#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_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_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
WNT9A	7483	hgsc.bcm.edu	37	1	228111953	228111954	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr1:228111953_228111954insC	ENST00000272164.5	-	3	510_511	c.500_501insG	c.(499-501)ggcfs	p.G167fs		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	167					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.G167fs*38(1)|p.C168fs*6(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				TGTCTCCGCAGCCCCCCCACTG	0.629																																					p.G167fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|pancreas(1)	c.501_502insG	1						.																																			226178577	SO:0001589	frameshift_variant	7483	exon3			AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.501dupG	1.37:g.228111960_228111960dupC	ENSP00000272164:p.Gly167fs		226178576	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Frame_Shift_Ins	INS	ENST00000272164.5	37	CCDS31045.1																																																																																				0.629	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
CHRM2	1129	hgsc.bcm.edu	37	7	136700131	136700131	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr7:136700131T>A	ENST00000445907.2	+	3	1047	c.519T>A	c.(517-519)gaT>gaA	p.D173E	hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000453373.1_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000401861.1_Missense_Mutation_p.D173E|CHRM2_ENST00000320658.5_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000397608.3_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000402486.3_Missense_Mutation_p.D173E|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	173					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.D173E(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	CTGTGGAGGATGGGGAGTGCT	0.483																																					p.D173E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T519A	7						.						114.0	106.0	109.0					7																	136700131		2203	4300	6503	136350671	SO:0001583	missense	1129	exon4				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1951	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 2"""	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.519T>A	7.37:g.136700131T>A	ENSP00000399745:p.Asp173Glu		136350671	NM_000739	Q4VBK6|Q9P1X9	Missense_Mutation	SNP	ENST00000445907.2	37	CCDS5843.1	.	.	.	.	.	.	.	.	.	.	T	2.030	-0.422677	0.04734	.	.	ENSG00000181072	ENST00000445907;ENST00000453373;ENST00000320658;ENST00000397608;ENST00000402486;ENST00000401861	T;T;T;T;T;T	0.36699	1.24;1.24;1.24;1.24;1.24;1.24	5.75	-3.77	0.04346	GPCR, rhodopsin-like superfamily (1);	0.236240	0.42821	D	0.000641	T	0.06416	0.0165	N	0.01048	-1.04	0.30656	N	0.754957	B	0.02656	0.0	B	0.06405	0.002	T	0.33137	-0.9880	10	0.02654	T	1	-17.3461	1.9467	0.03358	0.1821:0.306:0.0968:0.4151	.	173	P08172	ACM2_HUMAN	E	173	ENSP00000399745:D173E;ENSP00000415386:D173E;ENSP00000319984:D173E;ENSP00000380733:D173E;ENSP00000384937:D173E;ENSP00000384401:D173E	ENSP00000319984:D173E	D	+	3	2	CHRM2	136350671	0.195000	0.23338	0.997000	0.53966	0.980000	0.70556	-0.659000	0.05323	-0.146000	0.11274	0.533000	0.62120	GAT		0.483	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1		
CHRM2	1129	hgsc.bcm.edu	37	7	136700137	136700137	+	Silent	SNP	G	G	A	rs576281726	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr7:136700137G>A	ENST00000445907.2	+	3	1053	c.525G>A	c.(523-525)gaG>gaA	p.E175E	hsa-mir-490_ENST00000425981.2_RNA|CHRM2_ENST00000453373.1_Silent_p.E175E|hsa-mir-490_ENST00000586239.1_RNA|CHRM2_ENST00000401861.1_Silent_p.E175E|CHRM2_ENST00000320658.5_Silent_p.E175E|hsa-mir-490_ENST00000593789.1_RNA|CHRM2_ENST00000397608.3_Silent_p.E175E|hsa-mir-490_ENST00000592183.1_RNA|CHRM2_ENST00000402486.3_Silent_p.E175E|hsa-mir-490_ENST00000597642.1_RNA|hsa-mir-490_ENST00000439694.1_RNA|hsa-mir-490_ENST00000598184.1_RNA	NM_001006627.1|NM_001006629.1	NP_001006628.1|NP_001006630.1	P08172	ACM2_HUMAN	cholinergic receptor, muscarinic 2	175					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|nervous system development (GO:0007399)|phospholipase C-activating G-protein coupled acetylcholine receptor signaling pathway (GO:0007207)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|regulation of heart contraction (GO:0008016)|response to virus (GO:0009615)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled acetylcholine receptor activity (GO:0016907)	p.E175E(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(13)|liver(1)|lung(29)|ovary(4)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	68					Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Bethanechol(DB01019)|Brompheniramine(DB00835)|Carbachol(DB00411)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cocaine(DB00907)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Dicyclomine(DB00804)|Dimetindene(DB08801)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxacurium chloride(DB01135)|Doxepin(DB01142)|Ethopropazine(DB00392)|Fesoterodine(DB06702)|Flavoxate(DB01148)|Gallamine Triethiodide(DB00483)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Rocuronium(DB00728)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Triflupromazine(DB00508)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	AGGATGGGGAGTGCTACATTC	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.002				p.E175E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G525A	7						.						113.0	105.0	108.0					7																	136700137		2203	4300	6503	136350677	SO:0001819	synonymous_variant	1129	exon4				CCDS5843.1	7q35-q36	2014-09-17			ENSG00000181072	ENSG00000181072		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1951	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 2"""	118493					Standard	NM_000739		Approved		uc003vtl.1	P08172	OTTHUMG00000155658	ENST00000445907.2:c.525G>A	7.37:g.136700137G>A			136350677	NM_000739	Q4VBK6|Q9P1X9	Silent	SNP	ENST00000445907.2	37	CCDS5843.1																																																																																				0.488	CHRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341010.1		
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227087	99227087	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr7:99227087G>C	ENST00000394152.2	+	8	1406	c.1079G>C	c.(1078-1080)aGc>aCc	p.S360T	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.S288T|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.S360T	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	360					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S360T(1)									TTCAGTCGGAGCTCCAATCTC	0.562																																					p.S360T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1079C	7						.						75.0	69.0	71.0					7																	99227087		2203	4300	6503	99065023	SO:0001583	missense	221785	exon8			AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1079G>C	7.37:g.99227087G>C	ENSP00000377708:p.Ser360Thr		99065023	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	.	.	.	.	.	.	.	.	.	.	G	13.55	2.270188	0.40194	.	.	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.52983	0.64;0.64;0.64	3.89	3.89	0.44902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.53938	D	0.000044	T	0.34803	0.0910	L	0.37750	1.13	0.28610	N	0.908737	B;B	0.14012	0.007;0.009	B;B	0.15484	0.008;0.013	T	0.24297	-1.0164	10	0.59425	D	0.04	-20.7176	7.5921	0.28027	0.1122:0.0:0.8878:0.0	.	288;360	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	T	360;360;288	ENSP00000377708:S360T;ENSP00000334800:S360T;ENSP00000262941:S288T	ENSP00000262941:S288T	S	+	2	0	ZNF498	99065023	0.000000	0.05858	1.000000	0.80357	0.937000	0.57800	0.012000	0.13287	2.454000	0.82982	0.561000	0.74099	AGC		0.562	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138424341	138424341	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr7:138424341C>A	ENST00000310018.2	-	15	1798	c.1516G>T	c.(1516-1518)Gac>Tac	p.D506Y	ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.D506Y|ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.D506Y	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	506					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)	p.D506Y(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ATGGCTGGGTCCAGCTGCAGA	0.388																																					p.D506Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1516T	7						.						72.0	66.0	68.0					7																	138424341		2203	4300	6503	138074881	SO:0001583	missense	50617	exon14			AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1516G>T	7.37:g.138424341C>A	ENSP00000308122:p.Asp506Tyr		138074881	NM_130840	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.600363	0.66332	.	.	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.86097	-2.07;-2.07;-2.07	5.23	4.35	0.52113	.	0.000000	0.64402	D	0.000001	D	0.91717	0.7381	M	0.83483	2.645	0.53688	D	0.999976	D	0.89917	1.0	D	0.77004	0.989	D	0.92051	0.5648	10	0.87932	D	0	-32.9134	10.8407	0.46712	0.0:0.8478:0.0:0.1522	.	506	Q9HBG4	VPP4_HUMAN	Y	506	ENSP00000308122:D506Y;ENSP00000376774:D506Y;ENSP00000253856:D506Y	ENSP00000308122:D506Y	D	-	1	0	ATP6V0A4	138074881	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	2.217000	0.42880	1.183000	0.42943	0.643000	0.83706	GAC		0.388	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
FOXRED2	80020	hgsc.bcm.edu	37	22	36892062	36892062	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr22:36892062A>G	ENST00000397224.4	-	7	1669	c.1576T>C	c.(1576-1578)Tct>Cct	p.S526P	FOXRED2_ENST00000216187.6_Missense_Mutation_p.S526P|FOXRED2_ENST00000397223.4_Missense_Mutation_p.S526P|FOXRED2_ENST00000366463.3_Missense_Mutation_p.S78P	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	526					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)	p.S526P(1)		breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AGAAAGTTAGACTGCCAGGCA	0.527																																					p.S526P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1576C	22						.						108.0	100.0	102.0					22																	36892062		2203	4300	6503	35222008	SO:0001583	missense	80020	exon7			BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1576T>C	22.37:g.36892062A>G	ENSP00000380401:p.Ser526Pro		35222008	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	.	.	.	.	.	.	.	.	.	.	A	19.88	3.909693	0.72983	.	.	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000366463;ENST00000397223	T;T;T;T	0.57752	1.91;1.91;0.38;1.91	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.75398	0.3844	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.79838	-0.1634	10	0.66056	D	0.02	-23.3329	15.6826	0.77385	1.0:0.0:0.0:0.0	.	526	Q8IWF2	FXRD2_HUMAN	P	526;526;78;526	ENSP00000380401:S526P;ENSP00000216187:S526P;ENSP00000382543:S78P;ENSP00000380400:S526P	ENSP00000216187:S526P	S	-	1	0	FOXRED2	35222008	1.000000	0.71417	0.998000	0.56505	0.429000	0.31625	8.381000	0.90152	2.108000	0.64289	0.529000	0.55759	TCT		0.527	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
KIR3DL3	115653	hgsc.bcm.edu	37	19	55237553	55237553	+	Silent	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr19:55237553C>T	ENST00000291860.1	+	3	123	c.105C>T	c.(103-105)ccC>ccT	p.P35P	KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000538269.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P35P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		CTGCCTGGCCCGGCACTGTGG	0.577																																					p.P35P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C105T	19						.						1.0	1.0	1.0					19																	55237553		156	336	492	59929365	SO:0001819	synonymous_variant	115653	exon3			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.105C>T	19.37:g.55237553C>T			59929365	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Silent	SNP	ENST00000291860.1	37	CCDS12903.1																																																																																				0.577	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
NLRP4	147945	hgsc.bcm.edu	37	19	56392880	56392880	+	Missense_Mutation	SNP	C	C	T	rs374023533		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr19:56392880C>T	ENST00000301295.6	+	10	3334	c.2912C>T	c.(2911-2913)aCg>aTg	p.T971M	NLRP4_ENST00000346986.5_Missense_Mutation_p.T915M|NLRP4_ENST00000587891.1_Missense_Mutation_p.T896M	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	971					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.T971M(1)		breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GCACTTCTGACGGCTGAGGAA	0.423																																					p.T971M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2912T	19						.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	75.0	62.0	66.0		2912	-6.7	0.0	19		66	2,8598	2.2+/-6.3	0,2,4298	no	missense	NLRP4	NM_134444.4	81	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	971/995	56392880	3,13003	2203	4300	6503	61084692	SO:0001583	missense	147945	exon10			AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.2912C>T	19.37:g.56392880C>T	ENSP00000301295:p.Thr971Met		61084692	NM_134444	Q86W87|Q96AY6	Missense_Mutation	SNP	ENST00000301295.6	37	CCDS12936.1	.	.	.	.	.	.	.	.	.	.	C	2.304	-0.359501	0.05138	2.27E-4	2.33E-4	ENSG00000160505	ENST00000301295;ENST00000346986	T;T	0.53640	0.61;0.64	3.34	-6.67	0.01783	.	.	.	.	.	T	0.19565	0.0470	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.13594	0.008;0.005;0.003	B;B;B	0.11329	0.003;0.006;0.001	T	0.18745	-1.0327	9	0.38643	T	0.18	.	5.7472	0.18126	0.1235:0.5455:0.1253:0.2057	.	915;896;971	Q96MN2-2;Q96MN2-3;Q96MN2	.;.;NALP4_HUMAN	M	971;915	ENSP00000301295:T971M;ENSP00000344787:T915M	ENSP00000301295:T971M	T	+	2	0	NLRP4	61084692	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.944000	0.00681	-2.776000	0.00362	-0.966000	0.02617	ACG		0.423	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
ZNF121	7675	hgsc.bcm.edu	37	19	9677373	9677373	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr19:9677373G>C	ENST00000586602.1	-	6	832	c.416C>G	c.(415-417)aCt>aGt	p.T139S	ZNF121_ENST00000320451.6_Missense_Mutation_p.T139S			P58317	ZN121_HUMAN	zinc finger protein 121	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T139S(1)		breast(3)|kidney(4)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)	24						TTTTTCTACAGTATGCATTTT	0.378																																					p.T139S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C416G	19						.						83.0	76.0	79.0					19																	9677373		2203	4300	6503	9538373	SO:0001583	missense	7675	exon4			M99593	CCDS32902.1	19p13.2	2013-01-08	2006-08-22			ENSG00000197961		"""Zinc fingers, C2H2-type"""	12904	protein-coding gene	gene with protein product		194628	"""zinc finger protein 121 (clone ZHC32)"""	D19S204		8468057	Standard	NM_001008727		Approved	ZHC32, ZNF20	uc010xkp.1	P58317		ENST00000586602.1:c.416C>G	19.37:g.9677373G>C	ENSP00000468643:p.Thr139Ser		9538373	NM_001008727		Missense_Mutation	SNP	ENST00000586602.1	37		.	.	.	.	.	.	.	.	.	.	G	5.726	0.318503	0.10845	.	.	ENSG00000197961	ENST00000538300;ENST00000320451	T	0.24151	1.87	1.3	-1.41	0.08941	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16896	0.0406	L	0.39085	1.19	0.09310	N	1	B	0.12630	0.006	B	0.20955	0.032	T	0.30446	-0.9978	9	0.56958	D	0.05	.	3.3749	0.07234	0.1769:0.0:0.5768:0.2463	.	139	P58317	ZN121_HUMAN	S	139	ENSP00000326967:T139S	ENSP00000326967:T139S	T	-	2	0	ZNF121	9538373	0.966000	0.33281	0.001000	0.08648	0.005000	0.04900	1.490000	0.35573	-0.307000	0.08804	-0.327000	0.08410	ACT		0.378	ZNF121-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000449910.1	NM_001008727	
ZNF552	79818	hgsc.bcm.edu	37	19	58319947	58319947	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr19:58319947G>A	ENST00000391701.1	-	3	854	c.685C>T	c.(685-687)Cag>Tag	p.Q229*	ZNF586_ENST00000598885.1_Intron|ZNF586_ENST00000599802.1_Intron	NM_024762.3	NP_079038.2	Q9H707	ZN552_HUMAN	zinc finger protein 552	229					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q229*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	11		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0259)		CTCTCGTGCTGACTGAGTATA	0.433																																					p.Q229X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C685T	19						.						83.0	71.0	75.0					19																	58319947		2203	4300	6503	63011759	SO:0001587	stop_gained	79818	exon3			AK097041	CCDS12963.1	19q13.43	2013-09-20			ENSG00000178935	ENSG00000178935		"""Zinc fingers, C2H2-type"", ""-"""	26135	protein-coding gene	gene with protein product							Standard	XM_005259267		Approved	FLJ21603	uc002qqg.3	Q9H707	OTTHUMG00000183478	ENST00000391701.1:c.685C>T	19.37:g.58319947G>A	ENSP00000375582:p.Gln229*		63011759	NM_024762	B3KUE9|Q6P5A6	Nonsense_Mutation	SNP	ENST00000391701.1	37	CCDS12963.1	.	.	.	.	.	.	.	.	.	.	G	15.94	2.982381	0.53827	.	.	ENSG00000178935	ENST00000391701	.	.	.	1.96	-2.23	0.06930	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27785	T	0.31	.	0.3012	0.00273	0.2674:0.2101:0.3107:0.2118	.	.	.	.	X	229	.	ENSP00000375582:Q229X	Q	-	1	0	ZNF552	63011759	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-1.278000	0.02809	-0.681000	0.05204	0.205000	0.17691	CAG		0.433	ZNF552-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466829.1	NM_024762	
