#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
OR5B12	390191	hgsc.bcm.edu	37	11	58206796	58206797	+	Frame_Shift_Ins	INS	-	-	AAAGG			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr11:58206796_58206797insAAAGG	ENST00000302572.2	-	1	849_850	c.828_829insCCTTT	c.(826-831)tatgccfs	p.A277fs		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	277						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ATGACTATGGCATAGAACACAG	0.431																																					p.A277fs												.	.	0			c.829_830insCCTTT	11						.																																			57963373	SO:0001589	frameshift_variant	390191	exon1			AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.828_829insCCTTT	11.37:g.58206796_58206797insAAAGG	ENSP00000306657:p.Ala277fs		57963372	NM_001004733	B2RNL2|Q6IEV5	Frame_Shift_Ins	INS	ENST00000302572.2	37	CCDS31551.1																																																																																				0.431	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
KRT17	3872	hgsc.bcm.edu	37	17	39777264	39777265	+	In_Frame_Ins	INS	-	-	TCT	rs375243255		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:39777264_39777265insTCT	ENST00000311208.8	-	5	980_981	c.913_914insAGA	c.(913-915)cgc>cAGAgc	p.305_305R>QS	JUP_ENST00000540235.1_In_Frame_Ins_p.464_464R>QS	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	305	Coil 2.|Rod.			R -> C (in Ref. 4; AL353997/AC022596). {ECO:0000305}.	epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinization (GO:0031424)|morphogenesis of an epithelium (GO:0002009)|positive regulation of cell growth (GO:0030307)|positive regulation of hair follicle development (GO:0051798)|positive regulation of translation (GO:0045727)|signal transduction (GO:0007165)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	MHC class II protein binding (GO:0042289)|MHC class II receptor activity (GO:0032395)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|skin(1)	12		Breast(137;0.000307)				CTGCATGGTGCGCCGGAGCTCC	0.599																																					p.R305delinsQS	Pancreas(92;1242 2086 39193 50508)											.	.	0			c.914_915insAGA	17						.																																			37030791	SO:0001652	inframe_insertion	3872	exon5			X62571	CCDS11402.1	17q21.2	2014-06-12			ENSG00000128422	ENSG00000128422		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6427	protein-coding gene	gene with protein product		148069		PCHC1		7539673, 1281771, 16831889	Standard	NM_000422		Approved		uc002hxh.2	Q04695	OTTHUMG00000133505	ENST00000311208.8:c.913_914insAGA	17.37:g.39777264_39777265insTCT	ENSP00000308452:p.Arg305delinsGlnSer		37030790	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	In_Frame_Ins	INS	ENST00000311208.8	37	CCDS11402.1																																																																																				0.599	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422	
SLC10A4	201780	hgsc.bcm.edu	37	4	48486118	48486119	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr4:48486118_48486119insA	ENST00000273861.4	+	1	759_760	c.540_541insA	c.(541-543)aatfs	p.N181fs		NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	181						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)	p.N181fs*11(1)		central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						GTCCCGGCGGCAATCTCTCCAA	0.624																																					p.G180fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.540_541insA	4						.																																			48180876	SO:0001589	frameshift_variant	201780	exon1			BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"""Solute carriers"""	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.542dupA	4.37:g.48486120_48486120dupA	ENSP00000273861:p.Asn181fs		48180875	NM_152679	Q8WUZ2	Frame_Shift_Ins	INS	ENST00000273861.4	37	CCDS3482.1																																																																																				0.624	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679	
CPED1	79974	hgsc.bcm.edu	37	7	120629862	120629862	+	Missense_Mutation	SNP	A	A	C	rs370870472		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	A	A	A	A	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr7:120629862A>C	ENST00000310396.5	+	2	654	c.187A>C	c.(187-189)Aaa>Caa	p.K63Q	CPED1_ENST00000340646.5_Missense_Mutation_p.K63Q|CPED1_ENST00000495036.1_3'UTR|CPED1_ENST00000450913.2_Missense_Mutation_p.K63Q	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	63						endoplasmic reticulum (GO:0005783)											CAGATGCAAGAAAGGATTCTC	0.532																																					p.K63Q												.	.	0			c.A187C	7						.						110.0	115.0	113.0					7																	120629862		2203	4300	6503	120417098	SO:0001583	missense	79974	exon2				CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.187A>C	7.37:g.120629862A>C	ENSP00000309772:p.Lys63Gln		120417098	NM_024913	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	.	.	.	.	.	.	.	.	.	.	A	8.584	0.883039	0.17467	.	.	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000340646	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.78	-7.97	0.01139	.	1.040630	0.07523	N	0.910904	T	0.35885	0.0947	L	0.51422	1.61	0.09310	N	1	B;B	0.12630	0.002;0.006	B;B	0.13407	0.009;0.002	T	0.42275	-0.9461	10	0.54805	T	0.06	.	8.7329	0.34510	0.1758:0.3657:0.4585:0.0	.	63;63	A4D0V7-2;A4D0V7	.;CG058_HUMAN	Q	63	ENSP00000309772:K63Q;ENSP00000398082:K63Q;ENSP00000406122:K63Q;ENSP00000345235:K63Q	ENSP00000309772:K63Q	K	+	1	0	C7orf58	120417098	0.000000	0.05858	0.000000	0.03702	0.090000	0.18270	-0.131000	0.10482	-1.314000	0.02300	0.533000	0.62120	AAA		0.532	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
KLF14	136259	hgsc.bcm.edu	37	7	130418037	130418037	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr7:130418037C>A	ENST00000310992.4	-	1	851	c.824G>T	c.(823-825)cGc>cTc	p.R275L		NM_138693.2	NP_619638.2	Q8TD94	KLF14_HUMAN	Kruppel-like factor 14	275					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Melanoma(18;0.0435)					TGGGTGGCGGCGAGCATGCTT	0.652																																					p.R275L												.	.	0			c.G824T	7						.						58.0	53.0	54.0					7																	130418037		2203	4300	6503	130068577	SO:0001583	missense	136259	exon1			AF490374	CCDS5825.1	7q32.3	2014-05-06			ENSG00000174595	ENSG00000266265		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	23025	protein-coding gene	gene with protein product		609393				17480121	Standard	NM_138693		Approved	BTEB5	uc003vqk.2	Q8TD94	OTTHUMG00000188298	ENST00000310992.4:c.824G>T	7.37:g.130418037C>A	ENSP00000310878:p.Arg275Leu		130068577	NM_138693	Q19A42|Q19A43	Missense_Mutation	SNP	ENST00000310992.4	37	CCDS5825.1	.	.	.	.	.	.	.	.	.	.	C	19.97	3.925649	0.73213	.	.	ENSG00000174595	ENST00000310992	T	0.70282	-0.47	4.41	4.41	0.53225	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33670	N	0.004668	T	0.77718	0.4172	L	0.55990	1.75	0.36791	D	0.884852	D	0.89917	1.0	D	0.70716	0.97	T	0.81992	-0.0678	10	0.87932	D	0	.	9.0035	0.36097	0.0:0.8962:0.0:0.1038	.	275	Q8TD94	KLF14_HUMAN	L	275	ENSP00000310878:R275L	ENSP00000310878:R275L	R	-	2	0	KLF14	130068577	0.176000	0.23096	1.000000	0.80357	0.945000	0.59286	1.182000	0.32029	2.374000	0.81015	0.561000	0.74099	CGC		0.652	KLF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338013.1	NM_138693	
ZNF133	7692	hgsc.bcm.edu	37	20	18296626	18296626	+	Silent	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr20:18296626T>A	ENST00000316358.4	+	4	1228	c.1131T>A	c.(1129-1131)tcT>tcA	p.S377S	ZNF133_ENST00000396026.3_Silent_p.S380S|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000377671.3_Silent_p.S376S|ZNF133_ENST00000535822.1_Silent_p.S282S|ZNF133_ENST00000402618.2_Silent_p.S314S|ZNF133_ENST00000538547.1_Silent_p.S282S|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000401790.1_Silent_p.S377S	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	377					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.S376S(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						GGACGCACTCTGGGGAGAAGC	0.582																																					p.S376S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1128A	20						.						65.0	62.0	63.0					20																	18296626		2203	4300	6503	18244626	SO:0001819	synonymous_variant	7692	exon7			AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1131T>A	20.37:g.18296626T>A			18244626	NM_003434	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																					0.582	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
