAACGT	0.597																																																	0			21											61.0	60.0	61.0					21																	47418339		2203	4300	6503	46242767	SO:0001583	missense	1291			M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.1603G>A	21.37:g.47418339G>A	ENSP00000355180:p.Gly535Arg	Somatic		Capture	Illumina HiSeq	Phase_I	46242767	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451208	0.63290	.	.	ENSG00000142156	ENST00000361866;ENST00000538397	D	0.99353	-5.77	4.01	4.01	0.46588	.	0.135083	0.49305	D	0.000159	D	0.99674	0.9878	H	0.99169	4.455	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	D	0.97174	0.9846	10	0.87932	D	0	-9.0733	13.2368	0.59974	0.0:0.0:1.0:0.0	.	535	P12109	CO6A1_HUMAN	R	535	ENSP00000355180:G535R	ENSP00000355180:G535R	G	+	1	0	COL6A1	46242767	1.000000	0.71417	0.821000	0.32701	0.503000	0.33858	2.817000	0.48034	1.963000	0.57068	0.205000	0.17691	GGG		COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
SCN7A	6332	hgsc.bcm.edu	37	2	167330824	167330824	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:167330824T>C	ENST00000409855.1	-	3	391	c.265A>G	c.(265-267)Atc>Gtc	p.I89V		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	89					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	AATCTGAAGATTGTTCTATTT	0.313																																																	0			2											51.0	48.0	49.0					2																	167330824		1758	3949	5707	167039070	SO:0001583	missense	6332			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.265A>G	2.37:g.167330824T>C	ENSP00000386796:p.Ile89Val	Somatic		Capture	Illumina HiSeq	Phase_I	167039070		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.131703	0.37630	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98567	-4.6;-4.6;-5.0	4.52	2.06	0.26882	.	0.113548	0.38272	N	0.001743	D	0.97328	0.9126	M	0.93062	3.375	0.27687	N	0.946238	B	0.10296	0.003	B	0.10450	0.005	D	0.94362	0.7588	10	0.66056	D	0.02	.	4.1325	0.10156	0.149:0.171:0.0:0.6799	.	89	Q01118	SCN7A_HUMAN	V	89	ENSP00000386796:I89V;ENSP00000413699:I89V;ENSP00000403846:I89V	ENSP00000259060:I89V	I	-	1	0	SCN7A	167039070	1.000000	0.71417	0.974000	0.42286	0.871000	0.50021	3.196000	0.51020	0.332000	0.23536	0.383000	0.25322	ATC		SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
XIRP2	129446	hgsc.bcm.edu	37	2	167760306	167760306	+	Missense_Mutation	SNP	G	G	A	rs553364503		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:167760306G>A	ENST00000409728.1	+	2	403	c.314G>A	c.(313-315)cGc>cAc	p.R105H	XIRP2_ENST00000409043.1_Missense_Mutation_p.R105H|XIRP2_ENST00000409756.2_Missense_Mutation_p.R105H|XIRP2_ENST00000295237.9_Missense_Mutation_p.R105H|XIRP2_ENST00000420519.1_Missense_Mutation_p.R105H|XIRP2_ENST00000409195.1_Missense_Mutation_p.R105H	NM_001199143.1	NP_001186072.1	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	0					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AGCAGTCGGCGCAGGATTGAA	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		20520	0.0		0.0	False		,,,				2504	0.001																0			2											116.0	118.0	117.0					2																	167760306		2030	4161	6191	167468552	SO:0001583	missense	129446			AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409728.1:c.314G>A	2.37:g.167760306G>A	ENSP00000386619:p.Arg105His	Somatic		Capture	Illumina HiSeq	Phase_I	167468552	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409728.1	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	G	13.31	2.198409	0.38806	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409195;ENST00000409756;ENST00000420519;ENST00000295237	D;D;T;D;D;T	0.83163	-1.68;-1.69;3.7;-1.68;-1.69;3.7	5.12	5.12	0.69794	.	.	.	.	.	D	0.89757	0.6807	.	.	.	0.31070	N	0.713156	D;D	0.89917	1.0;1.0	D;D	0.74348	0.983;0.983	D	0.88217	0.2894	8	0.48119	T	0.1	-2.224	14.0425	0.64684	0.0:0.0:1.0:0.0	.	105;105	A4UGR9-4;A4UGR9-6	.;.	H	105	ENSP00000386454:R105H;ENSP00000386619:R105H;ENSP00000386840:R105H;ENSP00000386724:R105H;ENSP00000415541:R105H;ENSP00000295237:R105H	ENSP00000295237:R105H	R	+	2	0	XIRP2	167468552	1.000000	0.71417	0.993000	0.49108	0.295000	0.27426	2.351000	0.44071	2.390000	0.81377	0.655000	0.94253	CGC		XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381	
TTN	7273	hgsc.bcm.edu	37	2	179471982	179471982	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:179471982G>C	ENST00000591111.1	-	228	48648	c.48424C>G	c.(48424-48426)Ctt>Gtt	p.L16142V	TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.L8910V|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.L15215V|TTN_ENST00000589042.1_Missense_Mutation_p.L17783V|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.L8843V|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.L8718V|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16142	Fibronectin type-III 17. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GACCAGTTAAGTAGACACATT	0.358																																																	0			2											119.0	110.0	112.0					2																	179471982		1854	4102	5956	179180227	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48424C>G	2.37:g.179471982G>C	ENSP00000465570:p.Leu16142Val	Somatic		Capture	Illumina HiSeq	Phase_I	179180227	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	11.95	1.790922	0.31685	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.60548	0.18;0.18;0.18;0.18	5.99	5.99	0.97316	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73110	0.3545	L	0.46567	1.45	0.53005	D	0.999968	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.73135	-0.4078	9	0.87932	D	0	.	20.4777	0.99188	0.0:0.0:1.0:0.0	.	8718;8843;8910;16142	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	15215;8718;8910;8843;8718	ENSP00000343764:L15215V;ENSP00000434586:L8718V;ENSP00000340554:L8910V;ENSP00000352154:L8843V	ENSP00000340554:L8910V	L	-	1	0	TTN	179180227	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.646000	0.74348	2.840000	0.97914	0.655000	0.94253	CTT		TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ANKRD44	91526	hgsc.bcm.edu	37	2	197990136	197990136	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:197990136G>A	ENST00000328737.2	-	6	520	c.444C>T	c.(442-444)gaC>gaT	p.D148D	ANKRD44_ENST00000337207.5_Silent_p.D148D|ANKRD44_ENST00000409153.1_Silent_p.D173D|ANKRD44_ENST00000539527.1_Silent_p.D101D|ANKRD44_ENST00000409919.1_Silent_p.D173D|ANKRD44_ENST00000282272.8_Silent_p.D165D|ANKRD44_ENST00000450567.1_Silent_p.D148D			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	173										NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GAGCACGCCGGTCCTTCTTGT	0.418																																																	0			2											127.0	118.0	121.0					2																	197990136		2203	4300	6503	197698381	SO:0001819	synonymous_variant	91526			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.444C>T	2.37:g.197990136G>A		Somatic		Capture	Illumina HiSeq	Phase_I	197698381	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Silent	SNP	ENST00000328737.2	37																																																																																					ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
CLK1	1195	hgsc.bcm.edu	37	2	201728889	201728889	+	Intron	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:201728889T>C	ENST00000321356.4	-	1	136				CLK1_ENST00000434813.2_Missense_Mutation_p.R21G|CLK1_ENST00000492793.1_Intron|Y_RNA_ENST00000516950.1_RNA	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1						cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						AAATCCCCCCTCAACGGGGAG	0.637																																																	0			2											60.0	55.0	57.0					2																	201728889		692	1591	2283	201437134	SO:0001627	intron_variant	78989			L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.0+397A>G	2.37:g.201728889T>C		Somatic		Capture	Illumina HiSeq	Phase_I	201437134	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	.	.	.	.	.	.	.	.	.	.	T	3.630	-0.075828	0.07184	.	.	ENSG00000013441	ENST00000434813	T	0.70399	-0.48	1.8	-3.61	0.04556	.	.	.	.	.	T	0.41926	0.1180	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11275	-1.0594	9	0.87932	D	0	.	0.3931	0.00414	0.3209:0.1709:0.136:0.3721	.	21	B4DFW7	.	G	21	ENSP00000394734:R21G	ENSP00000394734:R21G	R	-	1	2	CLK1	201437134	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-6.303000	0.00071	-2.763000	0.00369	-0.765000	0.03448	AGG		CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2		
NRP2	8828	hgsc.bcm.edu	37	2	206608150	206608150	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:206608150A>G	ENST00000357785.5	+	9	1546	c.1515A>G	c.(1513-1515)ggA>ggG	p.G505G	NRP2_ENST00000540178.1_Silent_p.G505G|NRP2_ENST00000357118.4_Silent_p.G505G|NRP2_ENST00000360409.3_Silent_p.G505G|NRP2_ENST00000412873.2_Silent_p.G505G|NRP2_ENST00000417189.1_Silent_p.G505G|NRP2_ENST00000272849.3_Silent_p.G505G|NRP2_ENST00000355117.4_Silent_p.G505G|NRP2_ENST00000540841.1_Silent_p.G505G			Q99435	NELL2_HUMAN	neuropilin 2	0	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(14)|lung(19)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	52						TCATCCAGGGAGCCCGCGGAG	0.562																																																	0			2											68.0	72.0	71.0					2																	206608150		2203	4300	6503	206316395	SO:0001819	synonymous_variant	8828			AF016098	CCDS2364.1, CCDS2365.1, CCDS46496.1, CCDS46497.1, CCDS46498.1, CCDS46499.1	2q33.3	2008-05-23			ENSG00000118257	ENSG00000118257			8005	protein-coding gene	gene with protein product		602070				9529250, 9331348	Standard	NM_003872		Approved	VEGF165R2	uc002vaw.3	O60462	OTTHUMG00000132893	ENST00000357785.5:c.1515A>G	2.37:g.206608150A>G		Somatic		Capture	Illumina HiSeq	Phase_I	206316395	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Silent	SNP	ENST00000357785.5	37	CCDS46496.1																																																																																				NRP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336467.1		
NEFH	4744	hgsc.bcm.edu	37	22	29885564	29885564	+	Silent	SNP	A	A	G	rs202065964|rs371230849		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr22:29885564A>G	ENST00000310624.6	+	4	1968	c.1935A>G	c.(1933-1935)gaA>gaG	p.E645E		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	645	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CGAAGGAGGAAGCAAAGTCCC	0.562																																																	0			22											83.0	89.0	87.0					22																	29885564		2203	4300	6503	28215564	SO:0001819	synonymous_variant	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1935A>G	22.37:g.29885564A>G		Somatic		Capture	Illumina HiSeq	Phase_I	28215564	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
NEFH	4744	hgsc.bcm.edu	37	22	29885567	29885567	+	Silent	SNP	A	A	C	rs147489453|rs75808076|rs59279731		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr22:29885567A>C	ENST00000310624.6	+	4	1971	c.1938A>C	c.(1936-1938)gcA>gcC	p.A646A		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	652	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AGGAGGAAGCAAAGTCCCCTG	0.567																																																	0			22											78.0	77.0	77.0					22																	29885567		2133	4127	6260	28215567	SO:0001819	synonymous_variant	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1938A>C	22.37:g.29885567A>C		Somatic		Capture	Illumina HiSeq	Phase_I	28215567	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																				NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
COL6A3	1293	hgsc.bcm.edu	37	2	238253148	238253148	+	Missense_Mutation	SNP	C	C	T	rs545819982		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:238253148C>T	ENST00000295550.4	-	36	7965	c.7513G>A	c.(7513-7515)Gga>Aga	p.G2505R	COL6A3_ENST00000472056.1_Missense_Mutation_p.G1898R|COL6A3_ENST00000346358.4_Missense_Mutation_p.G2305R|COL6A3_ENST00000347401.3_Missense_Mutation_p.G2304R|COL6A3_ENST00000353578.4_Missense_Mutation_p.G2299R|COL6A3_ENST00000409809.1_Missense_Mutation_p.G2299R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2505	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		ATTAGGAATCCGTTCCTCACA	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		22006	0.0		0.0	False		,,,				2504	0.001																0			2											138.0	131.0	133.0					2																	238253148		2203	4300	6503	237917887	SO:0001583	missense	1293			X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7513G>A	2.37:g.238253148C>T	ENSP00000295550:p.Gly2505Arg	Somatic		Capture	Illumina HiSeq	Phase_I	237917887	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.322322	0.23994	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	T;T;T;T;T;T	0.16457	2.34;2.34;2.34;2.34;2.34;2.34	4.87	4.87	0.63330	von Willebrand factor, type A (3);	0.000000	0.52532	D	0.000073	T	0.47469	0.1447	M	0.82193	2.58	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.981	T	0.53294	-0.8459	10	0.59425	D	0.04	.	18.4072	0.90539	0.0:1.0:0.0:0.0	.	1898;1898;2299;2505	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	R	2505;2304;2299;1898;2299;2305	ENSP00000295550:G2505R;ENSP00000315609:G2304R;ENSP00000315873:G2299R;ENSP00000418285:G1898R;ENSP00000386844:G2299R;ENSP00000295546:G2305R	ENSP00000295550:G2505R	G	-	1	0	COL6A3	237917887	1.000000	0.71417	0.076000	0.20297	0.134000	0.20937	7.632000	0.83247	2.396000	0.81511	0.655000	0.94253	GGA		COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
SMEK2	57223	hgsc.bcm.edu	37	2	55831123	55831123	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:55831123T>G	ENST00000345102.5	-	3	589	c.288A>C	c.(286-288)aaA>aaC	p.K96N	SMEK2_ENST00000407823.3_Missense_Mutation_p.K96N|SMEK2_ENST00000272313.5_Missense_Mutation_p.K96N	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	96	WH1.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			CCTGACAAATTTTTTCCCAGA	0.323																																																	0			2											61.0	63.0	62.0					2																	55831123		2202	4300	6502	55684627	SO:0001583	missense	57223			AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.288A>C	2.37:g.55831123T>G	ENSP00000339769:p.Lys96Asn	Somatic		Capture	Illumina HiSeq	Phase_I	55684627	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	Missense_Mutation	SNP	ENST00000345102.5	37	CCDS46289.1	.	.	.	.	.	.	.	.	.	.	T	19.46	3.832188	0.71258	.	.	ENSG00000138041	ENST00000272313;ENST00000407823;ENST00000345102	T;T;T	0.46451	0.87;0.87;0.87	5.58	5.58	0.84498	Pleckstrin homology-type (1);	0.043066	0.85682	D	0.000000	T	0.48554	0.1506	L	0.51422	1.61	0.80722	D	1	D;D;P	0.56287	0.975;0.975;0.516	P;P;B	0.57468	0.791;0.821;0.281	T	0.38757	-0.9646	10	0.15066	T	0.55	-16.8615	10.8841	0.46957	0.0:0.0735:0.0:0.9265	.	96;96;96	Q5MIZ7-2;Q5MIZ7;Q5MIZ7-3	.;P4R3B_HUMAN;.	N	96	ENSP00000272313:K96N;ENSP00000385912:K96N;ENSP00000339769:K96N	ENSP00000272313:K96N	K	-	3	2	SMEK2	55684627	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.485000	0.45250	2.110000	0.64415	0.482000	0.46254	AAA		SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463	
AAK1	22848	hgsc.bcm.edu	37	2	69741756	69741756	+	Silent	SNP	T	T	C	rs66931661|rs3832159|rs55712143	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:69741756T>C	ENST00000409085.4	-	13	1999	c.1623A>G	c.(1621-1623)caA>caG	p.Q541Q	RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q541Q|AAK1_ENST00000406297.3_Silent_p.Q541Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	541	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gctgttgctgttgttgttgct	0.542																																																	0			2											27.0	24.0	25.0					2																	69741756		2177	4207	6384	69595260	SO:0001819	synonymous_variant	22848			AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1623A>G	2.37:g.69741756T>C		Somatic		Capture	Illumina HiSeq	Phase_I	69595260	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	37	CCDS1893.2																																																																																				AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
TCF7L1	83439	hgsc.bcm.edu	37	2	85529702	85529702	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:85529702T>C	ENST00000282111.3	+	5	896	c.621T>C	c.(619-621)ccT>ccC	p.P207P		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	207	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CCGGCTCCCCTCCCACCCACC	0.572																																																	0			2											82.0	85.0	84.0					2																	85529702		2203	4300	6503	85383213	SO:0001819	synonymous_variant	83439			X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.621T>C	2.37:g.85529702T>C		Somatic		Capture	Illumina HiSeq	Phase_I	85383213	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000282111.3	37	CCDS1971.1																																																																																				TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	
PRR21	643905	hgsc.bcm.edu	37	2	240981464	240981464	+	Silent	SNP	C	C	G	rs113555849	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:240981464C>G	ENST00000408934.1	-	1	935	c.936G>C	c.(934-936)tcG>tcC	p.S312S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	312	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GAGGCATGGACGAAGGGCCGT	0.607													N|||	3	0.000599042	0.0008	0.0	5008	,	,		18021	0.0		0.002	False		,,,				2504	0.0																0			2											75.0	67.0	70.0					2																	240981464		2203	4298	6501	240630137	SO:0001819	synonymous_variant	643905			AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.936G>C	2.37:g.240981464C>G		Somatic		Capture	Illumina HiSeq	Phase_I	240630137		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																				PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
COL6A5	256076	hgsc.bcm.edu	37	3	130095335	130095335	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:130095335T>C	ENST00000432398.2	+	3	817	c.323T>C	c.(322-324)cTg>cCg	p.L108P	COL6A5_ENST00000265379.6_Missense_Mutation_p.L108P	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	108	Nonhelical region.|VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						GGCGGGTCCCTGCAGATAGGA	0.502																																																	0			3											48.0	45.0	46.0					3																	130095335		692	1591	2283	131578025	SO:0001583	missense	256076			AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.323T>C	3.37:g.130095335T>C	ENSP00000390895:p.Leu108Pro	Somatic		Capture	Illumina HiSeq	Phase_I	131578025	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	T	9.534	1.111567	0.20714	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77489	-1.1;-1.1	5.14	3.98	0.46160	.	.	.	.	.	T	0.80486	0.4632	L	0.58302	1.8	0.42961	D	0.994402	D	0.52996	0.957	P	0.55667	0.781	T	0.80360	-0.1415	9	0.46703	T	0.11	.	9.6991	0.40175	0.0:0.0843:0.0:0.9157	.	108	A8TX70-2	.	P	108	ENSP00000390895:L108P;ENSP00000265379:L108P	ENSP00000265379:L108P	L	+	2	0	COL6A5	131578025	0.952000	0.32445	0.996000	0.52242	0.089000	0.18198	2.997000	0.49457	2.064000	0.61679	0.455000	0.32223	CTG		COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
COL6A6	131873	hgsc.bcm.edu	37	3	130318628	130318628	+	Missense_Mutation	SNP	G	G	C	rs376262924		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:130318628G>C	ENST00000358511.6	+	19	4658	c.4627G>C	c.(4627-4629)Ggg>Cgg	p.G1543R	COL6A6_ENST00000453409.2_Missense_Mutation_p.G1543R	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1543	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AGGCCCCCCCGGGACACCAGG	0.502																																																	0			3											45.0	49.0	48.0					3																	130318628		1849	4100	5949	131801318	SO:0001583	missense	131873			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.4627G>C	3.37:g.130318628G>C	ENSP00000351310:p.Gly1543Arg	Somatic		Capture	Illumina HiSeq	Phase_I	131801318	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.247298	0.80024	.	.	ENSG00000206384	ENST00000358511;ENST00000453409	D;D	0.99637	-6.29;-6.29	5.79	5.79	0.91817	.	.	.	.	.	D	0.99684	0.9881	M	0.91090	3.175	0.42268	D	0.992041	D	0.89917	1.0	D	0.91635	0.999	D	0.97789	1.0237	9	0.87932	D	0	.	15.5401	0.76035	0.0:0.0:1.0:0.0	.	1543	A6NMZ7	CO6A6_HUMAN	R	1543	ENSP00000351310:G1543R;ENSP00000399236:G1543R	ENSP00000351310:G1543R	G	+	1	0	COL6A6	131801318	1.000000	0.71417	0.883000	0.34634	0.919000	0.55068	4.888000	0.63164	2.733000	0.93635	0.655000	0.94253	GGG		COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
SLC22A13	9390	hgsc.bcm.edu	37	3	38307447	38307447	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:38307447T>C	ENST00000311856.4	+	1	145	c.96T>C	c.(94-96)tcT>tcC	p.S32S	SLC22A13_ENST00000450935.2_5'UTR	NM_004256.3	NP_004247.2	Q9Y226	S22AD_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 13	32					nicotinate transport (GO:2001142)|organic cation transport (GO:0015695)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	nicotinate transporter activity (GO:0090416)|organic cation transmembrane transporter activity (GO:0015101)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|urinary_tract(1)	20				KIRC - Kidney renal clear cell carcinoma(284;0.0533)|Kidney(284;0.067)		ACTTCCTGTCTCCCTTCTACT	0.498																																																	0			3											219.0	183.0	195.0					3																	38307447		2203	4300	6503	38282451	SO:0001819	synonymous_variant	9390			AB010438	CCDS2676.1	3p22.2	2013-07-18	2013-07-18	2003-10-15	ENSG00000172940	ENSG00000172940		"""Solute carriers"""	8494	protein-coding gene	gene with protein product		604047	"""organic cationic transporter-like 3"", ""solute carrier family 22 (organic anion transporter), member 13"""	ORCTL3		10072596, 18411268	Standard	NM_004256		Approved	OCTL1, OCTL3, OAT10	uc003chz.3	Q9Y226	OTTHUMG00000131086	ENST00000311856.4:c.96T>C	3.37:g.38307447T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38282451	B2RCV9|Q8IYG1	Silent	SNP	ENST00000311856.4	37	CCDS2676.1																																																																																				SLC22A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253746.2	NM_004256	