TMEM71	137835	hgsc.bcm.edu	37	8	133726435	133726435	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr8:133726435C>T	ENST00000356838.3	-	8	864	c.722G>A	c.(721-723)aGt>aAt	p.S241N	TMEM71_ENST00000377901.4_Missense_Mutation_p.S197N|TMEM71_ENST00000523829.1_Missense_Mutation_p.S260N	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	260						integral component of membrane (GO:0016021)		p.S241N(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|skin(2)	16	all_neural(3;2.72e-06)|Medulloblastoma(3;7.08e-05)|Ovarian(258;0.00438)|Esophageal squamous(12;0.00507)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;4.46e-05)			TGTGAAGACACTGGCTAATAT	0.353																																					p.S197N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G590A	8						.						141.0	137.0	139.0					8																	133726435		2203	4300	6503	133795617	SO:0001583	missense	137835	exon7			AK057631	CCDS6366.1, CCDS47921.1	8q24.22	2005-09-02				ENSG00000165071			26572	protein-coding gene	gene with protein product						12477932	Standard	NM_144649		Approved	FLJ33069	uc003ytn.3	Q6P5X7		ENST00000356838.3:c.722G>A	8.37:g.133726435C>T	ENSP00000349296:p.Ser241Asn		133795617	NM_001145153	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624509	0.28889	.	.	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901	.	.	.	5.59	1.36	0.22044	.	0.712158	0.14341	N	0.325698	T	0.34861	0.0912	M	0.68317	2.08	0.09310	N	1	B;B;B	0.32653	0.208;0.021;0.379	B;B;B	0.28553	0.077;0.027;0.091	T	0.33420	-0.9869	9	0.72032	D	0.01	-1.9095	4.565	0.12180	0.0:0.5207:0.2096:0.2697	.	260;197;241	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	N	260;241;197	.	ENSP00000349296:S241N	S	-	2	0	TMEM71	133795617	0.000000	0.05858	0.064000	0.19789	0.125000	0.20455	-0.264000	0.08658	0.405000	0.25532	0.561000	0.74099	AGT		0.353	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649	
TOX	9760	hgsc.bcm.edu	37	8	59720810	59720810	+	Missense_Mutation	SNP	C	C	T	rs372921240		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr8:59720810C>T	ENST00000361421.1	-	8	1631	c.1411G>A	c.(1411-1413)Gac>Aac	p.D471N		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	471						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D471N(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GTCTGATAGTCGGGTTGAAGA	0.423											OREG0018787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D471N	Pancreas(161;610 1969 17913 21374 22725)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1411A	8						.	C	ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	101.0	98.0	99.0		1411	6.2	1.0	8		99	0,8600		0,0,4300	no	missense	TOX	NM_014729.2	23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging	471/527	59720810	1,13005	2203	4300	6503	59883364	SO:0001583	missense	9760	exon8				CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.1411G>A	8.37:g.59720810C>T	ENSP00000354842:p.Asp471Asn	1040	59883364	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.698442	0.68386	2.27E-4	0.0	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.12569	2.67	6.17	6.17	0.99709	.	0.102660	0.64402	D	0.000005	T	0.09686	0.0238	N	0.17082	0.46	0.54753	D	0.999982	P	0.35551	0.509	B	0.26969	0.075	T	0.29882	-0.9997	9	.	.	.	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	471	O94900	TOX_HUMAN	N	471;221	ENSP00000354842:D471N	.	D	-	1	0	TOX	59883364	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.013000	0.70776	2.941000	0.99782	0.655000	0.94253	GAC		0.423	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729	
COMMD5	28991	hgsc.bcm.edu	37	8	146076065	146076065	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr8:146076065C>T	ENST00000305103.3	-	2	911	c.659G>A	c.(658-660)cGc>cAc	p.R220H	AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000450361.2_Missense_Mutation_p.R220H|COMMD5_ENST00000402718.3_Missense_Mutation_p.R220H	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	220						nucleus (GO:0005634)		p.R220H(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CTGCAGTCTGCGCTCACACCT	0.587																																					p.R220H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G659A	8						.						94.0	62.0	73.0					8																	146076065		2203	4300	6503	146046869	SO:0001583	missense	28991	exon2			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.659G>A	8.37:g.146076065C>T	ENSP00000304544:p.Arg220His		146046869	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	Missense_Mutation	SNP	ENST00000305103.3	37	CCDS6436.1	.	.	.	.	.	.	.	.	.	.	C	12.11	1.840990	0.32513	.	.	ENSG00000170619	ENST00000402718;ENST00000450361;ENST00000305103	T;T;T	0.32272	1.46;1.46;1.46	4.31	-1.44	0.08856	.	0.221722	0.36703	N	0.002445	T	0.18551	0.0445	L	0.36672	1.1	0.09310	N	0.999992	B	0.17268	0.021	B	0.10450	0.005	T	0.13308	-1.0514	10	0.36615	T	0.2	-23.815	6.7576	0.23523	0.6368:0.2681:0.0:0.0951	.	220	Q9GZQ3	COMD5_HUMAN	H	220	ENSP00000385793:R220H;ENSP00000394331:R220H;ENSP00000304544:R220H	ENSP00000304544:R220H	R	-	2	0	COMMD5	146046869	0.080000	0.21391	0.983000	0.44433	0.932000	0.56968	0.606000	0.24194	-0.089000	0.12484	0.557000	0.71058	CGC		0.587	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066	
RASAL2	9462	hgsc.bcm.edu	37	1	178426964	178426964	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr1:178426964G>A	ENST00000462775.1	+	12	2239	c.2114G>A	c.(2113-2115)cGg>cAg	p.R705Q	RASAL2_ENST00000448150.3_Missense_Mutation_p.R835Q|RASAL2_ENST00000367649.3_Missense_Mutation_p.R846Q	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	705					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)	p.R846Q(1)|p.R835Q(1)		biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CCTAATGGTCGGAGCGTCTCC	0.493																																					p.R846Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2537A	1						.						95.0	92.0	93.0					1																	178426964		2203	4300	6503	176693587	SO:0001583	missense	9462	exon14			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2114G>A	1.37:g.178426964G>A	ENSP00000420558:p.Arg705Gln		176693587	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965816	0.92855	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	T;T;T	0.13778	2.56;2.56;2.56	5.42	5.42	0.78866	.	0.061537	0.64402	D	0.000012	T	0.34366	0.0895	L	0.57536	1.79	0.80722	D	1	D;D;D	0.76494	0.999;0.982;0.976	D;P;P	0.63703	0.917;0.791;0.601	T	0.02320	-1.1177	10	0.66056	D	0.02	.	19.2521	0.93929	0.0:0.0:1.0:0.0	.	835;705;846	B1AKC7;Q9UJF2;F8W755	.;NGAP_HUMAN;.	Q	835;846;705	ENSP00000407768:R835Q;ENSP00000356621:R846Q;ENSP00000420558:R705Q	ENSP00000356621:R846Q	R	+	2	0	RASAL2	176693587	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.433000	0.97501	2.542000	0.85734	0.655000	0.94253	CGG		0.493	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	
SMG7	9887	hgsc.bcm.edu	37	1	183520213	183520213	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr1:183520213C>A	ENST00000347615.2	+	21	3307	c.3188C>A	c.(3187-3189)gCa>gAa	p.A1063E	SMG7_ENST00000508461.1_Missense_Mutation_p.A1071E|SMG7_ENST00000367537.3_Missense_Mutation_p.A1096E|SMG7_ENST00000507469.1_Missense_Mutation_p.A1067E|SMG7_ENST00000515829.2_Missense_Mutation_p.A1017E|SMG7_ENST00000456731.2_Missense_Mutation_p.A975E	NM_173156.2	NP_775179.1	Q92540	SMG7_HUMAN	SMG7 nonsense mediated mRNA decay factor	1063					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)	p.A1063E(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(16)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	46						TATCTCTCAGCAACGTCATCC	0.507																																					p.A1071E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3212A	1						.						81.0	75.0	77.0					1																	183520213		2203	4300	6503	181786836	SO:0001583	missense	9887	exon21			D87437	CCDS1355.1, CCDS41445.1, CCDS41445.2, CCDS53444.1, CCDS53445.1	1q25	2013-07-02	2013-07-02	2006-02-16	ENSG00000116698	ENSG00000116698			16792	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog C (S. cerevisiae)"""	610964	"""chromosome 1 open reading frame 16"", ""smg-7 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C1orf16		14636577, 15721257	Standard	NM_173156		Approved	KIAA0250, EST1C, SGA56M, SMG-7	uc001gqf.3	Q92540	OTTHUMG00000035221	ENST00000347615.2:c.3188C>A	1.37:g.183520213C>A	ENSP00000340766:p.Ala1063Glu		181786836	NM_001174061	B4DRB2|E9PCI0|E9PEH2|Q5T1Q0|Q6PIE0|Q7Z7H9|Q8IXC1|Q8IXC2	Missense_Mutation	SNP	ENST00000347615.2	37	CCDS1355.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.481611	0.44147	.	.	ENSG00000116698	ENST00000456731;ENST00000367537;ENST00000508461;ENST00000347615;ENST00000507469;ENST00000515829	T;T;T;T;T;T	0.23552	1.96;1.94;1.9;1.93;1.93;1.95	5.34	4.41	0.53225	.	0.335281	0.31734	N	0.007146	T	0.16557	0.0398	N	0.24115	0.695	0.09310	N	0.999995	B;B;B;B;B	0.31125	0.09;0.037;0.062;0.09;0.309	B;B;B;B;B	0.27608	0.031;0.035;0.076;0.051;0.081	T	0.17018	-1.0383	10	0.66056	D	0.02	-0.6955	9.7281	0.40344	0.0:0.7845:0.1419:0.0736	.	1071;975;1017;1063;1067	E9PCI0;E9PCE5;Q92540-2;Q92540;E9PEH2	.;.;.;SMG7_HUMAN;.	E	975;1096;1071;1063;1067;1017	ENSP00000407629:A975E;ENSP00000356507:A1096E;ENSP00000426915:A1071E;ENSP00000340766:A1063E;ENSP00000425133:A1067E;ENSP00000421358:A1017E	ENSP00000340766:A1063E	A	+	2	0	SMG7	181786836	0.968000	0.33430	0.388000	0.26195	0.783000	0.44284	4.301000	0.59086	1.327000	0.45338	0.650000	0.86243	GCA		0.507	SMG7-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000085432.1	NM_014837	
CACNA1S	779	hgsc.bcm.edu	37	1	201046094	201046094	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr1:201046094C>T	ENST00000362061.3	-	12	2007	c.1781G>A	c.(1780-1782)cGc>cAc	p.R594H	CACNA1S_ENST00000367338.3_Missense_Mutation_p.R594H	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	594					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R594H(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	AAAGTTGCTGCGCCGTACTTC	0.557																																					p.R594H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1781A	1						.						194.0	166.0	175.0					1																	201046094		2203	4300	6503	199312717	SO:0001583	missense	779	exon12			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1781G>A	1.37:g.201046094C>T	ENSP00000355192:p.Arg594His		199312717	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.922940	0.92319	.	.	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98474	-4.95;-4.95	4.55	4.55	0.56014	Ion transport (1);	.	.	.	.	D	0.98893	0.9625	M	0.80982	2.52	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	D	0.99857	1.1078	9	0.87932	D	0	.	17.6809	0.88242	0.0:1.0:0.0:0.0	.	594	Q13698	CAC1S_HUMAN	H	594	ENSP00000355192:R594H;ENSP00000356307:R594H	ENSP00000355192:R594H	R	-	2	0	CACNA1S	199312717	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.795000	0.85887	2.249000	0.74217	0.549000	0.68633	CGC		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
KIAA1377	57562	hgsc.bcm.edu	37	11	101832753	101832753	+	Silent	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr11:101832753T>C	ENST00000263468.8	+	6	1257	c.987T>C	c.(985-987)gaT>gaC	p.D329D	KIAA1377_ENST00000537689.1_Silent_p.D130D	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	329								p.D329D(1)		breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		CTTTCTCAGATATTTTAAGTA	0.308																																					p.D329D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T987C	11						.						41.0	43.0	43.0					11																	101832753		2203	4297	6500	101337963	SO:0001819	synonymous_variant	57562	exon6			AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.987T>C	11.37:g.101832753T>C			101337963	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																				0.308	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651120	1651120	+	Missense_Mutation	SNP	G	G	T	rs66665994		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	T	G	T	Unknown	Valid	Germline	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr11:1651120G>T	ENST00000399676.2	+	1	88	c.50G>T	c.(49-51)cGt>cTt	p.R17L		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	17				R -> L (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.R17L(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		tgtggaggccgtggctccggc	0.697																																					p.R17L												KRTAP5-5,lung,NS,Substitution - Missense,+1	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G50T	11						.						49.0	62.0	58.0					11																	1651120		2185	4288	6473	1607696	SO:0001583	missense	439915	exon1			AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.50G>T	11.37:g.1651120G>T	ENSP00000382584:p.Arg17Leu		1607696	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	1029	0.47115384615384615	280	0.5691056910569106	162	0.44751381215469616	221	0.38636363636363635	366	0.48284960422163586	G	7.595	0.671480	0.14776	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01005	5.45	2.63	2.63	0.31362	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.49389	P	2.1099999999996122E-4	B	0.24963	0.115	B	0.14023	0.01	T	0.01504	-1.1338	8	0.44086	T	0.13	.	9.323	0.37975	0.0:0.0:1.0:0.0	.	17	Q701N2	KRA55_HUMAN	L	17;15	ENSP00000382584:R17L	ENSP00000382584:R17L	R	+	2	0	KRTAP5-5	1607696	1.000000	0.71417	0.817000	0.32601	0.004000	0.04260	3.925000	0.56484	1.420000	0.47138	0.442000	0.29010	CGT		0.697	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
SLC22A25	387601	hgsc.bcm.edu	37	11	62996023	62996023	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr11:62996023C>A	ENST00000306494.6	-	2	415	c.416G>T	c.(415-417)tGc>tTc	p.C139F	SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25									p.C139F(1)		NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						TTGAGATTCGCATACCAGATC	0.418																																					p.C139F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G416T	11						.						107.0	96.0	100.0					11																	62996023		2201	4298	6499	62752599	SO:0001583	missense	387601	exon2			AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.416G>T	11.37:g.62996023C>A	ENSP00000307443:p.Cys139Phe		62752599	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.909086	0.33721	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.81163	-1.46	3.47	3.47	0.39725	Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	D	0.92941	0.7754	H	0.98238	4.18	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94893	0.8049	10	0.87932	D	0	.	12.9802	0.58559	0.0:1.0:0.0:0.0	.	137;139	A4IF29;Q6T423	.;S22AP_HUMAN	F	139	ENSP00000307443:C139F	ENSP00000307443:C139F	C	-	2	0	SLC22A25	62752599	1.000000	0.71417	0.900000	0.35374	0.183000	0.23260	4.531000	0.60602	1.698000	0.51180	0.478000	0.44815	TGC		0.418	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
ARHGAP20	57569	hgsc.bcm.edu	37	11	110477339	110477339	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr11:110477339G>A	ENST00000260283.4	-	10	1194	c.910C>T	c.(910-912)Cag>Tag	p.Q304*	ARHGAP20_ENST00000357139.3_Nonsense_Mutation_p.Q278*|ARHGAP20_ENST00000524756.1_Nonsense_Mutation_p.Q281*|ARHGAP20_ENST00000533353.1_Nonsense_Mutation_p.Q278*|ARHGAP20_ENST00000527598.1_Nonsense_Mutation_p.Q268*|ARHGAP20_ENST00000528829.1_Nonsense_Mutation_p.Q268*	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	304					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.Q304*(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		AACTGGCACTGCATCTCTCGG	0.527																																					p.Q304X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C910T	11						.						153.0	161.0	158.0					11																	110477339		2201	4298	6499	109982549	SO:0001587	stop_gained	57569	exon10			AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.910C>T	11.37:g.110477339G>A	ENSP00000260283:p.Gln304*		109982549	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Nonsense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	G	38	7.184560	0.98121	.	.	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	.	.	.	5.91	3.96	0.45880	.	0.111387	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.8896	0.58064	0.0:0.125:0.7449:0.1301	.	.	.	.	X	304;278;281;268;278;268	.	ENSP00000260283:Q304X	Q	-	1	0	ARHGAP20	109982549	1.000000	0.71417	0.424000	0.26647	0.755000	0.42902	6.422000	0.73357	0.750000	0.32877	0.650000	0.86243	CAG		0.527	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
GRM1	2911	hgsc.bcm.edu	37	6	146720520	146720520	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:146720520A>T	ENST00000282753.1	+	7	2580	c.2345A>T	c.(2344-2346)aAc>aTc	p.N782I	GRM1_ENST00000355289.4_Missense_Mutation_p.N782I|GRM1_ENST00000392299.2_Missense_Mutation_p.N782I|GRM1_ENST00000507907.1_Missense_Mutation_p.N782I|GRM1_ENST00000492807.2_Missense_Mutation_p.N782I|GRM1_ENST00000361719.2_Missense_Mutation_p.N782I			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	782					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)	p.N782I(1)		NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		GCCAACTTCAACGAGGCCAAA	0.502																																					p.N782I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2345T	6						.						170.0	146.0	154.0					6																	146720520		2203	4300	6503	146762213	SO:0001583	missense	2911	exon8			U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.2345A>T	6.37:g.146720520A>T	ENSP00000282753:p.Asn782Ile		146762213	NM_001114329	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.301296	0.81136	.	.	ENSG00000152822	ENST00000361719;ENST00000392299;ENST00000492807;ENST00000282753;ENST00000355289;ENST00000507907	D;D;D;D;D;D	0.91237	-2.81;-2.81;-2.81;-2.81;-2.81;-2.81	5.68	5.68	0.88126	GPCR, family 3, conserved site (1);GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.96812	0.8959	H	0.96691	3.865	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98206	1.0470	10	0.87932	D	0	.	15.9149	0.79503	1.0:0.0:0.0:0.0	.	782;782;782	F8W805;Q13255;Q13255-2	.;GRM1_HUMAN;.	I	782	ENSP00000354896:N782I;ENSP00000376119:N782I;ENSP00000424095:N782I;ENSP00000282753:N782I;ENSP00000347437:N782I;ENSP00000425599:N782I	ENSP00000282753:N782I	N	+	2	0	GRM1	146762213	1.000000	0.71417	0.970000	0.41538	0.985000	0.73830	9.339000	0.96797	2.169000	0.68431	0.477000	0.44152	AAC		0.502	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