ZNF133	7692	hgsc.bcm.edu	37	20	18296629	18296629	+	Silent	SNP	G	G	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr20:18296629G>C	ENST00000316358.4	+	4	1231	c.1134G>C	c.(1132-1134)ggG>ggC	p.G378G	ZNF133_ENST00000396026.3_Silent_p.G381G|ZNF133_ENST00000462170.1_3'UTR|ZNF133_ENST00000377671.3_Silent_p.G377G|ZNF133_ENST00000535822.1_Silent_p.G283G|ZNF133_ENST00000402618.2_Silent_p.G315G|ZNF133_ENST00000538547.1_Silent_p.G283G|RP4-568F9.3_ENST00000436848.1_RNA|ZNF133_ENST00000401790.1_Silent_p.G378G	NM_001282998.1|NM_001282999.1|NM_001283000.1|NM_001283001.1|NM_001283008.1	NP_001269927.1|NP_001269928.1|NP_001269929.1|NP_001269930.1|NP_001269937.1	P52736	ZN133_HUMAN	zinc finger protein 133	378					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.G377G(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	26						CGCACTCTGGGGAGAAGCCCT	0.577																																					p.G377G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1131C	20						.						66.0	63.0	64.0					20																	18296629		2203	4300	6503	18244629	SO:0001819	synonymous_variant	7692	exon7			AK123005	CCDS13134.1, CCDS63234.1, CCDS63235.1, CCDS74703.1, CCDS74704.1	20p11.23	2013-01-08	2006-06-13		ENSG00000125846	ENSG00000125846		"""Zinc fingers, C2H2-type"", ""-"""	12917	protein-coding gene	gene with protein product		604075	"""zinc finger protein 150 (pHZ-66)"", ""zinc finger protein 133 (clone pHZ-13)"""	ZNF150		7557990, 7649249	Standard	XM_005260819		Approved	pHZ-13, pHZ-66	uc010gcs.3	P52736	OTTHUMG00000031965	ENST00000316358.4:c.1134G>C	20.37:g.18296629G>C			18244629	NM_003434	A8K5S4|B4DHU7|B4DIB8|B7ZAS1|F5H289|J3KQ11|J3KQJ0|Q53XU1|Q5JXV8|Q9BUV2|Q9H443	Silent	SNP	ENST00000316358.4	37																																																																																					0.577	ZNF133-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000127616.1	NM_003434	
SALL4	57167	hgsc.bcm.edu	37	20	50407573	50407573	+	Silent	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr20:50407573T>C	ENST00000217086.4	-	2	1560	c.1449A>G	c.(1447-1449)gtA>gtG	p.V483V	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	483					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.V483V(1)		endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GAGGTAGCCCTACAGAGGTGG	0.557																																					p.V483V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1449G	20						.						97.0	103.0	101.0					20																	50407573		2203	4299	6502	49840980	SO:0001819	synonymous_variant	57167	exon2			AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1449A>G	20.37:g.50407573T>C			49840980	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																				0.557	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
LARGE	9215	hgsc.bcm.edu	37	22	34022287	34022287	+	Silent	SNP	G	G	A	rs201977889		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr22:34022287G>A	ENST00000354992.2	-	5	1003	c.432C>T	c.(430-432)tgC>tgT	p.C144C	LARGE_ENST00000337431.2_Silent_p.C144C|LARGE_ENST00000402320.1_Silent_p.C144C|LARGE_ENST00000397394.2_Silent_p.C144C|LARGE_ENST00000437602.2_Silent_p.C144C	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	144					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)	p.C144C(1)		breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				TGTATCCGGCGCAGACAATAG	0.532																																					p.C144C	Colon(70;397 1175 4573 19089 45288)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C432T	22						.	G	,	0,4406		0,0,2203	100.0	80.0	87.0		432,432	-0.6	1.0	22		87	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	,	144/757,144/757	34022287	3,13003	2203	4300	6503	32352287	SO:0001819	synonymous_variant	9215	exon4			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.432C>T	22.37:g.34022287G>A			32352287	NM_133642	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																				0.532	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642	
FAM83F	113828	hgsc.bcm.edu	37	22	40415324	40415324	+	Silent	SNP	T	T	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr22:40415324T>G	ENST00000333407.6	+	2	736	c.642T>G	c.(640-642)acT>acG	p.T214T	FAM83F_ENST00000473717.1_Silent_p.T46T	NM_138435.2	NP_612444.2	Q8NEG4	FA83F_HUMAN	family with sequence similarity 83, member F	214								p.T214T(1)		breast(1)|endometrium(2)|large_intestine(1)|lung(4)|skin(4)|urinary_tract(2)	14						TGCAGCTCACTGACTTCCGGA	0.577																																					p.T214T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T642G	22						.						131.0	101.0	111.0					22																	40415324		2203	4300	6503	38745270	SO:0001819	synonymous_variant	113828	exon2				CCDS14000.2	22q13.1	2006-03-22			ENSG00000133477	ENSG00000133477			25148	protein-coding gene	gene with protein product						12477932	Standard	NM_138435		Approved		uc003ayk.1	Q8NEG4	OTTHUMG00000150688	ENST00000333407.6:c.642T>G	22.37:g.40415324T>G			38745270	NM_138435	Q96FD6	Silent	SNP	ENST00000333407.6	37	CCDS14000.2																																																																																				0.577	FAM83F-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319624.3	NM_138435	
NAGA	4668	hgsc.bcm.edu	37	22	42466293	42466293	+	Silent	SNP	C	C	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr22:42466293C>A	ENST00000396398.3	-	1	541	c.9G>T	c.(7-9)ctG>ctT	p.L3L	NAGA_ENST00000403363.1_Silent_p.L3L|NAGA_ENST00000402937.1_Silent_p.L3L	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	3					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)	p.L3L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						TACCTGTCTTCAGCAGCATCG	0.547																																					p.L3L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G9T	22						.						239.0	203.0	216.0					22																	42466293		2203	4300	6503	40796239	SO:0001819	synonymous_variant	4668	exon1				CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.9G>T	22.37:g.42466293C>A			40796239	NM_000262		Silent	SNP	ENST00000396398.3	37	CCDS14030.1																																																																																				0.547	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1		
KIAA0930	23313	hgsc.bcm.edu	37	22	45601756	45601756	+	Missense_Mutation	SNP	C	C	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	C	C	C	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr22:45601756C>A	ENST00000336156.5	-	3	319	c.254G>T	c.(253-255)cGg>cTg	p.R85L	KIAA0930_ENST00000443310.3_Missense_Mutation_p.R67L|KIAA0930_ENST00000391627.2_Missense_Mutation_p.R51L|KIAA0930_ENST00000251993.7_Missense_Mutation_p.R90L	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930	85										endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						CTTGGAGTCCCGCCGGTACAC	0.622																																					p.R90L												.	.	0			c.G269T	22						.						57.0	54.0	55.0					22																	45601756		2203	4300	6503	43980420	SO:0001583	missense	23313	exon3			AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 9"""	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.254G>T	22.37:g.45601756C>A	ENSP00000336720:p.Arg85Leu		43980420	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Missense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.131869	0.77662	.	.	ENSG00000100364	ENST00000336156;ENST00000251993;ENST00000391627;ENST00000443310;ENST00000414854;ENST00000424508	.	.	.	4.22	4.22	0.49857	.	0.156057	0.56097	D	0.000038	T	0.63838	0.2545	M	0.80332	2.49	0.58432	D	0.999999	P;P;P;P	0.44521	0.546;0.608;0.553;0.837	B;B;B;P	0.46172	0.306;0.297;0.287;0.506	T	0.70263	-0.4920	9	0.72032	D	0.01	-9.8678	10.6491	0.45638	0.0:0.9108:0.0:0.0892	.	67;85;90;156	B0AZU2;Q6ICG6;Q6ICG6-2;Q8IUY4	.;K0930_HUMAN;.;.	L	85;90;51;67;51;67	.	ENSP00000251993:R90L	R	-	2	0	KIAA0930	43980420	1.000000	0.71417	0.991000	0.47740	0.991000	0.79684	5.522000	0.67092	2.095000	0.63458	0.561000	0.74099	CGG		0.622	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880	
CASP14	23581	hgsc.bcm.edu	37	19	15163075	15163075	+	Missense_Mutation	SNP	C	C	T	rs77227419	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr19:15163075C>T	ENST00000427043.3	+	2	321	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	CASP14_ENST00000221740.1_Missense_Mutation_p.R5W|AC004699.1_ENST00000411269.1_RNA	NM_012114.2	NP_036246.1	P31944	CASPE_HUMAN	caspase 14, apoptosis-related cysteine peptidase	5					cornification (GO:0070268)|epidermis development (GO:0008544)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinization (GO:0031424)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)	p.R5W(2)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|prostate(1)|skin(3)	26						GAGCAATCCGCGGTCTTTGGA	0.502													C|||	9	0.00179712	0.0068	0.0	5008	,	,		16614	0.0		0.0	False		,,,				2504	0.0				p.R5W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C13T	19						.	C	TRP/ARG	17,4389		0,17,2186	89.0	74.0	79.0		13	-0.8	0.0	19	dbSNP_131	79	0,8600		0,0,4300	yes	missense	CASP14	NM_012114.2	101	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	probably-damaging	5/243	15163075	17,12989	2203	4300	6503	15024075	SO:0001583	missense	23581	exon2				CCDS12323.1	19p13.1	2008-07-16	2005-08-17			ENSG00000105141			1502	protein-coding gene	gene with protein product	"""apoptosis-related cysteine protease"""	605848	"""caspase 14, apoptosis-related cysteine protease"""			10203698, 9792675	Standard	NM_012114		Approved	MICE, MGC119078, MGC119079	uc010dzv.2	P31944		ENST00000427043.3:c.13C>T	19.37:g.15163075C>T	ENSP00000393417:p.Arg5Trp		15024075	NM_012114	O95823|Q3SYC9	Missense_Mutation	SNP	ENST00000427043.3	37	CCDS12323.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	.	11.21	1.572012	0.28092	0.003858	0.0	ENSG00000105141	ENST00000427043;ENST00000221740	T;T	0.02944	4.1;4.1	4.2	-0.76	0.11041	.	4.671220	0.00166	N	0.000014	T	0.01124	0.0037	N	0.08118	0	0.09310	N	1	D	0.56968	0.978	B	0.38106	0.265	T	0.29212	-1.0019	10	0.59425	D	0.04	.	1.9888	0.03442	0.3634:0.3547:0.1773:0.1047	.	5	P31944	CASPE_HUMAN	W	5	ENSP00000393417:R5W;ENSP00000221740:R5W	ENSP00000221740:R5W	R	+	1	2	CASP14	15024075	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.245000	0.18142	0.082000	0.17018	0.491000	0.48974	CGG		0.502	CASP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465663.1	NM_012114	