DNAH1	25981	hgsc.bcm.edu	37	3	52430526	52430526	+	Missense_Mutation	SNP	G	G	A	rs12163565	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:52430526G>A	ENST00000420323.2	+	71	11663	c.11402G>A	c.(11401-11403)gGt>gAt	p.G3801D		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	3866	AAA 6. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		AGTAGCCTTGGTGAAGACTTC	0.602													G|||	831	0.165935	0.0219	0.1239	5008	,	,		17097	0.2927		0.1978	False		,,,				2504	0.227																0			3						G	ASP/GLY	203,4047		10,183,1932	52.0	57.0	56.0		11402	2.3	0.7	3	dbSNP_120	56	1603,6875		158,1287,2794	yes	missense	DNAH1	NM_015512.4	94	168,1470,4726	AA,AG,GG		18.9078,4.7765,14.1892	benign	3801/4266	52430526	1806,10922	2125	4239	6364	52405566	SO:0001583	missense	25981			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.11402G>A	3.37:g.52430526G>A	ENSP00000401514:p.Gly3801Asp	Somatic		Capture	Illumina HiSeq	Phase_I	52405566	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	363	0.1662087912087912	15	0.03048780487804878	52	0.143646408839779	144	0.2517482517482518	152	0.20052770448548812	G	0.006	-2.059211	0.00386	0.047765	0.189078	ENSG00000114841	ENST00000420323;ENST00000273600	T	0.07327	3.2	4.35	2.35	0.29111	.	0.375043	0.26684	N	0.023037	T	0.00012	0.0000	N	0.00602	-1.34	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.47018	-0.9149	9	0.02654	T	1	.	10.1318	0.42682	0.0878:0.1423:0.7698:0.0	rs12163565;rs52793948;rs57160821;rs12163565	3801;3866	C9JXH6;Q9P2D7-2	.;.	D	3801;554	ENSP00000401514:G3801D	ENSP00000273600:G554D	G	+	2	0	DNAH1	52405566	0.985000	0.35326	0.712000	0.30502	0.148000	0.21650	1.873000	0.39558	1.034000	0.39945	0.491000	0.48974	GGT		DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
CHDH	55349	hgsc.bcm.edu	37	3	53854534	53854534	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:53854534A>G	ENST00000315251.6	-	6	1524	c.1087T>C	c.(1087-1089)Tgc>Cgc	p.C363R		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	363					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	AGACCAATGCAGACCTTCCGC	0.557																																																	0			3											165.0	156.0	159.0					3																	53854534		2203	4300	6503	53829574	SO:0001583	missense	55349			AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.1087T>C	3.37:g.53854534A>G	ENSP00000319851:p.Cys363Arg	Somatic		Capture	Illumina HiSeq	Phase_I	53829574	Q9NY17	Missense_Mutation	SNP	ENST00000315251.6	37	CCDS2873.1	.	.	.	.	.	.	.	.	.	.	A	0.371	-0.933873	0.02340	.	.	ENSG00000016391	ENST00000315251	T	0.39229	1.09	5.26	-4.36	0.03645	.	0.669254	0.15227	N	0.273657	T	0.08268	0.0206	N	0.00138	-2.015	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.43228	-0.9404	10	0.24483	T	0.36	-2.0244	8.5686	0.33556	0.1814:0.0838:0.6259:0.1089	.	363	Q8NE62	CHDH_HUMAN	R	363	ENSP00000319851:C363R	ENSP00000319851:C363R	C	-	1	0	CHDH	53829574	0.348000	0.24861	0.002000	0.10522	0.021000	0.10359	0.496000	0.22499	-0.677000	0.05231	-1.054000	0.02325	TGC		CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
LRRC15	131578	hgsc.bcm.edu	37	3	194081016	194081016	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr3:194081016A>G	ENST00000347624.3	-	2	842	c.757T>C	c.(757-759)Tcc>Ccc	p.S253P	LRRC15_ENST00000439944.2_Missense_Mutation_p.S259P|LRRC15_ENST00000428839.1_Missense_Mutation_p.S259P	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	253					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TGGTTGTTGGACAGGTAGAGT	0.552																																																	0			3											157.0	169.0	165.0					3																	194081016		2203	4300	6503	195562311	SO:0001583	missense	131578			AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.757T>C	3.37:g.194081016A>G	ENSP00000306276:p.Ser253Pro	Somatic		Capture	Illumina HiSeq	Phase_I	195562311	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	A	18.38	3.610476	0.66558	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.12361	2.69;2.69;2.69	5.15	5.15	0.70609	.	0.088290	0.49305	D	0.000153	T	0.44030	0.1274	M	0.89095	3.005	0.47949	D	0.999556	D;D	0.89917	1.0;0.976	D;P	0.79784	0.993;0.775	T	0.51872	-0.8650	10	0.54805	T	0.06	.	15.2753	0.73737	1.0:0.0:0.0:0.0	.	253;259	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	P	253;259;259	ENSP00000306276:S253P;ENSP00000389128:S259P;ENSP00000413707:S259P	ENSP00000306276:S253P	S	-	1	0	LRRC15	195562311	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.335000	0.72949	2.074000	0.62210	0.533000	0.62120	TCC		LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2		
ANK2	287	hgsc.bcm.edu	37	4	114120225	114120225	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:114120225T>G	ENST00000357077.4	+	4	397	c.344T>G	c.(343-345)gTt>gGt	p.V115G	ANK2_ENST00000506722.1_Missense_Mutation_p.V94G|ANK2_ENST00000264366.6_Missense_Mutation_p.V115G|ANK2_ENST00000394537.3_Missense_Mutation_p.V115G	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	115					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		GTTGTCAAAGTTCTTGTTAAG	0.358																																																	0			4											130.0	129.0	130.0					4																	114120225		2203	4300	6503	114339674	SO:0001583	missense	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.344T>G	4.37:g.114120225T>G	ENSP00000349588:p.Val115Gly	Somatic		Capture	Illumina HiSeq	Phase_I	114339674	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	T	18.16	3.561769	0.65538	.	.	ENSG00000145362	ENST00000503271;ENST00000503423;ENST00000506722;ENST00000504454;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000508613;ENST00000343056	T;T;T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18;-0.18	5.82	5.82	0.92795	Ankyrin repeat-containing domain (3);	0.000000	0.46145	D	0.000307	T	0.77308	0.4111	M	0.72894	2.215	0.80722	D	1	D;P;D;D;D	0.62365	0.967;0.82;0.977;0.991;0.969	P;B;D;P;P	0.65684	0.901;0.433;0.937;0.844;0.792	T	0.78971	-0.1993	10	0.56958	D	0.05	.	15.858	0.79000	0.0:0.0:0.0:1.0	.	115;115;115;94;94	Q01484;Q01484-2;Q01484-4;Q01484-5;F8WEF9	ANK2_HUMAN;.;.;.;.	G	94;94;94;130;115;115;115;130;94	ENSP00000423799:V94G;ENSP00000421011:V94G;ENSP00000421067:V94G;ENSP00000424722:V130G;ENSP00000378044:V115G;ENSP00000349588:V115G;ENSP00000264366:V115G;ENSP00000422900:V130G	ENSP00000264366:V115G	V	+	2	0	ANK2	114339674	1.000000	0.71417	0.982000	0.44146	0.991000	0.79684	7.443000	0.80521	2.232000	0.73038	0.528000	0.53228	GTT		ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
FBXW7	55294	hgsc.bcm.edu	37	4	153247289	153247289	+	Missense_Mutation	SNP	G	G	A	rs149680468		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:153247289G>A	ENST00000281708.4	-	10	2742	c.1513C>T	c.(1513-1515)Cgc>Tgc	p.R505C	FBXW7_ENST00000393956.3_Missense_Mutation_p.R329C|FBXW7_ENST00000603841.1_Missense_Mutation_p.R505C|FBXW7_ENST00000296555.5_Missense_Mutation_p.R387C|FBXW7_ENST00000603548.1_Missense_Mutation_p.R505C|FBXW7_ENST00000263981.5_Missense_Mutation_p.R425C	NM_033632.3	NP_361014.1	Q969H0	FBXW7_HUMAN	F-box and WD repeat domain containing 7, E3 ubiquitin protein ligase	505			R -> L (in an ovarian cancer cell line). {ECO:0000269|PubMed:11565033, ECO:0000269|PubMed:16959974}.		cellular response to DNA damage stimulus (GO:0006974)|cellular response to UV (GO:0034644)|lipid homeostasis (GO:0055088)|lung development (GO:0030324)|negative regulation of DNA endoreduplication (GO:0032876)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of SREBP signaling pathway (GO:2000639)|negative regulation of triglyceride biosynthetic process (GO:0010868)|Notch signaling pathway (GO:0007219)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903378)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|regulation of cell cycle G1/S phase transition (GO:1902806)|regulation of lipid storage (GO:0010883)|regulation of protein localization (GO:0032880)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|sister chromatid cohesion (GO:0007062)|vasculature development (GO:0001944)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|protein complex (GO:0043234)|SCF ubiquitin ligase complex (GO:0019005)	cyclin binding (GO:0030332)|identical protein binding (GO:0042802)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)	p.R505C(60)|p.R505G(18)|p.R425C(14)|p.R266C(13)|p.R425G(9)|p.R266G(9)|p.R387G(6)|p.R387C(3)|p.R505S(3)|p.R387S(1)|p.?(1)|p.R425S(1)|p.R266S(1)		NS(1)|biliary_tract(8)|bone(1)|breast(5)|central_nervous_system(6)|cervix(2)|endometrium(36)|haematopoietic_and_lymphoid_tissue(159)|kidney(6)|large_intestine(155)|lung(31)|ovary(10)|pancreas(3)|prostate(2)|skin(6)|stomach(16)|upper_aerodigestive_tract(9)|urinary_tract(6)	462	all_hematologic(180;0.093)	Acute lymphoblastic leukemia(8;0.000629)|all_hematologic(8;0.067)				TGAACACAGCGGACTGCTGCA	0.468			"""Mis, N, D, F"""		"""colorectal, endometrial, T-ALL"""																																			Rec	yes		4	4q31.3	55294	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"""		"""E, L"""	139	Substitution - Missense(138)|Unknown(1)	haematopoietic_and_lymphoid_tissue(44)|large_intestine(26)|endometrium(20)|urinary_tract(15)|lung(15)|upper_aerodigestive_tract(8)|skin(8)|ovary(2)|biliary_tract(1)	4											167.0	156.0	160.0					4																	153247289		2203	4300	6503	153466739	SO:0001583	missense	55294			AF411971	CCDS3777.1, CCDS3778.1, CCDS34078.1, CCDS64082.1	4q31.23	2013-01-09	2012-02-23					"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	16712	protein-coding gene	gene with protein product	"""archipelago homolog (Drosophila)"""	606278	"""F-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)"", ""F-box and WD repeat domain containing 7"""			10531037, 11425854	Standard	NM_018315		Approved	AGO, FLJ11071, SEL-10, SEL10, FBW7, FBX30, CDC4, FBXW6	uc003ims.3	Q969H0		ENST00000281708.4:c.1513C>T	4.37:g.153247289G>A	ENSP00000281708:p.Arg505Cys	Somatic		Capture	Illumina HiSeq	Phase_I	153466739	B7ZLP9|Q68DR0|Q96A16|Q96LE0|Q96RI2|Q9NUX6	Missense_Mutation	SNP	ENST00000281708.4	37	CCDS3777.1	.	.	.	.	.	.	.	.	.	.	G	18.90	3.722220	0.68959	.	.	ENSG00000109670	ENST00000281708;ENST00000296555;ENST00000263981;ENST00000393956	T;T;T;T	0.61980	0.06;0.06;0.06;0.06	5.72	4.88	0.63580	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.101576	0.64402	D	0.000001	T	0.78679	0.4321	M	0.75085	2.285	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	T	0.81858	-0.0739	10	0.87932	D	0	-12.0024	15.0746	0.72066	0.0681:0.0:0.9319:0.0	.	329;505;387;425	B7Z2C8;Q969H0;Q969H0-4;Q969H0-2	.;FBXW7_HUMAN;.;.	C	505;387;425;329	ENSP00000281708:R505C;ENSP00000296555:R387C;ENSP00000263981:R425C;ENSP00000377528:R329C	ENSP00000263981:R425C	R	-	1	0	FBXW7	153466739	1.000000	0.71417	1.000000	0.80357	0.556000	0.35491	9.772000	0.98984	1.559000	0.49555	-0.145000	0.13849	CGC		FBXW7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469956.1		
GUCY1A3	2982	hgsc.bcm.edu	37	4	156634454	156634454	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:156634454A>G	ENST00000296518.7	+	7	1500	c.1291A>G	c.(1291-1293)Aag>Gag	p.K431E	GUCY1A3_ENST00000393832.3_Missense_Mutation_p.K173E|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.K431E|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.K431E|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.K431E			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	431					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		GAGGCTGGGGAAGCTGAAGGC	0.522																																																	0			4											82.0	85.0	84.0					4																	156634454		2203	4300	6503	156853904	SO:0001583	missense	2982				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.1291A>G	4.37:g.156634454A>G	ENSP00000296518:p.Lys431Glu	Somatic		Capture	Illumina HiSeq	Phase_I	156853904	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.849746	0.91277	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.88586	-2.4;-2.4;-2.4;-2.4;-2.4;-2.4;-2.4	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000002	D	0.92825	0.7718	L	0.56199	1.76	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.79108	0.992;0.992	D	0.92083	0.5674	10	0.39692	T	0.17	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	431;431	B3KU69;Q02108	.;GCYA3_HUMAN	E	431;431;431;431;173;431;431	ENSP00000424361:K431E;ENSP00000421493:K431E;ENSP00000426968:K431E;ENSP00000412201:K431E;ENSP00000377418:K173E;ENSP00000296518:K431E;ENSP00000426040:K431E	ENSP00000296518:K431E	K	+	1	0	GUCY1A3	156853904	1.000000	0.71417	0.996000	0.52242	0.992000	0.81027	8.930000	0.92872	2.308000	0.77769	0.533000	0.62120	AAG		GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
NEK1	4750	hgsc.bcm.edu	37	4	170345770	170345770	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:170345770T>C	ENST00000439128.2	-	29	3712	c.3072A>G	c.(3070-3072)aaA>aaG	p.K1024K	NEK1_ENST00000507142.1_Silent_p.K1052K|NEK1_ENST00000512193.1_Silent_p.K955K|NEK1_ENST00000511633.1_Silent_p.K1008K|NEK1_ENST00000510533.1_Silent_p.K980K	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	1024					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TGTTTTTATTTTTTGGTGGTA	0.383																																																	0			4											82.0	80.0	80.0					4																	170345770		1837	4083	5920	170582345	SO:0001819	synonymous_variant	4750			AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.3072A>G	4.37:g.170345770T>C		Somatic		Capture	Illumina HiSeq	Phase_I	170582345	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Silent	SNP	ENST00000439128.2	37	CCDS47162.1																																																																																				NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
TENM3	55714	hgsc.bcm.edu	37	4	183594202	183594202	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:183594202G>A	ENST00000511685.1	+	7	1279	c.1156G>A	c.(1156-1158)Gga>Aga	p.G386R	TENM3_ENST00000406950.2_Missense_Mutation_p.G386R			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	386					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.G386*(1)|p.G386R(1)									CATAGATTCCGGAGAACTTGA	0.363																																																	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	4											35.0	33.0	33.0					4																	183594202		1811	4083	5894	183831196	SO:0001583	missense	55714			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.1156G>A	4.37:g.183594202G>A	ENSP00000424226:p.Gly386Arg	Somatic		Capture	Illumina HiSeq	Phase_I	183831196	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862373	0.91511	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.40225	1.04;1.04	4.91	4.91	0.64330	.	.	.	.	.	T	0.67306	0.2879	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71361	-0.4616	9	0.87932	D	0	.	18.7292	0.91728	0.0:0.0:1.0:0.0	.	386	Q9P273	TEN3_HUMAN	R	386	ENSP00000424226:G386R;ENSP00000385276:G386R	ENSP00000385276:G386R	G	+	1	0	ODZ3	183831196	1.000000	0.71417	0.993000	0.49108	0.977000	0.68977	9.351000	0.97073	2.720000	0.93068	0.558000	0.71614	GGA		TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
SLIT2	9353	hgsc.bcm.edu	37	4	20512134	20512134	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:20512134A>G	ENST00000504154.1	+	10	1183	c.931A>G	c.(931-933)Aca>Gca	p.T311A	SLIT2_ENST00000503837.1_Missense_Mutation_p.T315A|SLIT2_ENST00000273739.5_Missense_Mutation_p.T315A|SLIT2_ENST00000503823.1_Missense_Mutation_p.T311A	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	311					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						GGAACAGAACACAATCAAAGT	0.318																																																	0			4											104.0	113.0	110.0					4																	20512134		2203	4300	6503	20121232	SO:0001583	missense	9353			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.931A>G	4.37:g.20512134A>G	ENSP00000422591:p.Thr311Ala	Somatic		Capture	Illumina HiSeq	Phase_I	20121232	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	A	8.767	0.924957	0.18056	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	5.5	2.94	0.34122	.	0.122223	0.56097	D	0.000026	T	0.19287	0.0463	N	0.00991	-1.07	0.25653	N	0.98608	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23583	-1.0184	10	0.13108	T	0.6	.	8.9132	0.35565	0.1266:0.0:0.1289:0.7445	.	311;311	O94813-3;O94813	.;SLIT2_HUMAN	A	311;311;315;315;315	ENSP00000427548:T311A;ENSP00000422591:T311A;ENSP00000273739:T315A;ENSP00000422261:T315A	ENSP00000273739:T315A	T	+	1	0	SLIT2	20121232	0.993000	0.37304	0.998000	0.56505	0.951000	0.60555	1.035000	0.30216	0.345000	0.23873	-0.429000	0.05907	ACA		SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
GABRA4	2557	hgsc.bcm.edu	37	4	46930361	46930361	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:46930361T>C	ENST00000264318.3	-	9	2528	c.1546A>G	c.(1546-1548)Agt>Ggt	p.S516G		NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	516			S -> R (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.S516R(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TCTATTTTACTTGTGCCAGAT	0.433																																					Ovarian(6;283 369 8234 12290 33402)												1	Substitution - Missense(1)	breast(1)	4											132.0	128.0	129.0					4																	46930361		2203	4300	6503	46625118	SO:0001583	missense	2557				CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.1546A>G	4.37:g.46930361T>C	ENSP00000264318:p.Ser516Gly	Somatic		Capture	Illumina HiSeq	Phase_I	46625118	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.826322	0.90955	.	.	ENSG00000109158	ENST00000264318	D	0.84800	-1.9	5.82	5.82	0.92795	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90521	0.7030	L	0.54323	1.7	0.51233	D	0.999913	D	0.89917	1.0	D	0.91635	0.999	D	0.91388	0.5133	10	0.87932	D	0	.	15.3777	0.74625	0.0:0.0:0.0:1.0	.	516	P48169	GBRA4_HUMAN	G	516	ENSP00000264318:S516G	ENSP00000264318:S516G	S	-	1	0	GABRA4	46625118	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	7.950000	0.87804	2.232000	0.73038	0.528000	0.53228	AGT		GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
DSPP	1834	hgsc.bcm.edu	37	4	88536019	88536019	+	Silent	SNP	T	T	C	rs554265208	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88536019T>C	ENST00000282478.7	+	4	2238	c.2205T>C	c.(2203-2205)agT>agC	p.S735S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S735S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	735	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcgatagcagtgacagcagca	0.502													t|||	10	0.00199681	0.0	0.0	5008	,	,		33236	0.0		0.007	False		,,,				2504	0.0031																0			4											65.0	73.0	70.0					4																	88536019		1654	2937	4591	88755043	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2205T>C	4.37:g.88536019T>C		Somatic		Capture	Illumina HiSeq	Phase_I	88755043	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
DSPP	1834	hgsc.bcm.edu	37	4	88537357	88537357	+	Silent	SNP	T	T	C	rs146317878	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88537357T>C	ENST00000282478.7	+	4	3576	c.3543T>C	c.(3541-3543)agT>agC	p.S1181S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1181S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1181	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gcaatagcagtgatagcagcg	0.567													t|||	285	0.0569089	0.0091	0.0879	5008	,	,		25184	0.003		0.168	False		,,,				2504	0.0409																0			4						C		80,3200		0,80,1560	55.0	74.0	67.0		3543	1.2	0.0	4	dbSNP_134	67	750,5074		47,656,2209	no	coding-synonymous	DSPP	NM_014208.3		47,736,3769	CC,CT,TT		12.8777,2.439,9.1169		1181/1302	88537357	830,8274	1640	2912	4552	88756381	SO:0001819	synonymous_variant	1834			AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3543T>C	4.37:g.88537357T>C		Somatic		Capture	Illumina HiSeq	Phase_I	88756381	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																				DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
MEPE	56955	hgsc.bcm.edu	37	4	88766391	88766391	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:88766391A>G	ENST00000424957.3	+	4	444	c.371A>G	c.(370-372)aAa>aGa	p.K124R	MEPE_ENST00000560249.1_Missense_Mutation_p.K11R|MEPE_ENST00000511670.1_3'UTR|MEPE_ENST00000395102.4_Missense_Mutation_p.K155R|MEPE_ENST00000497649.2_Missense_Mutation_p.K100R|MEPE_ENST00000540395.1_Missense_Mutation_p.K11R|MEPE_ENST00000508016.1_3'UTR|MEPE_ENST00000361056.3_Missense_Mutation_p.K124R	NM_001184694.1	NP_001171623.1	Q9NQ76	MEPE_HUMAN	matrix extracellular phosphoglycoprotein	124					biomineral tissue development (GO:0031214)|negative regulation of bone mineralization (GO:0030502)|regulation of bone remodeling (GO:0046850)|skeletal system development (GO:0001501)	proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(19)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000432)		ACTGGGAATAAAGGGTTTGAG	0.383																																																	0			4											73.0	72.0	72.0					4																	88766391		2203	4300	6503	88985415	SO:0001583	missense	56955			AJ276396	CCDS3625.1, CCDS54776.1	4q21.1	2008-08-29	2008-08-29		ENSG00000152595	ENSG00000152595			13361	protein-coding gene	gene with protein product		605912	"""matrix, extracellular phosphoglycoprotein with ASARM motif (bone)"""			10945470	Standard	NM_020203		Approved		uc003hqy.3	Q9NQ76	OTTHUMG00000130592	ENST00000424957.3:c.371A>G	4.37:g.88766391A>G	ENSP00000416984:p.Lys124Arg	Somatic		Capture	Illumina HiSeq	Phase_I	88985415	A1A4X9|A8MTA3|D2CFR4|F5H5C5	Missense_Mutation	SNP	ENST00000424957.3	37	CCDS3625.1	.	.	.	.	.	.	.	.	.	.	A	8.394	0.840329	0.16891	.	.	ENSG00000152595	ENST00000535138;ENST00000424957;ENST00000395102;ENST00000497649;ENST00000540395;ENST00000361056	T;T;T;T;T	0.46063	4.27;0.89;0.88;0.89;4.27	4.84	-2.05	0.07321	.	1.784080	0.02498	N	0.090183	T	0.31638	0.0803	L	0.39397	1.21	0.09310	N	1	B	0.13145	0.007	B	0.16289	0.015	T	0.09640	-1.0665	10	0.21540	T	0.41	-0.5334	5.4758	0.16695	0.3619:0.1929:0.4452:0.0	.	124	Q9NQ76	MEPE_HUMAN	R	124;124;155;100;11;124	ENSP00000416984:K124R;ENSP00000378534:K155R;ENSP00000422747:K100R;ENSP00000443491:K11R;ENSP00000354341:K124R	ENSP00000354341:K124R	K	+	2	0	MEPE	88985415	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.457000	0.06745	-0.171000	0.10797	0.533000	0.62120	AAA		MEPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253038.1		