OR2H1	26716	hgsc.bcm.edu	37	6	29429905	29429905	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:29429905G>A	ENST00000377136.1	+	4	824	c.359G>A	c.(358-360)cGa>cAa	p.R120Q	OR2H1_ENST00000377133.1_Missense_Mutation_p.R120Q|OR2H1_ENST00000442615.1_Missense_Mutation_p.R120Q|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377132.1_Missense_Mutation_p.R120Q|OR2H1_ENST00000396792.2_Missense_Mutation_p.R120Q			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	120						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R120Q(1)		large_intestine(5)|lung(12)	17						GCCTTTGACCGATACGTGGCT	0.577																																					p.R120Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G359A	6						.						166.0	169.0	168.0					6																	29429905		1509	2709	4218	29537884	SO:0001583	missense	26716	exon3			AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.359G>A	6.37:g.29429905G>A	ENSP00000366340:p.Arg120Gln		29537884	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475107	0.43942	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06	2.92	-1.05	0.10036	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41097	D	0.000946	T	0.70928	0.3280	M	0.91612	3.225	0.23126	N	0.998253	D	0.59357	0.985	P	0.48270	0.572	T	0.68318	-0.5440	10	0.87932	D	0	.	4.9109	0.13821	0.2665:0.0:0.5872:0.1463	.	120	Q9GZK4	OR2H1_HUMAN	Q	120	ENSP00000366340:R120Q;ENSP00000366337:R120Q;ENSP00000393254:R120Q;ENSP00000366336:R120Q;ENSP00000380010:R120Q	ENSP00000366336:R120Q	R	+	2	0	OR2H1	29537884	0.963000	0.33076	0.567000	0.28434	0.044000	0.14063	4.391000	0.59652	-0.274000	0.09232	-0.895000	0.02911	CGA		0.577	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
NOTCH4	4855	hgsc.bcm.edu	37	6	32163252	32163252	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:32163252C>A	ENST00000375023.3	-	30	6112	c.5974G>T	c.(5974-5976)Gaa>Taa	p.E1992*	GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000487761.1_5'Flank|GPSM3_ENST00000375043.3_5'UTR	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1992					cell differentiation (GO:0030154)|cell fate determination (GO:0001709)|embryo development (GO:0009790)|endothelial cell morphogenesis (GO:0001886)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|mammary gland development (GO:0030879)|morphogenesis of a branching structure (GO:0001763)|negative regulation of cell differentiation (GO:0045596)|negative regulation of endothelial cell differentiation (GO:0045602)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|patterning of blood vessels (GO:0001569)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)	p.E1992*(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(47)|ovary(5)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(1)	100						ATGGGCATTTCTTGGAGGGCT	0.517																																					p.L1992F												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C5974T	6						.						90.0	112.0	104.0					6																	32163252		1507	2707	4214	32271230	SO:0001587	stop_gained	4855	exon30				CCDS34420.1	6p21.3	2013-01-10	2010-06-24		ENSG00000204301	ENSG00000204301		"""Ankyrin repeat domain containing"""	7884	protein-coding gene	gene with protein product		164951	"""Notch (Drosophila) homolog 4"", ""Notch homolog 4 (Drosophila)"""	INT3		7835890	Standard	NM_004557		Approved		uc003obb.3	Q99466	OTTHUMG00000031044	ENST00000375023.3:c.5974G>T	6.37:g.32163252C>A	ENSP00000364163:p.Glu1992*		32271230	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Nonsense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	.	.	.	.	.	.	.	.	.	.	C	46	12.153790	0.99641	.	.	ENSG00000204301	ENST00000375023	.	.	.	4.0	4.0	0.46444	.	1.335850	0.05821	N	0.615832	.	.	.	.	.	.	0.58432	D	0.999992	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	11.7766	0.51989	0.0:1.0:0.0:0.0	.	.	.	.	X	1992	.	ENSP00000364163:E1992X	E	-	1	0	NOTCH4	32271230	0.015000	0.18098	0.005000	0.12908	0.032000	0.12392	2.997000	0.49457	2.246000	0.74042	0.655000	0.94253	GAA		0.517	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
TAPBP	6892	hgsc.bcm.edu	37	6	33271752	33271752	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:33271752T>C	ENST00000489157.1	-	6	1266	c.1054A>G	c.(1054-1056)Acc>Gcc	p.T352A	TAPBP_ENST00000456592.2_Missense_Mutation_p.T439A|TAPBP_ENST00000475304.1_Missense_Mutation_p.T457A|TAPBP_ENST00000426633.2_Missense_Mutation_p.T439A|TAPBP_ENST00000434618.2_Missense_Mutation_p.T439A			O15533	TPSN_HUMAN	TAP binding protein (tapasin)	439	Ig-like C1-type.				amide transport (GO:0042886)|antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|peptide antigen stabilization (GO:0050823)|peptide transport (GO:0015833)|protein complex assembly (GO:0006461)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of membrane (GO:0016021)|MHC class I peptide loading complex (GO:0042824)	MHC class I protein binding (GO:0042288)|peptide antigen binding (GO:0042605)|peptide antigen-transporting ATPase activity (GO:0015433)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)|unfolded protein binding (GO:0051082)	p.T439A(1)		endometrium(2)|large_intestine(5)|lung(8)|ovary(3)	18						TCCTTGCAGGTGGACAGGTAG	0.527																																					p.T439A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1315G	6						.						126.0	109.0	115.0					6																	33271752		2203	4300	6503	33379730	SO:0001583	missense	6892	exon7			Y13582	CCDS34426.1, CCDS34427.1, CCDS34428.1, CCDS34427.2, CCDS34428.2	6p21.3	2014-09-17			ENSG00000231925	ENSG00000231925		"""Immunoglobulin superfamily / C1-set domain containing"""	11566	protein-coding gene	gene with protein product		601962				9238042	Standard	NM_003190		Approved	TAPA	uc003odz.3	O15533	OTTHUMG00000031090	ENST00000489157.1:c.1054A>G	6.37:g.33271752T>C	ENSP00000419659:p.Thr352Ala		33379730	NM_172208	A2AB91|A2ABC0|B0V003|B0V0A6|B2ZUA4|E9PGM2|O15210|O15272|Q5STJ8|Q5STK6|Q5STQ5|Q5STQ6|Q66K65|Q96KK7|Q9HAN8|Q9UEE0|Q9UEE4|Q9UIZ6|Q9Y6K2	Missense_Mutation	SNP	ENST00000489157.1	37	CCDS34427.2	.	.	.	.	.	.	.	.	.	.	T	13.40	2.224544	0.39300	.	.	ENSG00000231925	ENST00000434618;ENST00000475304;ENST00000489157;ENST00000426633;ENST00000456592	T;T;T;T;T	0.30448	1.57;1.57;1.57;1.53;1.57	4.0	1.38	0.22167	.	0.554122	0.18317	N	0.144933	T	0.05777	0.0151	N	0.17674	0.51	0.09310	N	1	B;B;B;B	0.11235	0.001;0.001;0.003;0.004	B;B;B;B	0.10450	0.001;0.002;0.005;0.001	T	0.35674	-0.9779	10	0.35671	T	0.21	-0.1021	5.0817	0.14661	0.0:0.3167:0.0:0.6833	.	352;457;439;439	E9PGM2;A2AB90;O15533-3;O15533	.;.;.;TPSN_HUMAN	A	439;457;352;439;439	ENSP00000395701:T439A;ENSP00000417949:T457A;ENSP00000419659:T352A;ENSP00000404833:T439A;ENSP00000387803:T439A	ENSP00000404833:T439A	T	-	1	0	TAPBP	33379730	0.000000	0.05858	0.000000	0.03702	0.898000	0.52572	0.016000	0.13377	0.276000	0.22118	0.448000	0.29417	ACC		0.527	TAPBP-006	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276425.2		
TRERF1	55809	hgsc.bcm.edu	37	6	42200566	42200566	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:42200566G>T	ENST00000372922.4	-	17	3693	c.3131C>A	c.(3130-3132)aCc>aAc	p.T1044N	TRERF1_ENST00000541110.1_Missense_Mutation_p.T1064N|TRERF1_ENST00000354325.2_Missense_Mutation_p.T961N|TRERF1_ENST00000372917.4_Missense_Mutation_p.T973N|TRERF1_ENST00000340840.2_Missense_Mutation_p.T973N	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	1044	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.T1044N(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCGGGCCTTGGTCACCTGGTT	0.607																																					p.T1044N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3131A	6						.						43.0	37.0	39.0					6																	42200566		2203	4300	6503	42308544	SO:0001583	missense	55809	exon17			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.3131C>A	6.37:g.42200566G>T	ENSP00000362013:p.Thr1044Asn		42308544	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.540630	0.65085	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.54	5.54	0.83059	.	0.473238	0.19242	N	0.119150	T	0.14442	0.0349	N	0.19112	0.55	0.42849	D	0.994072	B;B;B;B;P	0.42692	0.161;0.1;0.1;0.161;0.787	B;B;B;B;B	0.44108	0.067;0.03;0.03;0.067;0.441	T	0.02983	-1.1086	10	0.31617	T	0.26	-5.9318	13.7851	0.63105	0.073:0.0:0.927:0.0	.	961;1064;1044;800;812	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	N	1064;973;1044;973;961	ENSP00000439689:T1064N;ENSP00000362008:T973N;ENSP00000362013:T1044N;ENSP00000339438:T973N;ENSP00000346285:T961N	ENSP00000339438:T973N	T	-	2	0	TRERF1	42308544	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.108000	0.64609	2.626000	0.88956	0.585000	0.79938	ACC		0.607	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
MDN1	23195	hgsc.bcm.edu	37	6	90377798	90377798	+	Missense_Mutation	SNP	C	C	T	rs370775568		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:90377798C>T	ENST00000369393.3	-	84	14144	c.14029G>A	c.(14029-14031)Gga>Aga	p.G4677R	MDN1_ENST00000468568.1_5'Flank|MDN1_ENST00000428876.1_Missense_Mutation_p.G4677R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4677					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.G4677R(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		ATTCCACCTCCCTCATAGTCA	0.433																																					p.G4677R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14029A	6						.						225.0	172.0	190.0					6																	90377798		2203	4300	6503	90434519	SO:0001583	missense	23195	exon84			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.14029G>A	6.37:g.90377798C>T	ENSP00000358400:p.Gly4677Arg		90434519	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520014	0.85495	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.13196	2.61;2.61	5.86	5.86	0.93980	.	0.063063	0.64402	D	0.000008	T	0.30916	0.0780	M	0.80746	2.51	0.58432	D	0.999999	D	0.59767	0.986	P	0.58577	0.841	T	0.05099	-1.0906	10	0.72032	D	0.01	.	20.1823	0.98208	0.0:1.0:0.0:0.0	.	4677	Q9NU22	MDN1_HUMAN	R	4677	ENSP00000358400:G4677R;ENSP00000413970:G4677R	ENSP00000358400:G4677R	G	-	1	0	MDN1	90434519	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.771000	0.95319	0.650000	0.86243	GGA		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
SMOC2	64094	hgsc.bcm.edu	37	6	168999543	168999543	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr6:168999543A>T	ENST00000356284.2	+	8	903	c.683A>T	c.(682-684)aAg>aTg	p.K228M	SMOC2_ENST00000354536.5_Missense_Mutation_p.K239M	NM_001166412.1	NP_001159884.1	Q9H3U7	SMOC2_HUMAN	SPARC related modular calcium binding 2	228	Thyroglobulin type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00500}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)|signal transduction (GO:0007165)	basement membrane (GO:0005604)|interstitial matrix (GO:0005614)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)	p.K239M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	32		Breast(66;0.000141)|Esophageal squamous(34;0.222)|Ovarian(120;0.231)		OV - Ovarian serous cystadenocarcinoma(33;1.31e-19)|BRCA - Breast invasive adenocarcinoma(81;3.06e-06)|GBM - Glioblastoma multiforme(31;0.00109)		GAGGAAGCCAAGCAGCCCAAG	0.607																																					p.K228M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A683T	6						.						195.0	144.0	161.0					6																	168999543		2203	4300	6503	168741468	SO:0001583	missense	64094	exon8			AB014730	CCDS5307.1, CCDS55076.1	6q27	2013-01-10			ENSG00000112562	ENSG00000112562		"""EF-hand domain containing"""	20323	protein-coding gene	gene with protein product		607223				12031507	Standard	NM_022138		Approved	SMAP2	uc003qwr.2	Q9H3U7	OTTHUMG00000016050	ENST00000356284.2:c.683A>T	6.37:g.168999543A>T	ENSP00000348630:p.Lys228Met		168741468	NM_001166412	B3KPS7|Q4G169|Q5TAT7|Q5TAT8|Q86VV9|Q96SF3|Q9H1L3|Q9H1L4|Q9H3U0|Q9H4F7|Q9HCV2	Missense_Mutation	SNP	ENST00000356284.2	37	CCDS55076.1	.	.	.	.	.	.	.	.	.	.	A	19.29	3.799490	0.70567	.	.	ENSG00000112562	ENST00000356284;ENST00000354536;ENST00000366793	T;T	0.65178	-0.14;-0.14	5.21	1.7	0.24286	Thyroglobulin type-1 (3);	0.324845	0.28398	N	0.015483	T	0.41166	0.1147	L	0.48877	1.53	0.28568	N	0.910753	P;P	0.42337	0.708;0.776	P;B	0.47102	0.537;0.445	T	0.32877	-0.9890	10	0.59425	D	0.04	-14.7243	6.8649	0.24088	0.665:0.0:0.335:0.0	.	228;239	Q9H3U7;Q9H3U7-2	SMOC2_HUMAN;.	M	228;239;228	ENSP00000348630:K228M;ENSP00000346537:K239M	ENSP00000346537:K239M	K	+	2	0	SMOC2	168741468	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	3.191000	0.50981	0.073000	0.16731	0.317000	0.21355	AAG		0.607	SMOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043201.1		
TP53	7157	hgsc.bcm.edu	37	17	7577588	7577588	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr17:7577588G>A	ENST00000269305.4	-	7	882	c.693C>T	c.(691-693)acC>acT	p.T231T	TP53_ENST00000359597.4_Silent_p.T231T|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000455263.2_Silent_p.T231T|TP53_ENST00000420246.2_Silent_p.T231T|TP53_ENST00000413465.2_Silent_p.T231T|TP53_ENST00000445888.2_Silent_p.T231T	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	231	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		T -> A (in sporadic cancers; somatic mutation).|T -> I (in sporadic cancers; somatic mutation).|T -> N (in sporadic cancers; somatic mutation).|T -> 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.0?(8)|p.T231T(7)|p.?(5)|p.T230fs*6(2)|p.C229_H233delCTTIH(2)|p.T230_Y234delTTIHY(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.T138T(1)|p.C229_I232del(1)|p.S227_I232delSDCTTI(1)|p.T231del(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)	TGTAGTGGATGGTGGTACAGT	0.547		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)																											p.T231T	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	.	.	31	Whole gene deletion(8)|Substitution - coding silent(8)|Deletion - In frame(6)|Unknown(5)|Deletion - Frameshift(4)	biliary_tract(5)|large_intestine(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|urinary_tract(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|oesophagus(2)|breast(2)|stomach(1)|lung(1)|ovary(1)|liver(1)	c.C693T	17						.						111.0	89.0	96.0					17																	7577588		2203	4300	6503	7518313	SO:0001819	synonymous_variant	7157	exon7	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.693C>T	17.37:g.7577588G>A			7518313	NM_001126114	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																																																																																				0.547	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
ACACA	31	hgsc.bcm.edu	37	17	35564696	35564696	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr17:35564696G>A	ENST00000394406.2	-	31	3805	c.3615C>T	c.(3613-3615)aaC>aaT	p.N1205N	ACACA_ENST00000335166.5_Silent_p.N1127N|ACACA_ENST00000360679.3_Silent_p.N1147N|ACACA_ENST00000353139.5_Silent_p.N1242N	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	1205					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)	p.N1147N(1)|p.N1242N(1)		NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	AGTGGTTGAGGTTGGAGGAGA	0.468																																					p.N1242N	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3726T	17						.						153.0	124.0	134.0					17																	35564696		2203	4300	6503	32638809	SO:0001819	synonymous_variant	31	exon31			U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.3615C>T	17.37:g.35564696G>A			32638809	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																				0.468	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
ZP2	7783	hgsc.bcm.edu	37	16	21212710	21212710	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr16:21212710C>G	ENST00000574002.1	-	15	2156	c.1674G>C	c.(1672-1674)caG>caC	p.Q558H	ZP2_ENST00000574091.1_Missense_Mutation_p.Q549H|ZP2_ENST00000219593.4_Missense_Mutation_p.Q558H|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	558	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)	p.Q558H(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		CAACGTTCCACTGGGGGAAAG	0.502																																					p.Q558H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1674C	16						.						146.0	131.0	136.0					16																	21212710		2200	4300	6500	21120211	SO:0001583	missense	7783	exon14			M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1674G>C	16.37:g.21212710C>G	ENSP00000460971:p.Gln558His		21120211	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	C	16.39	3.109892	0.56398	.	.	ENSG00000103310	ENST00000219593	D	0.83163	-1.69	5.31	2.2	0.27929	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	0.284895	0.29814	N	0.011126	D	0.91379	0.7280	M	0.93638	3.44	0.48696	D	0.999694	P;P	0.50272	0.881;0.933	D;D	0.64877	0.93;0.93	D	0.90827	0.4713	10	0.87932	D	0	-1.1199	8.7021	0.34332	0.0:0.7269:0.1273:0.1458	.	549;558	Q4VAP1;Q05996	.;ZP2_HUMAN	H	558	ENSP00000219593:Q558H	ENSP00000219593:Q558H	Q	-	3	2	ZP2	21120211	1.000000	0.71417	0.810000	0.32431	0.638000	0.38207	1.199000	0.32235	0.708000	0.31955	0.591000	0.81541	CAG		0.502	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