BRD4	23476	hgsc.bcm.edu	37	19	15375454	15375454	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	T	T	T	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr19:15375454T>C	ENST00000263377.2	-	6	1194	c.973A>G	c.(973-975)Agc>Ggc	p.S325G	BRD4_ENST00000360016.5_Missense_Mutation_p.S325G|BRD4_ENST00000371835.4_Missense_Mutation_p.S325G|BRD4_ENST00000602230.1_5'Flank	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	325					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			ACAGGCCGGCTGCTCTCCCGC	0.647			T	C15orf55	lethal midline carcinoma of young people						OREG0025319	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S325G			Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	.	0			c.A973G	19						.						48.0	44.0	45.0					19																	15375454		2203	4300	6503	15236454	SO:0001583	missense	23476	exon6			Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.973A>G	19.37:g.15375454T>C	ENSP00000263377:p.Ser325Gly	702	15236454	NM_014299	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	T	4.002	-0.002423	0.07819	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.26518	1.73;3.43;3.42	5.45	4.41	0.53225	.	0.241411	0.37577	N	0.002025	T	0.08179	0.0204	N	0.02539	-0.55	0.26035	N	0.981682	B;B;B	0.17852	0.0;0.024;0.0	B;B;B	0.20384	0.0;0.029;0.0	T	0.36841	-0.9731	10	0.06757	T	0.87	-10.7878	6.1256	0.20177	0.0:0.2185:0.0:0.7815	.	325;325;325	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	G	325	ENSP00000263377:S325G;ENSP00000360901:S325G;ENSP00000353112:S325G	ENSP00000263377:S325G	S	-	1	0	BRD4	15236454	0.839000	0.29477	1.000000	0.80357	0.992000	0.81027	0.448000	0.21726	0.930000	0.37217	0.460000	0.39030	AGC		0.647	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
FAM129C	199786	hgsc.bcm.edu	37	19	17654358	17654358	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr19:17654358C>T	ENST00000335393.4	+	13	1703	c.1565C>T	c.(1564-1566)gCg>gTg	p.A522V	FAM129C_ENST00000599164.1_Missense_Mutation_p.A491V|FAM129C_ENST00000595684.1_Missense_Mutation_p.A522V|FAM129C_ENST00000601861.1_Missense_Mutation_p.A491V|FAM129C_ENST00000600871.1_Missense_Mutation_p.A468V|FAM129C_ENST00000352727.3_Intron|FAM129C_ENST00000449408.2_Missense_Mutation_p.A248V|FAM129C_ENST00000332386.5_Missense_Mutation_p.A522V|FAM129C_ENST00000599124.1_Intron|FAM129C_ENST00000300971.2_Missense_Mutation_p.A522V	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	522								p.A522V(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						AGCGGGTTGGCGCAGAGGAGG	0.572																																					p.A522V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1565T	19						.						104.0	91.0	95.0					19																	17654358		2203	4300	6503	17515358	SO:0001583	missense	199786	exon13			AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.1565C>T	19.37:g.17654358C>T	ENSP00000335040:p.Ala522Val		17515358	NM_173544	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	.	.	.	.	.	.	.	.	.	.	c	4.310	0.056751	0.08339	.	.	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000300971;ENST00000449408;ENST00000435646	T;T;T;T	0.19394	2.5;2.53;2.26;2.15	5.01	3.94	0.45596	.	0.346122	0.24742	N	0.035962	T	0.14227	0.0344	L	0.43923	1.385	0.09310	N	1	P;P;P;P;P	0.52170	0.695;0.951;0.951;0.918;0.883	B;B;B;B;B	0.40134	0.177;0.242;0.32;0.185;0.241	T	0.12344	-1.0551	10	0.02654	T	1	-13.7759	11.2789	0.49181	0.0:0.8152:0.1848:0.0	.	468;522;522;248;522	E7ENP6;Q86XR2;Q86XR2-3;B4DNU3;Q86XR2-2	.;NIBL2_HUMAN;.;.;.	V	522;522;522;248;468	ENSP00000335040:A522V;ENSP00000333447:A522V;ENSP00000300971:A522V;ENSP00000394929:A248V	ENSP00000300971:A522V	A	+	2	0	FAM129C	17515358	0.000000	0.05858	0.001000	0.08648	0.131000	0.20780	-0.235000	0.09016	1.065000	0.40693	0.306000	0.20318	GCG		0.572	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38590710	38590710	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	A	Unknown	Valid	Germline	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr19:38590710G>A	ENST00000222345.6	+	5	2283	c.1774G>A	c.(1774-1776)Gag>Aag	p.E592K		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	592					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)	p.E592K(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			TGTCATCCCCGAGCTCAACAT	0.642																																					p.E592K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1774A	19						.						69.0	61.0	64.0					19																	38590710		2203	4300	6503	43282550	SO:0001583	missense	23094	exon5			AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.1774G>A	19.37:g.38590710G>A	ENSP00000222345:p.Glu592Lys		43282550	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	.	.	.	.	.	.	.	.	.	.	G	36	5.895053	0.97074	.	.	ENSG00000105738	ENST00000222345	D	0.94417	-3.42	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.93275	0.7857	M	0.73372	2.23	0.80722	D	1	P	0.38078	0.617	B	0.31101	0.124	D	0.93298	0.6674	10	0.62326	D	0.03	-41.2177	19.012	0.92877	0.0:0.0:1.0:0.0	.	592	O60292	SI1L3_HUMAN	K	592	ENSP00000222345:E592K	ENSP00000222345:E592K	E	+	1	0	SIPA1L3	43282550	1.000000	0.71417	0.968000	0.41197	0.918000	0.54935	9.692000	0.98682	2.797000	0.96272	0.561000	0.74099	GAG		0.642	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
CLPTM1	1209	hgsc.bcm.edu	37	19	45490670	45490670	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr19:45490670G>T	ENST00000337392.5	+	8	1177	c.1027G>T	c.(1027-1029)Gac>Tac	p.D343Y	CLPTM1_ENST00000541297.2_Missense_Mutation_p.D329Y|CLPTM1_ENST00000546079.1_Missense_Mutation_p.D241Y	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	343					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)		p.D343Y(2)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		TGAGGAGCAGGACTCGGTGAA	0.632																																					p.D343Y												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1027T	19						.						49.0	45.0	47.0					19																	45490670		2203	4300	6503	50182510	SO:0001583	missense	1209	exon8			AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1027G>T	19.37:g.45490670G>T	ENSP00000336994:p.Asp343Tyr		50182510	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013476	0.75161	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	4.51	4.51	0.55191	.	0.109050	0.64402	D	0.000012	D	0.85703	0.5758	M	0.93507	3.425	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.89525	0.3781	9	0.87932	D	0	-30.5248	14.8528	0.70309	0.0:0.0:1.0:0.0	.	329;343;343	F5H8J3;B3KQH2;O96005	.;.;CLPT1_HUMAN	Y	241;329;343;343	.	ENSP00000336994:D343Y	D	+	1	0	CLPTM1	50182510	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	8.953000	0.93041	2.357000	0.79964	0.650000	0.86243	GAC		0.632	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
PURG	29942	hgsc.bcm.edu	37	8	30889624	30889624	+	Silent	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr8:30889624T>C	ENST00000475541.1	-	1	1607	c.675A>G	c.(673-675)ccA>ccG	p.P225P	PURG_ENST00000339382.2_Silent_p.P225P|WRN_ENST00000298139.5_5'Flank	NM_013357.2	NP_037489.1	Q9UJV8	PURG_HUMAN	purine-rich element binding protein G	225						nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.P225P(2)		endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(542;0.0895)|Kidney(114;0.108)		TTCCTTGTGCTGGGAGGACAA	0.502																																					p.P225P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A675G	8						.						128.0	108.0	115.0					8																	30889624		2203	4300	6503	31009166	SO:0001819	synonymous_variant	29942	exon1			AF195513	CCDS34878.1, CCDS6081.1	8p11	2004-02-09			ENSG00000172733	ENSG00000172733			17930	protein-coding gene	gene with protein product						12034829	Standard	NM_013357		Approved	PURG-A, PURG-B	uc003xin.3	Q9UJV8	OTTHUMG00000157357	ENST00000475541.1:c.675A>G	8.37:g.30889624T>C			31009166	NM_001015508	Q8TE64	Silent	SNP	ENST00000475541.1	37	CCDS6081.1																																																																																				0.502	PURG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348565.1	NM_013357	