TENM3	55714	hgsc.bcm.edu	37	4	183696126	183696126	+	Silent	SNP	C	C	T	rs145946924	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr4:183696126C>T	ENST00000511685.1	+	24	5247	c.5124C>T	c.(5122-5124)taC>taT	p.Y1708Y	TENM3_ENST00000406950.2_Silent_p.Y1708Y|RP11-18D7.2_ENST00000513255.1_RNA			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1708					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)										GAATTATCTACGCCAGTGGCC	0.463													C|||	29	0.00579073	0.0	0.0288	5008	,	,		18933	0.0		0.0	False		,,,				2504	0.0092																0			4						C		2,3756		0,2,1877	40.0	40.0	40.0		5124	-5.2	0.5	4	dbSNP_134	40	6,8226		0,6,4110	no	coding-synonymous	ODZ3	NM_001080477.1		0,8,5987	TT,TC,CC		0.0729,0.0532,0.0667		1708/2700	183696126	8,11982	1879	4116	5995	183933120	SO:0001819	synonymous_variant	55714			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.5124C>T	4.37:g.183696126C>T		Somatic		Capture	Illumina HiSeq	Phase_I	183933120	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																				TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
APC	324	hgsc.bcm.edu	37	5	112175410	112175410	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175410T>C	ENST00000457016.1	+	16	4499	c.4119T>C	c.(4117-4119)ccT>ccC	p.P1373P	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.P1373P|APC_ENST00000508376.2_Silent_p.P1373P			P25054	APC_HUMAN	adenomatous polyposis coli	1373	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1374fs*2(1)|p.E1374fs*1(1)|p.P1373fs*41(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAGTCCACCTGAACACTATG	0.453		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	5	Insertion - Frameshift(2)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD011100	APC	D							83.0	80.0	81.0					5																	112175410		2202	4300	6502	112203309	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4119T>C	5.37:g.112175410T>C		Somatic		Capture	Illumina HiSeq	Phase_I	112203309	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175474	112175475	+	Missense_Mutation	DNP	AG	AG	GT	rs137854578		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A|G	A|G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175474_112175475AG>GT	ENST00000457016.1	+	16	4563_4564	c.4183_4184AG>GT	c.(4183-4185)AGt>GTt	p.S1395V	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.S1395V|APC_ENST00000508376.2_Missense_Mutation_p.S1395V			P25054	APC_HUMAN	adenomatous polyposis coli	1395	Ser-rich.		S -> C (in hepatoblastoma). {ECO:0000269|PubMed:8764128}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.S1395C(3)|p.E1397fs*1(2)|p.S1395fs*19(2)|p.Y1376fs*41(1)|p.?(1)|p.D1394fs*20(1)|p.K1192fs*3(1)|p.S1395fs*20(1)|p.?fs(1)|p.D1394fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTCACTTGATAGTTTTGAGAGT	0.475		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	14	Deletion - Frameshift(7)|Substitution - Missense(3)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(9)|liver(3)|soft_tissue(1)|skin(1)	5	GRCh37	CD972010|CP995074	APC	D|X	rs137854578																																			112203373|112203374	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	Exception_encountered	5.37:g.112175474_112175475delinsGT	ENSP00000413133:p.Ser1395Val	Somatic		Capture	Illumina HiSeq	Phase_I	112203373|112203374	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175682	112175682	+	Missense_Mutation	SNP	A	A	G	rs112961968		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175682A>G	ENST00000457016.1	+	16	4771	c.4391A>G	c.(4390-4392)gAg>gGg	p.E1464G	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.E1464G|APC_ENST00000508376.2_Missense_Mutation_p.E1464G			P25054	APC_HUMAN	adenomatous polyposis coli	1464	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1464fs*8(29)|p.?(1)|p.K1454fs*3(1)|p.K1192fs*3(1)|p.S1465fs*4(1)|p.S1465fs*3(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GAAAAGAGAGAGAGTGGACCT	0.453		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	34	Deletion - Frameshift(31)|Unknown(1)|Complex - frameshift(1)|Insertion - Frameshift(1)	large_intestine(21)|stomach(5)|small_intestine(3)|thyroid(1)|soft_tissue(1)|endometrium(1)|skin(1)|pancreas(1)	5	GRCh37	CD972012	APC	D	rs112961968						84.0	79.0	81.0					5																	112175682		2202	4300	6502	112203581	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4391A>G	5.37:g.112175682A>G	ENSP00000413133:p.Glu1464Gly	Somatic		Capture	Illumina HiSeq	Phase_I	112203581	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	13.05	2.121479	0.37436	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90676	-2.71;-2.71;-2.71	6.16	5.01	0.66863	.	0.103794	0.64402	D	0.000004	D	0.83289	0.5222	N	0.25647	0.755	0.48830	D	0.999711	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.002	T	0.76181	-0.3053	9	.	.	.	-16.9486	12.0784	0.53657	0.9336:0.0:0.0664:0.0	.	1466;1464	Q4LE70;P25054	.;APC_HUMAN	G	1464	ENSP00000413133:E1464G;ENSP00000257430:E1464G;ENSP00000427089:E1464G	.	E	+	2	0	APC	112203581	1.000000	0.71417	0.990000	0.47175	0.750000	0.42670	8.585000	0.90802	1.157000	0.42530	0.528000	0.53228	GAG		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175730	112175730	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175730A>G	ENST00000457016.1	+	16	4819	c.4439A>G	c.(4438-4440)cAg>cGg	p.Q1480R	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.Q1480R|APC_ENST00000508376.2_Missense_Mutation_p.Q1480R			P25054	APC_HUMAN	adenomatous polyposis coli	1480	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1454fs*3(1)|p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CAGAGGGTCCAGGTTCTTCCA	0.453		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	3	Unknown(1)|Complex - frameshift(1)|Deletion - Frameshift(1)	thyroid(1)|soft_tissue(1)|skin(1)	5											72.0	72.0	72.0					5																	112175730		2202	4300	6502	112203629	SO:0001583	missense	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4439A>G	5.37:g.112175730A>G	ENSP00000413133:p.Gln1480Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112203629	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	12.78	2.041642	0.35989	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.89681	-2.55;-2.55;-2.55	6.16	6.16	0.99307	.	0.059477	0.64402	D	0.000002	D	0.90909	0.7143	L	0.34521	1.04	0.54753	D	0.999981	D;D	0.60160	0.987;0.967	D;D	0.67725	0.953;0.932	D	0.89997	0.4112	9	.	.	.	-8.2076	16.8061	0.85666	1.0:0.0:0.0:0.0	.	1482;1480	Q4LE70;P25054	.;APC_HUMAN	R	1480	ENSP00000413133:Q1480R;ENSP00000257430:Q1480R;ENSP00000427089:Q1480R	.	Q	+	2	0	APC	112203629	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.425000	0.80255	2.367000	0.80283	0.528000	0.53228	CAG		APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175944	112175944	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175944A>G	ENST00000457016.1	+	16	5033	c.4653A>G	c.(4651-4653)aaA>aaG	p.K1551K	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.K1551K|APC_ENST00000508376.2_Silent_p.K1551K			P25054	APC_HUMAN	adenomatous polyposis coli	1551	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ACCAAGAGAAAGAGGCAGAAA	0.338		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	5											78.0	85.0	83.0					5																	112175944		2202	4300	6502	112203843	SO:0001819	synonymous_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4653A>G	5.37:g.112175944A>G		Somatic		Capture	Illumina HiSeq	Phase_I	112203843	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
SLC4A9	83697	hgsc.bcm.edu	37	5	139747350	139747350	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:139747350A>G	ENST00000230993.6	+	16	2328	c.2293A>G	c.(2293-2295)Atg>Gtg	p.M765V	SLC4A9_ENST00000506757.2_Missense_Mutation_p.M741V|SLC4A9_ENST00000506545.1_Missense_Mutation_p.M678V|SLC4A9_ENST00000432095.2_Missense_Mutation_p.M727V|SLC4A9_ENST00000507527.1_Missense_Mutation_p.M765V	NM_001258428.1	NP_001245357.1	Q96Q91	B3A4_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 9	765	Membrane (anion exchange).				bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			endometrium(4)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	14			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTGTGCTGATGCTACTCAC	0.587																																																	0			5											49.0	51.0	50.0					5																	139747350		2095	4217	6312	139727534	SO:0001583	missense	83697			AF313465	CCDS47278.1, CCDS58973.1, CCDS58974.1, CCDS58975.1	5q31.3	2013-05-22			ENSG00000113073	ENSG00000113073		"""Solute carriers"""	11035	protein-coding gene	gene with protein product		610207				11305939	Standard	NM_031467		Approved	AE4	uc003lfk.2	Q96Q91	OTTHUMG00000163352	ENST00000230993.6:c.2293A>G	5.37:g.139747350A>G	ENSP00000230993:p.Met765Val	Somatic		Capture	Illumina HiSeq	Phase_I	139727534	B7ZL63|D3DQD4|D3DQD5|D3DQD6|E9PDK1|Q96RM5|Q9BXF2|Q9BXN3	Missense_Mutation	SNP	ENST00000230993.6	37	CCDS58973.1	.	.	.	.	.	.	.	.	.	.	A	11.58	1.681351	0.29872	.	.	ENSG00000113073	ENST00000230993;ENST00000506757;ENST00000432095;ENST00000506545;ENST00000507527	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	5.12	1.24	0.21308	Bicarbonate transporter, C-terminal (1);	0.521018	0.20725	N	0.086823	T	0.67887	0.2941	L	0.41415	1.275	0.31044	N	0.715927	B;B;B;B	0.20550	0.003;0.046;0.037;0.037	B;B;B;B	0.30029	0.008;0.11;0.037;0.037	T	0.63646	-0.6590	10	0.49607	T	0.09	.	7.7721	0.29015	0.6691:0.2623:0.0686:0.0	.	678;765;727;741	E9PDK1;Q96Q91;Q96Q91-2;Q96Q91-3	.;B3A4_HUMAN;.;.	V	765;741;727;678;765	ENSP00000230993:M765V;ENSP00000424424:M741V;ENSP00000410056:M727V;ENSP00000422855:M678V;ENSP00000427661:M765V	ENSP00000230993:M765V	M	+	1	0	SLC4A9	139727534	1.000000	0.71417	0.968000	0.41197	0.889000	0.51656	2.841000	0.48223	0.130000	0.18549	0.482000	0.46254	ATG		SLC4A9-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372823.1	NM_031467	
PCYOX1L	78991	hgsc.bcm.edu	37	5	148743642	148743642	+	Silent	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:148743642C>T	ENST00000274569.4	+	3	401	c.339C>T	c.(337-339)ttC>ttT	p.F113F	PCYOX1L_ENST00000514349.1_Silent_p.F23F	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	113					prenylcysteine catabolic process (GO:0030328)	extracellular region (GO:0005576)|membrane (GO:0016020)	prenylcysteine oxidase activity (GO:0001735)			breast(2)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCATCTTCGGCGGGGAGC	0.622																																					Ovarian(62;1136 1477 27277 27495)												0			5											102.0	99.0	100.0					5																	148743642		2203	4300	6503	148723835	SO:0001819	synonymous_variant	78991				CCDS4296.1	5q33.1	2008-02-05			ENSG00000145882	ENSG00000145882			28477	protein-coding gene	gene with protein product						12477932	Standard	NM_024028		Approved	MGC3265	uc003lqk.2	Q8NBM8	OTTHUMG00000130052	ENST00000274569.4:c.339C>T	5.37:g.148743642C>T		Somatic		Capture	Illumina HiSeq	Phase_I	148723835	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Silent	SNP	ENST00000274569.4	37	CCDS4296.1																																																																																				PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149216623	149216623	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:149216623C>T	ENST00000309241.5	+	8	2637	c.2605C>T	c.(2605-2607)Cga>Tga	p.R869*	PPARGC1B_ENST00000403750.1_Nonsense_Mutation_p.R805*|PPARGC1B_ENST00000360453.4_Nonsense_Mutation_p.R830*|PPARGC1B_ENST00000394320.3_Nonsense_Mutation_p.R869*	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	869					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			ACCAGCCACTCGAAGGAACTT	0.652																																																	0			5											61.0	71.0	68.0					5																	149216623		2203	4300	6503	149196816	SO:0001587	stop_gained	133522			AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2605C>T	5.37:g.149216623C>T	ENSP00000312649:p.Arg869*	Somatic		Capture	Illumina HiSeq	Phase_I	149196816	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Nonsense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.541765|7.541765	0.98348|0.98348	.|.	.|.	ENSG00000155846|ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750|ENST00000434684	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.213744|.	0.32901|.	N|.	0.005520|.	.|T	.|0.65729	.|0.2719	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69247	.|-0.5195	.|3	0.02654|.	T|.	1|.	-7.9394|-7.9394	14.1067|14.1067	0.65093|0.65093	0.1592:0.8408:0.0:0.0|0.1592:0.8408:0.0:0.0	.|.	.|.	.|.	.|.	X|L	830;869;869;805|555	.|.	ENSP00000312649:R869X|.	R|S	+|+	1|2	2|0	PPARGC1B|PPARGC1B	149196816|149196816	0.958000|0.958000	0.32768|0.32768	0.259000|0.259000	0.24435|0.24435	0.730000|0.730000	0.41778|0.41778	0.924000|0.924000	0.28777|0.28777	2.747000|2.747000	0.94245|0.94245	0.462000|0.462000	0.41574|0.41574	CGA|TCG		PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
CCNJL	79616	hgsc.bcm.edu	37	5	159680550	159680550	+	Silent	SNP	C	C	T	rs141268151		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:159680550C>T	ENST00000393977.3	-	7	1428	c.1143G>A	c.(1141-1143)ccG>ccA	p.P381P	CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000257536.7_Silent_p.P333P	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	381						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GCGGTTGGTACGGGGTGTGGA	0.637																																																	0			5											74.0	81.0	79.0					5																	159680550		2121	4240	6361	159613128	SO:0001819	synonymous_variant	79616			BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.1143G>A	5.37:g.159680550C>T		Somatic		Capture	Illumina HiSeq	Phase_I	159613128	Q6ZN43|Q9H7W8	Silent	SNP	ENST00000393977.3	37	CCDS4350.2																																																																																				CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
GABRA1	2554	hgsc.bcm.edu	37	5	161300148	161300148	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:161300148G>A	ENST00000428797.2	+	6	636	c.281G>A	c.(280-282)cGt>cAt	p.R94H	GABRA1_ENST00000420560.1_Missense_Mutation_p.R94H|GABRA1_ENST00000437025.2_Missense_Mutation_p.R94H|GABRA1_ENST00000393943.4_Missense_Mutation_p.R94H|GABRA1_ENST00000444819.1_Missense_Mutation_p.R94H|GABRA1_ENST00000023897.6_Missense_Mutation_p.R94H	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	94					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.R94H(2)|p.R94L(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	GTATTTTTCCGTCAAAGCTGG	0.373																																																	3	Substitution - Missense(3)	urinary_tract(1)|ovary(1)|lung(1)	5											91.0	98.0	96.0					5																	161300148		2203	4300	6503	161232726	SO:0001583	missense	2554				CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.281G>A	5.37:g.161300148G>A	ENSP00000393097:p.Arg94His	Somatic		Capture	Illumina HiSeq	Phase_I	161232726	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	35	5.525396	0.96431	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819;ENST00000519621	T;T;T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35;-1.35;-1.35	5.75	5.75	0.90469	Neurotransmitter-gated ion-channel ligand-binding (3);	0.107484	0.64402	D	0.000008	D	0.91133	0.7208	M	0.84585	2.705	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	D	0.91782	0.5436	10	0.87932	D	0	.	19.9462	0.97183	0.0:0.0:1.0:0.0	.	94	P14867	GBRA1_HUMAN	H	94	ENSP00000023897:R94H;ENSP00000393097:R94H;ENSP00000377517:R94H;ENSP00000415441:R94H;ENSP00000408041:R94H;ENSP00000414232:R94H;ENSP00000430435:R94H	ENSP00000023897:R94H	R	+	2	0	GABRA1	161232726	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.751000	0.98889	2.717000	0.92951	0.585000	0.79938	CGT		GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	
LCP2	3937	hgsc.bcm.edu	37	5	169697858	169697858	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:169697858A>G	ENST00000046794.5	-	7	1003	c.388T>C	c.(388-390)Tcc>Ccc	p.S130P		NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	130					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TCATTGGGGGACTCATAGTCT	0.537																																																	0			5											73.0	89.0	84.0					5																	169697858		2132	4245	6377	169630436	SO:0001583	missense	3937				CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.388T>C	5.37:g.169697858A>G	ENSP00000046794:p.Ser130Pro	Somatic		Capture	Illumina HiSeq	Phase_I	169630436	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.484390	0.84854	.	.	ENSG00000043462	ENST00000046794	T	0.52526	0.66	5.4	5.4	0.78164	.	0.348432	0.30869	N	0.008715	T	0.64724	0.2624	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.65479	-0.6158	9	.	.	.	-29.6851	12.1086	0.53825	1.0:0.0:0.0:0.0	.	130	Q13094	LCP2_HUMAN	P	130	ENSP00000046794:S130P	.	S	-	1	0	LCP2	169630436	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	3.406000	0.52637	2.164000	0.68074	0.533000	0.62120	TCC		LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
UGT3A2	167127	hgsc.bcm.edu	37	5	36049170	36049170	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:36049170C>T	ENST00000282507.3	-	4	765	c.664G>A	c.(664-666)Gac>Aac	p.D222N	UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000545528.1_Intron|UGT3A2_ENST00000513300.1_Missense_Mutation_p.D188N	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	222					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATGGTGTTGTCAAATGTAGAC	0.438																																																	0			5											146.0	147.0	147.0					5																	36049170		2203	4300	6503	36084927	SO:0001583	missense	167127				CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"""UDP glucuronosyltransferases"""	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.664G>A	5.37:g.36049170C>T	ENSP00000282507:p.Asp222Asn	Somatic		Capture	Illumina HiSeq	Phase_I	36084927	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.035139	0.75617	.	.	ENSG00000168671	ENST00000282507;ENST00000513300	T;T	0.61510	0.1;0.1	3.45	3.45	0.39498	.	0.485483	0.19185	N	0.120581	T	0.70193	0.3196	M	0.74467	2.265	0.80722	D	1	B;D	0.59767	0.418;0.986	B;P	0.57502	0.206;0.822	T	0.73780	-0.3875	10	0.48119	T	0.1	.	14.8735	0.70478	0.0:1.0:0.0:0.0	.	188;222	E9PFK7;Q3SY77	.;UD3A2_HUMAN	N	222;188	ENSP00000282507:D222N;ENSP00000427404:D188N	ENSP00000282507:D222N	D	-	1	0	UGT3A2	36084927	0.902000	0.30710	0.016000	0.15963	0.268000	0.26511	1.898000	0.39809	2.242000	0.73789	0.655000	0.94253	GAC		UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
GZMA	3001	hgsc.bcm.edu	37	5	54404152	54404152	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:54404152A>G	ENST00000274306.6	+	4	592	c.557A>G	c.(556-558)aAt>aGt	p.N186S		NM_006144.3	NP_006135	P12544	GRAA_HUMAN	granzyme A (granzyme 1, cytotoxic T-lymphocyte-associated serine esterase 3)	186	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				apoptotic process (GO:0006915)|cytolysis (GO:0019835)|immune response (GO:0006955)|negative regulation of DNA binding (GO:0043392)|negative regulation of endodeoxyribonuclease activity (GO:0032078)|negative regulation of oxidoreductase activity (GO:0051354)|positive regulation of apoptotic process (GO:0043065)|proteolysis involved in cellular protein catabolic process (GO:0051603)	extracellular region (GO:0005576)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	25		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				AATCACTATAATTTTAACCCT	0.423																																																	0			5											80.0	81.0	80.0					5																	54404152		2203	4300	6503	54439909	SO:0001583	missense	3001				CCDS3965.1	5q11-q12	2008-07-18			ENSG00000145649	ENSG00000145649			4708	protein-coding gene	gene with protein product	"""CTL tryptase"", ""Granzyme A (Cytotoxic T-lymphocyte-associated serine esterase-3; Hanukah factor serine protease)"""	140050		HFSP, CTLA3		3262682, 3533635	Standard	NM_006144		Approved		uc003jpm.3	P12544	OTTHUMG00000097011	ENST00000274306.6:c.557A>G	5.37:g.54404152A>G	ENSP00000274306:p.Asn186Ser	Somatic		Capture	Illumina HiSeq	Phase_I	54439909	A4PHN1|Q6IB36	Missense_Mutation	SNP	ENST00000274306.6	37	CCDS3965.1	.	.	.	.	.	.	.	.	.	.	A	8.920	0.960938	0.18583	.	.	ENSG00000145649	ENST00000274306	D	0.88277	-2.36	5.93	4.77	0.60923	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.700801	0.15720	N	0.247943	T	0.77791	0.4183	L	0.35723	1.085	0.09310	N	1	P	0.39352	0.669	B	0.28709	0.093	T	0.65747	-0.6093	10	0.06365	T	0.9	.	9.837	0.40975	0.859:0.0:0.141:0.0	.	186	P12544	GRAA_HUMAN	S	186	ENSP00000274306:N186S	ENSP00000274306:N186S	N	+	2	0	GZMA	54439909	0.898000	0.30612	0.681000	0.30009	0.109000	0.19521	3.512000	0.53407	1.067000	0.40740	-0.250000	0.11733	AAT		GZMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214100.2	NM_006144	