MC2R	4158	hgsc.bcm.edu	37	18	13885364	13885364	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr18:13885364T>C	ENST00000327606.3	-	2	334	c.154A>G	c.(154-156)Aat>Gat	p.N52D		NM_000529.2	NP_000520.1	Q01718	ACTHR_HUMAN	melanocortin 2 receptor (adrenocorticotropic hormone)	52					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|neuropeptide signaling pathway (GO:0007218)|placenta development (GO:0001890)|positive regulation of cAMP biosynthetic process (GO:0030819)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotropin receptor activity (GO:0004978)|melanocortin receptor activity (GO:0004977)	p.N52D(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(8)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30					Corticotropin(DB01285)|Cosyntropin(DB01284)	AGATTCTTATTCTTGAACACA	0.428																																					p.N52D	Colon(141;1584 1782 35999 48227 48692)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A154G	18						.						84.0	79.0	81.0					18																	13885364		2203	4300	6503	13875364	SO:0001583	missense	4158	exon2				CCDS11869.1	18p11.2	2012-08-10			ENSG00000185231	ENSG00000185231		"""GPCR / Class A : Melanocortin receptors"""	6930	protein-coding gene	gene with protein product		607397				8390157	Standard	NM_001291911		Approved	ACTHR	uc002ksp.1	Q01718	OTTHUMG00000131721	ENST00000327606.3:c.154A>G	18.37:g.13885364T>C	ENSP00000333821:p.Asn52Asp		13875364	NM_000529	A8K016|Q3MI45|Q504X6	Missense_Mutation	SNP	ENST00000327606.3	37	CCDS11869.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.233183	0.79688	.	.	ENSG00000185231	ENST00000327606;ENST00000399821	T;T	0.72835	2.84;-0.69	4.13	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83124	0.5186	M	0.78344	2.41	0.50171	D	0.999857	D	0.89917	1.0	D	0.91635	0.999	D	0.85567	0.1231	10	0.72032	D	0.01	.	13.4468	0.61146	0.0:0.0:0.0:1.0	.	52	Q01718	ACTHR_HUMAN	D	52	ENSP00000333821:N52D;ENSP00000382718:N52D	ENSP00000333821:N52D	N	-	1	0	MC2R	13875364	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	7.355000	0.79434	1.643000	0.50594	0.528000	0.53228	AAT		0.428	MC2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254639.2		
SLC6A11	6538	hgsc.bcm.edu	37	3	10979978	10979978	+	Missense_Mutation	SNP	C	C	T	rs142712079	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr3:10979978C>T	ENST00000254488.2	+	14	1855	c.1789C>T	c.(1789-1791)Cgg>Tgg	p.R597W		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	597					brain development (GO:0007420)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter binding (GO:0042165)|neurotransmitter:sodium symporter activity (GO:0005328)	p.R597W(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(13)|ovary(1)|skin(4)	35				OV - Ovarian serous cystadenocarcinoma(96;0.229)	Clobazam(DB00349)	TCTGAAAATGCGGGGCAAGCT	0.547													C|||	7	0.00139776	0.0	0.0	5008	,	,		18261	0.0069		0.0	False		,,,				2504	0.0				p.R597W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1789T	3						.	C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	117.0	108.0	111.0		1789	1.5	1.0	3	dbSNP_134	111	0,8600		0,0,4300	yes	missense	SLC6A11	NM_014229.1	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	597/633	10979978	2,13004	2203	4300	6503	10954978	SO:0001583	missense	6538	exon14			S75989	CCDS2602.1	3p25.3	2013-07-19	2013-07-19		ENSG00000132164	ENSG00000132164		"""Solute carriers"""	11044	protein-coding gene	gene with protein product	"""GABA transporter 3"""	607952	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 11"""			7874447	Standard	NM_014229		Approved	GAT3	uc003bvz.3	P48066	OTTHUMG00000129718	ENST00000254488.2:c.1789C>T	3.37:g.10979978C>T	ENSP00000254488:p.Arg597Trp		10954978	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	37	CCDS2602.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	14.81	2.647594	0.47258	4.54E-4	0.0	ENSG00000132164	ENST00000254488	T	0.74842	-0.88	4.81	1.53	0.23141	.	0.361639	0.26542	N	0.023798	T	0.53997	0.1831	L	0.29908	0.895	0.80722	D	1	B	0.18863	0.031	B	0.12837	0.008	T	0.56189	-0.8020	10	0.51188	T	0.08	.	13.7065	0.62644	0.5834:0.4166:0.0:0.0	.	597	P48066	S6A11_HUMAN	W	597	ENSP00000254488:R597W	ENSP00000254488:R597W	R	+	1	2	SLC6A11	10954978	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	2.124000	0.42006	0.418000	0.25898	0.655000	0.94253	CGG		0.547	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229	
TRIM42	287015	hgsc.bcm.edu	37	3	140401925	140401925	+	Silent	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr3:140401925C>T	ENST00000286349.3	+	2	1154	c.963C>T	c.(961-963)caC>caT	p.H321H		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	321						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.H321H(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|large_intestine(11)|lung(33)|ovary(2)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ACAATGGCCACGACACCATTA	0.552																																					p.H321H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C963T	3						.						224.0	194.0	204.0					3																	140401925		2203	4300	6503	141884615	SO:0001819	synonymous_variant	287015	exon2			AF521868	CCDS3113.1	3q23	2014-02-17	2011-01-25		ENSG00000155890	ENSG00000155890		"""Tripartite motif containing / Tripartite motif containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	19014	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 40"""		"""tripartite motif-containing 42"""				Standard	NM_152616		Approved	FLJ40097, PPP1R40	uc003eto.2	Q8IWZ5	OTTHUMG00000160170	ENST00000286349.3:c.963C>T	3.37:g.140401925C>T			141884615	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																				0.552	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616	
FNDC3B	64778	hgsc.bcm.edu	37	3	172052861	172052861	+	Missense_Mutation	SNP	G	G	C	rs148414755		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr3:172052861G>C	ENST00000336824.4	+	15	1868	c.1769G>C	c.(1768-1770)aGt>aCt	p.S590T	FNDC3B_ENST00000416957.1_Missense_Mutation_p.S590T|FNDC3B_ENST00000415807.2_Missense_Mutation_p.S590T	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	590	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)	p.S590T(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		CATGGCTTTAGTGTCAAATGG	0.408													G|||	1	0.000199681	0.0	0.0	5008	,	,		14203	0.0		0.001	False		,,,				2504	0.0				p.S590T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1769C	3						.	G	THR/SER,THR/SER	0,4406		0,0,2203	223.0	213.0	216.0		1769,1769	6.2	1.0	3	dbSNP_134	216	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FNDC3B	NM_001135095.1,NM_022763.3	58,58	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	benign,benign	590/1205,590/1205	172052861	1,13005	2203	4300	6503	173535555	SO:0001583	missense	64778	exon15			AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.1769G>C	3.37:g.172052861G>C	ENSP00000338523:p.Ser590Thr		173535555	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Missense_Mutation	SNP	ENST00000336824.4	37	CCDS3217.1	.	.	.	.	.	.	.	.	.	.	G	11.07	1.530713	0.27387	0.0	1.16E-4	ENSG00000075420	ENST00000415807;ENST00000336824;ENST00000416957	T;T;T	0.55930	0.49;0.49;0.49	6.17	6.17	0.99709	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.167364	0.64402	D	0.000004	T	0.31295	0.0792	N	0.03268	-0.37	0.80722	D	1	B;B	0.20780	0.048;0.002	B;B	0.21360	0.034;0.01	T	0.18398	-1.0338	10	0.21014	T	0.42	-14.8476	16.2608	0.82541	0.0:0.1316:0.8683:0.0	.	590;590	Q53EP0-2;Q53EP0	.;FND3B_HUMAN	T	590	ENSP00000411242:S590T;ENSP00000338523:S590T;ENSP00000389094:S590T	ENSP00000338523:S590T	S	+	2	0	FNDC3B	173535555	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.042000	0.49815	2.941000	0.99782	0.655000	0.94253	AGT		0.408	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
EIF2B5	8893	hgsc.bcm.edu	37	3	183859765	183859765	+	Silent	SNP	G	G	A	rs143448763		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr3:183859765G>A	ENST00000273783.3	+	8	1331	c.1209G>A	c.(1207-1209)gcG>gcA	p.A403A	EIF2B5_ENST00000444495.1_Silent_p.A403A	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	403					astrocyte development (GO:0014002)|astrocyte differentiation (GO:0048708)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|positive regulation of translational initiation (GO:0045948)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)|nucleus (GO:0005634)	guanyl-nucleotide exchange factor activity (GO:0005085)|translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)	p.A403A(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(9)|ovary(5)|urinary_tract(1)	27	all_cancers(143;7.59e-11)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)			TTCGAGTGGCGGCTGGAGCAC	0.562																																					p.A403A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1209A	3						.	G		1,4405	2.1+/-5.4	0,1,2202	127.0	113.0	118.0		1209	-3.2	0.8	3	dbSNP_134	118	0,8600		0,0,4300	no	coding-synonymous	EIF2B5	NM_003907.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		403/722	183859765	1,13005	2203	4300	6503	185342459	SO:0001819	synonymous_variant	8893	exon8			U23028	CCDS3252.1	3q27.3	2006-07-18	2002-08-29		ENSG00000145191	ENSG00000145191			3261	protein-coding gene	gene with protein product		603945	"""eukaryotic translation initiation factor 2B, subunit 5 (epsilon, 82kD)"""			8688466	Standard	NM_003907		Approved	EIF2Bepsilon, EIF-2B	uc003fmp.3	Q13144	OTTHUMG00000156840	ENST00000273783.3:c.1209G>A	3.37:g.183859765G>A			185342459	NM_003907	Q541Z1|Q96D04	Silent	SNP	ENST00000273783.3	37	CCDS3252.1																																																																																				0.562	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1		
RFC4	5984	hgsc.bcm.edu	37	3	186508157	186508157	+	Silent	SNP	G	G	C	rs201614562		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr3:186508157G>C	ENST00000392481.2	-	9	1121	c.840C>G	c.(838-840)gcC>gcG	p.A280A	RFC4_ENST00000433496.1_Intron|SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000296273.2_Silent_p.A280A	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	280					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)	p.A280A(1)		breast(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26	all_cancers(143;2.92e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)	GBM - Glioblastoma multiforme(93;0.0739)		CACTCTGACAGGCAGCAAATA	0.388																																					p.A280A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C840G	3						.						110.0	111.0	111.0					3																	186508157		2203	4300	6503	187990851	SO:0001819	synonymous_variant	5984	exon9				CCDS3283.1	3q27	2010-04-21	2002-08-29		ENSG00000163918	ENSG00000163918		"""ATPases / AAA-type"""	9972	protein-coding gene	gene with protein product	"""A1 37 kDa subunit"", ""activator 1 37 kDa subunit"", ""RFC 37 kDa subunit"""	102577	"""replication factor C (activator 1) 4 (37kD)"""			7774928	Standard	NM_181573		Approved	A1, RFC37	uc003fqz.3	P35249	OTTHUMG00000156515	ENST00000392481.2:c.840C>G	3.37:g.186508157G>C			187990851	NM_002916	B4DM41|D3DNV2|Q6FHX7	Silent	SNP	ENST00000392481.2	37	CCDS3283.1																																																																																				0.388	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916	
ATF7IP	55729	hgsc.bcm.edu	37	12	14633967	14633967	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr12:14633967C>T	ENST00000540793.1	+	12	3283	c.3128C>T	c.(3127-3129)cCa>cTa	p.P1043L	ATF7IP_ENST00000261168.4_Missense_Mutation_p.P1043L|ATF7IP_ENST00000543189.1_Missense_Mutation_p.P1042L|ATF7IP_ENST00000544627.1_Missense_Mutation_p.P1051L|ATF7IP_ENST00000536444.1_Missense_Mutation_p.P1042L			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1043					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.P1043L(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						ACACATCGTCCAGTAACTCAG	0.443																																					p.P1043L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3128T	12						.						112.0	112.0	112.0					12																	14633967		2203	4300	6503	14525234	SO:0001583	missense	55729	exon13			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3128C>T	12.37:g.14633967C>T	ENSP00000444589:p.Pro1043Leu		14525234	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.597010	0.87055	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000540793	T;T;T;T;T	0.57907	1.62;0.37;1.6;1.62;1.62	5.43	5.43	0.79202	.	0.000000	0.64402	D	0.000007	T	0.72053	0.3413	M	0.61703	1.905	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	T	0.73792	-0.3871	10	0.87932	D	0	-13.311	19.6057	0.95580	0.0:1.0:0.0:0.0	.	1042;1043;1042	G3V1U0;Q6VMQ6;Q6VMQ6-2	.;MCAF1_HUMAN;.	L	1043;1042;1042;1051;1043	ENSP00000261168:P1043L;ENSP00000443179:P1042L;ENSP00000445955:P1042L;ENSP00000440440:P1051L;ENSP00000444589:P1043L	ENSP00000261168:P1043L	P	+	2	0	ATF7IP	14525234	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.042000	0.64202	2.693000	0.91896	0.650000	0.86243	CCA		0.443	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
OSBPL8	114882	hgsc.bcm.edu	37	12	76780014	76780014	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr12:76780014G>A	ENST00000261183.3	-	14	1946	c.1467C>T	c.(1465-1467)ggC>ggT	p.G489G	OSBPL8_ENST00000393250.4_Silent_p.G447G|OSBPL8_ENST00000393249.2_Silent_p.G447G	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	489					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)	p.G489G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						GGAAAGTCTCGCCAAGTATAG	0.308																																					p.G489G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1467T	12						.						50.0	50.0	50.0					12																	76780014		2203	4298	6501	75304145	SO:0001819	synonymous_variant	114882	exon14			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.1467C>T	12.37:g.76780014G>A			75304145	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Silent	SNP	ENST00000261183.3	37	CCDS31862.1																																																																																				0.308	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
MAP2K5	5607	hgsc.bcm.edu	37	15	67995740	67995740	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr15:67995740T>A	ENST00000178640.5	+	16	1665	c.1038T>A	c.(1036-1038)ttT>ttA	p.F346L	MAP2K5_ENST00000354498.5_Missense_Mutation_p.F310L|MAP2K5_ENST00000340972.4_Missense_Mutation_p.F156L|MAP2K5_ENST00000395476.2_Missense_Mutation_p.F346L	NM_145160.2	NP_660143.1	Q13163	MP2K5_HUMAN	mitogen-activated protein kinase kinase 5	346	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cellular response to growth factor stimulus (GO:0071363)|cellular response to laminar fluid shear stress (GO:0071499)|ERK5 cascade (GO:0070375)|heart development (GO:0007507)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleus (GO:0005634)|spindle (GO:0005819)	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)	p.F346L(2)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|skin(1)	16						GAATCTCTTTTATGGAGGTAC	0.393																																					p.F346L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1038A	15						.						147.0	139.0	142.0					15																	67995740		2200	4298	6498	65782794	SO:0001583	missense	5607	exon16			U25265	CCDS10224.1, CCDS42051.1, CCDS55970.1	15q22.31	2011-06-09			ENSG00000137764	ENSG00000137764		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6845	protein-coding gene	gene with protein product		602520		PRKMK5		7759517	Standard	NM_002757		Approved	MEK5, MAPKK5, HsT17454	uc002aqu.3	Q13163	OTTHUMG00000133264	ENST00000178640.5:c.1038T>A	15.37:g.67995740T>A	ENSP00000178640:p.Phe346Leu		65782794	NM_145160	B4DE43|Q92961|Q92962	Missense_Mutation	SNP	ENST00000178640.5	37	CCDS10224.1	.	.	.	.	.	.	.	.	.	.	T	5.103	0.204602	0.09704	.	.	ENSG00000137764	ENST00000541298;ENST00000395476;ENST00000178640;ENST00000354498;ENST00000340972	T;T;T;T	0.58652	0.32;0.32;0.32;0.32	5.96	3.91	0.45181	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.088940	0.85682	N	0.000000	T	0.14787	0.0357	N	0.00124	-2.055	0.54753	D	0.999984	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.32666	-0.9898	10	0.02654	T	1	-14.3721	8.5833	0.33642	0.0:0.6811:0.0:0.3189	.	156;346;346	A6NK28;Q13163-2;Q13163	.;.;MP2K5_HUMAN	L	346;346;346;310;156	ENSP00000378859:F346L;ENSP00000178640:F346L;ENSP00000346493:F310L;ENSP00000342101:F156L	ENSP00000178640:F346L	F	+	3	2	MAP2K5	65782794	0.999000	0.42202	1.000000	0.80357	0.963000	0.63663	0.714000	0.25808	0.703000	0.31848	-0.417000	0.06048	TTT		0.393	MAP2K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257041.1	NM_145162	
QRFPR	84109	hgsc.bcm.edu	37	4	122254012	122254012	+	Missense_Mutation	SNP	C	C	T	rs543792498	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:122254012C>T	ENST00000394427.2	-	4	1172	c.761G>A	c.(760-762)cGa>cAa	p.R254Q	QRFPR_ENST00000334383.5_Intron	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	254				VILFLLPLMVMLILYSKIGYELWIKKRVGDGSVLRTIHGKE MSKIAR -> SSSSSCLLW (in Ref. 1; AAL26488). {ECO:0000305}.	G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)	p.R254Q(1)		endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						ATGAATAGTTCGAAGCACTGA	0.353													C|||	2	0.000399361	0.0	0.0014	5008	,	,		14668	0.001		0.0	False		,,,				2504	0.0				p.R254Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G761A	4						.						84.0	81.0	82.0					4																	122254012		2203	4300	6503	122473462	SO:0001583	missense	84109	exon4			AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.761G>A	4.37:g.122254012C>T	ENSP00000377948:p.Arg254Gln		122473462	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	C	0.817	-0.750009	0.03041	.	.	ENSG00000186867	ENST00000394427	T	0.74315	-0.83	6.17	0.811	0.18739	GPCR, rhodopsin-like superfamily (1);	0.459160	0.25857	N	0.027850	T	0.49236	0.1545	N	0.12961	0.28	0.29769	N	0.834915	B	0.14012	0.009	B	0.08055	0.003	T	0.38845	-0.9642	10	0.06625	T	0.88	.	9.4707	0.38839	0.0:0.3941:0.0:0.6058	.	254	Q96P65	QRFPR_HUMAN	Q	254	ENSP00000377948:R254Q	ENSP00000377948:R254Q	R	-	2	0	QRFPR	122473462	0.996000	0.38824	0.819000	0.32651	0.170000	0.22686	0.324000	0.19610	-0.020000	0.14032	-0.797000	0.03246	CGA		0.353	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