DDOST	1650	hgsc.bcm.edu	37	1	20980730	20980730	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:20980730C>T	ENST00000375048.3	-	7	936	c.831G>A	c.(829-831)gcG>gcA	p.A277A	DDOST_ENST00000415136.2_Silent_p.A240A|PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000602624.2_Silent_p.A260A	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	277					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)	p.A277A(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGGAGCCGGGCGCCGCCTTCT	0.622																																					p.A277A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G831A	1						.						16.0	17.0	17.0					1																	20980730		2052	4023	6075	20853317	SO:0001819	synonymous_variant	1650	exon7			D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.831G>A	1.37:g.20980730C>T			20853317	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																				0.622	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
RPL11	6135	hgsc.bcm.edu	37	1	24022845	24022845	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:24022845C>T	ENST00000374550.3	+	6	564	c.519C>T	c.(517-519)atC>atT	p.I173I	RPL11_ENST00000482370.1_3'UTR	NM_000975.3|NM_001199802.1	NP_000966.2|NP_001186731.1	P62913	RL11_HUMAN	ribosomal protein L11	173					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein localization to nucleus (GO:0034504)|protein targeting (GO:0006605)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)	p.I173I(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(2)	6		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.13e-24)|Colorectal(126;5.06e-08)|COAD - Colon adenocarcinoma(152;2.92e-06)|GBM - Glioblastoma multiforme(114;4.4e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|KIRC - Kidney renal clear cell carcinoma(1967;0.00322)|STAD - Stomach adenocarcinoma(196;0.0124)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0837)|LUSC - Lung squamous cell carcinoma(448;0.185)		ATGATGGGATCATCCTTCCTG	0.373																																					p.I173I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C519T	1						.						91.0	89.0	90.0					1																	24022845		2203	4300	6503	23895432	SO:0001819	synonymous_variant	6135	exon6			L05092	CCDS238.1	1p36.1-p35	2011-04-06			ENSG00000142676	ENSG00000142676		"""L ribosomal proteins"""	10301	protein-coding gene	gene with protein product		604175				9582194, 10343117	Standard	NM_000975		Approved	L11	uc001bhk.3	P62913	OTTHUMG00000002926	ENST00000374550.3:c.519C>T	1.37:g.24022845C>T			23895432	NM_000975	P25121|P39026|Q8TDH2|Q9Y674	Silent	SNP	ENST00000374550.3	37	CCDS238.1																																																																																				0.373	RPL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008168.1	NM_000975	
COL11A1	1301	hgsc.bcm.edu	37	1	103488320	103488320	+	Missense_Mutation	SNP	T	T	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:103488320T>G	ENST00000370096.3	-	8	1535	c.1223A>C	c.(1222-1224)gAa>gCa	p.E408A	COL11A1_ENST00000353414.4_Missense_Mutation_p.E369A|COL11A1_ENST00000512756.1_Intron|COL11A1_ENST00000358392.2_Missense_Mutation_p.E420A	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	408	Nonhelical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.E420A(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		AATATCAGTTTCTGCTGGTAC	0.343																																					p.E408A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1223C	1						.						100.0	100.0	100.0					1																	103488320		2203	4300	6503	103260908	SO:0001583	missense	1301	exon8			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.1223A>C	1.37:g.103488320T>G	ENSP00000359114:p.Glu408Ala		103260908	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.231650	0.39399	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000427239	D;T;D;T	0.88124	-2.34;-0.5;-2.34;-0.61	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.90126	0.6915	M	0.82517	2.595	0.51482	D	0.999921	D;D;P	0.67145	0.974;0.996;0.956	D;D;D	0.76071	0.969;0.987;0.931	D	0.89545	0.3795	10	0.09590	T	0.72	.	14.0148	0.64517	0.0:0.0:0.0:1.0	.	369;420;408	P12107-3;P12107-2;P12107	.;.;COBA1_HUMAN	A	408;420;369;420	ENSP00000359114:E408A;ENSP00000351163:E420A;ENSP00000302551:E369A;ENSP00000408640:E420A	ENSP00000302551:E369A	E	-	2	0	COL11A1	103260908	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.998000	0.76277	2.038000	0.60285	0.523000	0.50628	GAA		0.343	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
EFCAB2	84288	hgsc.bcm.edu	37	1	245222746	245222746	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:245222746G>T	ENST00000366522.2	+	4	718	c.577G>T	c.(577-579)Gat>Tat	p.D193Y	EFCAB2_ENST00000366523.1_Missense_Mutation_p.D57Y|EFCAB2_ENST00000487845.1_3'UTR|EFCAB2_ENST00000447569.2_Missense_Mutation_p.D57Y			Q5VUJ9	EFCB2_HUMAN	EF-hand calcium binding domain 2	193							calcium ion binding (GO:0005509)	p.D57Y(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|stomach(2)	13	all_cancers(71;2.93e-06)|all_epithelial(71;2.13e-05)|all_lung(81;0.0337)|Lung NSC(105;0.0472)|Ovarian(71;0.0584)|Breast(184;0.0716)|all_neural(11;0.0982)		OV - Ovarian serous cystadenocarcinoma(106;0.015)			AGAGCTGCATGATCTGATTGC	0.398																																					p.D57Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G169T	1						.						88.0	83.0	85.0					1																	245222746		2203	4300	6503	243289369	SO:0001583	missense	84288	exon3			AB209286	CCDS31082.1, CCDS44341.1	1q44	2014-07-18			ENSG00000203666	ENSG00000203666		"""EF-hand domain containing"""	28166	protein-coding gene	gene with protein product	"""dynein regulatory complex subunit 8"""					23427265	Standard	NM_032328		Approved	MGC12458, DRC8, CFAP200	uc001ibc.2	Q5VUJ9	OTTHUMG00000040474	ENST00000366522.2:c.577G>T	1.37:g.245222746G>T	ENSP00000355479:p.Asp193Tyr		243289369	NM_001143943	B4DZE9|Q59G23|Q9BS36	Missense_Mutation	SNP	ENST00000366522.2	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	19.99|19.99|19.99	3.929011|3.929011|3.929011	0.73327|0.73327|0.73327	.|.|.	.|.|.	ENSG00000203666|ENSG00000203666|ENSG00000203666	ENST00000366523;ENST00000366522;ENST00000447569|ENST00000551317;ENST00000425550|ENST00000366521	T;T;D|.|.	0.82526|.|.	-1.22;-1.21;-1.62|.|.	5.79|5.79|5.79	5.79|5.79|5.79	0.91817|0.91817|0.91817	EF-hand-like domain (1);|.|.	0.229068|.|.	0.33217|.|.	N|.|.	0.005147|.|.	D|D|.	0.86781|0.86781|.	0.6015|0.6015|.	M|M|M	0.93939|0.93939|0.93939	3.475|3.475|3.475	0.49213|0.49213|0.49213	D|D|D	0.999768|0.999768|0.999768	D;D;D;D|.|.	0.71674|.|.	0.996;0.998;0.998;0.996|.|.	P;D;D;D|.|.	0.68353|.|.	0.868;0.926;0.952;0.957|.|.	D|D|.	0.89593|0.89593|.	0.3829|0.3829|.	10|5|.	0.87932|.|.	D|.|.	0|.|.	.|.|.	17.5436|17.5436|17.5436	0.87855|0.87855|0.87855	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.|.	57;115;193;57|.|.	B4DZE9;B1AN33;Q5VUJ9;Q5VUJ9-2|.|.	.;.;EFCB2_HUMAN;.|.|.	Y|I|L	57;193;57|48|115	ENSP00000355480:D57Y;ENSP00000355479:D193Y;ENSP00000408661:D57Y|.|.	ENSP00000355479:D193Y|.|.	D|M|X	+|+|+	1|3|2	0|0|2	EFCAB2|EFCAB2|EFCAB2	243289369|243289369|243289369	0.995000|0.995000|0.995000	0.38212|0.38212|0.38212	0.681000|0.681000|0.681000	0.30009|0.30009|0.30009	0.984000|0.984000|0.984000	0.73092|0.73092|0.73092	4.281000|4.281000|4.281000	0.58965|0.58965|0.58965	2.753000|2.753000|2.753000	0.94483|0.94483|0.94483	0.557000|0.557000|0.557000	0.71058|0.71058|0.71058	GAT|ATG|TGA		0.398	EFCAB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000097407.2		
CNKSR1	10256	hgsc.bcm.edu	37	1	26507258	26507258	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:26507258G>A	ENST00000374253.5	+	3	302	c.263G>A	c.(262-264)gGg>gAg	p.G88E	CNKSR1_ENST00000361530.6_Missense_Mutation_p.G88E|CNKSR1_ENST00000531191.1_5'UTR|CNKSR1_ENST00000480348.2_3'UTR	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	88	CRIC. {ECO:0000255|PROSITE- ProRule:PRU00621}.				Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)	p.G88E(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		GGACTTCTGGGGGCAACCCAT	0.587																																					p.G88E	NSCLC(180;1396 2109 28270 30756 34275)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G263A	1						.						52.0	53.0	53.0					1																	26507258		2203	4300	6503	26379845	SO:0001583	missense	10256	exon3			AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.263G>A	1.37:g.26507258G>A	ENSP00000363371:p.Gly88Glu		26379845	NM_006314	B1AMW9|O95381	Missense_Mutation	SNP	ENST00000374253.5	37		.	.	.	.	.	.	.	.	.	.	G	1.025	-0.683563	0.03353	.	.	ENSG00000142675	ENST00000361530;ENST00000422547;ENST00000374253	T;T	0.12774	2.65;2.65	4.93	-1.8	0.07907	CRIC domain (1);CRIC domain, Chordata (1);	0.710106	0.13550	N	0.379532	T	0.03434	0.0099	N	0.01800	-0.715	0.28868	N	0.895134	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.34925	-0.9809	10	0.30078	T	0.28	-1.8163	1.2498	0.01980	0.2629:0.3008:0.2902:0.1461	.	88;88	Q969H4;Q53GM7	CNKR1_HUMAN;.	E	88	ENSP00000354609:G88E;ENSP00000363371:G88E	ENSP00000354609:G88E	G	+	2	0	CNKSR1	26379845	0.002000	0.14202	0.065000	0.19835	0.012000	0.07955	-0.241000	0.08940	-0.191000	0.10448	-0.302000	0.09304	GGG		0.587	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