PDE4D	5144	hgsc.bcm.edu	37	5	58270649	58270649	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:58270649C>T	ENST00000340635.6	-	15	2447	c.2272G>A	c.(2272-2274)Gaa>Aaa	p.E758K	PDE4D_ENST00000405755.2_Missense_Mutation_p.E636K|PDE4D_ENST00000507116.1_Missense_Mutation_p.E694K|PDE4D_ENST00000360047.5_Missense_Mutation_p.E622K|PDE4D_ENST00000358923.6_Missense_Mutation_p.E456K|PDE4D_ENST00000503258.1_Missense_Mutation_p.E628K|PDE4D_ENST00000546160.1_Missense_Mutation_p.E697K|PDE4D_ENST00000502484.2_Missense_Mutation_p.E697K|PDE4D_ENST00000317118.8_Missense_Mutation_p.E467K	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	758					adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CTAGTGTCTTCTTCCACTTGA	0.483																																																	0			5											269.0	273.0	272.0					5																	58270649		1984	4161	6145	58306406	SO:0001583	missense	5144				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"""Phosphodiesterases"""	8783	protein-coding gene	gene with protein product	"""phosphodiesterase E3 dunce homolog (Drosophila)"""	600129	"""phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"""	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.2272G>A	5.37:g.58270649C>T	ENSP00000345502:p.Glu758Lys	Somatic		Capture	Illumina HiSeq	Phase_I	58306406	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Missense_Mutation	SNP	ENST00000340635.6	37	CCDS47213.1	.	.	.	.	.	.	.	.	.	.	C	15.63	2.890084	0.52014	.	.	ENSG00000113448	ENST00000340635;ENST00000356665;ENST00000360047;ENST00000507116;ENST00000358923;ENST00000317118;ENST00000503258;ENST00000405755;ENST00000502484;ENST00000546160	T;T;T;T;T;T;T;T;T	0.67345	-0.26;-0.24;-0.24;-0.04;-0.05;-0.24;-0.24;-0.25;-0.25	5.22	5.22	0.72569	.	0.159021	0.47455	D	0.000234	T	0.74543	0.3730	L	0.42245	1.32	0.80722	D	1	D;P;D;B;B;D;B;B	0.56035	0.974;0.956;0.974;0.003;0.103;0.974;0.202;0.108	D;D;D;B;B;D;B;B	0.70487	0.969;0.931;0.969;0.003;0.058;0.969;0.138;0.089	T	0.66156	-0.5994	10	0.11182	T	0.66	.	18.9581	0.92668	0.0:1.0:0.0:0.0	.	697;758;694;621;636;628;533;467	Q08499-11;Q08499;Q08499-6;Q08499-2;Q08499-9;Q08499-10;Q08499-4;Q08499-8	.;PDE4D_HUMAN;.;.;.;.;.;.	K	758;627;622;694;456;467;628;636;697;697	ENSP00000345502:E758K;ENSP00000353152:E622K;ENSP00000424852:E694K;ENSP00000351800:E456K;ENSP00000321739:E467K;ENSP00000425605:E628K;ENSP00000384806:E636K;ENSP00000423094:E697K;ENSP00000442734:E697K	ENSP00000321739:E467K	E	-	1	0	PDE4D	58306406	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.095000	0.76952	2.728000	0.93425	0.655000	0.94253	GAA		PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3		
LRRC70	100130733	hgsc.bcm.edu	37	5	61876446	61876446	+	Missense_Mutation	SNP	G	G	A	rs139239583		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:61876446G>A	ENST00000334994.5	+	2	1420	c.1181G>A	c.(1180-1182)aGa>aAa	p.R394K	IPO11_ENST00000325324.6_Intron|IPO11_ENST00000409296.3_Intron|LRRC70_ENST00000448151.2_3'UTR|LRRC70_ENST00000491184.2_3'UTR|IPO11_ENST00000409534.1_Intron	NM_181506.4	NP_852607.3	Q7Z2Q7	LRR70_HUMAN	leucine rich repeat containing 70	394	LRRCT.					integral component of membrane (GO:0016021)				breast(1)|endometrium(1)	2						ATGCGTGGCAGAGCATTACGT	0.398																																																	0			5											63.0	52.0	55.0					5																	61876446		692	1590	2282	61912202	SO:0001583	missense	100130733				CCDS47218.1	5q12.1	2008-12-18			ENSG00000186105	ENSG00000186105			35155	protein-coding gene	gene with protein product	"""synleurin"""						Standard	NM_181506		Approved	SLRN, LOC100130733	uc011cqs.1	Q7Z2Q7	OTTHUMG00000154401	ENST00000334994.5:c.1181G>A	5.37:g.61876446G>A	ENSP00000399441:p.Arg394Lys	Somatic		Capture	Illumina HiSeq	Phase_I	61912202	Q6ZWI5	Missense_Mutation	SNP	ENST00000334994.5	37	CCDS47218.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.623300	0.46840	.	.	ENSG00000186105	ENST00000334994	T	0.23552	1.9	4.97	3.19	0.36642	Cysteine-rich flanking region, C-terminal (1);	.	.	.	.	T	0.09862	0.0242	N	0.03071	-0.42	0.80722	D	1	B	0.22276	0.067	B	0.21151	0.033	T	0.12785	-1.0534	9	0.09590	T	0.72	.	11.3691	0.49690	0.1475:0.0:0.8525:0.0	.	394	Q7Z2Q7	LRR70_HUMAN	K	394	ENSP00000399441:R394K	ENSP00000399441:R394K	R	+	2	0	LRRC70	61912202	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	4.004000	0.57068	0.792000	0.33850	-0.136000	0.14681	AGA		LRRC70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335067.3	XR_042302	
CMYA5	202333	hgsc.bcm.edu	37	5	79031477	79031477	+	Missense_Mutation	SNP	G	G	A	rs377265303		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:79031477G>A	ENST00000446378.2	+	2	6920	c.6889G>A	c.(6889-6891)Gat>Aat	p.D2297N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	2297					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		AATCTCAGGCGATTCAGAGGA	0.338																																																	0			5						G	ASN/ASP	1,3651		0,1,1825	91.0	89.0	89.0		6889	-1.8	0.0	5		89	0,8158		0,0,4079	no	missense	CMYA5	NM_153610.3	23	0,1,5904	AA,AG,GG		0.0,0.0274,0.0085	benign	2297/4070	79031477	1,11809	1826	4079	5905	79067233	SO:0001583	missense	202333			AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.6889G>A	5.37:g.79031477G>A	ENSP00000394770:p.Asp2297Asn	Somatic		Capture	Illumina HiSeq	Phase_I	79067233	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.676871	0.00102	2.74E-4	0.0	ENSG00000164309	ENST00000446378	T	0.16597	2.33	6.02	-1.84	0.07809	.	2.353210	0.01435	N	0.014865	T	0.10294	0.0252	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30736	-0.9968	10	0.02654	T	1	.	8.1801	0.31305	0.2042:0.0:0.4518:0.344	.	2297	Q8N3K9	CMYA5_HUMAN	N	2297	ENSP00000394770:D2297N	ENSP00000394770:D2297N	D	+	1	0	CMYA5	79067233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.127000	0.15790	-0.357000	0.08175	-2.337000	0.00247	GAT		CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
PCSK1	5122	hgsc.bcm.edu	37	5	95729007	95729007	+	Missense_Mutation	SNP	G	G	A	rs200614230	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:95729007G>A	ENST00000311106.3	-	14	2197	c.1960C>T	c.(1960-1962)Cgg>Tgg	p.R654W	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.R607W|PCSK1_ENST00000513085.1_5'UTR	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	654					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|metabolic process (GO:0008152)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of insulin secretion (GO:0050796)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|secretory granule lumen (GO:0034774)	serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(14)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	36		all_cancers(142;2.67e-06)|all_epithelial(76;6.92e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.0112)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;3.44e-16)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TCATCCCTCCGGCCCCCTACG	0.547													G|||	2	0.000399361	0.0	0.0	5008	,	,		17878	0.0		0.001	False		,,,				2504	0.001																0			5											67.0	71.0	70.0					5																	95729007		2203	4300	6503	95754763	SO:0001583	missense	5122				CCDS4081.1, CCDS54881.1	5q15-q21	2008-07-18			ENSG00000175426	ENSG00000175426			8743	protein-coding gene	gene with protein product	"""prohormone convertase 3"", ""prohormone convertase 1"", ""neuroendocrine convertase 1"", ""proprotein convertase 1"""	162150		NEC1		1765368	Standard	NM_000439		Approved	PC1, PC3, SPC3	uc003kls.2	P29120	OTTHUMG00000122089	ENST00000311106.3:c.1960C>T	5.37:g.95729007G>A	ENSP00000308024:p.Arg654Trp	Somatic		Capture	Illumina HiSeq	Phase_I	95754763	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	12.07	1.826852	0.32329	.	.	ENSG00000175426	ENST00000311106;ENST00000508626	T;T	0.68903	-0.21;-0.36	5.62	1.9	0.25705	.	0.359981	0.32918	N	0.005481	T	0.45236	0.1332	L	0.36672	1.1	0.09310	N	1	P;P	0.44260	0.561;0.83	B;B	0.28638	0.092;0.075	T	0.41360	-0.9513	10	0.66056	D	0.02	-5.6154	7.2964	0.26395	0.0:0.0811:0.4678:0.4511	.	607;654	E9PHA1;P29120	.;NEC1_HUMAN	W	654;607	ENSP00000308024:R654W;ENSP00000421600:R607W	ENSP00000308024:R654W	R	-	1	2	PCSK1	95754763	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.042000	0.13949	0.081000	0.16988	-0.262000	0.10625	CGG		PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439	
FGFR4	2264	hgsc.bcm.edu	37	5	176520243	176520243	+	Missense_Mutation	SNP	G	G	A	rs351855	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:176520243G>A	ENST00000292408.4	+	9	1407	c.1162G>A	c.(1162-1164)Ggg>Agg	p.G388R	FGFR4_ENST00000393648.2_Intron|FGFR4_ENST00000393637.1_Intron|FGFR4_ENST00000292410.3_Intron|FGFR4_ENST00000502906.1_Missense_Mutation_p.G388R	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	388			G -> R (prolonged FGFR4 activity, increased cell motility and tumor cell invasion, possibly due to increased stability of the protease MMP14; dbSNP:rs351855). {ECO:0000269|PubMed:11781352, ECO:0000269|PubMed:21882254, ECO:0000269|Ref.8}.		alveolar secondary septum development (GO:0061144)|cell migration (GO:0016477)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphate ion homeostasis (GO:0055062)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of proteolysis (GO:0045862)|protein autophosphorylation (GO:0046777)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cholesterol homeostasis (GO:2000188)|regulation of extracellular matrix disassembly (GO:0010715)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	34	all_cancers(89;5.93e-05)|Renal(175;0.000269)|Lung NSC(126;0.0088)|all_lung(126;0.0142)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Palifermin(DB00039)|Ponatinib(DB08901)	GCTGCTGGCCGGGCTGTATCG	0.711										TSP Lung(9;0.080)			G|||	1500	0.299521	0.1097	0.3098	5008	,	,		12765	0.4633		0.2942	False		,,,				2504	0.3855																0			5	GRCh37	CM023917	FGFR4	M	rs351855	G	ARG/GLY,,ARG/GLY	567,3839	240.9+/-251.5	34,499,1670	35.0	32.0	33.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1162,,1162	4.3	0.9	5	dbSNP_79	33	2583,6011	393.4+/-344.3	429,1725,2143	yes	missense,intron,missense	FGFR4	NM_002011.3,NM_022963.2,NM_213647.1	125,,125	463,2224,3813	AA,AG,GG		30.0559,12.8688,24.2308	possibly-damaging,,possibly-damaging	388/803,,388/803	176520243	3150,9850	2203	4297	6500	176452849	SO:0001583	missense	2264			AF202063	CCDS4410.1, CCDS4411.1	5q35.2	2013-09-19			ENSG00000160867	ENSG00000160867		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3691	protein-coding gene	gene with protein product		134935					Standard	XM_005265837		Approved	JTK2, CD334	uc003mfm.3	P22455	OTTHUMG00000151523	ENST00000292408.4:c.1162G>A	5.37:g.176520243G>A	ENSP00000292408:p.Gly388Arg	Somatic		Capture	Illumina HiSeq	Phase_I	176452849	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	661|661	0.30265567765567764|0.30265567765567764	61|61	0.12398373983739837|0.12398373983739837	123|123	0.3397790055248619|0.3397790055248619	258|258	0.45104895104895104|0.45104895104895104	219|219	0.28891820580474936|0.28891820580474936	G|G	19.01|19.01	3.743077|3.743077	0.69418|0.69418	0.128688|0.128688	0.300559|0.300559	ENSG00000160867|ENSG00000160867	ENST00000292408;ENST00000502906;ENST00000377207|ENST00000511076	D;D|.	0.82984|.	-1.67;-1.67|.	4.29|4.29	4.29|4.29	0.51040|0.51040	.|.	0.316526|.	0.32753|.	N|.	0.005687|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	P|P	1.0|1.0	D|.	0.71674|.	0.998|.	P|.	0.52481|.	0.7|.	T|T	0.50338|0.50338	-0.8840|-0.8840	9|4	0.59425|.	D|.	0.04|.	.|.	11.2123|11.2123	0.48806|0.48806	0.0906:0.0:0.9094:0.0|0.0906:0.0:0.9094:0.0	rs351855;rs56695235;rs351855|rs351855;rs56695235;rs351855	388|.	P22455|.	FGFR4_HUMAN|.	R|Q	388;388;616|23	ENSP00000292408:G388R;ENSP00000424960:G388R|.	ENSP00000292408:G388R|.	G|R	+|+	1|2	0|0	FGFR4|FGFR4	176452849|176452849	0.995000|0.995000	0.38212|0.38212	0.911000|0.911000	0.35937|0.35937	0.721000|0.721000	0.41392|0.41392	4.235000|4.235000	0.58666|0.58666	2.233000|2.233000	0.73108|0.73108	0.561000|0.561000	0.74099|0.74099	GGG|CGG		FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1		
PREP	5550	hgsc.bcm.edu	37	6	105736747	105736747	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:105736747C>T	ENST00000369110.3	-	11	1532	c.1340G>A	c.(1339-1341)gGt>gAt	p.G447D		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	447					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	AATCTTCGTACCATCCTTGCT	0.353																																																	0			6											111.0	106.0	108.0					6																	105736747		2203	4300	6503	105843440	SO:0001583	missense	5550				CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.1340G>A	6.37:g.105736747C>T	ENSP00000358106:p.Gly447Asp	Somatic		Capture	Illumina HiSeq	Phase_I	105843440	Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.739413	0.89573	.	.	ENSG00000085377	ENST00000369110	T	0.65549	-0.16	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.74015	0.3661	H	0.95365	3.66	0.80722	D	1	P	0.40731	0.728	B	0.42882	0.401	T	0.81167	-0.1056	10	0.62326	D	0.03	-20.1991	20.2469	0.98398	0.0:1.0:0.0:0.0	.	447	P48147	PPCE_HUMAN	D	447	ENSP00000358106:G447D	ENSP00000358106:G447D	G	-	2	0	PREP	105843440	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.757000	0.68766	2.781000	0.95711	0.555000	0.69702	GGT		PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
MCM9	254394	hgsc.bcm.edu	37	6	119252789	119252789	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:119252789C>T	ENST00000316316.6	-	2	386	c.100G>A	c.(100-102)Gaa>Aaa	p.E34K	MCM9_ENST00000316068.3_Missense_Mutation_p.E34K	NM_017696.2	NP_060166.2	Q9NXL9	MCM9_HUMAN	minichromosome maintenance complex component 9	34					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)	MCM8-MCM9 complex (GO:0097362)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		all_cancers(87;0.122)|all_epithelial(87;0.179)		GBM - Glioblastoma multiforme(226;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.194)		TGAGCATCTTCATCCCTTTCC	0.398																																																	0			6											129.0	116.0	121.0					6																	119252789		2203	4300	6503	119294488	SO:0001583	missense	254394			BC031658	CCDS5121.1, CCDS56447.1	6q22.31	2009-11-16	2007-04-04	2007-04-04	ENSG00000111877	ENSG00000111877			21484	protein-coding gene	gene with protein product		610098	"""minichromosome maintenance deficient domain containing 1"", ""chromosome 6 open reading frame 61"""	MCMDC1, C6orf61		16226853, 15850810, 16495042	Standard	NM_153255		Approved	MGC35304, dJ329L24.3, FLJ20170	uc021zeh.1	Q9NXL9	OTTHUMG00000015468	ENST00000316316.6:c.100G>A	6.37:g.119252789C>T	ENSP00000314505:p.Glu34Lys	Somatic		Capture	Illumina HiSeq	Phase_I	119294488	B4DR30|B9DI77|Q2KHJ0|Q8N5S5|Q9HCV5	Missense_Mutation	SNP	ENST00000316316.6	37	CCDS56447.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613254	0.87359	.	.	ENSG00000111877	ENST00000316316;ENST00000316068;ENST00000425154;ENST00000505446	T;T;T;T	0.04275	3.66;3.66;3.66;3.66	5.91	5.91	0.95273	.	.	.	.	.	T	0.03695	0.0105	M	0.64997	1.995	0.80722	D	1	P	0.38504	0.634	B	0.33620	0.167	T	0.51220	-0.8733	9	0.19147	T	0.46	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	34	Q9NXL9-2	.	K	34	ENSP00000314505:E34K;ENSP00000312870:E34K;ENSP00000394776:E34K;ENSP00000426890:E34K	ENSP00000312870:E34K	E	-	1	0	MCM9	119294488	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.707000	0.68370	2.793000	0.96121	0.655000	0.94253	GAA		MCM9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042005.4	NM_153255	
TBC1D32	221322	hgsc.bcm.edu	37	6	121625558	121625558	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:121625558A>T	ENST00000398212.2	-	8	937	c.888T>A	c.(886-888)aaT>aaA	p.N296K	TBC1D32_ENST00000275159.6_Missense_Mutation_p.N296K	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	296					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCTGATATTCATTTAGAAGAC	0.368																																																	0			6											83.0	80.0	81.0					6																	121625558		1817	4083	5900	121667257	SO:0001583	missense	221322			AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.888T>A	6.37:g.121625558A>T	ENSP00000381270:p.Asn296Lys	Somatic		Capture	Illumina HiSeq	Phase_I	121667257	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392106	0.62066	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.23552	1.9;1.9	5.05	2.56	0.30785	.	0.053903	0.64402	D	0.000001	T	0.33030	0.0849	M	0.75264	2.295	0.43330	D	0.995361	D	0.76494	0.999	D	0.65874	0.939	T	0.14364	-1.0475	10	0.66056	D	0.02	.	9.5036	0.39033	0.8523:0.0:0.1477:0.0	.	296	Q96NH3	BROMI_HUMAN	K	296	ENSP00000275159:N296K;ENSP00000381270:N296K	ENSP00000275159:N296K	N	-	3	2	C6orf170	121667257	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.895000	0.48648	0.226000	0.20979	0.528000	0.53228	AAT		TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
FARS2	10667	hgsc.bcm.edu	37	6	5771573	5771573	+	Missense_Mutation	SNP	C	C	T	rs145697325		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:5771573C>T	ENST00000324331.6	+	7	1603	c.1267C>T	c.(1267-1269)Cgg>Tgg	p.R423W	FARS2_ENST00000274680.4_Missense_Mutation_p.R423W			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	423	FDX-ACB. {ECO:0000255|PROSITE- ProRule:PRU00778}.				gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	CCACATGGAACGGACTCTGTC	0.587																																																	0			6											173.0	130.0	144.0					6																	5771573		2203	4300	6503	5716572	SO:0001583	missense	10667			AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	21062	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 2, mitochondrial"""	611592	"""phenylalanine-tRNA synthetase 1 (mitochondrial)"""	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.1267C>T	6.37:g.5771573C>T	ENSP00000316335:p.Arg423Trp	Somatic		Capture	Illumina HiSeq	Phase_I	5716572	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	37	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	C	18.42	3.621024	0.66787	.	.	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.79352	-1.26;-1.26	5.81	2.71	0.32032	Phenylalanyl-tRNA synthetase, beta subunit, ferrodoxin-fold anticodon-binding (5);	0.000000	0.64402	D	0.000002	D	0.88066	0.6337	M	0.93638	3.44	0.52099	D	0.999948	D	0.89917	1.0	D	0.91635	0.999	D	0.90661	0.4590	10	0.72032	D	0.01	-36.8389	13.5071	0.61489	0.4852:0.5148:0.0:0.0	.	423	O95363	SYFM_HUMAN	W	423	ENSP00000274680:R423W;ENSP00000316335:R423W	ENSP00000274680:R423W	R	+	1	2	FARS2	5716572	1.000000	0.71417	0.980000	0.43619	0.778000	0.44026	1.436000	0.34980	0.756000	0.33013	0.655000	0.94253	CGG		FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567	
MYLIP	29116	hgsc.bcm.edu	37	6	16145473	16145473	+	Silent	SNP	C	C	T	rs1060901	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:16145473C>T	ENST00000356840.3	+	6	1371	c.1173C>T	c.(1171-1173)tgC>tgT	p.C391C	MYLIP_ENST00000349606.4_Silent_p.C210C	NM_013262.3	NP_037394.2	Q8WY64	MYLIP_HUMAN	myosin regulatory light chain interacting protein	391					cellular component movement (GO:0006928)|cholesterol homeostasis (GO:0042632)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|nervous system development (GO:0007399)|positive regulation of protein catabolic process (GO:0045732)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of low-density lipoprotein particle receptor catabolic process (GO:0032803)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	cytoskeletal protein binding (GO:0008092)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28	Breast(50;0.0799)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.241)			TGGTGTGCTGCGAGGAGGAGA	0.612													C|||	125	0.0249601	0.003	0.0375	5008	,	,		20576	0.001		0.0736	False		,,,				2504	0.0204																0			6						C		72,4334	63.5+/-100.7	1,70,2132	103.0	89.0	94.0		1173	-5.6	0.6	6	dbSNP_86	94	773,7827	184.6+/-232.5	34,705,3561	no	coding-synonymous	MYLIP	NM_013262.3		35,775,5693	TT,TC,CC		8.9884,1.6341,6.497		391/446	16145473	845,12161	2203	4300	6503	16253452	SO:0001819	synonymous_variant	29116			AF187016	CCDS4536.1	6p23-p22.3	2011-11-17			ENSG00000007944	ENSG00000007944			21155	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase-inducible degrader of the low density lipoprotein receptor"""	610082				10593918, 11162443, 19688294	Standard	NM_013262		Approved	MIR, IDOL	uc003nbq.3	Q8WY64	OTTHUMG00000016405	ENST00000356840.3:c.1173C>T	6.37:g.16145473C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16253452	Q5TIA4|Q9BU73|Q9NRL9|Q9UHE7	Silent	SNP	ENST00000356840.3	37	CCDS4536.1																																																																																				MYLIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043864.1	NM_013262	