FAT4	79633	hgsc.bcm.edu	37	4	126371394	126371394	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:126371394G>C	ENST00000394329.3	+	9	9236	c.9223G>C	c.(9223-9225)Gtt>Ctt	p.V3075L	FAT4_ENST00000335110.5_Missense_Mutation_p.V1373L	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3075	Cadherin 29. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V3075L(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CCAAGCAACTGTTCACATAAC	0.438																																					p.V3075L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G9223C	4						.						98.0	93.0	94.0					4																	126371394		2203	4300	6503	126590844	SO:0001583	missense	79633	exon9			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9223G>C	4.37:g.126371394G>C	ENSP00000377862:p.Val3075Leu		126590844	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	10.66	1.411790	0.25465	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.57107	0.42;1.81	5.63	4.78	0.61160	Cadherin (4);Cadherin-like (1);	0.275170	0.18282	U	0.145996	T	0.44726	0.1307	L	0.38692	1.165	0.58432	D	0.999999	B;B;B	0.11235	0.003;0.004;0.003	B;B;B	0.15052	0.005;0.012;0.007	T	0.24941	-1.0146	10	0.32370	T	0.25	.	14.9304	0.70911	0.0691:0.0:0.9309:0.0	.	1373;3075;3075	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	L	3075;1373	ENSP00000377862:V3075L;ENSP00000335169:V1373L	ENSP00000335169:V1373L	V	+	1	0	FAT4	126590844	1.000000	0.71417	0.894000	0.35097	0.463000	0.32649	3.729000	0.54999	1.353000	0.45828	0.655000	0.94253	GTT		0.438	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FGA	2243	hgsc.bcm.edu	37	4	155507733	155507733	+	Missense_Mutation	SNP	G	G	A	rs555704618		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:155507733G>A	ENST00000302053.3	-	5	926	c.848C>T	c.(847-849)aCg>aTg	p.T283M	FGA_ENST00000403106.3_Missense_Mutation_p.T283M	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	283					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)	p.T283M(1)		NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	GGGGCTTTCCGTCTCTGATCC	0.542													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18029	0.0		0.0	False		,,,				2504	0.0				p.T283M	NSCLC(143;340 1922 20892 22370 48145)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C848T	4						.						99.0	107.0	104.0					4																	155507733		2203	4300	6503	155727183	SO:0001583	missense	2243	exon5				CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.848C>T	4.37:g.155507733G>A	ENSP00000306361:p.Thr283Met		155727183	NM_021871	A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Missense_Mutation	SNP	ENST00000302053.3	37	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.630623	0.46944	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	D;D	0.82619	-1.63;-1.63	4.91	-2.44	0.06502	.	32.388400	0.00166	N	0.000000	T	0.72566	0.3476	L	0.38175	1.15	0.09310	N	1	P;P	0.49862	0.929;0.928	B;B	0.38712	0.28;0.109	T	0.65413	-0.6174	10	0.59425	D	0.04	.	4.3068	0.10951	0.0741:0.3172:0.3568:0.2519	.	283;283	P02671-2;P02671	.;FIBA_HUMAN	M	283	ENSP00000306361:T283M;ENSP00000385981:T283M	ENSP00000306361:T283M	T	-	2	0	FGA	155727183	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.274000	0.18680	-0.382000	0.07870	-0.344000	0.07964	ACG		0.542	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
EVC2	132884	hgsc.bcm.edu	37	4	5690922	5690922	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:5690922G>A	ENST00000344408.5	-	5	721	c.668C>T	c.(667-669)tCg>tTg	p.S223L	EVC2_ENST00000310917.2_Missense_Mutation_p.S143L|EVC2_ENST00000344938.1_Missense_Mutation_p.S223L	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	223					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.S223L(1)		NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						GAATCCTTCCGAGGTCCTGTT	0.488																																					p.S143L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C428T	4						.						100.0	92.0	94.0					4																	5690922		2203	4300	6503	5741823	SO:0001583	missense	132884	exon5			AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.668C>T	4.37:g.5690922G>A	ENSP00000342144:p.Ser223Leu		5741823	NM_001166136	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	G	5.073	0.199175	0.09652	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.75050	-0.9;-0.89;-0.89	4.54	2.7	0.31948	.	0.000000	0.85682	D	0.000000	T	0.56949	0.2020	L	0.42245	1.32	0.09310	N	1	P	0.43633	0.813	B	0.25405	0.06	T	0.50558	-0.8814	10	0.48119	T	0.1	-1.4813	9.8406	0.40996	0.0:0.0:0.6552:0.3448	.	223	Q86UK5	LBN_HUMAN	L	223;143;223	ENSP00000339954:S223L;ENSP00000311683:S143L;ENSP00000342144:S223L	ENSP00000311683:S143L	S	-	2	0	EVC2	5741823	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.417000	0.21214	0.403000	0.25479	0.561000	0.74099	TCG		0.488	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
NFXL1	152518	hgsc.bcm.edu	37	4	47907326	47907326	+	Silent	SNP	A	A	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:47907326A>G	ENST00000507489.1	-	4	620	c.444T>C	c.(442-444)taT>taC	p.Y148Y	NFXL1_ENST00000381538.3_Silent_p.Y148Y|NFXL1_ENST00000329043.3_Silent_p.Y148Y	NM_001278624.1	NP_001265553.1	Q6ZNB6	NFXL1_HUMAN	nuclear transcription factor, X-box binding-like 1	148						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Y148Y(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(4)	27						CTTCATTTACATATTGTTTTG	0.333																																					p.Y148Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T444C	4						.						156.0	163.0	160.0					4																	47907326		2203	4300	6503	47602083	SO:0001819	synonymous_variant	152518	exon4			AY134856	CCDS3478.2	4p12	2008-02-05			ENSG00000170448	ENSG00000170448			18726	protein-coding gene	gene with protein product	"""ovarian zinc finger protein"""						Standard	NM_152995		Approved	HOZFP	uc003gxp.3	Q6ZNB6	OTTHUMG00000128621	ENST00000507489.1:c.444T>C	4.37:g.47907326A>G			47602083	NM_152995	B1Q2K1|Q86VG1|Q8WVH1	Silent	SNP	ENST00000507489.1	37	CCDS3478.2																																																																																				0.333	NFXL1-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361636.1	NM_152995	
FAM47E-STBD1	100631383	hgsc.bcm.edu	37	4	77231020	77231020	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:77231020C>T	ENST00000237642.6	+	2	1688	c.944C>T	c.(943-945)gCa>gTa	p.A315V	FAM47E_ENST00000515604.1_3'UTR|FAM47E-STBD1_ENST00000539752.1_Missense_Mutation_p.A166V	NM_003943.4	NP_003934.1			FAM47E-STBD1 readthrough									p.A315V(1)									TTCCTGCCTGCAGATACAGTG	0.483																																					p.A315V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C944T	4						.						187.0	178.0	181.0					4																	77231020		2203	4300	6503	77450044	SO:0001583	missense	8987	exon2				CCDS58908.1	4q21.1	2013-04-23			ENSG00000118804	ENSG00000118804			44667	other	readthrough							Standard	NM_001242939		Approved				OTTHUMG00000160966	ENST00000237642.6:c.944C>T	4.37:g.77231020C>T	ENSP00000237642:p.Ala315Val		77450044	NM_003943		Missense_Mutation	SNP	ENST00000237642.6	37	CCDS3578.1	.	.	.	.	.	.	.	.	.	.	C	11.08	1.534899	0.27475	.	.	ENSG00000118804	ENST00000539752;ENST00000237642	D;D	0.94497	-3.44;-3.44	5.4	4.48	0.54585	Carbohydrate-binding-like fold (1);Glycoside hydrolase, carbohydrate-binding (2);Immunoglobulin-like fold (1);	0.218818	0.29438	N	0.012146	D	0.92244	0.7540	L	0.52759	1.655	0.19775	N	0.999957	P	0.39094	0.659	P	0.44673	0.457	D	0.85032	0.0918	10	0.34782	T	0.22	-14.9282	7.997	0.30273	0.0:0.8423:0.0:0.1577	.	315	O95210	STBD1_HUMAN	V	166;315	ENSP00000442265:A166V;ENSP00000237642:A315V	ENSP00000237642:A315V	A	+	2	0	STBD1	77450044	0.013000	0.17824	0.770000	0.31555	0.105000	0.19272	0.168000	0.16622	2.805000	0.96524	0.655000	0.94253	GCA		0.483	FAM47E-STBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252415.2		
PRIMPOL	201973	hgsc.bcm.edu	37	4	185612854	185612854	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr4:185612854T>A	ENST00000314970.6	+	13	1846	c.1413T>A	c.(1411-1413)ttT>ttA	p.F471L	PRIMPOL_ENST00000515774.1_Missense_Mutation_p.F342L|PRIMPOL_ENST00000503752.1_Missense_Mutation_p.F471L|PRIMPOL_ENST00000512834.1_Missense_Mutation_p.F470L	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	471					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)	p.F471L(1)									GTCTCCTGTTTCTTTTCAAAG	0.353																																					p.F471L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1413A	4						.						158.0	156.0	156.0					4																	185612854		2202	4300	6502	185849848	SO:0001583	missense	201973	exon13			AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.1413T>A	4.37:g.185612854T>A	ENSP00000313816:p.Phe471Leu		185849848	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Missense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	T	11.78	1.741093	0.30865	.	.	ENSG00000164306	ENST00000314970;ENST00000515774;ENST00000503752;ENST00000512834;ENST00000508001	T;T;T;T	0.30448	1.54;1.53;1.54;1.54	4.84	1.15	0.20763	.	0.596983	0.19257	N	0.118768	T	0.25121	0.0610	L	0.59436	1.845	0.80722	D	1	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.06405	0.002;0.002;0.002	T	0.05084	-1.0907	10	0.41790	T	0.15	-9.7233	5.6268	0.17487	0.0:0.2281:0.1515:0.6204	.	342;471;470	D3DP56;Q96LW4;D6RDM1	.;CC111_HUMAN;.	L	471;342;471;470;145	ENSP00000313816:F471L;ENSP00000421913:F342L;ENSP00000420860:F471L;ENSP00000425316:F470L	ENSP00000313816:F471L	F	+	3	2	CCDC111	185849848	0.315000	0.24571	0.045000	0.18777	0.800000	0.45204	0.511000	0.22739	0.115000	0.18071	0.260000	0.18958	TTT		0.353	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
RGAG1	57529	hgsc.bcm.edu	37	X	109696873	109696873	+	Missense_Mutation	SNP	G	G	A	rs148401387	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:109696873G>A	ENST00000465301.2	+	3	3274	c.3028G>A	c.(3028-3030)Gtg>Atg	p.V1010M	RGAG1_ENST00000540313.1_Missense_Mutation_p.V1010M	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1010								p.V1010M(1)		NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						AACATATACCGTGTCTGGAAG	0.498																																					p.V1010M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3028A	X						.	G	MET/VAL	5,3830		1,3,1628,571	230.0	200.0	210.0		3028	0.1	0.0	X	dbSNP_134	210	0,6728		0,0,2428,1872	yes	missense	RGAG1	NM_020769.2	21	1,3,4056,2443	AA,AG,GG,G		0.0,0.1304,0.0473	possibly-damaging	1010/1389	109696873	5,10558	2203	4300	6503	109583529	SO:0001583	missense	57529	exon3			AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3028G>A	X.37:g.109696873G>A	ENSP00000419786:p.Val1010Met		109583529	NM_020769	Q9P2M8	Missense_Mutation	SNP	ENST00000465301.2	37	CCDS14552.1	.	.	.	.	.	.	.	.	.	.	G	6.766	0.510246	0.12883	0.001304	0.0	ENSG00000243978	ENST00000465301;ENST00000540313;ENST00000540483	T;T	0.46451	0.87;0.87	4.24	0.0714	0.14382	.	1.266790	0.06086	N	0.662793	T	0.34106	0.0886	L	0.40543	1.245	0.09310	N	1	D	0.64830	0.994	P	0.44597	0.454	T	0.23190	-1.0195	9	.	.	.	0.9452	4.6263	0.12479	0.2612:0.3264:0.4124:0.0	.	1010	Q8NET4	RGAG1_HUMAN	M	1010;1010;571	ENSP00000419786:V1010M;ENSP00000441452:V1010M	.	V	+	1	0	RGAG1	109583529	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	0.403000	0.20982	-0.123000	0.11745	-0.192000	0.12808	GTG		0.498	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769	
DOCK11	139818	hgsc.bcm.edu	37	X	117695437	117695437	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:117695437C>A	ENST00000276202.7	+	7	713	c.650C>A	c.(649-651)tCg>tAg	p.S217*	DOCK11_ENST00000276204.6_Nonsense_Mutation_p.S217*	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	217	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S217W(1)|p.S217*(1)		breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						TCAAAAGAATCGAAAGGTTGC	0.363																																					p.S217X												.	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|lung(1)	c.C650A	X						.						108.0	98.0	102.0					X																	117695437		2203	4300	6503	117579465	SO:0001587	stop_gained	139818	exon7			AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.650C>A	X.37:g.117695437C>A	ENSP00000276202:p.Ser217*		117579465	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Nonsense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	c	38	6.854179	0.97889	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	.	.	.	5.41	5.41	0.78517	.	0.185584	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.20046	T	0.44	-4.9426	18.1276	0.89591	0.0:1.0:0.0:0.0	.	.	.	.	X	217	.	ENSP00000276202:S217X	S	+	2	0	DOCK11	117579465	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.373000	0.79623	2.405000	0.81733	0.417000	0.27973	TCG		0.363	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
MSN	4478	hgsc.bcm.edu	37	X	64951047	64951047	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:64951047G>A	ENST00000360270.5	+	5	718	c.546G>A	c.(544-546)atG>atA	p.M182I		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	182	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.M182I(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						ACCGTGGCATGCTCAGGTAAG	0.537			T	ALK	ALCL																																p.M182I			Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G546A	X						.						104.0	66.0	79.0					X																	64951047		2203	4300	6503	64867772	SO:0001583	missense	4478	exon5			M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.546G>A	X.37:g.64951047G>A	ENSP00000353408:p.Met182Ile		64867772	NM_002444		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017043	0.75161	.	.	ENSG00000147065	ENST00000360270	T	0.78595	-1.19	5.8	5.8	0.92144	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	0.000000	0.85682	D	0.000000	T	0.81211	0.4775	M	0.78344	2.41	0.80722	D	1	B	0.21606	0.058	B	0.30855	0.121	T	0.78453	-0.2198	10	0.51188	T	0.08	.	17.4025	0.87464	0.0:0.0:1.0:0.0	.	182	P26038	MOES_HUMAN	I	182	ENSP00000353408:M182I	ENSP00000353408:M182I	M	+	3	0	MSN	64867772	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.732000	0.98816	2.434000	0.82447	0.600000	0.82982	ATG		0.537	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444	
NONO	4841	hgsc.bcm.edu	37	X	70517755	70517755	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:70517755G>C	ENST00000276079.8	+	9	1303	c.1098G>C	c.(1096-1098)caG>caC	p.Q366H	NONO_ENST00000373841.1_Missense_Mutation_p.Q366H|NONO_ENST00000373856.3_Missense_Mutation_p.Q366H|NONO_ENST00000490044.1_3'UTR|NONO_ENST00000535149.1_Missense_Mutation_p.Q277H	NM_007363.4	NP_031389.3	Q15233	NONO_HUMAN	non-POU domain containing, octamer-binding	366	DBHS.			QQ -> HE (in Ref. 3; CAA72157 and 4; AAA03427). {ECO:0000305}.	circadian rhythm (GO:0007623)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|mRNA processing (GO:0006397)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of circadian rhythm (GO:0042752)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|paraspeckles (GO:0042382)	core promoter binding (GO:0001047)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.Q366H(1)	NONO/TFE3(2)	endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	19	Renal(35;0.156)					TGCGGCGACAGCAGGAAGGAT	0.517			T	TFE3	papillary renal cancer																																p.Q277H			Dom	yes		X	Xq13.1	4841	"""non-POU domain containing, octamer-binding"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G831C	X						.						91.0	68.0	76.0					X																	70517755		2203	4300	6503	70434480	SO:0001583	missense	4841	exon7			L14599	CCDS14410.1, CCDS55445.1	Xq13.1	2014-06-13	2002-01-14		ENSG00000147140	ENSG00000147140		"""RNA binding motif (RRM) containing"""	7871	protein-coding gene	gene with protein product	"""Nuclear RNA-binding protein, 54-kD"", ""non-Pou domain-containing octamer (ATGCAAAT) binding protein"", ""protein phosphatase 1, regulatory subunit 114"""	300084	"""non-POU-domain-containing, octamer-binding"""			8371983, 9360842	Standard	NM_007363		Approved	NRB54, NMT55, P54NRB, P54, PPP1R114	uc004dzp.3	Q15233	OTTHUMG00000021798	ENST00000276079.8:c.1098G>C	X.37:g.70517755G>C	ENSP00000276079:p.Gln366His		70434480	NM_001145410	B7Z4C2|D3DVV4|F5GYZ3|O00201|P30807|Q12786|Q9BQC5	Missense_Mutation	SNP	ENST00000276079.8	37	CCDS14410.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	15.57|15.57	2.872809|2.872809	0.51695|0.51695	.|.	.|.	ENSG00000147140|ENSG00000147140	ENST00000535149;ENST00000276079;ENST00000373856;ENST00000373841|ENST00000418921	T;T;T;T|.	0.23552|.	1.95;1.9;1.9;1.9|.	5.23|5.23	5.23|5.23	0.72850|0.72850	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.70482|0.70482	0.3229|0.3229	M|M	0.67625|0.67625	2.065|2.065	0.80722|0.80722	D|D	1|1	D|.	0.61080|.	0.989|.	P|.	0.50708|.	0.648|.	T|T	0.69993|0.69993	-0.4994|-0.4994	10|5	0.54805|.	T|.	0.06|.	-9.9515|-9.9515	12.2602|12.2602	0.54647|0.54647	0.0825:0.0:0.9175:0.0|0.0825:0.0:0.9175:0.0	.|.	366|.	Q15233|.	NONO_HUMAN|.	H|T	277;366;366;366|228	ENSP00000441364:Q277H;ENSP00000276079:Q366H;ENSP00000362963:Q366H;ENSP00000362947:Q366H|.	ENSP00000276079:Q366H|.	Q|S	+|+	3|2	2|0	NONO|NONO	70434480|70434480	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.257000|5.257000	0.65473|0.65473	2.427000|2.427000	0.82271|0.82271	0.529000|0.529000	0.55759|0.55759	CAG|AGC		0.517	NONO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057138.1	NM_007363	