PTPRU	10076	hgsc.bcm.edu	37	1	29641954	29641954	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:29641954G>A	ENST00000345512.3	+	24	3457	c.3328G>A	c.(3328-3330)Gtc>Atc	p.V1110I	PTPRU_ENST00000428026.2_Missense_Mutation_p.V1097I|PTPRU_ENST00000356870.3_Missense_Mutation_p.V1106I|PTPRU_ENST00000460170.2_Missense_Mutation_p.V1106I|PTPRU_ENST00000323874.8_Missense_Mutation_p.V1106I|PTPRU_ENST00000373779.3_Missense_Mutation_p.V1100I	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	1110	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|homotypic cell-cell adhesion (GO:0034109)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|organ regeneration (GO:0031100)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|response to glucocorticoid (GO:0051384)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.V1110I(1)		breast(4)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(26)|ovary(1)|prostate(3)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	79		Colorectal(325;0.000399)|Lung NSC(340;0.00953)|all_lung(284;0.0112)|Breast(348;0.0126)|all_neural(195;0.0199)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0563)|Medulloblastoma(700;0.123)		Colorectal(126;6.99e-07)|COAD - Colon adenocarcinoma(152;3.18e-05)|STAD - Stomach adenocarcinoma(196;0.0234)|READ - Rectum adenocarcinoma(331;0.0686)|BRCA - Breast invasive adenocarcinoma(304;0.0871)		GTGTGAGGGCGTCGTGGACAT	0.592																																					p.V1110I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3328A	1						.						132.0	120.0	124.0					1																	29641954		2203	4300	6503	29514541	SO:0001583	missense	10076	exon24			U71075	CCDS334.1, CCDS335.1, CCDS44098.1, CCDS44098.2, CCDS53290.1	1p35.3	2013-02-11			ENSG00000060656	ENSG00000060656		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9683	protein-coding gene	gene with protein product	"""pi R-PTP-Psi"""	602454				8700514, 9434160	Standard	NM_133178		Approved	PTPRO, hPTP-J, PCP-2, FMI, PTP	uc001bru.3	Q92729	OTTHUMG00000003699	ENST00000345512.3:c.3328G>A	1.37:g.29641954G>A	ENSP00000334941:p.Val1110Ile		29514541	NM_005704	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	32	5.142054	0.94560	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	4.66	4.66	0.58398	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);	0.000000	0.64402	D	0.000001	D	0.85703	0.5758	L	0.31371	0.925	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.80764	0.989;0.989;0.989;0.994;0.994	D	0.84377	0.0547	9	.	.	.	.	17.0877	0.86615	0.0:0.0:1.0:0.0	.	1097;1106;1100;1106;1110	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	I	1110;1100;1106;1106;1097;1106	ENSP00000334941:V1110I;ENSP00000362884:V1100I;ENSP00000349333:V1106I;ENSP00000314987:V1106I;ENSP00000392332:V1097I;ENSP00000432906:V1106I	.	V	+	1	0	PTPRU	29514541	1.000000	0.71417	0.927000	0.36925	0.996000	0.88848	9.657000	0.98554	2.579000	0.87056	0.561000	0.74099	GTC		0.592	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1		
IQCC	55721	hgsc.bcm.edu	37	1	32673149	32673149	+	Silent	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:32673149A>G	ENST00000291358.6	+	5	888	c.867A>G	c.(865-867)tcA>tcG	p.S289S	IQCC_ENST00000537469.1_Silent_p.S369S|RP4-622L5.7_ENST00000373604.4_RNA|DCDC2B_ENST00000409358.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	289								p.S289S(1)		endometrium(4)|large_intestine(1)|lung(3)|ovary(4)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTATACCATCAAACAGCCAGG	0.542																																					p.S369S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1107G	1						.						57.0	57.0	57.0					1																	32673149		2203	4300	6503	32445736	SO:0001819	synonymous_variant	55721	exon5			AL049795	CCDS355.1, CCDS53293.1	1p36.11-p34.2	2008-02-05			ENSG00000160051	ENSG00000160051			25545	protein-coding gene	gene with protein product							Standard	NM_018134		Approved	FLJ10547	uc001bum.2	Q4KMZ1	OTTHUMG00000005739	ENST00000291358.6:c.867A>G	1.37:g.32673149A>G			32445736	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Silent	SNP	ENST00000291358.6	37	CCDS355.1																																																																																				0.542	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134	
LRRC40	55631	hgsc.bcm.edu	37	1	70614267	70614267	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:70614267G>A	ENST00000370952.3	-	14	1685	c.1606C>T	c.(1606-1608)Cag>Tag	p.Q536*		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	536						membrane (GO:0016020)		p.Q536*(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TTCATTTTCTGAGGGTCCACA	0.353																																					p.Q536X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1606T	1						.						155.0	155.0	155.0					1																	70614267		2203	4300	6503	70386855	SO:0001587	stop_gained	55631	exon14				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1606C>T	1.37:g.70614267G>A	ENSP00000359990:p.Gln536*		70386855	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Nonsense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	G	37	6.318975	0.97471	.	.	ENSG00000066557	ENST00000370952	.	.	.	5.46	3.52	0.40303	.	0.972957	0.08504	N	0.935927	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	16.4263	0.83815	0.0:0.3693:0.6307:0.0	.	.	.	.	X	536	.	ENSP00000359990:Q536X	Q	-	1	0	LRRC40	70386855	0.980000	0.34600	0.998000	0.56505	0.998000	0.95712	1.146000	0.31589	0.615000	0.30124	0.650000	0.86243	CAG		0.353	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768	
ABCA4	24	hgsc.bcm.edu	37	1	94476936	94476936	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:94476936C>T	ENST00000370225.3	-	39	5552	c.5466G>A	c.(5464-5466)ctG>ctA	p.L1822L	ABCA4_ENST00000536513.1_Silent_p.L92L|ABCA4_ENST00000535881.1_5'UTR|ABCA4_ENST00000465352.1_5'Flank	NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1822					phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)	p.L1822L(1)		NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		TGAACCTGAGCAGCGTCTGAA	0.602																																					p.L1822L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5466A	1						.						80.0	80.0	80.0					1																	94476936		2203	4300	6503	94249524	SO:0001819	synonymous_variant	24	exon39			U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.5466G>A	1.37:g.94476936C>T			94249524	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Silent	SNP	ENST00000370225.3	37	CCDS747.1																																																																																				0.602	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
ZNF496	84838	hgsc.bcm.edu	37	1	247473095	247473095	+	Silent	SNP	G	G	A	rs75453877	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr1:247473095G>A	ENST00000294753.4	-	7	1262	c.798C>T	c.(796-798)gcC>gcT	p.A266A	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Silent_p.A302A	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	266	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.A266A(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			GATCTGGCTGGGCAGCTAGGT	0.542													G|||	21	0.00419329	0.0	0.0058	5008	,	,		18623	0.0		0.0149	False		,,,				2504	0.002				p.A266A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C798T	1						.	G		16,4390	23.3+/-48.9	0,16,2187	66.0	64.0	65.0		798	2.6	0.5	1	dbSNP_132	65	150,8450	72.0+/-134.6	0,150,4150	no	coding-synonymous	ZNF496	NM_032752.1		0,166,6337	AA,AG,GG		1.7442,0.3631,1.2763		266/588	247473095	166,12840	2203	4300	6503	245539718	SO:0001819	synonymous_variant	84838	exon7			BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.798C>T	1.37:g.247473095G>A			245539718	NM_032752	Q8TBS2	Silent	SNP	ENST00000294753.4	37	CCDS1631.1																																																																																				0.542	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
FCHSD2	9873	hgsc.bcm.edu	37	11	72553764	72553764	+	Missense_Mutation	SNP	C	C	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr11:72553764C>G	ENST00000409418.4	-	17	2211	c.1828G>C	c.(1828-1830)Ggg>Cgg	p.G610R	ATG16L2_ENST00000534905.1_3'UTR|FCHSD2_ENST00000409314.1_Missense_Mutation_p.G634R|FCHSD2_ENST00000311172.7_Missense_Mutation_p.G554R|FCHSD2_ENST00000458644.2_Missense_Mutation_p.G474R|FCHSD2_ENST00000409263.1_Intron	NM_014824.2	NP_055639.2	O94868	FCSD2_HUMAN	FCH and double SH3 domains 2	610	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.							p.G554R(1)		endometrium(2)|large_intestine(11)|lung(5)|ovary(2)|prostate(1)|skin(1)	22			BRCA - Breast invasive adenocarcinoma(5;3.3e-05)			TTGAATTCCCCTTCCCAGAAG	0.443																																					p.G610R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1828C	11						.						152.0	144.0	146.0					11																	72553764		2200	4293	6493	72231412	SO:0001583	missense	9873	exon17			AB018312	CCDS8218.2	11q13.3	2008-02-05	2004-04-14	2004-04-16	ENSG00000137478	ENSG00000137478			29114	protein-coding gene	gene with protein product			"""SH3 multiple domains 3"""	SH3MD3		9872452, 15067381	Standard	NM_014824		Approved	KIAA0769	uc009ytl.3	O94868	OTTHUMG00000153082	ENST00000409418.4:c.1828G>C	11.37:g.72553764C>G	ENSP00000386722:p.Gly610Arg		72231412	NM_014824	B4DNI3|Q7L8J9|Q8WVM2|Q96FV7|Q9UF77	Missense_Mutation	SNP	ENST00000409418.4	37	CCDS8218.2	.	.	.	.	.	.	.	.	.	.	C	25.4	4.636300	0.87760	.	.	