HLA-A	3105	hgsc.bcm.edu	37	6	29910759	29910759	+	Missense_Mutation	SNP	T	T	A	rs1071742	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:29910759T>A	ENST00000396634.1	+	4	640	c.299T>A	c.(298-300)gTg>gAg	p.V100E	HLA-A_ENST00000376806.5_Missense_Mutation_p.V100E|HLA-A_ENST00000376809.5_Missense_Mutation_p.V100E|HLA-A_ENST00000376802.2_Missense_Mutation_p.V100E			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	100	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						ACTGACCGAGTGGACCTGGGG	0.687									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			N|||	1111	0.221845	0.2345	0.2522	5008	,	,		10249	0.2222		0.1938	False		,,,				2504	0.2117																0			6											60.0	64.0	63.0					6																	29910759		2194	4284	6478	30018738	SO:0001583	missense	3105	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.299T>A	6.37:g.29910759T>A	ENSP00000379873:p.Val100Glu	Somatic		Capture	Illumina HiSeq	Phase_I	30018738	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	345	0.15796703296703296	79	0.16056910569105692	84	0.23204419889502761	95	0.1660839160839161	87	0.11477572559366754	.	5.377	0.254742	0.10185	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00695	5.83;5.83;5.83;5.83	3.33	-6.67	0.01783	MHC class I, alpha chain, alpha1/alpha2 (6);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	15.776400	0.01836	U	0.034989	T	0.00271	0.0008	L	0.58428	1.81	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.002	T	0.46898	-0.9158	10	0.30854	T	0.27	.	0.4643	0.00521	0.2856:0.2905:0.146:0.2778	rs1071742;rs2231002;rs3129019;rs3173422;rs3200152;rs3200155;rs9256981;rs17423971;rs41551313	100;100;100;100;100	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	E	100	ENSP00000379873:V100E;ENSP00000366002:V100E;ENSP00000366005:V100E;ENSP00000365998:V100E	ENSP00000348012:V100E	V	+	2	0	HLA-A	30018738	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.538000	0.00938	-1.834000	0.01193	-3.111000	0.00062	GTG		HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
MUC21	394263	hgsc.bcm.edu	37	6	30954491	30954491	+	Missense_Mutation	SNP	C	C	T	rs34126344	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:30954491C>T	ENST00000376296.3	+	2	780	c.539C>T	c.(538-540)gCc>gTc	p.A180V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	180	28 X 15 AA approximate tandem repeats.|Ser-rich.			A -> V (in Ref. 4; CAQ07653). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GCCAGCACAGCCACCAACTCT	0.607													C|||	312	0.0623003	0.0166	0.0994	5008	,	,		27275	0.1319		0.0596	False		,,,				2504	0.0286																0			6						C	VAL/ALA	162,4244	108.6+/-147.0	1,160,2042	159.0	151.0	154.0		539	1.9	0.0	6	dbSNP_126	154	585,8015	155.4+/-209.4	23,539,3738	no	missense	MUC21	NM_001010909.2	64	24,699,5780	TT,TC,CC		6.8023,3.6768,5.7435	benign	180/567	30954491	747,12259	2203	4300	6503	31062470	SO:0001583	missense	394263			AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.539C>T	6.37:g.30954491C>T	ENSP00000365473:p.Ala180Val	Somatic		Capture	Illumina HiSeq	Phase_I	31062470	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	148	0.06776556776556776	10	0.02032520325203252	30	0.08287292817679558	62	0.10839160839160839	46	0.06068601583113457	C	9.071	0.996786	0.19043	0.036768	0.068023	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02787	4.16	3.72	1.89	0.25635	.	.	.	.	.	T	0.00695	0.0023	N	0.19112	0.55	0.80722	P	0.0	B	0.33044	0.395	B	0.36289	0.221	T	0.49725	-0.8909	7	.	.	.	-0.31	3.2061	0.06666	0.2079:0.5615:0.0:0.2305	rs34126344	180	Q5SSG8	MUC21_HUMAN	V	180	ENSP00000365473:A180V	.	A	+	2	0	MUC21	31062470	0.000000	0.05858	0.000000	0.03702	0.065000	0.16274	0.279000	0.18771	0.360000	0.24265	0.485000	0.47835	GCC		MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
LY6G6D	58530	hgsc.bcm.edu	37	6	31685453	31685453	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:31685453G>T	ENST00000375825.3	+	3	274	c.274G>T	c.(274-276)Gcc>Tcc	p.A92S	MEGT1_ENST00000503322.1_Missense_Mutation_p.A341S|LY6G6F_ENST00000556581.1_Missense_Mutation_p.A341S	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	92	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						GACTTATCCAGCCCACAGGGA	0.602																																																	0			6											156.0	158.0	158.0					6																	31685453		2203	4300	6503	31793432	SO:0001583	missense	259215				CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"""chromosome 6 open reading frame 23"""	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.274G>T	6.37:g.31685453G>T	ENSP00000364985:p.Ala92Ser	Somatic		Capture	Illumina HiSeq	Phase_I	31793432	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Missense_Mutation	SNP	ENST00000375825.3	37	CCDS34404.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	7.565|7.565	0.665501|0.665501	0.14710|0.14710	.|.	.|.	ENSG00000204424;ENSG00000250641;ENSG00000244355|ENSG00000244355	ENST00000556581;ENST00000503322;ENST00000375825|ENST00000375824	T;T;T|T	0.69685|0.37058	2.53;2.53;-0.42|1.22	5.54|5.54	0.0731|0.0731	0.14389|0.14389	.|.	1.740850|.	0.03400|.	N|.	0.203239|.	T|T	0.08447|0.08447	0.0210|0.0210	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B|.	0.14012|.	0.009;0.005|.	B;B|.	0.09377|.	0.004;0.004|.	T|T	0.29305|0.29305	-1.0016|-1.0016	10|7	0.54805|0.72032	T|D	0.06|0.01	.|.	3.99|3.99	0.09533|0.09533	0.6057:0.0:0.2494:0.1449|0.6057:0.0:0.2494:0.1449	.|.	92;341|.	O95868;Q9NZJ1|.	LY66D_HUMAN;.|.	S|I	341;341;92|132	ENSP00000452432:A341S;ENSP00000421232:A341S;ENSP00000364985:A92S|ENSP00000364984:S132I	ENSP00000364985:A92S|ENSP00000364984:S132I	A|S	+|+	1|2	0|0	LY6G6D;XXbac-BPG32J3.19;LY6G6F|LY6G6D	31793432|31793432	0.042000|0.042000	0.20092|0.20092	0.024000|0.024000	0.17045|0.17045	0.240000|0.240000	0.25518|0.25518	0.426000|0.426000	0.21363|0.21363	0.072000|0.072000	0.16694|0.16694	-0.792000|-0.792000	0.03331|0.03331	GCC|AGC		LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2		
LY6G6D	58530	hgsc.bcm.edu	37	6	31685455	31685455	+	Silent	SNP	C	C	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:31685455C>A	ENST00000375825.3	+	3	276	c.276C>A	c.(274-276)gcC>gcA	p.A92A	MEGT1_ENST00000503322.1_Silent_p.A341A|LY6G6F_ENST00000556581.1_Silent_p.A341A	NM_021246.2	NP_067069.2	O95868	LY66D_HUMAN	lymphocyte antigen 6 complex, locus G6D	92	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|plasma membrane (GO:0005886)				central_nervous_system(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	5						CTTATCCAGCCCACAGGGACT	0.602																																																	0			6											155.0	157.0	156.0					6																	31685455		2203	4300	6503	31793434	SO:0001819	synonymous_variant	259215				CCDS34404.1	6p21.3	2008-08-29	2002-07-29	2002-08-01	ENSG00000244355	ENSG00000244355			13935	protein-coding gene	gene with protein product		606038	"""chromosome 6 open reading frame 23"""	C6orf23		12079290	Standard	NM_021246		Approved	MEGT1, Ly6-D, G6D, LY6-D, NG25		O95868	OTTHUMG00000137370	ENST00000375825.3:c.276C>A	6.37:g.31685455C>A		Somatic		Capture	Illumina HiSeq	Phase_I	31793434	A2BEY8|B0UXC1|B0V019|B0V1Y6|Q4VX50	Silent	SNP	ENST00000375825.3	37	CCDS34404.1	.	.	.	.	.	.	.	.	.	.	c	12.93	2.084495	0.36758	.	.	ENSG00000244355	ENST00000375824	T	0.38240	1.15	5.54	1.65	0.23941	.	.	.	.	.	T	0.17195	0.0413	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	T	0.24870	-1.0148	6	0.87932	D	0	.	4.6608	0.12641	0.1502:0.5976:0.0:0.2522	.	.	.	.	T	133	ENSP00000364984:P133T	ENSP00000364984:P133T	P	+	1	0	LY6G6D	31793434	0.262000	0.24073	0.091000	0.20842	0.329000	0.28539	0.403000	0.20982	0.284000	0.22305	0.645000	0.84053	CCA		LY6G6D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144875.2		
MAPK13	5603	hgsc.bcm.edu	37	6	36106492	36106492	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:36106492T>C	ENST00000211287.4	+	10	1038	c.776T>C	c.(775-777)aTc>aCc	p.I259T	Z95152.1_ENST00000408816.1_RNA|MAPK13_ENST00000373761.6_Missense_Mutation_p.I249T|MAPK13_ENST00000373759.1_Silent_p.H130H|MAPK13_ENST00000373766.5_Silent_p.H208H	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	259	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						AAATCCTACATCCAGTCCCTG	0.597																																																	0			6											58.0	60.0	59.0					6																	36106492		2203	4300	6503	36214470	SO:0001583	missense	5603			Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.776T>C	6.37:g.36106492T>C	ENSP00000211287:p.Ile259Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36214470	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Missense_Mutation	SNP	ENST00000211287.4	37	CCDS4818.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.145620	0.77888	.	.	ENSG00000156711	ENST00000373761;ENST00000211287	T;T	0.43688	0.94;0.94	5.25	5.25	0.73442	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	0.64402	D	0.000017	T	0.45657	0.1353	M	0.62209	1.925	0.80722	D	1	P	0.45126	0.851	P	0.53809	0.735	T	0.51309	-0.8722	10	0.87932	D	0	-29.7119	14.3162	0.66452	0.0:0.0:0.0:1.0	.	259	O15264	MK13_HUMAN	T	249;259	ENSP00000362866:I249T;ENSP00000211287:I259T	ENSP00000211287:I259T	I	+	2	0	MAPK13	36214470	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.717000	0.84732	1.976000	0.57569	0.397000	0.26171	ATC		MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1		
GLP1R	2740	hgsc.bcm.edu	37	6	39034026	39034026	+	Silent	SNP	C	C	T	rs200564025		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:39034026C>T	ENST00000373256.4	+	5	499	c.456C>T	c.(454-456)taC>taT	p.Y152Y		NM_002062.3	NP_002053.3	P43220	GLP1R_HUMAN	glucagon-like peptide 1 receptor	152					activation of adenylate cyclase activity (GO:0007190)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|learning or memory (GO:0007611)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of heart contraction (GO:0008016)|regulation of insulin secretion (GO:0050796)|response to stress (GO:0006950)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glucagon receptor activity (GO:0004967)|transmembrane signaling receptor activity (GO:0004888)	p.Y152Y(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	31					Exenatide(DB01276)|Glucagon recombinant(DB00040)|Liraglutide(DB06655)	CGGTGGGCTACGCACTCTCCT	0.617																																																	1	Substitution - coding silent(1)	endometrium(1)	6											176.0	130.0	146.0					6																	39034026		2203	4300	6503	39142004	SO:0001819	synonymous_variant	2740				CCDS4839.1	6p21	2012-08-10			ENSG00000112164	ENSG00000112164		"""GPCR / Class B : Glucagon receptors"""	4324	protein-coding gene	gene with protein product		138032					Standard	NM_002062		Approved		uc003ooj.4	P43220	OTTHUMG00000014638	ENST00000373256.4:c.456C>T	6.37:g.39034026C>T		Somatic		Capture	Illumina HiSeq	Phase_I	39142004	Q2M229|Q99669	Silent	SNP	ENST00000373256.4	37	CCDS4839.1																																																																																				GLP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040443.1		
POLH	5429	hgsc.bcm.edu	37	6	43550100	43550100	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:43550100A>G	ENST00000372236.4	+	2	339	c.44A>G	c.(43-45)gAc>gGc	p.D15G	POLH_ENST00000535400.1_Intron|POLH_ENST00000372226.1_Missense_Mutation_p.D15G	NM_006502.2	NP_006493.1	O75417	DPOLQ_HUMAN	polymerase (DNA directed), eta	0					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			breast(4)|endometrium(5)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_cancers(18;1.89e-05)|Lung NSC(15;0.00161)|all_lung(25;0.004)		all cancers(41;0.000753)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0826)|OV - Ovarian serous cystadenocarcinoma(102;0.167)			GTGGACATGGACTGTTTTTTT	0.418								DNA polymerases (catalytic subunits)	Xeroderma Pigmentosum																																								0			6											234.0	217.0	222.0					6																	43550100		2203	4300	6503	43658078	SO:0001583	missense	10721	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AB024313	CCDS4902.1	6p21	2014-09-17			ENSG00000170734	ENSG00000170734			9181	protein-coding gene	gene with protein product		603968				10385124, 10398605	Standard	NM_006502		Approved	RAD30A, XP-V	uc003ovq.4	Q9Y253	OTTHUMG00000014743	ENST00000372236.4:c.44A>G	6.37:g.43550100A>G	ENSP00000361310:p.Asp15Gly	Somatic		Capture	Illumina HiSeq	Phase_I	43658078	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000372236.4	37	CCDS4902.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.840285	0.91117	.	.	ENSG00000170734	ENST00000372236;ENST00000372226	D;D	0.83755	-1.76;-1.76	5.56	5.56	0.83823	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.000000	0.85682	D	0.000000	D	0.93298	0.7864	H	0.96691	3.865	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95253	0.8361	10	0.87932	D	0	0.3493	14.2865	0.66249	1.0:0.0:0.0:0.0	.	15	Q9Y253	POLH_HUMAN	G	15	ENSP00000361310:D15G;ENSP00000361300:D15G	ENSP00000361300:D15G	D	+	2	0	POLH	43658078	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.613000	0.82986	2.245000	0.73994	0.454000	0.30748	GAC		POLH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040666.1	NM_006502	
PDE7B	27115	hgsc.bcm.edu	37	6	136429947	136429947	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr6:136429947T>C	ENST00000308191.6	+	3	464	c.161T>C	c.(160-162)cTt>cCt	p.L54P	RP13-143G15.4_ENST00000585946.1_RNA|RP13-143G15.4_ENST00000591521.1_RNA|RP13-143G15.4_ENST00000417643.1_RNA	NM_018945.3	NP_061818.1	Q9NP56	PDE7B_HUMAN	phosphodiesterase 7B	54					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(1)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Colorectal(23;0.24)			OV - Ovarian serous cystadenocarcinoma(155;0.0136)|GBM - Glioblastoma multiforme(68;0.0147)	Caffeine(DB00201)|Dyphylline(DB00651)|Ketotifen(DB00920)	TTCCGCCTACTTAACAGTGAG	0.433																																																	0			6											105.0	104.0	104.0					6																	136429947		2203	4300	6503	136471640	SO:0001583	missense	27115			AB038040	CCDS5175.1	6q23-q24	2008-03-18			ENSG00000171408	ENSG00000171408	3.1.4.17	"""Phosphodiesterases"""	8792	protein-coding gene	gene with protein product		604645				10618442	Standard	XM_005266931		Approved		uc003qgp.3	Q9NP56	OTTHUMG00000015641	ENST00000308191.6:c.161T>C	6.37:g.136429947T>C	ENSP00000310661:p.Leu54Pro	Somatic		Capture	Illumina HiSeq	Phase_I	136471640	Q5W154	Missense_Mutation	SNP	ENST00000308191.6	37	CCDS5175.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049803	0.75846	.	.	ENSG00000171408	ENST00000308191;ENST00000367787	T	0.73897	-0.79	5.97	5.97	0.96955	.	3.163210	0.00424	N	0.000070	T	0.77260	0.4104	L	0.58101	1.795	0.80722	D	1	D;P	0.54397	0.966;0.929	P;P	0.54629	0.641;0.757	T	0.62034	-0.6939	10	0.37606	T	0.19	.	13.9684	0.64223	0.0:0.0:0.0:1.0	.	106;54	A1E5M1;Q9NP56	.;PDE7B_HUMAN	P	54;190	ENSP00000310661:L54P	ENSP00000310661:L54P	L	+	2	0	PDE7B	136471640	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.757000	0.62213	2.281000	0.76405	0.528000	0.53228	CTT		PDE7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042371.1		
TMEM168	64418	hgsc.bcm.edu	37	7	112424142	112424142	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:112424142A>G	ENST00000312814.6	-	2	1299	c.739T>C	c.(739-741)Tca>Cca	p.S247P	TMEM168_ENST00000454074.1_Missense_Mutation_p.S247P	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168	247						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)		p.S247T(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(2)|stomach(1)	32						TCAGTTACTGAAAGTCCACTA	0.348																																																	1	Substitution - Missense(1)	central_nervous_system(1)	7											100.0	111.0	107.0					7																	112424142		2203	4300	6503	112211378	SO:0001583	missense	64418				CCDS5757.1	7q31.32	2006-08-08			ENSG00000146802	ENSG00000146802			25826	protein-coding gene	gene with protein product						12477932	Standard	XM_005250527		Approved	DKFZp564C012,FLJ13576	uc003vgn.3	Q9H0V1	OTTHUMG00000155188	ENST00000312814.6:c.739T>C	7.37:g.112424142A>G	ENSP00000323068:p.Ser247Pro	Somatic		Capture	Illumina HiSeq	Phase_I	112211378	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Missense_Mutation	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	A	19.13	3.768042	0.69878	.	.	ENSG00000146802	ENST00000312814;ENST00000454074	.	.	.	6.06	6.06	0.98353	.	0.246149	0.42294	D	0.000740	T	0.73118	0.3546	L	0.55481	1.735	0.80722	D	1	D	0.69078	0.997	P	0.59487	0.858	T	0.75402	-0.3330	9	0.72032	D	0.01	-27.2205	16.6245	0.84952	1.0:0.0:0.0:0.0	.	247	Q9H0V1	TM168_HUMAN	P	247	.	ENSP00000323068:S247P	S	-	1	0	TMEM168	112211378	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.353000	0.79414	2.323000	0.78572	0.528000	0.53228	TCA		TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484	
MKLN1	4289	hgsc.bcm.edu	37	7	131155643	131155643	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:131155643A>G	ENST00000352689.6	+	16	2011	c.1971A>G	c.(1969-1971)aaA>aaG	p.K657K	MKLN1_ENST00000421797.2_Silent_p.K565K|MKLN1_ENST00000498778.1_3'UTR	NM_013255.4	NP_037387.2	Q9UL63	MKLN1_HUMAN	muskelin 1, intracellular mediator containing kelch motifs	657					signal transduction (GO:0007165)	cytoplasm (GO:0005737)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28	Melanoma(18;0.162)					GTGCTCTGAAATATTTACAAA	0.323																																																	0			7											72.0	76.0	75.0					7																	131155643		2203	4297	6500	130806183	SO:0001819	synonymous_variant	4289			AF047489	CCDS34754.1	7q32	2008-07-18			ENSG00000128585	ENSG00000128585			7109	protein-coding gene	gene with protein product		605623				10640805	Standard	NM_001145354		Approved	TWA2	uc011kpm.2	Q9UL63	OTTHUMG00000154880	ENST00000352689.6:c.1971A>G	7.37:g.131155643A>G		Somatic		Capture	Illumina HiSeq	Phase_I	130806183	A4D1M8|A6NG43|Q9NSK4|Q9NUS8	Silent	SNP	ENST00000352689.6	37	CCDS34754.1																																																																																				MKLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337473.4	NM_013255	
BRAF	673	hgsc.bcm.edu	37	7	140453170	140453170	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:140453170T>C	ENST00000288602.6	-	15	1825	c.1765A>G	c.(1765-1767)Aca>Gca	p.T589A		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	589	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ATTTTTACTGTGAGGTCTTCA	0.383		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)			Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	0			7											98.0	94.0	95.0					7																	140453170		2203	4300	6503	140099639	SO:0001583	missense	673	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1765A>G	7.37:g.140453170T>C	ENSP00000288602:p.Thr589Ala	Somatic		Capture	Illumina HiSeq	Phase_I	140099639	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.616302	0.87359	.	.	ENSG00000157764	ENST00000288602	D	0.98958	-5.27	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98451	0.9484	L	0.49640	1.575	0.80722	D	1	P	0.35780	0.52	P	0.51701	0.677	D	0.99846	1.1066	10	0.87932	D	0	.	15.9326	0.79675	0.0:0.0:0.0:1.0	.	589	P15056	BRAF_HUMAN	A	589	ENSP00000288602:T589A	ENSP00000288602:T589A	T	-	1	0	BRAF	140099639	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.921000	0.87530	2.169000	0.68431	0.529000	0.55759	ACA		BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
TNRC18	84629	hgsc.bcm.edu	37	7	5363928	5363928	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:5363928T>C	ENST00000430969.1	-	21	6707	c.6359A>G	c.(6358-6360)gAc>gGc	p.D2120G	TNRC18_ENST00000399537.4_Missense_Mutation_p.D2120G	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2120							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGTTCAAAGTCCTCCTCGGC	0.637																																																	0			7											46.0	49.0	48.0					7																	5363928		1568	3581	5149	5330454	SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.6359A>G	7.37:g.5363928T>C	ENSP00000395538:p.Asp2120Gly	Somatic		Capture	Illumina HiSeq	Phase_I	5330454	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	18.97|18.97	3.735255|3.735255	0.69189|0.69189	.|.	.|.	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000455076	T;T|.	0.23147|.	1.92;1.92|.	4.07|4.07	4.07|4.07	0.47477|0.47477	.|.	.|.	.|.	.|.	.|.	T|T	0.51075|0.51075	0.1653|0.1653	L|L	0.28115|0.28115	0.83|0.83	0.43330|0.43330	D|D	0.995362|0.995362	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.46498|0.46498	-0.9187|-0.9187	9|5	0.66056|.	D|.	0.02|.	.|.	12.9664|12.9664	0.58485|0.58485	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2120|.	O15417|.	TNC18_HUMAN|.	G|A	2120|168	ENSP00000382452:D2120G;ENSP00000395538:D2120G|.	ENSP00000382452:D2120G|.	D|T	-|-	2|1	0|0	TNRC18|TNRC18	5330454|5330454	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.566000|0.566000	0.35808|0.35808	7.178000|7.178000	0.77657|0.77657	1.614000|1.614000	0.50241|0.50241	0.260000|0.260000	0.18958|0.18958	GAC|ACT		TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
C7orf26	79034	hgsc.bcm.edu	37	7	6634106	6634106	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:6634106T>C	ENST00000344417.5	+	3	722	c.455T>C	c.(454-456)cTt>cCt	p.L152P	C7orf26_ENST00000472693.1_3'UTR|C7orf26_ENST00000359073.5_Missense_Mutation_p.L133P	NM_024067.2	NP_076972.2	Q96N11	CG026_HUMAN	chromosome 7 open reading frame 26	152										endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	11		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)		GCCAAGGCCCTTGTAGATGAC	0.527																																																	0			7											243.0	218.0	226.0					7																	6634106		2203	4300	6503	6600631	SO:0001583	missense	79034			BC005121	CCDS5353.1	7p22.1	2011-11-24			ENSG00000146576	ENSG00000146576			21702	protein-coding gene	gene with protein product							Standard	NM_024067		Approved	MGC2718	uc003sqo.1	Q96N11	OTTHUMG00000125517	ENST00000344417.5:c.455T>C	7.37:g.6634106T>C	ENSP00000340220:p.Leu152Pro	Somatic		Capture	Illumina HiSeq	Phase_I	6600631	Q9BQ43	Missense_Mutation	SNP	ENST00000344417.5	37	CCDS5353.1	.	.	.	.	.	.	.	.	.	.	T	17.50	3.404955	0.62288	.	.	ENSG00000146576	ENST00000344417;ENST00000359073	T;T	0.53206	0.63;0.63	4.66	4.66	0.58398	.	0.065009	0.56097	D	0.000023	T	0.63628	0.2527	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.67055	-0.5767	10	0.87932	D	0	-22.1337	12.6786	0.56908	0.0:0.0:0.0:1.0	.	133;152	Q96N11-2;Q96N11	.;CG026_HUMAN	P	152;133	ENSP00000340220:L152P;ENSP00000351974:L133P	ENSP00000340220:L152P	L	+	2	0	C7orf26	6600631	1.000000	0.71417	0.948000	0.38648	0.986000	0.74619	7.931000	0.87625	2.033000	0.60031	0.533000	0.62120	CTT		C7orf26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246844.2	NM_024067	