ITM2A	9452	hgsc.bcm.edu	37	X	78618104	78618104	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:78618104G>C	ENST00000373298.2	-	4	669	c.526C>G	c.(526-528)Ctg>Gtg	p.L176V	ITM2A_ENST00000434584.2_Missense_Mutation_p.L132V|ITM2A_ENST00000469541.1_5'UTR	NM_004867.4	NP_004858.1	O43736	ITM2A_HUMAN	integral membrane protein 2A	176	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)		p.L176V(1)		breast(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	18						AGCTCTACCAGATTTTTTGGA	0.373																																					p.L176V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C526G	X						.						66.0	61.0	63.0					X																	78618104		2203	4299	6502	78504760	SO:0001583	missense	9452	exon4			BC034485	CCDS14444.1, CCDS55455.1	Xq13.3-q21.2	2012-10-10			ENSG00000078596	ENSG00000078596		"""BRICHOS domain containing"""	6173	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2A"""	300222				9892734, 8702637	Standard	NM_004867		Approved	BRICD2A, E25A	uc004edh.3	O43736	OTTHUMG00000021900	ENST00000373298.2:c.526C>G	X.37:g.78618104G>C	ENSP00000362395:p.Leu176Val		78504760	NM_004867	B2R7X5|B4E062|Q6IBC9	Missense_Mutation	SNP	ENST00000373298.2	37	CCDS14444.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.472995	0.26423	.	.	ENSG00000078596	ENST00000373298;ENST00000434584	D;D	0.83992	-1.79;-1.79	4.95	3.16	0.36331	BRICHOS (2);	0.000000	0.64402	D	0.000002	D	0.87597	0.6217	M	0.76170	2.325	0.45239	D	0.998247	D;D	0.56746	0.961;0.977	P;P	0.61328	0.887;0.735	D	0.85693	0.1308	10	0.72032	D	0.01	-12.0285	7.8383	0.29382	0.0883:0.0:0.7508:0.1609	.	132;176	B4E062;O43736	.;ITM2A_HUMAN	V	176;132	ENSP00000362395:L176V;ENSP00000415533:L132V	ENSP00000362395:L176V	L	-	1	2	ITM2A	78504760	1.000000	0.71417	0.996000	0.52242	0.053000	0.15095	1.011000	0.29911	0.328000	0.23435	-0.245000	0.11935	CTG		0.373	ITM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057329.1	NM_004867	
TBX22	50945	hgsc.bcm.edu	37	X	79281207	79281207	+	Silent	SNP	C	C	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:79281207C>A	ENST00000373294.5	+	4	592	c.564C>A	c.(562-564)acC>acA	p.T188T	TBX22_ENST00000442340.1_Silent_p.T68T|TBX22_ENST00000373296.3_Silent_p.T188T|TBX22_ENST00000373291.1_Silent_p.T68T	NM_016954.2	NP_058650.1	Q9Y458	TBX22_HUMAN	T-box 22	188					multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T188T(1)		breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(13)|lung(38)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CGGGAGAGACCTGGATGCGGC	0.502																																					p.T188T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C564A	X						.						107.0	72.0	84.0					X																	79281207		2203	4300	6503	79167863	SO:0001819	synonymous_variant	50945	exon5			AL031000	CCDS14445.1, CCDS43975.1	Xq21.1	2011-02-11			ENSG00000122145	ENSG00000122145		"""T-boxes"""	11600	protein-coding gene	gene with protein product		300307	"""cleft palate and/or ankyloglossia"""	CPX, CLPA		11559848, 14729838	Standard	NM_001109878		Approved		uc004edj.1	Q9Y458	OTTHUMG00000021901	ENST00000373294.5:c.564C>A	X.37:g.79281207C>A			79167863	NM_001109878	Q5JZ06|Q96LC0|Q9HBF1	Silent	SNP	ENST00000373294.5	37	CCDS14445.1																																																																																				0.502	TBX22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057334.1	NM_016954	
L1CAM	3897	hgsc.bcm.edu	37	X	153134140	153134140	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chrX:153134140G>T	ENST00000370060.1	-	13	1611	c.1422C>A	c.(1420-1422)ttC>ttA	p.F474L	L1CAM_ENST00000361981.3_Missense_Mutation_p.F469L|L1CAM_ENST00000361699.4_Missense_Mutation_p.F474L|L1CAM_ENST00000370057.3_Missense_Mutation_p.F474L|L1CAM_ENST00000538883.1_Missense_Mutation_p.F476L|L1CAM_ENST00000370055.1_Missense_Mutation_p.F469L|L1CAM_ENST00000543994.1_Missense_Mutation_p.F476L	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	474	Ig-like C2-type 5.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cell-cell adhesion mediated by integrin (GO:0033631)|chemotaxis (GO:0006935)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|homotypic cell-cell adhesion (GO:0034109)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	sialic acid binding (GO:0033691)	p.F474L(1)|p.F474F(1)		NS(1)|breast(4)|central_nervous_system(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|liver(1)|lung(31)|ovary(13)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	81	all_cancers(53;6.72e-15)|all_epithelial(53;3.19e-09)|all_lung(58;3.39e-06)|all_hematologic(71;4.25e-06)|Lung NSC(58;4.7e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CATAGGGGAAGAAGCGTTCGT	0.617																																					p.F469L												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|breast(1)	c.C1407A	X						.						144.0	104.0	118.0					X																	153134140		2203	4300	6503	152787334	SO:0001583	missense	3897	exon11			M74387	CCDS14733.1, CCDS14734.1, CCDS48192.1	Xq28	2014-09-17	2003-04-07		ENSG00000198910	ENSG00000198910		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	6470	protein-coding gene	gene with protein product		308840	"""antigen identified by monoclonal antibody R1"""	HSAS1, SPG1, HSAS, MASA, MIC5, S10			Standard	NM_001278116		Approved	CD171	uc031tks.1	P32004	OTTHUMG00000024221	ENST00000370060.1:c.1422C>A	X.37:g.153134140G>T	ENSP00000359077:p.Phe474Leu		152787334	NM_001143963	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	G	16.78	3.216898	0.58452	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000361699	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.62	3.49	0.39957	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000004	T	0.60728	0.2291	N	0.20304	0.555	0.39560	D	0.969112	D;B;P	0.55800	0.973;0.257;0.948	P;B;P	0.57152	0.718;0.202;0.814	T	0.63782	-0.6559	10	0.66056	D	0.02	.	6.5262	0.22303	0.3927:0.0:0.6073:0.0	.	469;474;474	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	L	474;476;474;476;469;469;474	ENSP00000359077:F474L;ENSP00000438430:F476L;ENSP00000359074:F474L;ENSP00000439645:F476L;ENSP00000354712:F469L;ENSP00000359072:F469L;ENSP00000355380:F474L	ENSP00000355380:F474L	F	-	3	2	L1CAM	152787334	1.000000	0.71417	1.000000	0.80357	0.783000	0.44284	1.559000	0.36320	1.128000	0.42052	0.529000	0.55759	TTC		0.617	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003	
TPO	7173	hgsc.bcm.edu	37	2	1497771	1497771	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:1497771C>G	ENST00000345913.4	+	11	2057	c.1966C>G	c.(1966-1968)Ctc>Gtc	p.L656V	TPO_ENST00000349624.3_Missense_Mutation_p.L483V|TPO_ENST00000346956.3_Missense_Mutation_p.L656V|TPO_ENST00000329066.4_Missense_Mutation_p.L656V|TPO_ENST00000382201.3_Missense_Mutation_p.L599V|TPO_ENST00000497517.2_3'UTR|TPO_ENST00000337415.3_Missense_Mutation_p.L656V|TPO_ENST00000382198.1_Missense_Mutation_p.L483V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	656					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)	p.L656V(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	GTTTGCCTGTCTCATTGGGAA	0.567																																					p.L656V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1966G	2						.						83.0	81.0	82.0					2																	1497771		2203	4300	6503	1476778	SO:0001583	missense	7173	exon10				CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.1966C>G	2.37:g.1497771C>G	ENSP00000318820:p.Leu656Val		1476778	NM_175721	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	C	14.01	2.407133	0.42715	.	.	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607	T;T;T;T;T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76;-0.76	4.84	-2.62	0.06152	.	0.402568	0.27622	N	0.018553	T	0.71626	0.3362	L	0.55213	1.73	0.80722	D	1	D;P;P;D	0.55385	0.964;0.543;0.633;0.971	P;B;B;P	0.51079	0.527;0.215;0.221;0.658	T	0.70753	-0.4786	10	0.72032	D	0.01	-23.9214	10.0126	0.41995	0.2684:0.5388:0.0:0.1928	.	656;483;599;656	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	V	656;656;656;483;656;599;483;585;130	ENSP00000337263:L656V;ENSP00000318820:L656V;ENSP00000263886:L656V;ENSP00000332044:L483V;ENSP00000329869:L656V;ENSP00000371636:L599V;ENSP00000371633:L483V;ENSP00000405788:L585V;ENSP00000419461:L130V	ENSP00000329869:L656V	L	+	1	0	TPO	1476778	0.193000	0.23313	0.245000	0.24217	0.509000	0.34042	0.273000	0.18662	-0.654000	0.05394	-0.314000	0.08810	CTC		0.567	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
LPIN1	23175	hgsc.bcm.edu	37	2	11960606	11960606	+	Silent	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:11960606C>T	ENST00000256720.2	+	19	2572	c.2479C>T	c.(2479-2481)Ctg>Ttg	p.L827L	LPIN1_ENST00000404113.2_Silent_p.L328L|LPIN1_ENST00000449576.2_Silent_p.L912L|LPIN1_ENST00000425416.2_Silent_p.L833L|LPIN1_ENST00000396097.1_Silent_p.L557L|LPIN1_ENST00000396099.1_Silent_p.L869L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	827	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.L827L(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TAAAGGAGAGCTGGTACAGGA	0.358																																					p.L827L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2479T	2						.						126.0	115.0	118.0					2																	11960606		2203	4300	6503	11878057	SO:0001819	synonymous_variant	23175	exon19			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.2479C>T	2.37:g.11960606C>T			11878057	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																				0.358	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
DPP10	57628	hgsc.bcm.edu	37	2	116548684	116548684	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:116548684T>C	ENST00000410059.1	+	18	2039	c.1559T>C	c.(1558-1560)aTg>aCg	p.M520T	DPP10_ENST00000310323.8_Missense_Mutation_p.M513T|DPP10_ENST00000409163.1_Missense_Mutation_p.M470T|DPP10_ENST00000393147.2_Missense_Mutation_p.M524T	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	520						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)	p.M513T(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						AGCAATTCTATGCTGAAGGAA	0.328																																					p.M470T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1409C	2						.						61.0	64.0	63.0					2																	116548684		2202	4297	6499	116265154	SO:0001583	missense	57628	exon19			AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.1559T>C	2.37:g.116548684T>C	ENSP00000386565:p.Met520Thr		116265154	NM_001178036	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	T	6.504	0.461244	0.12342	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323;ENST00000476155	T;T;T;T	0.28454	1.61;1.61;1.61;1.61	5.54	3.1	0.35709	.	0.638830	0.17490	N	0.172389	T	0.19927	0.0479	L	0.36672	1.1	0.21652	N	0.999601	B;B;B;B	0.12630	0.006;0.005;0.003;0.003	B;B;B;B	0.09377	0.003;0.004;0.001;0.001	T	0.28618	-1.0038	10	0.13853	T	0.58	-1.6166	7.2627	0.26212	0.1447:0.0:0.1519:0.7035	.	513;524;516;520	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	T	520;470;524;513;470	ENSP00000386565:M520T;ENSP00000387038:M470T;ENSP00000376855:M524T;ENSP00000309066:M513T	ENSP00000309066:M513T	M	+	2	0	DPP10	116265154	0.995000	0.38212	0.925000	0.36789	0.956000	0.61745	2.876000	0.48498	0.489000	0.27749	0.528000	0.53228	ATG		0.328	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
MARCH7	64844	hgsc.bcm.edu	37	2	160619487	160619487	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:160619487C>G	ENST00000259050.4	+	8	2112	c.1990C>G	c.(1990-1992)Cca>Gca	p.P664A	MARCH7_ENST00000409591.1_Missense_Mutation_p.P626A|MARCH7_ENST00000539065.1_Missense_Mutation_p.P608A|MARCH7_ENST00000409175.1_Missense_Mutation_p.P664A	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	664					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.P664A(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						TACAAATGAACCAAGCACACG	0.428																																					p.P664A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1990G	2						.						116.0	104.0	108.0					2																	160619487		2203	4300	6503	160327733	SO:0001583	missense	64844	exon8			AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.1990C>G	2.37:g.160619487C>G	ENSP00000259050:p.Pro664Ala		160327733	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	C	3.163	-0.171718	0.06421	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591;ENST00000420397	T;T;T;T;T	0.39406	3.09;2.99;3.09;3.07;1.08	5.11	4.16	0.48862	.	0.054440	0.64402	D	0.000001	T	0.11665	0.0284	N	0.00538	-1.39	0.33402	D	0.57746	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.09377	0.004;0.003;0.002	T	0.21999	-1.0229	10	0.02654	T	1	-13.7879	12.4292	0.55565	0.0:0.5886:0.4114:0.0	.	608;626;664	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	A	664;608;664;626;97	ENSP00000386830:P664A;ENSP00000442992:P608A;ENSP00000259050:P664A;ENSP00000387238:P626A;ENSP00000391493:P97A	ENSP00000259050:P664A	P	+	1	0	MARCH7	160327733	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.995000	0.63908	2.527000	0.85204	0.650000	0.86243	CCA		0.428	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
SDPR	8436	hgsc.bcm.edu	37	2	192701302	192701302	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:192701302G>A	ENST00000304141.4	-	2	954	c.625C>T	c.(625-627)Ccc>Tcc	p.P209S		NM_004657.5	NP_004648.1			serum deprivation response									p.P209S(1)		NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			TCATCGTGGGGCAAATCATCA	0.527																																					p.P209S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C625T	2						.						90.0	95.0	93.0					2																	192701302		2203	4300	6503	192409547	SO:0001583	missense	8436	exon2			AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"""phosphatidylserine binding protein"""	606728	"""serum deprivation response (phosphatidylserine-binding protein)"", ""serum deprivation response (phosphatidylserine binding protein)"""			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.625C>T	2.37:g.192701302G>A	ENSP00000305675:p.Pro209Ser		192409547	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	37	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	G	1.432	-0.570067	0.03910	.	.	ENSG00000168497	ENST00000304141	T	0.58358	0.34	5.16	-0.0679	0.13758	.	0.464038	0.23069	N	0.052299	T	0.39226	0.1070	L	0.54323	1.7	0.09310	N	1	B	0.28933	0.228	B	0.27796	0.083	T	0.32561	-0.9902	10	0.09843	T	0.71	-15.744	9.289	0.37775	0.063:0.5258:0.303:0.1083	.	209	O95810	SDPR_HUMAN	S	209	ENSP00000305675:P209S	ENSP00000305675:P209S	P	-	1	0	SDPR	192409547	0.433000	0.25562	0.019000	0.16419	0.009000	0.06853	1.035000	0.30216	-0.185000	0.10550	-0.344000	0.07964	CCC		0.527	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
C2orf44	80304	hgsc.bcm.edu	37	2	24261324	24261324	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:24261324A>T	ENST00000295148.4	-	2	1098	c.1041T>A	c.(1039-1041)ttT>ttA	p.F347L	C2orf44_ENST00000406895.3_Missense_Mutation_p.F347L	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	347								p.F347L(1)	C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTTAAGATTAAATGCTATCA	0.403			T	ALK	NSCLC																																p.F347L			Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1041A	2						.						56.0	55.0	55.0					2																	24261324		2201	4296	6497	24114828	SO:0001583	missense	80304	exon2			AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.1041T>A	2.37:g.24261324A>T	ENSP00000295148:p.Phe347Leu		24114828	NM_025203	D6W532|Q8IYK0|Q9HBP5	Missense_Mutation	SNP	ENST00000295148.4	37	CCDS1705.1	.	.	.	.	.	.	.	.	.	.	A	15.84	2.951580	0.53186	.	.	ENSG00000163026	ENST00000295148;ENST00000406895	T;T	0.49139	0.79;0.79	5.38	0.371	0.16168	WD40/YVTN repeat-like-containing domain (1);	0.046236	0.85682	D	0.000000	T	0.54303	0.1850	M	0.76328	2.33	0.44036	D	0.99676	P;D	0.55385	0.944;0.971	P;P	0.53146	0.719;0.719	T	0.54768	-0.8244	10	0.51188	T	0.08	-17.5121	9.0493	0.36367	0.715:0.0:0.285:0.0	.	347;347	Q9H6R7-2;Q9H6R7	.;CB044_HUMAN	L	347	ENSP00000295148:F347L;ENSP00000385816:F347L	ENSP00000295148:F347L	F	-	3	2	C2orf44	24114828	0.999000	0.42202	0.004000	0.12327	0.783000	0.44284	0.924000	0.28777	0.113000	0.18004	0.533000	0.62120	TTT		0.403	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