ENSG00000137478	ENST00000311172;ENST00000409314;ENST00000409418;ENST00000458644	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	6.03	6.03	0.97812	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	D	0.86331	0.5907	H	0.95470	3.675	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.995;1.0	D	0.89344	0.3656	10	0.87932	D	0	-20.5438	19.5548	0.95338	0.0:1.0:0.0:0.0	.	474;610	E7ENZ2;O94868	.;FCSD2_HUMAN	R	554;634;610;474	ENSP00000308978:G554R;ENSP00000386987:G634R;ENSP00000386722:G610R;ENSP00000402972:G474R	ENSP00000308978:G554R	G	-	1	0	FCHSD2	72231412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.854000	0.98071	0.655000	0.94253	GGG		0.443	FCHSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329429.2	NM_014824	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7662817	7662817	+	Missense_Mutation	SNP	C	C	T	rs150660067		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr11:7662817C>T	ENST00000299492.4	+	16	1871	c.1483C>T	c.(1483-1485)Cgg>Tgg	p.R495W	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.R337W|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.R352W|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.R383W|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	495					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)	p.R495W(1)		breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGATGGTAAACGGAATCCCAA	0.453													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21042	0.0		0.0	False		,,,				2504	0.0				p.R495W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1483T	11						.	C	TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	146.0	129.0	135.0		1483	4.1	1.0	11	dbSNP_134	135	1,8591	1.2+/-3.3	0,1,4295	no	missense	PPFIBP2	NM_003621.2	101	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	495/877	7662817	2,12992	2201	4296	6497	7619393	SO:0001583	missense	8495	exon16			AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.1483C>T	11.37:g.7662817C>T	ENSP00000299492:p.Arg495Trp		7619393	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.9|20.9	4.071203|4.071203	0.76301|0.76301	2.27E-4|2.27E-4	1.16E-4|1.16E-4	ENSG00000166387|ENSG00000166387	ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000530081|ENST00000534409	T;T;T;T|.	0.36878|.	1.66;1.24;1.66;1.23|.	6.03|6.03	4.05|4.05	0.47172|0.47172	.|.	0.084158|.	0.49916|.	D|.	0.000133|.	T|T	0.58836|0.58836	0.2150|0.2150	L|L	0.47716|0.47716	1.5|1.5	0.50467|0.50467	D|D	0.999878|0.999878	D;D;D;D;D;D|.	0.89917|.	0.999;0.997;1.0;1.0;1.0;0.999|.	P;P;D;D;D;P|.	0.67382|.	0.895;0.821;0.951;0.92;0.92;0.895|.	T|T	0.56360|0.56360	-0.7992|-0.7992	10|5	0.72032|.	D|.	0.01|.	-23.3711|-23.3711	11.8116|11.8116	0.52185|0.52185	0.4353:0.5647:0.0:0.0|0.4353:0.5647:0.0:0.0	.|.	383;383;418;337;352;495|.	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30|.	.;.;.;.;.;LIPB2_HUMAN|.	W|M	495;337;337;418;383;352;156|185	ENSP00000299492:R495W;ENSP00000436498:R337W;ENSP00000435469:R383W;ENSP00000437321:R352W|.	ENSP00000299492:R495W|.	R|T	+|+	1|2	2|0	PPFIBP2|PPFIBP2	7619393|7619393	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	4.870000|4.870000	0.63035|0.63035	1.531000|1.531000	0.49152|0.49152	-0.182000|-0.182000	0.12963|0.12963	CGG|ACG		0.453	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
ATG2A	23130	hgsc.bcm.edu	37	11	64665208	64665209	+	Frame_Shift_Del	DEL	GG	GG	-	rs376529700		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	GG	GG	GG	GG	GG	GG	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr11:64665208_64665209delGG	ENST00000377264.3	-	36	5113_5114	c.5001_5002delCC	c.(4999-5004)ttccgcfs	p.FR1667fs	ATG2A_ENST00000421419.2_Frame_Shift_Del_p.FR1669fs	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1667					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(19)|ovary(3)|prostate(5)|skin(1)|stomach(1)|urinary_tract(3)	55						GACGTGAAGCGGAACTCTCTGG	0.644																																					p.1667_1668del												.	.	0			c.5001_5002del	11						.																																			64421785	SO:0001589	frameshift_variant	23130	exon36				CCDS31602.1	11q13.1	2014-02-12	2012-06-06		ENSG00000110046	ENSG00000110046			29028	protein-coding gene	gene with protein product			"""ATG2 autophagy related 2 homolog A (S. cerevisiae)"""			21887408	Standard	NM_015104		Approved	KIAA0404	uc001obx.3	Q2TAZ0	OTTHUMG00000066831	ENST00000377264.3:c.5001_5002delCC	11.37:g.64665208_64665209delGG	ENSP00000366475:p.Phe1667fs		64421784	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Frame_Shift_Del	DEL	ENST00000377264.3	37	CCDS31602.1																																																																																				0.644	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73076590	73076590	+	Silent	SNP	C	C	T	rs61749197	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr11:73076590C>T	ENST00000263674.3	+	19	6056	c.5706C>T	c.(5704-5706)ccC>ccT	p.P1902P		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1902					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.P1902P(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						TCACTCCTCCCGTGCACAGGA	0.577													C|||	162	0.0323482	0.0068	0.0418	5008	,	,		22002	0.003		0.0924	False		,,,				2504	0.0286				p.P1902P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5706T	11						.	C		81,4319	70.3+/-108.2	0,81,2119	140.0	107.0	118.0		5706	-11.6	0.5	11	dbSNP_129	118	788,7798	184.9+/-232.8	36,716,3541	no	coding-synonymous	ARHGEF17	NM_014786.3		36,797,5660	TT,TC,CC		9.1777,1.8409,6.6918		1902/2064	73076590	869,12117	2200	4293	6493	72754238	SO:0001819	synonymous_variant	9828	exon19			AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.5706C>T	11.37:g.73076590C>T			72754238	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Silent	SNP	ENST00000263674.3	37	CCDS8221.1																																																																																				0.577	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
NOS2	4843	hgsc.bcm.edu	37	17	26101433	26101433	+	Silent	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:26101433G>T	ENST00000313735.6	-	12	1559	c.1326C>A	c.(1324-1326)tcC>tcA	p.S442S		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	442					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)	p.S442S(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	ACTTCATGAAGGATTCTGCAG	0.562																																					p.S442S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1326A	17						.						101.0	95.0	97.0					17																	26101433		2203	4300	6503	23125560	SO:0001819	synonymous_variant	4843	exon12			U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.1326C>A	17.37:g.26101433G>T			23125560	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																				0.562	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
CDC27	996	hgsc.bcm.edu	37	17	45216210	45216210	+	Silent	SNP	A	A	G	rs62075659		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:45216210A>G	ENST00000066544.3	-	13	1692	c.1599T>C	c.(1597-1599)gtT>gtC	p.V533V	CDC27_ENST00000531206.1_Silent_p.V539V|CDC27_ENST00000446365.2_Silent_p.V472V|CDC27_ENST00000527547.1_Silent_p.V532V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	533					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.V533V(1)|p.V539V(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CCATGCCTTCAACTCTATAAT	0.318																																					p.V539V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1617C	17						.						36.0	40.0	39.0					17																	45216210		2200	4297	6497	42571209	SO:0001819	synonymous_variant	996	exon13			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1599T>C	17.37:g.45216210A>G			42571209	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																				0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
GGT6	124975	hgsc.bcm.edu	37	17	4461463	4461463	+	Silent	SNP	A	A	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:4461463A>T	ENST00000574154.1	-	4	1625	c.1329T>A	c.(1327-1329)ccT>ccA	p.P443P	GGT6_ENST00000301395.3_Silent_p.P411P|MYBBP1A_ENST00000381556.2_5'Flank|MYBBP1A_ENST00000254718.4_5'Flank|GGT6_ENST00000381550.3_Silent_p.P449P|GGT6_ENST00000573591.1_Silent_p.P295P			Q6P531	GGT6_HUMAN	gamma-glutamyltransferase 6	443					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.P411P(1)		endometrium(2)|large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						GGGCCTGGGTAGGGGGCCTTG	0.622																																					p.P443P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1329A	17						.						91.0	80.0	84.0					17																	4461463		2203	4300	6503	4408212	SO:0001819	synonymous_variant	124975	exon4			AK074646	CCDS11047.1, CCDS45582.1, CCDS73942.1	17p13.2	2014-08-12	2008-03-10		ENSG00000167741	ENSG00000167741		"""Gamma-glutamyltransferases"""	26891	protein-coding gene	gene with protein product		612341	"""gamma-glutamyltransferase 6 homolog (rat)"""			18357469	Standard	NM_001122890		Approved	FLJ90165	uc002fyd.4	Q6P531	OTTHUMG00000177827	ENST00000574154.1:c.1329T>A	17.37:g.4461463A>T			4408212	NM_001122890	B4DUH4|Q8NCM0	Silent	SNP	ENST00000574154.1	37	CCDS45582.1																																																																																				0.622	GGT6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439122.1	NM_153338	