ZNF853	54753	hgsc.bcm.edu	37	7	6656830	6656830	+	Missense_Mutation	SNP	G	G	A	rs2243563	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:6656830G>A	ENST00000457543.3	+	2	580	c.22G>A	c.(22-24)Ggg>Agg	p.G8R		NM_017560.1	NP_060030.1	P0CG23	ZN853_HUMAN	zinc finger protein 853	8			G -> R (in dbSNP:rs2243563).				metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|kidney(1)	2						GCCGACTCCCGGGAATCGGGG	0.637													G|||	3712	0.741214	0.823	0.683	5008	,	,		18907	0.753		0.5427	False		,,,				2504	0.864																0			7						G	ARG/GLY	1085,299		429,227,36	24.0	31.0	29.0		22	-7.7	0.0	7	dbSNP_100	29	1749,1433		478,793,320	yes	missense	ZNF853	NM_017560.1	125	907,1020,356	AA,AG,GG		45.0346,21.604,37.9325	benign	8/660	6656830	2834,1732	692	1591	2283	6623355	SO:0001583	missense	54753			AL133055	CCDS59048.1	7p22.1	2013-01-08				ENSG00000236609		"""Zinc fingers, C2H2-type"""	21767	protein-coding gene	gene with protein product							Standard	NM_017560		Approved	DKFZp434J1015	uc011jwz.2	P0CG23		ENST00000457543.3:c.22G>A	7.37:g.6656830G>A	ENSP00000455585:p.Gly8Arg	Somatic		Capture	Illumina HiSeq	Phase_I	6623355		Missense_Mutation	SNP	ENST00000457543.3	37	CCDS59048.1																																																																																				ZNF853-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324169.2	NM_017560	
MEOX2	4223	hgsc.bcm.edu	37	7	15725797	15725797	+	Silent	SNP	A	A	G	rs113582077	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:15725797A>G	ENST00000262041.5	-	1	640	c.231T>C	c.(229-231)caT>caC	p.H77H	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	77	Poly-His.				angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		gatggtggtgatggtggtggt	0.617																																					Esophageal Squamous(140;197 1769 16409 18257 29929)												0			7											21.0	22.0	22.0					7																	15725797		2203	4300	6503	15692322	SO:0001819	synonymous_variant	4223				CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"""Homeoboxes / ANTP class : HOXL subclass"""	7014	protein-coding gene	gene with protein product	"""growth arrest-specific homeobox"""	600535	"""mesenchyme homeo box 2 (growth arrest-specific homeo box)"", ""mesenchyme homeobox 2 (growth arrest-specific homeo box)"""	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.231T>C	7.37:g.15725797A>G		Somatic		Capture	Illumina HiSeq	Phase_I	15692322	B2R8I7|O75263|Q9UPL6	Silent	SNP	ENST00000262041.5	37	CCDS34605.1																																																																																				MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924	
SNX13	23161	hgsc.bcm.edu	37	7	17854565	17854565	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:17854565T>A	ENST00000409389.1	-	20	2161	c.1989A>T	c.(1987-1989)ttA>ttT	p.L663F	SNX13_ENST00000496855.1_5'UTR|SNX13_ENST00000428135.3_Missense_Mutation_p.L652F			Q9Y5W8	SNX13_HUMAN	sorting nexin 13	663	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					GAGCTAACAGTAACTAACAAG	0.323																																																	0			7											51.0	45.0	47.0					7																	17854565		1824	4065	5889	17821090	SO:0001583	missense	23161			AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1989A>T	7.37:g.17854565T>A	ENSP00000386705:p.Leu663Phe	Somatic		Capture	Illumina HiSeq	Phase_I	17821090	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Missense_Mutation	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	T	14.98	2.698102	0.48307	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	T;T	0.53206	0.63;0.63	5.8	3.34	0.38264	.	0.000000	0.64402	D	0.000001	T	0.45935	0.1367	L	0.37507	1.11	0.80722	D	1	D;B;D	0.60575	0.983;0.034;0.988	P;B;P	0.59115	0.852;0.18;0.769	T	0.48614	-0.9020	10	0.59425	D	0.04	-11.5493	1.9056	0.03276	0.116:0.145:0.251:0.4879	.	449;663;652	B3KN60;B8ZZT9;Q9Y5W8-2	.;.;.	F	663;652;700	ENSP00000386705:L663F;ENSP00000398789:L652F	ENSP00000242044:L700F	L	-	3	2	SNX13	17821090	1.000000	0.71417	0.831000	0.32960	0.261000	0.26267	1.455000	0.35190	1.025000	0.39708	0.460000	0.39030	TTA		SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	
SP4	6671	hgsc.bcm.edu	37	7	21470070	21470070	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:21470070A>G	ENST00000222584.3	+	3	1505	c.1287A>G	c.(1285-1287)tcA>tcG	p.S429S		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	429					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						AACTCCAGTCAGGGCAGACGA	0.473																																																	0			7											118.0	118.0	118.0					7																	21470070		2203	4300	6503	21436595	SO:0001819	synonymous_variant	6671				CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.1287A>G	7.37:g.21470070A>G		Somatic		Capture	Illumina HiSeq	Phase_I	21436595	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																				SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112	
DNAH11	8701	hgsc.bcm.edu	37	7	21737770	21737770	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:21737770G>A	ENST00000409508.3	+	36	6150	c.6119G>A	c.(6118-6120)cGt>cAt	p.R2040H	DNAH11_ENST00000328843.6_Missense_Mutation_p.R2047H	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	2047	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GTGGATGCGCGTGCATTAGCC	0.418									Kartagener syndrome																																								0			7																																								21704295	SO:0001583	missense	8701	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.6119G>A	7.37:g.21737770G>A	ENSP00000475939:p.Arg2040His	Somatic		Capture	Illumina HiSeq	Phase_I	21704295	Q9UJ82	Silent	SNP	ENST00000409508.3	37		.	.	.	.	.	.	.	.	.	.	G	15.56	2.869856	0.51588	.	.	ENSG00000105877	ENST00000328843	T	0.11821	2.74	5.33	5.33	0.75918	.	0.072264	0.51477	D	0.000095	T	0.40694	0.1127	.	.	.	0.53005	D	0.999962	D	0.76494	0.999	D	0.68943	0.961	T	0.32025	-0.9922	9	0.72032	D	0.01	.	19.0193	0.92906	0.0:0.0:1.0:0.0	.	2047	Q96DT5	DYH11_HUMAN	H	2047	ENSP00000330671:R2047H	ENSP00000330671:R2047H	R	+	2	0	DNAH11	21704295	0.688000	0.27680	0.105000	0.21289	0.028000	0.11728	3.849000	0.55910	2.493000	0.84123	0.655000	0.94253	CGT		DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
DDC	1644	hgsc.bcm.edu	37	7	50605570	50605570	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:50605570T>C	ENST00000444124.2	-	4	623	c.423A>G	c.(421-423)ggA>ggG	p.G141G	DDC_ENST00000431062.1_Silent_p.G141G|DDC_ENST00000426377.1_Intron|DDC_ENST00000380984.4_Silent_p.G141G|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000357936.5_Silent_p.G141G|DDC_ENST00000489162.1_5'UTR	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	141	2 X approximate tandem repeats.				catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	GGATCACTCCTCCCCCTTCTC	0.557																																																	0			7											118.0	109.0	112.0					7																	50605570		2203	4300	6503	50573064	SO:0001819	synonymous_variant	1644				CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.423A>G	7.37:g.50605570T>C		Somatic		Capture	Illumina HiSeq	Phase_I	50573064	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1																																																																																				DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
POM121	9883	hgsc.bcm.edu	37	7	72413443	72413443	+	Missense_Mutation	SNP	G	G	A	rs62463429	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:72413443G>A	ENST00000434423.2	+	11	2911	c.2911G>A	c.(2911-2913)Gca>Aca	p.A971T	POM121_ENST00000395270.1_Missense_Mutation_p.A706T|POM121_ENST00000446813.1_Missense_Mutation_p.A706T|POM121_ENST00000358357.3_Missense_Mutation_p.A706T|POM121_ENST00000257622.4_Missense_Mutation_p.A706T			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	971	Pore side. {ECO:0000255}.			A -> T (in Ref. 3; BAB14097). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CCCCCAGCCCGCATTTGGGGC	0.642																																																	0			7											13.0	19.0	17.0					7																	72413443		2073	4153	6226	72051379	SO:0001583	missense	22932			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.2911G>A	7.37:g.72413443G>A	ENSP00000405562:p.Ala971Thr	Somatic		Capture	Illumina HiSeq	Phase_I	72051379	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	37		806	0.36904761904761907	111	0.22560975609756098	135	0.3729281767955801	269	0.47027972027972026	291	0.3839050131926121	G	0.019	-1.453214	0.01071	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.06849	3.25;3.27;3.25;3.27;3.54	2.33	-4.66	0.03329	.	1.040150	0.07705	N	0.941009	T	0.00012	0.0000	N	0.17838	0.53	0.80722	P	0.0	B;B	0.23650	0.089;0.008	B;B	0.16722	0.016;0.004	T	0.45396	-0.9264	9	0.25106	T	0.35	.	10.3771	0.44088	0.524:0.0:0.476:0.0	rs62463429	706;971	A8MXF9;Q96HA1	.;P121A_HUMAN	T	706;706;706;706;971	ENSP00000393020:A706T;ENSP00000257622:A706T;ENSP00000378687:A706T;ENSP00000351124:A706T;ENSP00000405562:A971T	ENSP00000257622:A706T	A	+	1	0	POM121	72051379	0.000000	0.05858	0.055000	0.19348	0.038000	0.13279	-1.922000	0.01568	-1.455000	0.01923	-1.195000	0.01675	GCA		POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
TMEM130	222865	hgsc.bcm.edu	37	7	98460916	98460916	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:98460916C>T	ENST00000416379.2	-	2	197	c.193G>A	c.(193-195)Gct>Act	p.A65T	TMEM130_ENST00000450876.1_5'UTR|TMEM130_ENST00000546258.1_Missense_Mutation_p.A46T|TMEM130_ENST00000345589.4_Intron|TMEM130_ENST00000339375.4_Missense_Mutation_p.A65T			Q8N3G9	TM130_HUMAN	transmembrane protein 130	65						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.A65T(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	25	all_cancers(62;4.05e-09)|all_epithelial(64;2.62e-09)|Lung NSC(181;0.01)|all_lung(186;0.0115)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGGGCGTCAGCGGGCAGGGCC	0.642																																																	1	Substitution - Missense(1)	urinary_tract(1)	7											54.0	50.0	51.0					7																	98460916		2203	4300	6503	98298852	SO:0001583	missense	222865				CCDS5658.1, CCDS47649.1, CCDS47650.1	7q22.1	2006-03-09			ENSG00000166448	ENSG00000166448			25429	protein-coding gene	gene with protein product						12975309	Standard	NM_152913		Approved	DKFZp761L1417, FLJ42643	uc003upo.3	Q8N3G9	OTTHUMG00000154419	ENST00000416379.2:c.193G>A	7.37:g.98460916C>T	ENSP00000413163:p.Ala65Thr	Somatic		Capture	Illumina HiSeq	Phase_I	98298852	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Missense_Mutation	SNP	ENST00000416379.2	37	CCDS47650.1	.	.	.	.	.	.	.	.	.	.	C	0.009	-1.799256	0.00617	.	.	ENSG00000166448	ENST00000416379;ENST00000339375;ENST00000546258	T;T;T	0.12569	2.67;2.67;2.67	4.28	-3.09	0.05331	.	0.877727	0.09755	N	0.760081	T	0.03520	0.0101	N	0.01576	-0.805	0.09310	N	1	B;B;B	0.10296	0.001;0.001;0.003	B;B;B	0.04013	0.001;0.001;0.001	T	0.44847	-0.9301	10	0.12766	T	0.61	-6.2021	5.9152	0.19052	0.0:0.4178:0.1431:0.4391	.	65;46;65	Q8N3G9-2;B7Z2F1;Q8N3G9	.;.;TM130_HUMAN	T	65;65;46	ENSP00000413163:A65T;ENSP00000341256:A65T;ENSP00000445869:A46T	ENSP00000341256:A65T	A	-	1	0	TMEM130	98298852	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-3.422000	0.00476	-0.814000	0.04352	0.505000	0.49811	GCT		TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913	
KPNA7	402569	hgsc.bcm.edu	37	7	98775543	98775543	+	Splice_Site	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:98775543C>T	ENST00000327442.6	-	9	1503	c.1464G>A	c.(1462-1464)gaG>gaA	p.E488E		NM_001145715.1	NP_001139187.1	A9QM74	IMA8_HUMAN	karyopherin alpha 7 (importin alpha 8)	488					cytokine-mediated signaling pathway (GO:0019221)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	protein transporter activity (GO:0008565)			breast(3)|endometrium(2)|kidney(1)|prostate(1)|skin(1)	8						AGTCACTTACCTCACCAAAGT	0.552																																																	0			7											175.0	143.0	153.0					7																	98775543		692	1591	2283	98613479	SO:0001630	splice_region_variant	402569				CCDS47651.1	7q22.1	2013-02-14			ENSG00000185467	ENSG00000185467		"""Importins"", ""Armadillo repeat containing"""	21839	protein-coding gene	gene with protein product		614107					Standard	NM_001145715		Approved		uc010lft.2	A9QM74	OTTHUMG00000154412	ENST00000327442.6:c.1464+1G>A	7.37:g.98775543C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98613479	A4D277	Silent	SNP	ENST00000327442.6	37	CCDS47651.1																																																																																				KPNA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335118.1	NM_001145715	Silent
GIMAP5	55340	hgsc.bcm.edu	37	7	150439391	150439391	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr7:150439391C>G	ENST00000358647.3	+	3	531	c.164C>G	c.(163-165)tCc>tGc	p.S55C	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	55	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)	p.S55Y(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTGTTTGAGTCCAAGCTGAGG	0.562																																																	1	Substitution - Missense(1)	central_nervous_system(1)	7											90.0	76.0	80.0					7																	150439391		2203	4300	6503	150070324	SO:0001583	missense	0			AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.164C>G	7.37:g.150439391C>G	ENSP00000351473:p.Ser55Cys	Somatic		Capture	Illumina HiSeq	Phase_I	150070324	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Missense_Mutation	SNP	ENST00000358647.3	37	CCDS5907.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111174	0.37242	.	.	ENSG00000196329	ENST00000358647;ENST00000447239	T	0.11712	2.75	4.35	4.35	0.52113	AIG1 (1);	0.063252	0.64402	D	0.000003	T	0.34135	0.0887	M	0.84326	2.69	0.09310	N	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.09530	-1.0670	10	0.66056	D	0.02	.	12.225	0.54455	0.0:1.0:0.0:0.0	.	55	Q96F15	GIMA5_HUMAN	C	55;91	ENSP00000351473:S55C	ENSP00000351473:S55C	S	+	2	0	GIMAP5	150070324	0.000000	0.05858	0.982000	0.44146	0.285000	0.27093	0.614000	0.24314	2.251000	0.74343	0.655000	0.94253	TCC		GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
DLC1	10395	hgsc.bcm.edu	37	8	13356870	13356870	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:13356870T>C	ENST00000276297.4	-	2	1120	c.711A>G	c.(709-711)aaA>aaG	p.K237K	DLC1_ENST00000511869.1_Silent_p.K237K|DLC1_ENST00000316609.5_Silent_p.K237K	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	237					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.K237N(1)		NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						GGGGGTCAGGTTTCCTTCGTT	0.403																																																	1	Substitution - Missense(1)	lung(1)	8											155.0	156.0	155.0					8																	13356870		2203	4300	6503	13401241	SO:0001819	synonymous_variant	10395			AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.711A>G	8.37:g.13356870T>C		Somatic		Capture	Illumina HiSeq	Phase_I	13401241	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																				DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
CLVS1	157807	hgsc.bcm.edu	37	8	62212613	62212613	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:62212613T>C	ENST00000519846.1	+	3	699	c.227T>C	c.(226-228)aTc>aCc	p.I76T	CLVS1_ENST00000518592.1_Intron|CLVS1_ENST00000325897.4_Missense_Mutation_p.I76T|RP11-787D18.1_ENST00000518064.1_RNA|RP11-787D18.1_ENST00000521801.1_RNA			Q8IUQ0	CLVS1_HUMAN	clavesin 1	76					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						GATGCCTTCATCCTGAGATTT	0.458																																																	0			8											113.0	96.0	102.0					8																	62212613		2203	4300	6503	62375167	SO:0001583	missense	0			AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.227T>C	8.37:g.62212613T>C	ENSP00000428402:p.Ile76Thr	Somatic		Capture	Illumina HiSeq	Phase_I	62375167	B2R7M5|C8UZT3|Q8NB32	Missense_Mutation	SNP	ENST00000519846.1	37	CCDS6176.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384999	0.82792	.	.	ENSG00000177182	ENST00000522621;ENST00000519846;ENST00000325897	D;D	0.85702	-2.02;-2.02	5.79	5.79	0.91817	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.048550	0.85682	N	0.000000	D	0.89760	0.6808	L	0.48642	1.525	0.80722	D	1	D;D;D	0.71674	0.998;0.971;0.998	D;P;D	0.71184	0.94;0.901;0.972	D	0.90766	0.4668	10	0.87932	D	0	0.203	16.1303	0.81428	0.0:0.0:0.0:1.0	.	76;76;76	E5RK22;Q8IUQ0;Q8IUQ0-2	.;CLVS1_HUMAN;.	T	76	ENSP00000428402:I76T;ENSP00000325506:I76T	ENSP00000325506:I76T	I	+	2	0	CLVS1	62375167	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	2.218000	0.71995	0.533000	0.62120	ATC		CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
TRPA1	8989	hgsc.bcm.edu	37	8	72935336	72935336	+	Silent	SNP	A	A	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:72935336A>G	ENST00000262209.4	-	27	3372	c.3165T>C	c.(3163-3165)acT>acC	p.T1055T	RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron|RP11-383H13.1_ENST00000524152.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	1055					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	CCAGGAGAAAAGTAAGATCCT	0.373																																																	0			8											88.0	79.0	82.0					8																	72935336		2203	4300	6503	73097890	SO:0001819	synonymous_variant	8989			Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.3165T>C	8.37:g.72935336A>G		Somatic		Capture	Illumina HiSeq	Phase_I	73097890	A6NIN6	Silent	SNP	ENST00000262209.4	37	CCDS34908.1																																																																																				TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
MPDZ	8777	hgsc.bcm.edu	37	9	13192158	13192158	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:13192158T>C	ENST00000319217.7	-	15	2187	c.1940A>G	c.(1939-1941)gAc>gGc	p.D647G	MPDZ_ENST00000541718.1_Missense_Mutation_p.D647G|MPDZ_ENST00000381015.4_Missense_Mutation_p.D647G|MPDZ_ENST00000536827.1_Missense_Mutation_p.D647G|MPDZ_ENST00000447879.1_Missense_Mutation_p.D647G|MPDZ_ENST00000546205.1_Missense_Mutation_p.D647G|MPDZ_ENST00000381022.2_Missense_Mutation_p.D647G	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	647					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		ATCACATAAGTCCAGGCTATC	0.388																																																	0			9											120.0	113.0	116.0					9																	13192158		1919	4132	6051	13182158	SO:0001583	missense	84708			AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.1940A>G	9.37:g.13192158T>C	ENSP00000320006:p.Asp647Gly	Somatic		Capture	Illumina HiSeq	Phase_I	13182158	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.00|14.00	2.406213|2.406213	0.42715|0.42715	.|.	.|.	ENSG00000107186|ENSG00000107186	ENST00000399902|ENST00000319217;ENST00000541718;ENST00000381022;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000546205	.|T;T;T;T;T;T;T	.|0.10960	.|2.87;2.82;2.82;2.82;2.86;2.87;2.87	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.139921	.|0.32416	.|N	.|0.006125	.|T	.|0.06005	.|0.0156	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.34615	.|0.179;0.459;0.459	.|B;B;B	.|0.33960	.|0.084;0.115;0.173	.|T	.|0.47959	.|-0.9076	.|10	.|0.18276	.|T	.|0.48	.|.	8.0925|8.0925	0.30809|0.30809	0.0:0.093:0.0:0.907|0.0:0.093:0.0:0.907	.|.	.|647;647;647	.|B7ZMI4;O75970-3;O75970-2	.|.;.;.	.|G	-1|647	.|ENSP00000320006:D647G;ENSP00000439807:D647G;ENSP00000370410:D647G;ENSP00000444151:D647G;ENSP00000415208:D647G;ENSP00000370403:D647G;ENSP00000446358:D647G	.|ENSP00000320006:D647G	.|D	-|-	.|2	.|0	MPDZ|MPDZ	13182158|13182158	0.999000|0.999000	0.42202|0.42202	0.999000|0.999000	0.59377|0.59377	0.983000|0.983000	0.72400|0.72400	1.278000|1.278000	0.33179|0.33179	2.199000|2.199000	0.70637|0.70637	0.533000|0.533000	0.62120|0.62120	.|GAC		MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
CYLC2	1539	hgsc.bcm.edu	37	9	105767414	105767414	+	Silent	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:105767414T>C	ENST00000374798.3	+	5	571	c.501T>C	c.(499-501)gaT>gaC	p.D167D	CYLC2_ENST00000487798.1_Silent_p.D167D	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	167	3 X approximate tandem repeats.|31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				gtaaaaaggatgcagagaagg	0.333																																																	0			9											71.0	68.0	69.0					9																	105767414		2203	4300	6503	104807235	SO:0001819	synonymous_variant	1539			Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.501T>C	9.37:g.105767414T>C		Somatic		Capture	Illumina HiSeq	Phase_I	104807235	B2R8F4|Q5VVJ9	Silent	SNP	ENST00000374798.3	37	CCDS35085.1																																																																																				CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340	