GTF2A1L	11036	hgsc.bcm.edu	37	2	48873903	48873903	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:48873903T>C	ENST00000403751.3	+	6	737	c.700T>C	c.(700-702)Tgt>Cgt	p.C234R	GTF2A1L_ENST00000430487.2_Missense_Mutation_p.C200R|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.C938R|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.C891R|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.C938R|LHCGR_ENST00000420913.3_Intron	NM_006872.3	NP_006863.2	Q9UNN4	TF2AY_HUMAN	general transcription factor IIA, 1-like	234					cognition (GO:0050890)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIIA complex (GO:0005672)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.C938R(1)		lung(7)	7		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCTTTGTTGTGTCATCAGGA	0.418																																					p.C234R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T700C	2						.						131.0	117.0	122.0					2																	48873903		2203	4300	6503	48727407	SO:0001583	missense	286749	exon6			AF106857	CCDS46281.1, CCDS54359.1	2p16.3	2007-08-02			ENSG00000242441	ENSG00000242441			30727	protein-coding gene	gene with protein product	"""TFIIA alpha/beta like factor"""	605358				10364255, 11889132, 16525715	Standard	NM_006872		Approved	ALF		Q9UNN4	OTTHUMG00000152038	ENST00000403751.3:c.700T>C	2.37:g.48873903T>C	ENSP00000384597:p.Cys234Arg		48727407	NM_006872	B4DY14|Q53FD9|Q5D050	Missense_Mutation	SNP	ENST00000403751.3	37	CCDS46281.1	.	.	.	.	.	.	.	.	.	.	T	0.406	-0.915918	0.02415	.	.	ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000242441;ENSG00000242441;ENSG00000242441	ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751;ENST00000394749;ENST00000437125;ENST00000430487;ENST00000403751	T;T;T;T;T;T	0.43688	3.02;3.0;3.02;3.02;3.2;0.94	4.88	1.03	0.20045	.	0.441341	0.22106	N	0.064546	T	0.15478	0.0373	N	0.02539	-0.55	0.09310	N	1	B;B;B;B;B	0.14012	0.0;0.0;0.009;0.0;0.0	B;B;B;B;B	0.18871	0.0;0.0;0.023;0.0;0.0	T	0.20672	-1.0268	10	0.27082	T	0.32	.	6.5697	0.22531	0.5515:0.3021:0.0:0.1464	.	200;891;938;234;938	Q9UNN4-2;A8MXJ1;B5MCF5;Q9UNN4;Q53S48	.;.;.;TF2AY_HUMAN;.	R	938;938;938;938;891;233;243;200;234	ENSP00000385499:C938R;ENSP00000385701:C938R;ENSP00000378236:C938R;ENSP00000311493:C938R;ENSP00000378234:C891R;ENSP00000396702:C243R	ENSP00000384597:C234R	C	+	1	0	STON1-GTF2A1L;GTF2A1L	48727407	0.261000	0.24063	0.006000	0.13384	0.004000	0.04260	0.633000	0.24598	0.023000	0.15187	-1.616000	0.00795	TGT		0.418	GTF2A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323852.4	NM_006872	
CCDC88A	55704	hgsc.bcm.edu	37	2	55561549	55561549	+	Missense_Mutation	SNP	A	A	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:55561549A>T	ENST00000436346.1	-	15	3249	c.2408T>A	c.(2407-2409)cTa>cAa	p.L803Q	AC012358.8_ENST00000599352.1_RNA|AC012358.8_ENST00000599475.1_RNA|CCDC88A_ENST00000263630.8_Missense_Mutation_p.L803Q|CCDC88A_ENST00000413716.2_Missense_Mutation_p.L803Q|CCDC88A_ENST00000336838.6_Missense_Mutation_p.L803Q|AC012358.8_ENST00000600219.1_RNA|AC012358.8_ENST00000594078.1_RNA|AC012358.8_ENST00000608103.1_RNA	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	803					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)	p.L803Q(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						AGATATTTTTAGTTCTTCTAG	0.318																																					p.L803Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2408A	2						.						90.0	89.0	89.0					2																	55561549		2202	4298	6500	55415053	SO:0001583	missense	55704	exon15			AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.2408T>A	2.37:g.55561549A>T	ENSP00000410608:p.Leu803Gln		55415053	NM_001135597	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Missense_Mutation	SNP	ENST00000436346.1	37		.	.	.	.	.	.	.	.	.	.	A	17.39	3.377157	0.61735	.	.	ENSG00000115355	ENST00000336838;ENST00000263630;ENST00000436346;ENST00000413716	T;T;T;T	0.19806	2.12;2.38;2.33;2.15	5.03	5.03	0.67393	.	0.000000	0.37577	U	0.002040	T	0.47358	0.1441	M	0.76838	2.35	0.80722	D	1	D;D;D;D;D	0.89917	0.98;1.0;0.996;1.0;1.0	P;D;P;D;D	0.91635	0.814;0.999;0.882;0.997;0.999	T	0.45249	-0.9274	10	0.39692	T	0.17	-5.2718	15.1059	0.72322	1.0:0.0:0.0:0.0	.	803;803;803;803;803	B7ZM78;Q3V6T2-2;Q3V6T2;Q3V6T2-3;Q3V6T2-4	.;.;GRDN_HUMAN;.;.	Q	803	ENSP00000338728:L803Q;ENSP00000263630:L803Q;ENSP00000410608:L803Q;ENSP00000404431:L803Q	ENSP00000263630:L803Q	L	-	2	0	CCDC88A	55415053	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.300000	0.78841	2.034000	0.60081	0.369000	0.22263	CTA		0.318	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571	
RNF103	7844	hgsc.bcm.edu	37	2	86847522	86847522	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:86847522G>A	ENST00000237455.4	-	2	1265	c.297C>T	c.(295-297)acC>acT	p.T99T	AC015971.2_ENST00000439077.1_RNA|RNF103_ENST00000477307.1_5'UTR|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000426549.1_RNA|RNF103-CHMP3_ENST00000604011.1_Silent_p.T21T|CHMP3_ENST00000439940.2_Silent_p.T21T	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	99					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T99T(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						CACTGAAATTGGTACTAGAAA	0.398																																					p.T99T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C297T	2						.						99.0	96.0	97.0					2																	86847522		2203	4300	6503	86701033	SO:0001819	synonymous_variant	7844	exon2			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"""RING-type (C3HC4) zinc fingers"""	12859	protein-coding gene	gene with protein product		602507	"""zinc finger protein 103 homolog (mouse)"""	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.297C>T	2.37:g.86847522G>A			86701033	NM_001198952	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Silent	SNP	ENST00000237455.4	37	CCDS33237.1																																																																																				0.398	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667	
SNRNP200	23020	hgsc.bcm.edu	37	2	96944361	96944361	+	Silent	SNP	G	G	A	rs142524062		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:96944361G>A	ENST00000323853.5	-	38	5489	c.5412C>T	c.(5410-5412)atC>atT	p.I1804I	SNRNP200_ENST00000349783.5_Intron	NM_014014.4	NP_054733.2	O75643	U520_HUMAN	small nuclear ribonucleoprotein 200kDa (U5)	1804					ATP catabolic process (GO:0006200)|cis assembly of pre-catalytic spliceosome (GO:0000354)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U5 snRNP (GO:0005682)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)	p.I1804I(1)		breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|lung(37)|ovary(7)|prostate(4)|skin(5)|stomach(1)|urinary_tract(1)	90						TCTCGTCCTCGATGCTGATGC	0.582																																					p.I1804I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5412T	2						.	G		0,4406		0,0,2203	105.0	96.0	99.0		5412	-8.4	0.7	2	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SNRNP200	NM_014014.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		1804/2137	96944361	1,13005	2203	4300	6503	96308088	SO:0001819	synonymous_variant	23020	exon38			AL831994	CCDS2020.1	2q11.2	2013-05-13	2008-10-29	2008-10-29	ENSG00000144028	ENSG00000144028			30859	protein-coding gene	gene with protein product	"""U5 snRNP specific protein, 200 KD"""	601664	"""activating signal cointegrator 1 complex subunit 3-like 1"", ""retinitis pigmentosa 33 (autosomal dominant)"""	ASCC3L1, RP33		9872452, 8670905, 9774689, 9539711, 16612614, 19878916	Standard	NM_014014		Approved	U5-200KD, HELIC2, KIAA0788, BRR2	uc002svu.3	O75643	OTTHUMG00000130455	ENST00000323853.5:c.5412C>T	2.37:g.96944361G>A			96308088	NM_014014	O94884|Q6NZY0|Q6PX59|Q8NBE6|Q96IF2|Q9H7S0	Silent	SNP	ENST00000323853.5	37	CCDS2020.1																																																																																				0.582	SNRNP200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252846.2	NM_014014	
FN1	2335	hgsc.bcm.edu	37	2	216274441	216274441	+	Missense_Mutation	SNP	G	G	A	rs144664306	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr2:216274441G>A	ENST00000359671.1	-	15	2409	c.2144C>T	c.(2143-2145)aCg>aTg	p.T715M	FN1_ENST00000345488.5_Missense_Mutation_p.T715M|FN1_ENST00000446046.1_Missense_Mutation_p.T715M|FN1_ENST00000356005.4_Missense_Mutation_p.T715M|FN1_ENST00000323926.6_Missense_Mutation_p.T715M|FN1_ENST00000336916.4_Missense_Mutation_p.T715M|FN1_ENST00000432072.2_Missense_Mutation_p.T715M|FN1_ENST00000443816.1_Missense_Mutation_p.T715M|FN1_ENST00000346544.3_Missense_Mutation_p.T715M|FN1_ENST00000354785.4_Missense_Mutation_p.T715M|FN1_ENST00000357009.2_Missense_Mutation_p.T715M|FN1_ENST00000421182.1_Missense_Mutation_p.T715M|FN1_ENST00000357867.4_Missense_Mutation_p.T715M			P02751	FINC_HUMAN	fibronectin 1	715					acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)	p.T715M(3)	FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	AAAGGGAGTCGTCTCTCCTGT	0.502													G|||	6	0.00119808	0.0008	0.0	5008	,	,		19769	0.001		0.0	False		,,,				2504	0.0041				p.T715M												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.C2144T	2						.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	49.0	43.0	45.0		2144,2144,2144,2144,2144	3.9	0.7	2	dbSNP_134	45	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense,missense,missense	FN1	NM_002026.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	81,81,81,81,81	0,9,6494	AA,AG,GG		0.1047,0.0,0.0692	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/2356,715/2177,715/2297,715/2331,715/2478	216274441	9,12997	2203	4300	6503	215982686	SO:0001583	missense	2335	exon15				CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.2144C>T	2.37:g.216274441G>A	ENSP00000352696:p.Thr715Met		215982686	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	37		2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	G	18.71	3.683226	0.68157	0.0	0.001047	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005	T;T;T;T;T;T;T;T;T;T;T;T;T	0.52295	0.67;2.03;2.21;0.74;2.26;1.89;2.25;1.91;2.2;1.92;1.41;0.75;1.32	5.81	3.94	0.45596	.	0.166645	0.41823	D	0.000804	T	0.63780	0.2540	M	0.61703	1.905	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.996;0.992;0.998;0.997;1.0;0.999;0.998;0.998;0.995	D;D;P;P;B;D;P;P;P;P	0.71656	0.911;0.913;0.72;0.633;0.43;0.974;0.869;0.633;0.633;0.892	T	0.66069	-0.6015	10	0.72032	D	0.01	.	13.0344	0.58862	0.0:0.124:0.7468:0.1292	.	715;715;715;715;715;715;715;715;715;715	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	M	715	ENSP00000394423:T715M;ENSP00000323534:T715M;ENSP00000338200:T715M;ENSP00000350534:T715M;ENSP00000346839:T715M;ENSP00000352696:T715M;ENSP00000265312:T715M;ENSP00000273049:T715M;ENSP00000349509:T715M;ENSP00000410422:T715M;ENSP00000415018:T715M;ENSP00000399538:T715M;ENSP00000348285:T715M	ENSP00000265313:T715M	T	-	2	0	FN1	215982686	1.000000	0.71417	0.667000	0.29798	0.619000	0.37552	7.539000	0.82063	0.836000	0.34901	0.655000	0.94253	ACG		0.502	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
DDX58	23586	hgsc.bcm.edu	37	9	32457312	32457312	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr9:32457312T>C	ENST00000379883.2	-	18	2743	c.2586A>G	c.(2584-2586)atA>atG	p.I862M	DDX58_ENST00000542096.1_Missense_Mutation_p.I791M|DDX58_ENST00000379868.1_Missense_Mutation_p.I659M|DDX58_ENST00000379882.1_Missense_Mutation_p.I817M	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	862	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.I862M(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GGGCACAGAATATCTTTGCTC	0.413																																					p.I862M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2586G	9						.						115.0	108.0	111.0					9																	32457312		2203	4300	6503	32447312	SO:0001583	missense	23586	exon18			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2586A>G	9.37:g.32457312T>C	ENSP00000369213:p.Ile862Met		32447312	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	T	11.08	1.533196	0.27387	.	.	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	5.83	2.06	0.26882	C-terminal domain of RIG-I (1);	0.062472	0.64402	D	0.000006	T	0.40743	0.1129	L	0.38838	1.175	0.80722	D	1	B;B	0.33266	0.404;0.059	B;B	0.40165	0.321;0.059	T	0.13737	-1.0498	10	0.39692	T	0.17	-14.8116	3.5993	0.08019	0.1196:0.0709:0.293:0.5165	.	791;862	B3KWW1;O95786	.;DDX58_HUMAN	M	817;862;659;791	ENSP00000369212:I817M;ENSP00000369213:I862M;ENSP00000369197:I659M;ENSP00000442160:I791M	ENSP00000369197:I659M	I	-	3	3	DDX58	32447312	1.000000	0.71417	0.998000	0.56505	0.831000	0.47069	1.089000	0.30890	0.086000	0.17137	0.528000	0.53228	ATA		0.413	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
CCL21	6366	hgsc.bcm.edu	37	9	34709648	34709648	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr9:34709648G>A	ENST00000259607.2	-	3	277	c.220C>T	c.(220-222)Cta>Tta	p.L74L	CCL21_ENST00000378792.1_Silent_p.L74L	NM_002989.2	NP_002980.1	O00585	CCL21_HUMAN	chemokine (C-C motif) ligand 21	74					activation of Rho GTPase activity (GO:0032862)|cell chemotaxis (GO:0060326)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|dendritic cell chemotaxis (GO:0002407)|dendritic cell dendrite assembly (GO:0097026)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|immunological synapse formation (GO:0001771)|inflammatory response (GO:0006954)|mesangial cell-matrix adhesion (GO:0035759)|negative regulation of dendritic cell dendrite assembly (GO:2000548)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative regulation of leukocyte tethering or rolling (GO:1903237)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of chemotaxis (GO:0050921)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process (GO:0010560)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myeloid dendritic cell chemotaxis (GO:2000529)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of T cell migration (GO:2000406)|release of sequestered calcium ion into cytosol (GO:0051209)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)|T cell costimulation (GO:0031295)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	CCR7 chemokine receptor binding (GO:0031732)|chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)	p.L74L(1)		large_intestine(4)	4	all_epithelial(49;0.0899)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		TCTGCACATAGCTCTGCCTGA	0.617																																					p.L74L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C220T	9						.						43.0	43.0	43.0					9																	34709648		2203	4300	6503	34699648	SO:0001819	synonymous_variant	6366	exon3			AB002409	CCDS6571.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000137077	ENSG00000137077		"""Chemokine ligands"", ""Endogenous ligands"""	10620	protein-coding gene	gene with protein product	"""beta chemokine exodus-2"", ""secondary lymphoid tissue chemokine"", ""Efficient Chemoattractant for Lymphocytes"""	602737	"""small inducible cytokine subfamily A (Cys-Cys), member 21"""	SCYA21		9235955	Standard	NM_002989		Approved	SLC, exodus-2, TCA4, CKb9, 6Ckine, ECL	uc003zvo.4	O00585	OTTHUMG00000019838	ENST00000259607.2:c.220C>T	9.37:g.34709648G>A			34699648	NM_002989		Silent	SNP	ENST00000259607.2	37	CCDS6571.1																																																																																				0.617	CCL21-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052245.1	NM_002989	
FREM2	341640	hgsc.bcm.edu	37	13	39343884	39343884	+	Silent	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr13:39343884C>T	ENST00000280481.7	+	4	5796	c.5580C>T	c.(5578-5580)ccC>ccT	p.P1860P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1860					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P1860P(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TCTCAGAGCCCGTGCTGGCTG	0.547																																					p.P1860P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5580T	13						.						121.0	100.0	107.0					13																	39343884		2203	4300	6503	38241884	SO:0001819	synonymous_variant	341640	exon4			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.5580C>T	13.37:g.39343884C>T			38241884	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																				0.547	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
GPC6	10082	hgsc.bcm.edu	37	13	94482694	94482694	+	Missense_Mutation	SNP	G	G	A	rs376951709		TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr13:94482694G>A	ENST00000377047.4	+	3	1222	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	203					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.V203L(1)|p.V203M(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				ATTTGGAGACGTGCCCCGGAA	0.512																																					p.V203M												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G607A	13						.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	76.0	71.0	73.0		607	5.5	1.0	13		73	0,8600		0,0,4300	no	missense	GPC6	NM_005708.3	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	203/556	94482694	1,13005	2203	4300	6503	93280695	SO:0001583	missense	10082	exon3			AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"""Proteoglycans / Cell Surface : Glypicans"""	4454	protein-coding gene	gene with protein product	"""glypican proteoglycan 6"""	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.607G>A	13.37:g.94482694G>A	ENSP00000366246:p.Val203Met		93280695	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.330632	0.81690	2.27E-4	0.0	ENSG00000183098	ENST00000377047	T	0.54071	0.59	5.49	5.49	0.81192	.	0.000000	0.64402	D	0.000001	T	0.74566	0.3733	M	0.89414	3.03	0.44234	D	0.997074	D;D	0.71674	0.998;0.998	D;D	0.67900	0.954;0.954	T	0.78625	-0.2131	10	0.66056	D	0.02	.	13.0682	0.59046	0.0736:0.0:0.9264:0.0	.	203;203	B4E2M1;Q9Y625	.;GPC6_HUMAN	M	203	ENSP00000366246:V203M	ENSP00000366246:V203M	V	+	1	0	GPC6	93280695	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.536000	0.60636	2.771000	0.95319	0.644000	0.83932	GTG		0.512	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708	