USP6	9098	hgsc.bcm.edu	37	17	5036224	5036224	+	Missense_Mutation	SNP	C	C	G	rs72830922		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	C	C	G	Unknown	Valid	LOH	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:5036224C>G	ENST00000574788.1	+	13	2445	c.215C>G	c.(214-216)aCa>aGa	p.T72R	USP6_ENST00000572429.1_3'UTR|USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Missense_Mutation_p.T72R|USP6_ENST00000332776.4_Missense_Mutation_p.T72R			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	72					cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)	p.T72R(8)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						CGGGAGATGACACGAACGAGC	0.537			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																p.T72R			Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	.	8	Substitution - Missense(8)	kidney(6)|large_intestine(2)	c.C215G	17						.						152.0	171.0	165.0					17																	5036224		2203	4300	6503	4976948	SO:0001583	missense	9098	exon5			X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.215C>G	17.37:g.5036224C>G	ENSP00000460380:p.Thr72Arg		4976948	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	2.172	-0.389573	0.04932	.	.	ENSG00000129204	ENST00000332776;ENST00000250066	T;T	0.29917	1.55;1.55	0.0465	-0.093	0.13652	Rab-GAP/TBC domain (1);	0.262826	0.38959	N	0.001520	T	0.09202	0.0227	N	0.01505	-0.83	0.80722	D	1	B;B	0.13145	0.007;0.003	B;B	0.06405	0.002;0.001	T	0.32348	-0.9910	9	0.87932	D	0	.	.	.	.	.	72;72	B9A6N0;P35125	.;UBP6_HUMAN	R	72	ENSP00000328010:T72R;ENSP00000250066:T72R	ENSP00000250066:T72R	T	+	2	0	USP6	4976948	0.870000	0.30015	0.001000	0.08648	0.001000	0.01503	0.250000	0.18235	-1.539000	0.01732	-1.549000	0.00901	ACA		0.537	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
CDC27	996	hgsc.bcm.edu	37	17	45216216	45216216	+	Silent	SNP	A	A	G	rs62077260		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:45216216A>G	ENST00000066544.3	-	13	1686	c.1593T>C	c.(1591-1593)taT>taC	p.Y531Y	CDC27_ENST00000531206.1_Silent_p.Y537Y|CDC27_ENST00000446365.2_Silent_p.Y470Y|CDC27_ENST00000527547.1_Silent_p.Y530Y	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	531					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.Y537Y(1)|p.Y531Y(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTTCAACTCTATAATTCTCAA	0.318																																					p.Y537Y												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T1611C	17						.						34.0	39.0	37.0					17																	45216216		2200	4297	6497	42571215	SO:0001819	synonymous_variant	996	exon13			U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1593T>C	17.37:g.45216216A>G			42571215	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																				0.318	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
KCNJ16	3773	hgsc.bcm.edu	37	17	68129146	68129146	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:68129146G>A	ENST00000589377.1	+	2	1081	c.918G>A	c.(916-918)tgG>tgA	p.W306*	KCNJ16_ENST00000392670.1_Nonsense_Mutation_p.W306*|KCNJ16_ENST00000283936.1_Nonsense_Mutation_p.W306*|KCNJ16_ENST00000585558.1_Nonsense_Mutation_p.W341*|KCNJ16_ENST00000586462.1_Nonsense_Mutation_p.W345*|KCNJ16_ENST00000392671.1_Nonsense_Mutation_p.W306*	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	306					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)	p.W306*(1)		breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					AAATTCTCTGGGGCCATAGGT	0.398																																					p.W306X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G918A	17						.						72.0	77.0	75.0					17																	68129146		2203	4300	6503	65640741	SO:0001587	stop_gained	3773	exon5			AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.918G>A	17.37:g.68129146G>A	ENSP00000465967:p.Trp306*		65640741	NM_018658		Nonsense_Mutation	SNP	ENST00000589377.1	37	CCDS11687.1	.	.	.	.	.	.	.	.	.	.	G	38	6.869311	0.97897	.	.	ENSG00000153822	ENST00000283936;ENST00000392671;ENST00000392670	.	.	.	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5977	0.95547	0.0:0.0:1.0:0.0	.	.	.	.	X	306	.	.	W	+	3	0	KCNJ16	65640741	1.000000	0.71417	1.000000	0.80357	0.268000	0.26511	9.771000	0.98977	2.722000	0.93159	0.650000	0.86243	TGG		0.398	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658	
QRICH2	84074	hgsc.bcm.edu	37	17	74288615	74288615	+	Silent	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:74288615G>T	ENST00000262765.5	-	4	1874	c.1695C>A	c.(1693-1695)gtC>gtA	p.V565V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	565	Gln-rich.							p.V565V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(2)|stomach(4)	62						CTCCAGGTTGGACCAAACCAT	0.527																																					p.V565V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1695A	17						.						198.0	158.0	171.0					17																	74288615		2203	4300	6503	71800210	SO:0001819	synonymous_variant	84074	exon4			AK058102	CCDS32741.1	17q25.1	2009-03-19			ENSG00000129646	ENSG00000129646			25326	protein-coding gene	gene with protein product							Standard	NM_032134		Approved	DKFZP434P0316	uc002jrd.1	Q9H0J4	OTTHUMG00000167578	ENST00000262765.5:c.1695C>A	17.37:g.74288615G>T			71800210	NM_032134	A2RRE1|Q96LM3	Silent	SNP	ENST00000262765.5	37	CCDS32741.1																																																																																				0.527	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134	
ODF4	146852	hgsc.bcm.edu	37	17	8249110	8249110	+	Silent	SNP	A	A	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:8249110A>C	ENST00000328248.2	+	3	902	c.714A>C	c.(712-714)acA>acC	p.T238T	ODF4_ENST00000584943.1_Silent_p.T123T	NM_153007.4	NP_694552.2	Q2M2E3	ODFP4_HUMAN	outer dense fiber of sperm tails 4	238					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|outer dense fiber (GO:0001520)		p.T238T(1)		endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|stomach(1)	8						AGACGATCACAGACACCCCCA	0.522																																					p.T238T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A714C	17						.						93.0	92.0	93.0					17																	8249110		2203	4300	6503	8189835	SO:0001819	synonymous_variant	146852	exon3			AB081120	CCDS11140.1	17p13	2010-09-27			ENSG00000184650	ENSG00000184650			19056	protein-coding gene	gene with protein product	"""cancer/testis antigen 136"""	610097					Standard	NM_153007		Approved	OPPO1, CT136	uc002gle.1	Q2M2E3	OTTHUMG00000108190	ENST00000328248.2:c.714A>C	17.37:g.8249110A>C			8189835	NM_153007	Q8J021	Silent	SNP	ENST00000328248.2	37	CCDS11140.1																																																																																				0.522	ODF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226996.1		
BAIAP2	10458	hgsc.bcm.edu	37	17	79027481	79027481	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr17:79027481A>G	ENST00000321300.6	+	2	161	c.68A>G	c.(67-69)cAg>cGg	p.Q23R	BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000321280.7_Missense_Mutation_p.Q23R|BAIAP2_ENST00000392411.3_Intron|BAIAP2_ENST00000435091.3_Missense_Mutation_p.Q23R|BAIAP2_ENST00000428708.2_Missense_Mutation_p.Q23R|BAIAP2_ENST00000575712.1_Missense_Mutation_p.Q23R|BAIAP2_ENST00000575245.1_Missense_Mutation_p.Q56R	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	23	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)	p.Q23R(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			ATCATGGAGCAGTTCAACCCT	0.582																																					p.Q23R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A68G	17						.						172.0	147.0	155.0					17																	79027481		2203	4300	6503	76642076	SO:0001583	missense	10458	exon2			AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.68A>G	17.37:g.79027481A>G	ENSP00000316338:p.Gln23Arg		76642076	NM_006340	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	37	CCDS11775.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.505427	0.85282	.	.	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000435091;ENST00000321280	T;T;T;T	0.34667	1.35;1.35;1.35;1.35	5.34	5.34	0.76211	IRSp53/MIM homology domain (IMD) (3);	0.000000	0.85682	D	0.000000	T	0.57504	0.2058	M	0.69823	2.125	0.80722	D	1	D;D;D;D;D;D	0.76494	0.999;0.997;0.994;0.999;0.999;0.997	D;P;P;D;D;P	0.75020	0.985;0.825;0.873;0.946;0.946;0.872	T	0.56535	-0.7963	10	0.34782	T	0.22	-2.4451	14.3024	0.66362	1.0:0.0:0.0:0.0	.	23;23;23;23;23;23	Q9UQB8;Q9UQB8-2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-6;Q9UQB8-4	BAIP2_HUMAN;.;.;.;.;.	R	23	ENSP00000316338:Q23R;ENSP00000401022:Q23R;ENSP00000413069:Q23R;ENSP00000315685:Q23R	ENSP00000315685:Q23R	Q	+	2	0	BAIAP2	76642076	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	8.341000	0.90046	2.019000	0.59389	0.533000	0.62120	CAG		0.582	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