SNAPC3	6619	hgsc.bcm.edu	37	9	15422893	15422893	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:15422893C>T	ENST00000380821.3	+	1	192	c.16C>T	c.(16-18)Cga>Tga	p.R6*		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	6					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		TGAAGGAAGCCGAGGTGGCCC	0.612																																																	0			9											27.0	24.0	25.0					9																	15422893		2109	4170	6279	15412893	SO:0001587	stop_gained	6619			U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.16C>T	9.37:g.15422893C>T	ENSP00000370200:p.Arg6*	Somatic		Capture	Illumina HiSeq	Phase_I	15412893	D3DRI8|Q2VPI6|Q5T285	Nonsense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.809522	0.90707	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	.	.	.	4.86	-3.17	0.05202	.	2.010380	0.02238	N	0.065449	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.9315	0.4719	0.00533	0.2577:0.2913:0.1262:0.3248	.	.	.	.	X	6	.	ENSP00000370185:R6X	R	+	1	2	SNAPC3	15412893	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.646000	0.05403	-0.536000	0.06298	-0.379000	0.06801	CGA		SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
CCDC171	203238	hgsc.bcm.edu	37	9	15848930	15848930	+	Missense_Mutation	SNP	A	A	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:15848930A>C	ENST00000380701.3	+	23	3781	c.3453A>C	c.(3451-3453)gaA>gaC	p.E1151D	CCDC171_ENST00000297641.3_Missense_Mutation_p.E1151D	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1151																	GAGCAGTAGAAAATACGCTTC	0.299																																																	0			9											79.0	87.0	85.0					9																	15848930		2201	4294	6495	15838930	SO:0001583	missense	203238			AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3453A>C	9.37:g.15848930A>C	ENSP00000370077:p.Glu1151Asp	Somatic		Capture	Illumina HiSeq	Phase_I	15838930	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.14|19.14	3.769386|3.769386	0.69992|0.69992	.|.	.|.	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701;ENST00000359391|ENST00000449575;ENST00000432954	T;T|.	0.69561|.	-0.41;-0.41|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.050681|.	0.85682|.	D|.	0.000000|.	T|T	0.55097|0.55097	0.1899|0.1899	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	D;P;D|.	0.55385|.	0.971;0.952;0.971|.	P;P;P|.	0.50934|.	0.654;0.452;0.654|.	T|T	0.51834|0.51834	-0.8655|-0.8655	10|5	0.62326|.	D|.	0.03|.	-18.9668|-18.9668	14.6699|14.6699	0.68937|0.68937	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1159;418;1151|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	D|T	1151;418;1151;5|391;205	ENSP00000297641:E1151D;ENSP00000370077:E1151D|.	ENSP00000297641:E1151D|.	E|K	+|+	3|2	2|0	C9orf93|C9orf93	15838930|15838930	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.628000|0.628000	0.37860|0.37860	2.614000|2.614000	0.46359|0.46359	2.274000|2.274000	0.75844|0.75844	0.477000|0.477000	0.44152|0.44152	GAA|AAA		CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
CDKN2A	1029	hgsc.bcm.edu	37	9	21974593	21974593	+	Intron	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:21974593G>A	ENST00000304494.5	-	1	421				CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000446177.1_Intron|CDKN2A_ENST00000498124.1_Intron|CDKN2A_ENST00000530628.2_Intron|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000579122.1_Intron	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A						cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(10)|p.0(1)|p.V28_V51del(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GAATCGAAGCGCTACCTGATT	0.607		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																																							1327	Whole gene deletion(1316)|Unknown(10)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(277)|skin(167)|central_nervous_system(162)|lung(143)|urinary_tract(90)|bone(73)|soft_tissue(57)|pleura(51)|oesophagus(48)|upper_aerodigestive_tract(47)|ovary(34)|kidney(30)|breast(30)|pancreas(29)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(7)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	9											162.0	186.0	178.0					9																	21974593		2203	4300	6503	21964593	SO:0001627	intron_variant	1029			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.150+83C>T	9.37:g.21974593G>A		Somatic		Capture	Illumina HiSeq	Phase_I	21964593	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Silent	SNP	ENST00000304494.5	37	CCDS6510.1																																																																																				CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
HSD17B3	3293	hgsc.bcm.edu	37	9	99064377	99064377	+	Missense_Mutation	SNP	C	C	T	rs377018679		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:99064377C>T	ENST00000375263.3	-	1	57	c.10G>A	c.(10-12)Gtc>Atc	p.V4I	HSD17B3_ENST00000375262.2_Missense_Mutation_p.V4I	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	4					androgen biosynthetic process (GO:0006702)|male genitalia development (GO:0030539)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			breast(1)|endometrium(3)|large_intestine(2)|lung(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13		Acute lymphoblastic leukemia(62;0.0171)|all_hematologic(171;0.214)				TGTTCCAGGACGTCCCCCATG	0.567																																																	0			9						C	ILE/VAL	0,4406		0,0,2203	85.0	74.0	78.0		10	-2.2	0.0	9		78	3,8597	3.0+/-9.4	0,3,4297	no	missense	HSD17B3	NM_000197.1	29	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	4/311	99064377	3,13003	2203	4300	6503	98104198	SO:0001583	missense	3293				CCDS6716.1	9q22	2011-09-20			ENSG00000130948	ENSG00000130948	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5212	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 12C, member 2"""	605573				8075637, 19027726	Standard	NM_000197		Approved	SDR12C2	uc004awa.1	P37058	OTTHUMG00000020292	ENST00000375263.3:c.10G>A	9.37:g.99064377C>T	ENSP00000364412:p.Val4Ile	Somatic		Capture	Illumina HiSeq	Phase_I	98104198	Q5U0Q6	Missense_Mutation	SNP	ENST00000375263.3	37	CCDS6716.1	.	.	.	.	.	.	.	.	.	.	C	2.860	-0.236340	0.05944	0.0	3.49E-4	ENSG00000130948	ENST00000375263;ENST00000375262	D;D	0.84800	-1.9;-1.9	4.55	-2.25	0.06888	.	0.928961	0.09089	N	0.850088	T	0.61726	0.2370	N	0.12182	0.205	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.52193	-0.8608	10	0.05959	T	0.93	-11.1653	1.3859	0.02240	0.2015:0.3857:0.2466:0.1662	.	4;4	Q5U0Q6;P37058	.;DHB3_HUMAN	I	4	ENSP00000364412:V4I;ENSP00000364411:V4I	ENSP00000364411:V4I	V	-	1	0	HSD17B3	98104198	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.660000	0.05317	-0.242000	0.09667	-0.794000	0.03295	GTC		HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197	
SURF6	6838	hgsc.bcm.edu	37	9	136199466	136199466	+	Missense_Mutation	SNP	G	G	A	rs886089	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr9:136199466G>A	ENST00000372022.4	-	4	789	c.524C>T	c.(523-525)aCg>aTg	p.T175M	SURF6_ENST00000468290.1_5'UTR	NM_006753.4	NP_006744.2	O75683	SURF6_HUMAN	surfeit 6	175			T -> M (in dbSNP:rs886089).		ribosome biogenesis (GO:0042254)	granular component (GO:0001652)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	12				OV - Ovarian serous cystadenocarcinoma(145;1.16e-06)|Epithelial(140;8.34e-06)|all cancers(34;7.08e-05)		CTGGGCCTCCGTGGCCTCCTC	0.657													G|||	1407	0.28095	0.0386	0.3501	5008	,	,		15252	0.2986		0.3569	False		,,,				2504	0.4632																0			9						G	MET/THR	372,4034	184.0+/-211.4	20,332,1851	88.0	92.0	90.0		524	-8.3	0.0	9	dbSNP_86	90	3017,5583	460.5+/-365.2	543,1931,1826	yes	missense	SURF6	NM_006753.4	81	563,2263,3677	AA,AG,GG		35.0814,8.443,26.0572	possibly-damaging	175/362	136199466	3389,9617	2203	4300	6503	135189287	SO:0001583	missense	6838			AF186772	CCDS6962.1	9q33-q34	2010-07-06			ENSG00000148296	ENSG00000148296			11478	protein-coding gene	gene with protein product	"""surfeit locus protein 6"""	185642				9740673, 15629442	Standard	NM_006753		Approved	FLJ30322, RRP14	uc004cdb.4	O75683	OTTHUMG00000020871	ENST00000372022.4:c.524C>T	9.37:g.136199466G>A	ENSP00000361092:p.Thr175Met	Somatic		Capture	Illumina HiSeq	Phase_I	135189287	Q5T8U1|Q9BRK9|Q9BTZ5|Q9UK24	Missense_Mutation	SNP	ENST00000372022.4	37	CCDS6962.1	584	0.2673992673992674	31	0.06300813008130081	122	0.3370165745856354	154	0.2692307692307692	277	0.3654353562005277	G	8.549	0.875047	0.17395	0.08443	0.350814	ENSG00000148296	ENST00000372022	T	0.14516	2.5	4.14	-8.28	0.01013	.	1.762280	0.02976	N	0.145022	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.36010	0.532	B	0.31191	0.125	T	0.25847	-1.0120	9	0.48119	T	0.1	.	1.6707	0.02811	0.2994:0.1487:0.0953:0.4565	rs886089;rs886089	175	O75683	SURF6_HUMAN	M	175	ENSP00000361092:T175M	ENSP00000361092:T175M	T	-	2	0	SURF6	135189287	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.892000	0.01610	-3.813000	0.00104	-1.250000	0.01514	ACG		SURF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054905.1	NM_006753	
AMELX	265	hgsc.bcm.edu	37	X	11316978	11316978	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:11316978T>C	ENST00000380714.3	+	5	523	c.455T>C	c.(454-456)cTg>cCg	p.L152P	AMELX_ENST00000348912.4_Missense_Mutation_p.L136P|ARHGAP6_ENST00000380732.3_Intron|ARHGAP6_ENST00000380736.1_Intron|ARHGAP6_ENST00000380718.1_Intron|ARHGAP6_ENST00000337414.4_Intron|ARHGAP6_ENST00000413512.3_Intron|AMELX_ENST00000380712.3_Missense_Mutation_p.L166P	NM_001142.2	NP_001133.1	Q99217	AMELX_HUMAN	amelogenin, X-linked	152					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|enamel mineralization (GO:0070166)|epithelial to mesenchymal transition (GO:0001837)|ion homeostasis (GO:0050801)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of tooth mineralization (GO:0070172)|signal transduction (GO:0007165)|tooth mineralization (GO:0034505)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|hydroxyapatite binding (GO:0046848)|identical protein binding (GO:0042802)|structural constituent of tooth enamel (GO:0030345)			endometrium(3)|kidney(2)|large_intestine(1)|lung(9)	15						ATGCAGCCCCTGCCGCCACAG	0.662																																																	0			X											47.0	41.0	43.0					X																	11316978		2203	4300	6503	11226899	SO:0001583	missense	265				CCDS14144.1, CCDS14145.1, CCDS14146.1	Xp22.31-p22.1	2010-04-20	2010-04-20		ENSG00000125363	ENSG00000125363			461	protein-coding gene	gene with protein product	"""amelogenesis imperfecta 1"""	300391	"""amelogenin (X chromosome, amelogenesis imperfecta 1)"""	AMG, AIH1		1734713	Standard	NM_182680		Approved		uc004cus.3	Q99217	OTTHUMG00000021130	ENST00000380714.3:c.455T>C	X.37:g.11316978T>C	ENSP00000370090:p.Leu152Pro	Somatic		Capture	Illumina HiSeq	Phase_I	11226899	Q96NW6|Q9UCA7	Missense_Mutation	SNP	ENST00000380714.3	37	CCDS14144.1	.	.	.	.	.	.	.	.	.	.	T	10.46	1.357285	0.24598	.	.	ENSG00000125363	ENST00000380714;ENST00000380712;ENST00000348912	D;D;D	0.89123	-2.47;-2.47;-2.47	4.79	3.62	0.41486	.	0.616605	0.14622	N	0.308371	D	0.85396	0.5687	M	0.68952	2.095	0.34886	D	0.745065	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.10450	0.003;0.005;0.003	D	0.84731	0.0745	10	0.51188	T	0.08	-2.7216	5.0054	0.14286	0.0:0.1001:0.1851:0.7148	.	136;152;166	Q99217-2;Q99217;Q99217-3	.;AMELX_HUMAN;.	P	152;166;136	ENSP00000370090:L152P;ENSP00000370088:L166P;ENSP00000335312:L136P	ENSP00000335312:L136P	L	+	2	0	AMELX	11226899	0.973000	0.33851	0.993000	0.49108	0.968000	0.65278	0.883000	0.28200	1.712000	0.51347	0.339000	0.21740	CTG		AMELX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055746.1	NM_001142	
ALG13	79868	hgsc.bcm.edu	37	X	110987999	110987999	+	Silent	SNP	T	T	A	rs56717389|rs13440710		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:110987999T>A	ENST00000394780.3	+	24	2811	c.2799T>A	c.(2797-2799)ccT>ccA	p.P933P	ALG13_ENST00000251943.4_Intron|ALG13_ENST00000470971.1_3'UTR	NM_001099922.2|NM_001257231.1	NP_001093392.1|NP_001244160.1	Q9NP73	ALG13_HUMAN	ALG13, UDP-N-acetylglucosaminyltransferase subunit	933	Pro-rich.				cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipid glycosylation (GO:0030259)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)	carbohydrate binding (GO:0030246)|cysteine-type peptidase activity (GO:0008234)|N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase activity (GO:0004577)|poly(A) RNA binding (GO:0044822)	p.P933P(9)		endometrium(2)|lung(10)|skin(1)	13						caccaccacctcctcctcctc	0.562																																																	9	Substitution - coding silent(9)	endometrium(9)	X											10.0	8.0	9.0					X																	110987999		1498	3409	4907	110874655	SO:0001819	synonymous_variant	79868			AF220051	CCDS14559.1, CCDS55477.1, CCDS59173.1, CCDS76011.1, CCDS76012.1, CCDS76013.1	Xq23	2014-02-24	2013-02-21	2006-11-07	ENSG00000101901	ENSG00000101901	2.4.1.141	"""Tudor domain containing"", ""OTU domain containing"""	30881	protein-coding gene	gene with protein product	"""tudor domain containing 13"", ""N-acetylglucosaminyldiphosphodolichol N-acetylglucosaminyltransferase"""	300776	"""glycosyltransferase 28 domain containing 1"", ""chromosome X open reading frame 45"", ""asparagine-linked glycosylation 13 homolog (S. cerevisiae)"""	GLT28D1, CXorf45		12477932	Standard	NM_018466		Approved	MDS031, YGL047W, FLJ23018, TDRD13	uc011msy.2	Q9NP73	OTTHUMG00000022209	ENST00000394780.3:c.2799T>A	X.37:g.110987999T>A		Somatic		Capture	Illumina HiSeq	Phase_I	110874655	B1AKD6|B1AKM1|B2R5L5|B7Z6J0|B7Z804|B7Z847|B7Z9A8|B7ZAJ1|B7ZB57|Q17RC3|Q5JXY9|Q9H5U8	Silent	SNP	ENST00000394780.3	37	CCDS55477.1																																																																																				ALG13-011	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272895.1	NM_018466	
NKRF	55922	hgsc.bcm.edu	37	X	118724855	118724855	+	Missense_Mutation	SNP	G	G	A	rs144370117		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:118724855G>A	ENST00000371527.1	-	2	1185	c.533C>T	c.(532-534)aCg>aTg	p.T178M	NKRF_ENST00000542113.1_Missense_Mutation_p.T193M|NKRF_ENST00000304449.5_Missense_Mutation_p.T178M|NKRF_ENST00000487600.1_Intron	NM_001173488.1	NP_001166959.1	O15226	NKRF_HUMAN	NFKB repressing factor	178	Active repression domain.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(9)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	30						GATTGTCGCCGTTAATTTTTC	0.398																																																	0			X						G	MET/THR,MET/THR,MET/THR	1,3834		0,1,1631,571	76.0	75.0	75.0		578,533,533	5.7	1.0	X	dbSNP_134	75	1,6727		0,1,2427,1872	yes	missense,missense,missense	NKRF	NM_001173487.1,NM_001173488.1,NM_017544.3	81,81,81	0,2,4058,2443	AA,AG,GG,G		0.0149,0.0261,0.0189	possibly-damaging,possibly-damaging,possibly-damaging	193/706,178/691,178/691	118724855	2,10561	2203	4300	6503	118608883	SO:0001583	missense	55922			AJ011812	CCDS35375.1, CCDS55486.1	Xq24	2013-01-28	2008-03-26		ENSG00000186416	ENSG00000186416		"""G patch domain containing"""	19374	protein-coding gene	gene with protein product		300440	"""NF-kappaB repressing factor"""			10562553	Standard	NM_017544		Approved	ITBA4, NRF	uc022cdk.1	O15226	OTTHUMG00000022277	ENST00000371527.1:c.533C>T	X.37:g.118724855G>A	ENSP00000360582:p.Thr178Met	Somatic		Capture	Illumina HiSeq	Phase_I	118608883	G3V1N1|Q4VC41|Q9UJ91	Missense_Mutation	SNP	ENST00000371527.1	37	CCDS35375.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303557	0.40795	2.61E-4	1.49E-4	ENSG00000186416	ENST00000371527;ENST00000304449;ENST00000542113	T;T;T	0.44482	0.92;0.92;0.92	5.7	5.7	0.88788	.	0.242716	0.42053	D	0.000776	T	0.23886	0.0578	N	0.08118	0	0.42964	D	0.994417	P	0.52170	0.951	B	0.35182	0.197	T	0.22521	-1.0214	10	0.66056	D	0.02	-12.8891	17.6846	0.88253	0.0:0.0:1.0:0.0	.	178	O15226	NKRF_HUMAN	M	178;178;193	ENSP00000360582:T178M;ENSP00000304803:T178M;ENSP00000442308:T193M	ENSP00000304803:T178M	T	-	2	0	NKRF	118608883	1.000000	0.71417	0.994000	0.49952	0.912000	0.54170	4.929000	0.63455	2.394000	0.81467	0.600000	0.82982	ACG		NKRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058044.1	NM_017544	
RS1	6247	hgsc.bcm.edu	37	X	18674815	18674815	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:18674815C>T	ENST00000379984.3	-	3	182	c.142G>A	c.(142-144)Gct>Act	p.A48T		NM_000330.3	NP_000321.1	O15537	XLRS1_HUMAN	retinoschisin 1	48					adaptation of rhodopsin mediated signaling (GO:0016062)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|retina layer formation (GO:0010842)|visual perception (GO:0007601)	extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(4)|large_intestine(5)|lung(2)|ovary(2)|skin(1)	15	Hepatocellular(33;0.183)					GACCACAGAGCATTGGGTCCT	0.552																																																	0			X											238.0	185.0	203.0					X																	18674815		2203	4300	6503	18584736	SO:0001583	missense	6248			AF014459	CCDS14187.1	Xp22.2-p22.1	2014-09-17	2008-07-29		ENSG00000102104	ENSG00000102104			10457	protein-coding gene	gene with protein product		300839	"""retinoschisis (X-linked, juvenile) 1"""	RS		9326935, 17804407	Standard	NM_000330		Approved	XLRS1	uc004cyo.3	O15537	OTTHUMG00000021216	ENST00000379984.3:c.142G>A	X.37:g.18674815C>T	ENSP00000369320:p.Ala48Thr	Somatic		Capture	Illumina HiSeq	Phase_I	18584736	Q0QD39	Missense_Mutation	SNP	ENST00000379984.3	37	CCDS14187.1	.	.	.	.	.	.	.	.	.	.	C	2.347	-0.349822	0.05173	.	.	ENSG00000102104	ENST00000379984	D	0.98221	-4.8	5.15	-5.06	0.02946	.	0.747484	0.13638	N	0.373159	D	0.91513	0.7320	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	D	0.85527	0.1207	10	0.10111	T	0.7	.	7.4925	0.27471	0.1835:0.2027:0.0:0.6138	.	48	O15537	XLRS1_HUMAN	T	48	ENSP00000369320:A48T	ENSP00000369320:A48T	A	-	1	0	RS1	18584736	0.070000	0.21116	0.000000	0.03702	0.004000	0.04260	-0.074000	0.11450	-1.038000	0.03279	-0.853000	0.03031	GCT		RS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055949.1		
EIF2S3	1968	hgsc.bcm.edu	37	X	24082408	24082408	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:24082408T>C	ENST00000253039.4	+	7	981	c.728T>C	c.(727-729)aTt>aCt	p.I243T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	243	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GTAAAGAAAATTCCAGTACCC	0.388																																																	0			X											111.0	116.0	114.0					X																	24082408		2203	4297	6500	23992329	SO:0001583	missense	1968			L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.728T>C	X.37:g.24082408T>C	ENSP00000253039:p.Ile243Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23992329	B5BTZ4	Missense_Mutation	SNP	ENST00000253039.4	37	CCDS14210.1	.	.	.	.	.	.	.	.	.	.	T	17.45	3.393795	0.62066	.	.	ENSG00000130741	ENST00000253039	T	0.72615	-0.67	5.11	5.11	0.69529	Protein synthesis factor, GTP-binding (1);	0.000000	0.85682	D	0.000000	D	0.82949	0.5148	H	0.96777	3.88	0.80722	D	1	B	0.24675	0.109	B	0.34418	0.182	D	0.84634	0.0691	10	0.87932	D	0	.	14.2471	0.65995	0.0:0.0:0.0:1.0	.	243	P41091	IF2G_HUMAN	T	243	ENSP00000253039:I243T	ENSP00000253039:I243T	I	+	2	0	EIF2S3	23992329	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.628000	0.83189	1.811000	0.52892	0.486000	0.48141	ATT		EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
FAM47B	170062	hgsc.bcm.edu	37	X	34961582	34961582	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:34961582C>T	ENST00000329357.5	+	1	670	c.634C>T	c.(634-636)Cgc>Tgc	p.R212C		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	212	Pro-rich.									breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						GTCCAGTCGCCGCCCAGAGCC	0.652																																																	0			X											35.0	39.0	37.0					X																	34961582		2202	4297	6499	34871503	SO:0001583	missense	170062			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.634C>T	X.37:g.34961582C>T	ENSP00000328307:p.Arg212Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34871503	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	3.551	-0.091646	0.07053	.	.	ENSG00000189132	ENST00000329357	T	0.21543	2.0	0.217	0.217	0.15264	.	.	.	.	.	T	0.10680	0.0261	N	0.17278	0.47	0.22552	N	0.998993	B	0.15473	0.013	B	0.06405	0.002	T	0.28267	-1.0049	9	0.51188	T	0.08	.	3.053	0.06175	0.4809:0.5188:2.0E-4:1.0E-4	.	212	Q8NA70	FA47B_HUMAN	C	212	ENSP00000328307:R212C	ENSP00000328307:R212C	R	+	1	0	FAM47B	34871503	0.075000	0.21258	0.002000	0.10522	0.002000	0.02628	-0.209000	0.09358	0.273000	0.22049	0.277000	0.19347	CGC		FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
FAM47C	442444	hgsc.bcm.edu	37	X	37028775	37028775	+	Silent	SNP	G	G	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:37028775G>A	ENST00000358047.3	+	1	2344	c.2292G>A	c.(2290-2292)ccG>ccA	p.P764P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	764										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ATCTCCGCCCGGAGCCTCCTG	0.622																																																	0			X											42.0	42.0	42.0					X																	37028775		2202	4300	6502	36938696	SO:0001819	synonymous_variant	442444			AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2292G>A	X.37:g.37028775G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36938696	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																				FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
BGN	633	hgsc.bcm.edu	37	X	152771509	152771509	+	Silent	SNP	C	C	T	rs1126499	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrX:152771509C>T	ENST00000331595.4	+	4	726	c.540C>T	c.(538-540)agC>agT	p.S180S	BGN_ENST00000480756.1_3'UTR	NM_001711.4	NP_001702.1	P21810	PGS1_HUMAN	biglycan	180					blood vessel remodeling (GO:0001974)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|transport vesicle (GO:0030133)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|glycosaminoglycan binding (GO:0005539)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GAGTGTTCAGCGGGCTCCGGA	0.607													C|||	1266	0.335364	0.0726	0.2853	3775	,	,		11034	0.3016		0.3767	False		,,,				2504	0.2955																0			X						C		628,3207		40,453,95,1139,476	50.0	46.0	47.0		540	-9.4	0.5	X	dbSNP_86	47	3135,3593		508,1207,912,713,960	no	coding-synonymous	BGN	NM_001711.4		548,1660,1007,1852,1436	TT,TC,T,CC,C		46.5963,16.3755,35.6243		180/369	152771509	3763,6800	2203	4300	6503	152424703	SO:0001819	synonymous_variant	633			AK092954	CCDS14721.1	Xq28	2008-02-05			ENSG00000182492	ENSG00000182492		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1044	protein-coding gene	gene with protein product	"""biglycan proteoglycan"""	301870				1612609	Standard	NM_001711		Approved	DSPG1, SLRR1A	uc004fhr.2	P21810	OTTHUMG00000024205	ENST00000331595.4:c.540C>T	X.37:g.152771509C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152424703	D3DWU3|P13247	Silent	SNP	ENST00000331595.4	37	CCDS14721.1																																																																																				BGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060981.1	NM_001711	