PDZD8	118987	hgsc.bcm.edu	37	10	119042953	119042953	+	Silent	SNP	G	G	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr10:119042953G>A	ENST00000334464.5	-	5	3530	c.3291C>T	c.(3289-3291)ggC>ggT	p.G1097G	PDZD8_ENST00000482496.1_5'Flank	NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	1097					cytoskeleton organization (GO:0007010)|intracellular signal transduction (GO:0035556)|regulation of cell morphogenesis (GO:0022604)|viral process (GO:0016032)	membrane (GO:0016020)	metal ion binding (GO:0046872)	p.G1097G(1)		kidney(3)|large_intestine(8)|lung(24)|upper_aerodigestive_tract(3)	38		Colorectal(252;0.19)		all cancers(201;0.0121)		TATCTTCAATGCCTGCTCTGT	0.363																																					p.G1097G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3291T	10						.						133.0	126.0	128.0					10																	119042953		2203	4300	6503	119032943	SO:0001819	synonymous_variant	118987	exon5			AL122051	CCDS7600.1	10q26.12	2006-01-24		2006-01-24	ENSG00000165650	ENSG00000165650			26974	protein-coding gene	gene with protein product		614235		PDZK8		12477932	Standard	NM_173791		Approved	bA129M16.2, FLJ34427	uc001lde.1	Q8NEN9	OTTHUMG00000019122	ENST00000334464.5:c.3291C>T	10.37:g.119042953G>A			119032943	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Silent	SNP	ENST00000334464.5	37	CCDS7600.1																																																																																				0.363	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791	
TSPAN14	81619	hgsc.bcm.edu	37	10	82273790	82273790	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr10:82273790A>G	ENST00000429989.3	+	7	815	c.592A>G	c.(592-594)Aca>Gca	p.T198A	TSPAN14_ENST00000372164.3_Missense_Mutation_p.T181A|TSPAN14_ENST00000372156.1_Missense_Mutation_p.T198A|TSPAN14_ENST00000372158.1_Missense_Mutation_p.T198A|TSPAN14_ENST00000481124.1_Missense_Mutation_p.T75A|TSPAN14_ENST00000341863.6_Missense_Mutation_p.T141A	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	198					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)	p.T198A(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			AGTTGTGAACACACAGTGTGG	0.403																																					p.T198A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A592G	10						.						122.0	111.0	115.0					10																	82273790		2203	4300	6503	82263770	SO:0001583	missense	81619	exon7			AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.592A>G	10.37:g.82273790A>G	ENSP00000396270:p.Thr198Ala		82263770	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Missense_Mutation	SNP	ENST00000429989.3	37	CCDS7369.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.161814	0.78226	.	.	ENSG00000108219	ENST00000429989;ENST00000481124;ENST00000372157;ENST00000372164;ENST00000372158;ENST00000341863;ENST00000372156	T;T;T;T;T;T;T	0.46819	1.92;0.86;2.98;2.99;1.92;2.22;1.92	4.87	4.87	0.63330	Tetraspanin, EC2 domain (1);	0.093442	0.64402	D	0.000001	T	0.61726	0.2370	L	0.57536	1.79	0.58432	D	0.999993	D;P;P	0.76494	0.999;0.767;0.918	D;P;P	0.73380	0.98;0.685;0.604	T	0.59177	-0.7503	10	0.30854	T	0.27	-17.4747	12.7185	0.57129	1.0:0.0:0.0:0.0	.	75;198;181	B4DHY6;Q8NG11;Q8NG11-2	.;TSN14_HUMAN;.	A	198;75;168;181;198;141;198	ENSP00000396270:T198A;ENSP00000418195:T75A;ENSP00000361230:T168A;ENSP00000361237:T181A;ENSP00000361231:T198A;ENSP00000344076:T141A;ENSP00000361229:T198A	ENSP00000344076:T141A	T	+	1	0	TSPAN14	82263770	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.952000	0.93031	1.956000	0.56807	0.459000	0.35465	ACA		0.403	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
MKI67	4288	hgsc.bcm.edu	37	10	129910475	129910475	+	Missense_Mutation	SNP	T	T	C	rs997983	byFrequency	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr10:129910475T>C	ENST00000368654.3	-	9	2266	c.1891A>G	c.(1891-1893)Atc>Gtc	p.I631V	MKI67_ENST00000484853.1_5'UTR|MKI67_ENST00000368653.3_Missense_Mutation_p.I271V	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	631			I -> L (in dbSNP:rs997983).		cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.I631V(1)|p.I631L(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTTCGGCTGATAGACACTCTC	0.443																																					p.I271V												.	.	2	Substitution - Missense(2)	large_intestine(1)|stomach(1)	c.A811G	10						.						112.0	100.0	104.0					10																	129910475		2203	4300	6503	129800465	SO:0001583	missense	4288	exon8			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.1891A>G	10.37:g.129910475T>C	ENSP00000357643:p.Ile631Val		129800465	NM_001145966	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	2.392	-0.339566	0.05243	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01295	5.07;5.04	4.03	-8.06	0.01102	.	0.788319	0.11269	N	0.581682	T	0.00998	0.0033	L	0.44542	1.39	0.80722	P	0.0	B;B;B	0.21225	0.053;0.011;0.006	B;B;B	0.20767	0.031;0.023;0.01	T	0.46359	-0.9197	9	0.17832	T	0.49	.	1.3818	0.02232	0.1695:0.3373:0.2008:0.2923	.	630;271;631	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	V	631;271;630;206	ENSP00000357643:I631V;ENSP00000357642:I271V	ENSP00000357641:I206V	I	-	1	0	MKI67	129800465	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.743000	0.04845	-2.155000	0.00791	-0.291000	0.09656	ATC		0.443	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
SLCO6A1	133482	hgsc.bcm.edu	37	5	101816000	101816000	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:101816000C>T	ENST00000506729.1	-	2	668	c.497G>A	c.(496-498)gGa>gAa	p.G166E	SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.G166E|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.G166E|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.G166E|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.G166E			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	166						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.G166E(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		TTTTCTGTCTCCATAGAATGC	0.328																																					p.G166E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G497A	5						.						117.0	120.0	119.0					5																	101816000		2203	4300	6503	101843899	SO:0001583	missense	133482	exon2			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.497G>A	5.37:g.101816000C>T	ENSP00000421339:p.Gly166Glu		101843899	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.784825	0.31593	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35	4.56	2.67	0.31697	Major facilitator superfamily domain, general substrate transporter (1);	0.257140	0.32640	N	0.005823	T	0.72859	0.3513	M	0.90542	3.125	0.22127	N	0.99935	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.993;1.0	T	0.63391	-0.6648	10	0.87932	D	0	.	7.4958	0.27487	0.1902:0.6261:0.1837:0.0	.	166;166;166	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	E	166	ENSP00000421339:G166E;ENSP00000369135:G166E;ENSP00000373671:G166E;ENSP00000421990:G166E;ENSP00000369138:G166E	ENSP00000369135:G166E	G	-	2	0	SLCO6A1	101843899	0.993000	0.37304	0.503000	0.27626	0.096000	0.18686	1.244000	0.32778	0.583000	0.29574	0.655000	0.94253	GGA		0.328	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
APC	324	hgsc.bcm.edu	37	5	112175348	112175348	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:112175348G>T	ENST00000457016.1	+	16	4437	c.4057G>T	c.(4057-4059)Gaa>Taa	p.E1353*	APC_ENST00000257430.4_Nonsense_Mutation_p.E1353*|CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000508376.2_Nonsense_Mutation_p.E1353*			P25054	APC_HUMAN	adenomatous polyposis coli	1353	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.E1353*(12)|p.E1353fs*19(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)		CAAAGCTGTTGAATTTTCTTC	0.483		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)																											p.E1335X	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"""	APC,large_intestine,right,Substitution - Nonsense,0	.	15	Substitution - Nonsense(12)|Deletion - Frameshift(2)|Unknown(1)	large_intestine(13)|soft_tissue(1)|skin(1)	c.G4003T	5	GRCh37	CD972008	APC	D		.						62.0	65.0	64.0					5																	112175348		2202	4300	6502	112203247	SO:0001587	stop_gained	324	exon14	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.4057G>T	5.37:g.112175348G>T	ENSP00000413133:p.Glu1353*		112203247	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	40	8.431314	0.98808	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	.	.	.	6.03	6.03	0.97812	.	0.111916	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.8759	20.1672	0.98154	0.0:0.0:1.0:0.0	.	.	.	.	X	1353	.	.	E	+	1	0	APC	112203247	1.000000	0.71417	0.993000	0.49108	0.986000	0.74619	5.308000	0.65768	2.861000	0.98227	0.655000	0.94253	GAA		0.483	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
DMXL1	1657	hgsc.bcm.edu	37	5	118483022	118483022	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:118483022T>A	ENST00000311085.8	+	17	2848	c.2768T>A	c.(2767-2769)cTa>cAa	p.L923Q	DMXL1_ENST00000539542.1_Missense_Mutation_p.L923Q	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	923								p.L923Q(1)		breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GAGAAGATCCTATCTCCTTTT	0.378																																					p.L923Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2768A	5						.						62.0	66.0	65.0					5																	118483022		2202	4300	6502	118510921	SO:0001583	missense	1657	exon17			AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.2768T>A	5.37:g.118483022T>A	ENSP00000309690:p.Leu923Gln		118510921	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	0.897	-0.723556	0.03158	.	.	ENSG00000172869	ENST00000311085;ENST00000539542	T;T	0.29397	1.57;1.57	5.82	-1.89	0.07689	.	0.855312	0.10769	N	0.636297	T	0.08714	0.0216	N	0.01800	-0.715	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.37079	-0.9721	10	0.12430	T	0.62	1.5231	4.7123	0.12879	0.4428:0.2477:0.0:0.3096	.	923;923	F5H269;Q9Y485	.;DMXL1_HUMAN	Q	923	ENSP00000309690:L923Q;ENSP00000439479:L923Q	ENSP00000309690:L923Q	L	+	2	0	DMXL1	118510921	0.000000	0.05858	0.000000	0.03702	0.359000	0.29487	-0.029000	0.12329	-0.143000	0.11334	-0.376000	0.06991	CTA		0.378	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
SNX2	6643	hgsc.bcm.edu	37	5	122165298	122165298	+	Silent	SNP	A	A	T			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:122165298A>T	ENST00000379516.2	+	15	1623	c.1515A>T	c.(1513-1515)atA>atT	p.I505I	SNX2_ENST00000510372.1_3'UTR|CTB-36H16.2_ENST00000565823.1_RNA|SNX2_ENST00000514949.1_Silent_p.I388I	NM_003100.2	NP_003091.2	O60749	SNX2_HUMAN	sorting nexin 2	505					endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|protein complex (GO:0043234)|retromer complex (GO:0030904)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)	p.I505I(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)|skin(1)	19		all_cancers(142;1.14e-44)|all_lung(232;1.03e-13)|Lung NSC(810;2.5e-13)|Breast(839;0.000812)|Myeloproliferative disorder(839;0.0122)|Prostate(80;0.0235)|all_hematologic(541;0.0592)|all_neural(839;0.243)	KIRC - Kidney renal clear cell carcinoma(527;0.0897)|Kidney(363;0.137)	all cancers(49;2.13e-24)|Epithelial(69;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(64;5.6e-11)|BRCA - Breast invasive adenocarcinoma(61;0.00013)|GBM - Glioblastoma multiforme(465;0.000357)|COAD - Colon adenocarcinoma(49;0.000887)|Lung(113;0.0109)		CACAGCTGATAAAATACTGGG	0.333																																					p.I505I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1515T	5						.						93.0	95.0	95.0					5																	122165298		2203	4300	6503	122193197	SO:0001819	synonymous_variant	6643	exon15			AF043453	CCDS34217.1, CCDS64234.1	5q23.2	2011-05-03			ENSG00000205302	ENSG00000205302		"""Sorting nexins"""	11173	protein-coding gene	gene with protein product		605929				9819414	Standard	NM_003100		Approved		uc003kte.4	O60749	OTTHUMG00000163020	ENST00000379516.2:c.1515A>T	5.37:g.122165298A>T			122193197	NM_003100	B3KN44|B4DEK4|B7Z408|O43650|P82862|Q53XK8|Q597H6|Q9BTS8	Silent	SNP	ENST00000379516.2	37	CCDS34217.1																																																																																				0.333	SNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371392.1	NM_003100	
SLC22A5	6584	hgsc.bcm.edu	37	5	131722803	131722803	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:131722803A>G	ENST00000245407.3	+	5	1132	c.911A>G	c.(910-912)aAt>aGt	p.N304S	SLC22A5_ENST00000435065.2_Missense_Mutation_p.N328S	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	304					carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)	p.N304S(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	GCCAAAGCCAATGGGATTGTT	0.552											OREG0016767	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N304S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A911G	5						.						307.0	261.0	276.0					5																	131722803		2203	4300	6503	131750702	SO:0001583	missense	6584	exon5			AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.911A>G	5.37:g.131722803A>G	ENSP00000245407:p.Asn304Ser	1589	131750702	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	37	CCDS4154.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342404	0.61073	.	.	ENSG00000197375	ENST00000245407;ENST00000435065;ENST00000415928	T;T;T	0.57752	0.38;0.38;0.38	5.4	5.4	0.78164	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.042955	0.85682	D	0.000000	T	0.81791	0.4897	H	0.96576	3.845	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.91635	0.992;0.999	D	0.88218	0.2895	10	0.87932	D	0	.	15.4222	0.75022	1.0:0.0:0.0:0.0	.	328;304	A2Q0V1;O76082	.;S22A5_HUMAN	S	304;328;227	ENSP00000245407:N304S;ENSP00000402760:N328S;ENSP00000388838:N227S	ENSP00000245407:N304S	N	+	2	0	SLC22A5	131750702	1.000000	0.71417	0.912000	0.35992	0.029000	0.11900	8.842000	0.92136	2.048000	0.60808	0.460000	0.39030	AAT		0.552	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
IQGAP2	10788	hgsc.bcm.edu	37	5	75973062	75973062	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:75973062T>G	ENST00000274364.6	+	28	3844	c.3547T>G	c.(3547-3549)Tgt>Ggt	p.C1183G	IQGAP2_ENST00000502745.1_Missense_Mutation_p.C679G|IQGAP2_ENST00000396234.3_Missense_Mutation_p.C679G|IQGAP2_ENST00000379730.3_Missense_Mutation_p.C685G	NM_006633.2	NP_006624	Q13576	IQGA2_HUMAN	IQ motif containing GTPase activating protein 2	1183					negative regulation of catalytic activity (GO:0043086)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microvillus (GO:0005902)	actin binding (GO:0003779)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Ras GTPase activator activity (GO:0005099)	p.C1183G(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(23)|ovary(6)|prostate(1)|skin(3)|stomach(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	68		all_lung(232;0.000514)|Lung NSC(167;0.00135)|Prostate(461;0.00838)|Ovarian(174;0.0149)		all cancers(79;1.38e-36)		CAAAGAAGCATGTAATGTCCC	0.343																																					p.C1183G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3547G	5						.						72.0	73.0	73.0					5																	75973062		2203	4300	6503	76008818	SO:0001583	missense	10788	exon28			U51903	CCDS34188.1, CCDS68897.1, CCDS68898.1, CCDS75262.1	5q	2008-07-18			ENSG00000145703	ENSG00000145703			6111	protein-coding gene	gene with protein product		605401				8756646	Standard	XM_005248409		Approved		uc003kek.3	Q13576	OTTHUMG00000162432	ENST00000274364.6:c.3547T>G	5.37:g.75973062T>G	ENSP00000274364:p.Cys1183Gly		76008818	NM_006633	A8K4V1|B7Z8A4|J3KR91	Missense_Mutation	SNP	ENST00000274364.6	37	CCDS34188.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.088412	0.76756	.	.	ENSG00000145703	ENST00000274364;ENST00000379730;ENST00000505766;ENST00000396234;ENST00000502745	T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1	5.15	5.15	0.70609	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.000000	0.85682	D	0.000000	T	0.81446	0.4824	M	0.86953	2.85	0.80722	D	1	D;D;D	0.60575	0.988;0.988;0.965	D;D;D	0.75484	0.986;0.986;0.917	D	0.85149	0.0985	10	0.87932	D	0	-14.4369	15.1126	0.72372	0.0:0.0:0.0:1.0	.	685;679;1183	F5H7S7;Q13576-2;Q13576	.;.;IQGA2_HUMAN	G	1183;685;1133;679;679	ENSP00000274364:C1183G;ENSP00000442313:C685G;ENSP00000421097:C1133G;ENSP00000379535:C679G;ENSP00000426027:C679G	ENSP00000274364:C1183G	C	+	1	0	IQGAP2	76008818	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.771000	0.85420	2.162000	0.67917	0.482000	0.46254	TGT		0.343	IQGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368877.1	NM_006633	
ZNF454	285676	hgsc.bcm.edu	37	5	178392836	178392836	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3593-01A-01W-0831-10	TCGA-AG-3593-10A-01W-0831-10	g.chr5:178392836T>A	ENST00000320129.3	+	5	1734	c.1431T>A	c.(1429-1431)ttT>ttA	p.F477L	ZNF454_ENST00000519564.1_Missense_Mutation_p.F477L	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	477					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F477L(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		AGAAAGCCTTTATCCGAAGCA	0.393																																					p.F477L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1431A	5						.						73.0	78.0	77.0					5																	178392836		2203	4300	6503	178325442	SO:0001583	missense	285676	exon5			AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.1431T>A	5.37:g.178392836T>A	ENSP00000326249:p.Phe477Leu		178325442	NM_182594	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.271478	0.40194	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.46063	0.88;0.88	4.46	2.11	0.27256	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40469	N	0.001081	T	0.60235	0.2253	M	0.83483	2.645	0.33249	D	0.558288	D	0.89917	1.0	D	0.91635	0.999	T	0.67837	-0.5567	10	0.87932	D	0	-13.3973	5.3466	0.16012	0.0:0.3117:0.0:0.6883	.	477	Q8N9F8	ZN454_HUMAN	L	477	ENSP00000326249:F477L;ENSP00000430354:F477L	ENSP00000326249:F477L	F	+	3	2	ZNF454	178325442	0.000000	0.05858	1.000000	0.80357	0.019000	0.09904	-0.770000	0.04705	0.853000	0.35312	0.528000	0.53228	TTT		0.393	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718	