ZNF669	79862	hgsc.bcm.edu	37	1	247264093	247264094	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr1:247264093_247264094delCC	ENST00000343381.6	-	4	1149_1150	c.977_978delGG	c.(976-978)aggfs	p.R326fs	ZNF669_ENST00000358785.4_3'UTR|ZNF669_ENST00000448299.2_Frame_Shift_Del_p.R240fs	NM_024804.2	NP_079080.2	Q96BR6	ZN669_HUMAN	zinc finger protein 669	326					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(4)|large_intestine(2)|lung(6)	17	all_cancers(71;4.09e-05)|all_epithelial(71;6.72e-06)|Breast(184;0.0226)|Ovarian(71;0.0283)|all_lung(81;0.0488)|Lung NSC(105;0.053)		OV - Ovarian serous cystadenocarcinoma(106;0.00427)			CAGTGTGAGTCCTTTCATGCGT	0.406																																																	0			1																																								245330717	SO:0001589	frameshift_variant	79862				CCDS31088.1, CCDS44345.1	1q44	2013-01-08			ENSG00000188295	ENSG00000188295		"""Zinc fingers, C2H2-type"", ""-"""	25736	protein-coding gene	gene with protein product						12477932	Standard	NM_024804		Approved	FLJ12606	uc001ice.2	Q96BR6	OTTHUMG00000040869	ENST00000343381.6:c.977_978delGG	1.37:g.247264093_247264094delCC	ENSP00000342818:p.Arg326fs	Somatic		Capture	Illumina HiSeq	Phase_I	245330716	B3KP94|Q5VT39|Q9H9Q6	Frame_Shift_Del	DEL	ENST00000343381.6	37	CCDS31088.1																																																																																				ZNF669-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000098394.4	NM_024804	
MGAT4A	11320	hgsc.bcm.edu	37	2	99342737	99342737	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:99342737delG	ENST00000264968.3	-	1	422	c.59delC	c.(58-60)actfs	p.T20fs	MGAT4A_ENST00000393487.1_Frame_Shift_Del_p.T20fs|MGAT4A_ENST00000409391.1_Frame_Shift_Del_p.T20fs|MGAT4A_ENST00000495056.2_Frame_Shift_Del_p.T20fs			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	20					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						CCAAGACAAAGTAAGGAAGGA	0.408																																																	0			2											124.0	111.0	115.0					2																	99342737		2203	4300	6503	98709169	SO:0001589	frameshift_variant	11320			AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.59delC	2.37:g.99342737delG	ENSP00000264968:p.Thr20fs	Somatic		Capture	Illumina HiSeq	Phase_I	98709169	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Frame_Shift_Del	DEL	ENST00000264968.3	37	CCDS2036.1																																																																																				MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
SPATA3	130560	hgsc.bcm.edu	37	2	231861033	231861059	+	In_Frame_Del	DEL	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA	-	rs13005918|rs72362780	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CAGCAGCCTAGCCCTGAATCCACACCA	CAGCAGCCTAGCCCTGAATCCACACCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr2:231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENST00000452881.1	+	1	193_219	c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	c.(85-111)cagcagcctagccctgaatccacaccadel	p.QQPSPESTP47del	SPATA3_ENST00000455816.1_In_Frame_Del_p.QQPSPESTP47del|SPATA3_ENST00000433428.2_In_Frame_Del_p.QQPSPESTP47del|AC105344.2_ENST00000414876.1_lincRNA|SPATA3_ENST00000424440.1_In_Frame_Del_p.QQPSPESTP47del			Q8NHX4	SPTA3_HUMAN	spermatogenesis associated 3	47			Missing.							endometrium(2)|lung(1)	3						TTCCACCTCTCAGCAGCCTAGCCCTGAATCCACACCACAGCAGCCTA	0.564																																																	0			2								924,1842		222,480,681						-8.0	0.0		dbSNP_130	187	2754,2350		871,1012,669	no	coding	SPATA3	NM_139073.3		1093,1492,1350	A1A1,A1R,RR		46.0423,33.4056,46.7344				3678,4192				231569303	SO:0001651	inframe_deletion	130560			AY032925	CCDS2481.1	2q37.1	2008-02-05			ENSG00000173699	ENSG00000173699			17884	protein-coding gene	gene with protein product							Standard	NM_139073		Approved	TSARG1	uc010zmd.2	Q8NHX4	OTTHUMG00000133221	ENST00000452881.1:c.85_111delCAGCAGCCTAGCCCTGAATCCACACCA	2.37:g.231861033_231861059delCAGCAGCCTAGCCCTGAATCCACACCA	ENSP00000388895:p.Gln47_Pro55del	Somatic		Capture	Illumina HiSeq	Phase_I	231569277	Q86WX5|Q8N9Y6	In_Frame_Del	DEL	ENST00000452881.1	37	CCDS2481.1																																																																																				SPATA3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256956.2	NM_139073	
APC	324	hgsc.bcm.edu	37	5	112174366	112174366	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112174366delA	ENST00000457016.1	+	16	3455	c.3075delA	c.(3073-3075)atafs	p.I1025fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.I1025fs|APC_ENST00000508376.2_Frame_Shift_Del_p.I1025fs			P25054	APC_HUMAN	adenomatous polyposis coli	1025	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		ATACACCAATAAATTATAGTC	0.373		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	1	Unknown(1)	skin(1)	5											71.0	76.0	74.0					5																	112174366		2202	4299	6501	112202265	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3075delA	5.37:g.112174366delA	ENSP00000413133:p.Ile1025fs	Somatic		Capture	Illumina HiSeq	Phase_I	112202265	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112175475	112175476	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:112175475_112175476insT	ENST00000457016.1	+	16	4564_4565	c.4184_4185insT	c.(4183-4188)agttttfs	p.SF1395fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Ins_p.SF1395fs|APC_ENST00000508376.2_Frame_Shift_Ins_p.SF1395fs			P25054	APC_HUMAN	adenomatous polyposis coli	1395	Ser-rich.		S -> C (in hepatoblastoma). {ECO:0000269|PubMed:8764128}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1397fs*1(2)|p.S1395fs*19(2)|p.Y1376fs*41(1)|p.?(1)|p.K1192fs*3(1)|p.?fs(1)|p.F1396fs*19(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCACTTGATAGTTTTGAGAGTC	0.475		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)		yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	9	Deletion - Frameshift(5)|Insertion - Frameshift(3)|Unknown(1)	large_intestine(7)|soft_tissue(1)|skin(1)	5	GRCh37	CD972010	APC	D																																				112203375	SO:0001589	frameshift_variant	324	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.4188dupT	5.37:g.112175479_112175479dupT	ENSP00000413133:p.Ser1395fs	Somatic		Capture	Illumina HiSeq	Phase_I	112203374	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Ins	INS	ENST00000457016.1	37	CCDS4107.1																																																																																				APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDH12	51294	hgsc.bcm.edu	37	5	141335623	141335624	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr5:141335623_141335624insA	ENST00000231484.3	-	1	3003_3004	c.1793_1794insT	c.(1792-1794)ttgfs	p.L598fs	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	598					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCGCTGGGCCCAAGCCATTGGG	0.604																																																	0			5																																								141315808	SO:0001589	frameshift_variant	51294			AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.1794dupT	5.37:g.141335625_141335625dupA	ENSP00000231484:p.Leu598fs	Somatic		Capture	Illumina HiSeq	Phase_I	141315807	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Frame_Shift_Ins	INS	ENST00000231484.3	37	CCDS4269.1																																																																																				PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
SH2D4A	63898	hgsc.bcm.edu	37	8	19190463	19190468	+	Splice_Site	DEL	CAGAGA	CAGAGA	-	rs529179009		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CAGAGA	CAGAGA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr8:19190463_19190468delCAGAGA	ENST00000265807.3	+	3	592_595	c.181_184delCAGAGA	c.(181-186)cagaga>ga	p.QR61del	SH2D4A_ENST00000519207.1_Splice_Site_p.QR61del|SH2D4A_ENST00000518040.1_Splice_Site_p.QR16del	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	61					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TGTTTGTTTGCAGAGAATGGCAAATC	0.364																																																	0			8																																								19234748	SO:0001630	splice_region_variant	63898			AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.182-1CAGAGA>-	8.37:g.19190463_19190468delCAGAGA		Somatic		Capture	Illumina HiSeq	Phase_I	19234743	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Frame_Shift_Del	DEL	ENST00000265807.3	37	CCDS6009.1																																																																																				SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	In_Frame_Del
DNA2	1763	hgsc.bcm.edu	37	10	70182521	70182521	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr10:70182521delA	ENST00000358410.3	-	15	2385	c.2335delT	c.(2335-2337)tcafs	p.S779fs	DNA2_ENST00000399179.2_Intron|DNA2_ENST00000399180.2_Frame_Shift_Del_p.S865fs	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	779	Helicase activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)	p.S779fs*6(1)|p.S865fs*6(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						AATCTCCGTGAAAAAAAAAGG	0.403																																																	2	Deletion - Frameshift(2)	large_intestine(2)	10								36,47,3383		0,0,36,2,43,1652	30.0	31.0	31.0			5.7	1.0	10		32	74,113,7597		0,0,74,8,97,3713	no	codingComplex	DNA2	NM_001080449.2		0,0,110,10,140,5365	A1A1,A1A2,A1R,A2A2,A2R,RR		2.4024,2.3947,2.4			70182521	110,160,10980	1797	4062	5859	69852527	SO:0001589	frameshift_variant	1763			D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.2335delT	10.37:g.70182521delA	ENSP00000351185:p.Ser779fs	Somatic		Capture	Illumina HiSeq	Phase_I	69852527	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Frame_Shift_Del	DEL	ENST00000358410.3	37																																																																																					DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
KRT3	3850	hgsc.bcm.edu	37	12	53184999	53185000	+	Frame_Shift_Ins	INS	-	-	CGCC	rs57872071		TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr12:53184999_53185000insCGCC	ENST00000417996.2	-	7	1599_1600	c.1525_1526insGGCG	c.(1525-1527)gagfs	p.E509fs	KRT3_ENST00000309505.3_Frame_Shift_Ins_p.E509fs	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	509	Coil 2.|Rod.		E -> K (in MECD; dbSNP:rs57872071). {ECO:0000269|PubMed:9171831}.		epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						CCTGTACTCCTCGCCCTCCAGC	0.609																																																	0			12	GRCh37	CM970845	KRT3	M	rs57872071																																			51471267	SO:0001589	frameshift_variant	3850				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1522_1525dupGGCG	12.37:g.53185000_53185003dupCGCC	ENSP00000413479:p.Glu509fs	Somatic		Capture	Illumina HiSeq	Phase_I	51471266	A6NIS2|Q701L8	Frame_Shift_Ins	INS	ENST00000417996.2	37	CCDS44895.1																																																																																				KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
Unknown	0	hgsc.bcm.edu	37	Unknown	0	0	+	IGR	INS	-	-	G			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chrUnknown:0_0insG								None (None upstream) : None (None downstream)																								0																																																	0			17																																								3423920	SO:0001628	intergenic_variant	7442																															Unknown.37:g.0_0insG		Somatic		Capture	Illumina HiSeq	Phase_I	3423919		Frame_Shift_Ins	INS		37																																																																																				0								
SMAD4	4089	hgsc.bcm.edu	37	18	48591811	48591812	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CC	CC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr18:48591811_48591812delCC	ENST00000342988.3	+	9	1512_1513	c.974_975delCC	c.(973-975)tccfs	p.S325fs	SMAD4_ENST00000398417.2_Frame_Shift_Del_p.S325fs|SMAD4_ENST00000588745.1_Frame_Shift_Del_p.S229fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	325	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				atrioventricular canal development (GO:0036302)|atrioventricular valve formation (GO:0003190)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|brainstem development (GO:0003360)|branching involved in ureteric bud morphogenesis (GO:0001658)|cardiac septum development (GO:0003279)|cell proliferation (GO:0008283)|developmental growth (GO:0048589)|endocardial cell differentiation (GO:0060956)|endoderm development (GO:0007492)|endothelial cell activation (GO:0042118)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|formation of anatomical boundary (GO:0048859)|gastrulation with mouth forming second (GO:0001702)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|metanephric mesenchyme morphogenesis (GO:0072133)|negative regulation of cell death (GO:0060548)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neural crest cell differentiation (GO:0014033)|neuron fate commitment (GO:0048663)|palate development (GO:0060021)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation involved in heart valve morphogenesis (GO:0003251)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of binding (GO:0051098)|regulation of hair follicle development (GO:0051797)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of transforming growth factor beta2 production (GO:0032909)|response to hypoxia (GO:0001666)|response to transforming growth factor beta (GO:0071559)|sebaceous gland development (GO:0048733)|SMAD protein complex assembly (GO:0007183)|SMAD protein signal transduction (GO:0060395)|somite rostral/caudal axis specification (GO:0032525)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	activin responsive factor complex (GO:0032444)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|R-SMAD binding (GO:0070412)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity (GO:0030616)	p.0?(36)|p.?(2)|p.W323fs*11(1)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TATTGGTGTTCCATTGCTTACT	0.421																																																	39	Whole gene deletion(36)|Unknown(2)|Deletion - Frameshift(1)	pancreas(26)|large_intestine(3)|breast(3)|stomach(2)|lung(2)|upper_aerodigestive_tract(1)|small_intestine(1)|oesophagus(1)	18																																								46845810	SO:0001589	frameshift_variant	4089			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646		"""SMADs"""	6770	protein-coding gene	gene with protein product		600993	"""MAD, mothers against decapentaplegic homolog 4 (Drosophila)"", ""SMAD, mothers against DPP homolog 4 (Drosophila)"""	MADH4		8553070, 8774881	Standard	NM_005359		Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000342988.3:c.974_975delCC	18.37:g.48591811_48591812delCC	ENSP00000341551:p.Ser325fs	Somatic		Capture	Illumina HiSeq	Phase_I	46845809	A8K405	Frame_Shift_Del	DEL	ENST00000342988.3	37	CCDS11950.1																																																																																				SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	NM_005359	
ZNF83	55769	hgsc.bcm.edu	37	19	53116934	53117017	+	In_Frame_Del	DEL	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	-	rs78562523|rs573424533|rs561268356|rs575275768|rs542853549|rs7248435|rs201794892|rs557033862|rs144905073|rs560464978|rs199821089|rs201460258|rs542573550|rs201157018|rs199590691|rs556550175|rs367946778|rs146207784|rs200250390|rs7247691|rs7247690|rs113015820|rs75857698|rs78207921|rs140513277	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	CCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr19:53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENST00000597597.1	-	2	3054_3137	c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	c.(799-885)ggaaaggtcttccatcatatttcacaccttgcacaacatcagagaatccacactggagagaaaccttacaaatgtaatgagtgtggc>ggc	p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G	ZNF83_ENST00000536937.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000301096.3_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000601257.1_Intron|ZNF83_ENST00000600714.1_Intron|ZNF83_ENST00000594682.2_3'UTR|ZNF83_ENST00000545872.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000541777.2_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G|ZNF83_ENST00000391789.4_Splice_Site_p.KV268del|ZNF83_ENST00000544146.1_In_Frame_Del_p.267_295GKVFHHISHLAQHQRIHTGEKPYKCNECG>G			P51522	ZNF83_HUMAN	zinc finger protein 83	267					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				OV - Ovarian serous cystadenocarcinoma(262;0.00841)|GBM - Glioblastoma multiforme(134;0.0244)		GAAGACCTTGCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTTCCACATACAT	0.405																																																	0			19							,,,,,,,,	1161,3099		263,635,1232					,,,,,,,,	-2.2	0.0			87	1473,6779		168,1137,2821	no	coding,coding-near-splice,coding-near-splice,coding-near-splice,coding-near-splice,coding,coding,coding,coding	ZNF83	NM_018300.3,NM_001242538.1,NM_001242531.1,NM_001105554.1,NM_001105553.1,NM_001105552.1,NM_001105551.1,NM_001105550.1,NM_001105549.1	,,,,,,,,	431,1772,4053	A1A1,A1R,RR		17.8502,27.2535,21.0518	,,,,,,,,	,,,,,,,,		2634,9878				57808829	SO:0001651	inframe_deletion	55769			M27877	CCDS12854.1	19q13.3	2013-01-08	2006-05-12			ENSG00000167766		"""Zinc fingers, C2H2-type"""	13158	protein-coding gene	gene with protein product		194558	"""zinc finger protein 83 (HPF1)"", ""zinc finger protein 816B"""	ZNF816B		8088807	Standard	NM_018300		Approved	FLJ11015, HPF1	uc010epy.3	P51522		ENST00000597597.1:c.801_884delAAAGGTCTTCCATCATATTTCACACCTTGCACAACATCAGAGAATCCACACTGGAGAGAAACCTTACAAATGTAATGAGTGTGG	19.37:g.53116934_53117017delCCACACTCATTACATTTGTAAGGTTTCTCTCCAGTGTGGATTCTCTGATGTTGTGCAAGGTGTGAAATATGATGGAAGACCTTT	ENSP00000472619:p.Gly267_Cys294del	Somatic		Capture	Illumina HiSeq	Phase_I	57808746	A8MT75|Q3ZCX0|Q6PI08	In_Frame_Del	DEL	ENST00000597597.1	37	CCDS12854.1																																																																																				ZNF83-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463700.1	NM_018300	
TOX2	84969	hgsc.bcm.edu	37	20	42694558	42694559	+	In_Frame_Ins	INS	-	-	CCG	rs199841880|rs34604629	byFrequency	TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr20:42694558_42694559insCCG	ENST00000358131.5	+	6	1321_1322	c.1113_1114insCCG	c.(1114-1116)ccg>CCGccg	p.372_372P>PP	TOX2_ENST00000341197.4_In_Frame_Ins_p.390_390P>PP|TOX2_ENST00000372999.1_In_Frame_Ins_p.348_348P>PP|TOX2_ENST00000423191.2_In_Frame_Ins_p.348_348P>PP|TOX2_ENST00000435864.2_3'UTR	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	372	Pro-rich.			P -> PP (in Ref. 1; BAF82595). {ECO:0000305}.	female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S347_P348insR(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			TCAGTGCGTCCCCGCCGCCGCC	0.713														176	0.0351438	0.0045	0.0648	5008	,	,		13049	0.0		0.1044	False		,,,				2504	0.0204																1	Insertion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	20							,,,	79,4179		2,75,2052					,,,	1.5	0.1		dbSNP_126	33	928,7320		58,812,3254	no	coding,coding,coding,coding	TOX2	NM_032883.2,NM_001098798.1,NM_001098797.1,NM_001098796.1	,,,	60,887,5306	A1A1,A1R,RR		11.2512,1.8553,8.0521	,,,	,,,		1007,11499				42127973	SO:0001652	inframe_insertion	84969			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.1120_1122dupCCG	20.37:g.42694565_42694567dupCCG	ENSP00000350849:p.Pro376dup	Somatic		Capture	Illumina HiSeq	Phase_I	42127972	A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	In_Frame_Ins	INS	ENST00000358131.5	37	CCDS42875.1																																																																																				TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2		
URB1	9875	hgsc.bcm.edu	37	21	33744896	33744909	+	Frame_Shift_Del	DEL	AACAAGCTCCCGCA	AACAAGCTCCCGCA	-			TCGA-AG-3885-01A-01W-0899-10	TCGA-AG-3885-10A-01W-0901-10	AACAAGCTCCCGCA	AACAAGCTCCCGCA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	7a748a19-12e6-43b6-8389-97945d7be392	466f3612-0dc1-4e8e-a7e8-0f18e6f74b94	g.chr21:33744896_33744909delAACAAGCTCCCGCA	ENST00000382751.3	-	8	1023_1036	c.908_921delTGCGGGAGCTTGTT	c.(907-921)gtgcgggagcttgttfs	p.VRELV303fs		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	303						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GGAAGTTATGAACAAGCTCCCGCACCATGGTTTT	0.379																																																	0			21																																								32666780	SO:0001589	frameshift_variant	9875			AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.908_921delTGCGGGAGCTTGTT	21.37:g.33744896_33744909delAACAAGCTCCCGCA	ENSP00000372199:p.Val303fs	Somatic		Capture	Illumina HiSeq	Phase_I	32666767	D3DSE5|Q96NX1|Q9NYQ1	Frame_Shift_Del	DEL	ENST00000382751.3	37	CCDS46645.1																																																																																				URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