SIM2	6493	hgsc.bcm.edu	37	21	38092190	38092190	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr21:38092190C>T	ENST00000290399.6	+	4	1030	c.417C>T	c.(415-417)gtC>gtT	p.V139V	SIM2_ENST00000430056.3_Silent_p.V139V	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	139	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|embryonic pattern specification (GO:0009880)|lung development (GO:0030324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.V139V(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(6)|prostate(1)|skin(2)	16						TGACCGCTGTCCTCACGGCCC	0.512																																					p.V139V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C417T	21						.						81.0	81.0	81.0					21																	38092190		2203	4300	6503	37014060	SO:0001819	synonymous_variant	6493	exon4				CCDS13646.1	21q22.2	2013-10-17	2013-10-17		ENSG00000159263	ENSG00000159263		"""Basic helix-loop-helix proteins"""	10883	protein-coding gene	gene with protein product	"""transcription factor SIM2"""	600892	"""single-minded (Drosophila) homolog 2"", ""single-minded homolog 2 (Drosophila)"""	SIM		7485157	Standard	NM_009586		Approved	MGC119447, bHLHe15	uc002yvr.2	Q14190	OTTHUMG00000086637	ENST00000290399.6:c.417C>T	21.37:g.38092190C>T			37014060	NM_009586	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Silent	SNP	ENST00000290399.6	37	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	10.70	1.424142	0.25639	.	.	ENSG00000159263	ENST00000431229	.	.	.	4.93	-1.31	0.09230	.	.	.	.	.	T	0.42854	0.1221	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31194	-0.9952	4	.	.	.	.	3.4661	0.07550	0.2175:0.2659:0.4057:0.1109	.	.	.	.	S	77	.	.	P	+	1	0	SIM2	37014060	0.001000	0.12720	0.837000	0.33122	0.994000	0.84299	-2.206000	0.01231	0.082000	0.17018	0.655000	0.94253	CCT		0.512	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586	
SEPT12	124404	hgsc.bcm.edu	37	16	4836036	4836036	+	Silent	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr16:4836036T>A	ENST00000268231.8	-	3	500	c.237A>T	c.(235-237)ccA>ccT	p.P79P	SEPT12_ENST00000591861.1_5'UTR|SMIM22_ENST00000589721.1_5'Flank|SMIM22_ENST00000589327.1_5'Flank|SEPT12_ENST00000396693.5_Silent_p.P79P	NM_144605.4	NP_653206.2	Q8IYM1	SEP12_HUMAN	septin 12	79	Septin-type G.				cell cycle (GO:0007049)|cell division (GO:0051301)	cleavage furrow (GO:0032154)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|septin complex (GO:0031105)|sperm annulus (GO:0097227)|spindle (GO:0005819)|stress fiber (GO:0001725)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)	p.P79P(1)		NS(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|skin(2)|stomach(3)	23						CCAAGCCCGGTGGGTTTGACT	0.627																																					p.P79P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A237T	16						.						54.0	47.0	49.0					16																	4836036		2197	4300	6497	4776037	SO:0001819	synonymous_variant	124404	exon3			AK058139	CCDS10522.1, CCDS53987.1	16p13.3	2013-01-21			ENSG00000140623	ENSG00000140623		"""Septins"""	26348	protein-coding gene	gene with protein product		611562				14611653, 15915442	Standard	NM_001154458		Approved	FLJ25410	uc002cxq.3	Q8IYM1	OTTHUMG00000129481	ENST00000268231.8:c.237A>T	16.37:g.4836036T>A			4776037	NM_144605	Q0P6B0|Q1PBH0|Q96LL0	Silent	SNP	ENST00000268231.8	37	CCDS10522.1																																																																																				0.627	SEPT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251645.2	NM_144605	
KAT8	84148	hgsc.bcm.edu	37	16	31131563	31131563	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr16:31131563T>C	ENST00000543774.2	+	3	603	c.268T>C	c.(268-270)Tat>Cat	p.Y90H	KAT8_ENST00000448516.2_Missense_Mutation_p.Y90H|KAT8_ENST00000219797.4_Missense_Mutation_p.Y90H|RP11-196G11.4_ENST00000576336.1_RNA			Q9H7Z6	KAT8_HUMAN	K(lysine) acetyltransferase 8	90	Chromo.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|myeloid cell differentiation (GO:0030099)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	histone acetyltransferase complex (GO:0000123)|kinetochore (GO:0000776)|MLL1 complex (GO:0071339)|MSL complex (GO:0072487)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|transcription factor binding (GO:0008134)	p.Y90H(1)									AGAGGAATTCTATGTACACTA	0.537																																					p.Y90H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T268C	16						.						152.0	137.0	142.0					16																	31131563		2197	4300	6497	31039064	SO:0001583	missense	84148	exon2			AF217501	CCDS10706.1, CCDS45468.1	16p11.1	2013-01-10	2011-07-21	2011-07-21	ENSG00000103510	ENSG00000103510	2.3.1.48	"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	17933	protein-coding gene	gene with protein product		609912	"""MYST histone acetyltransferase 1"""	MYST1		10786633	Standard	NM_032188		Approved	MOF, FLJ14040, hMOF, ZC2HC8	uc002eax.3	Q9H7Z6	OTTHUMG00000132410	ENST00000543774.2:c.268T>C	16.37:g.31131563T>C	ENSP00000456933:p.Tyr90His		31039064	NM_032188	A8K4Z1|G5E9P2|Q659G0|Q7LC17|Q8IY59|Q8WYB4|Q8WZ14|Q9HAC5|Q9NR35	Missense_Mutation	SNP	ENST00000543774.2	37	CCDS10706.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.601576	0.87055	.	.	ENSG00000103510	ENST00000219797;ENST00000448516	T;T	0.55930	0.49;0.49	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.77598	0.4154	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.81976	-0.0686	10	0.59425	D	0.04	-14.9295	15.1835	0.72978	0.0:0.0:0.0:1.0	.	90;90	Q9H7Z6;G5E9P2	KAT8_HUMAN;.	H	90	ENSP00000219797:Y90H;ENSP00000406037:Y90H	ENSP00000219797:Y90H	Y	+	1	0	KAT8	31039064	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.131000	0.77243	2.235000	0.73313	0.533000	0.62120	TAT		0.537	KAT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000255546.3	NM_032188	
AMFR	267	hgsc.bcm.edu	37	16	56397907	56397907	+	Silent	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr16:56397907G>A	ENST00000290649.5	-	13	1920	c.1710C>T	c.(1708-1710)cgC>cgT	p.R570R		NM_001144.5	NP_001135.3	Q9UKV5	AMFR_HUMAN	autocrine motility factor receptor, E3 ubiquitin protein ligase	570					aging (GO:0007568)|cellular component movement (GO:0006928)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|learning or memory (GO:0007611)|protein oligomerization (GO:0051259)|protein polyubiquitination (GO:0000209)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)	dendrite (GO:0030425)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	ligase activity (GO:0016874)|receptor activity (GO:0004872)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R570R(1)		NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17						ACTTGGAGAAGCGGCTCCCAC	0.612																																					p.R570R	Pancreas(2;144 323 39528)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1710T	16						.						59.0	50.0	53.0					16																	56397907		2198	4300	6498	54955408	SO:0001819	synonymous_variant	267	exon13			L35233	CCDS10758.1	16q21	2013-01-09	2012-02-23		ENSG00000159461	ENSG00000159461		"""RING-type (C3HC4) zinc fingers"""	463	protein-coding gene	gene with protein product		603243	"""autocrine motility factor receptor"""			1649192	Standard	NM_001144		Approved	RNF45, gp78	uc002eiy.4	Q9UKV5	OTTHUMG00000133239	ENST00000290649.5:c.1710C>T	16.37:g.56397907G>A			54955408	NM_001144	P26442|Q8IZ70	Silent	SNP	ENST00000290649.5	37	CCDS10758.1																																																																																				0.612	AMFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256978.2		
GAS8	2622	hgsc.bcm.edu	37	16	90097861	90097861	+	Missense_Mutation	SNP	G	G	T	rs884928	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr16:90097861G>T	ENST00000268699.4	+	3	367	c.245G>T	c.(244-246)cGg>cTg	p.R82L	C16orf3_ENST00000408886.2_5'Flank|GAS8_ENST00000536122.1_Missense_Mutation_p.R57L|GAS8_ENST00000540721.1_3'UTR	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8	82	Regulates microtubule-binding. {ECO:0000250}.				cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		AACAAAGACCGGGAGATGGAA	0.602													G|||	2	0.000399361	0.0015	0.0	5008	,	,		16514	0.0		0.0	False		,,,				2504	0.0				p.R82L												.	.	0			c.G245T	16						.						95.0	106.0	102.0					16																	90097861		2193	4297	6490	88625362	SO:0001583	missense	2622	exon3			AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.245G>T	16.37:g.90097861G>T	ENSP00000268699:p.Arg82Leu		88625362	NM_001481	B2RCT1|B7Z4U1|G3V1L5|Q2M234	Missense_Mutation	SNP	ENST00000268699.4	37	CCDS10992.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.699185	0.88830	.	.	ENSG00000141013	ENST00000536122;ENST00000268699;ENST00000540721;ENST00000537797	T;T	0.38560	1.15;1.13	5.88	5.88	0.94601	.	0.052785	0.85682	D	0.000000	T	0.74824	0.3767	M	0.92077	3.27	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.79688	-0.1699	9	.	.	.	-42.1888	20.2366	0.98359	0.0:0.0:1.0:0.0	.	53;82;82	B7Z1X3;B7Z9B0;O95995	.;.;GAS8_HUMAN	L	57;82;53;82	ENSP00000440977:R57L;ENSP00000268699:R82L	.	R	+	2	0	GAS8	88625362	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	6.392000	0.73213	2.792000	0.96026	0.557000	0.71058	CGG		0.602	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
SLC2A2	6514	hgsc.bcm.edu	37	3	170723098	170723098	+	Silent	SNP	A	A	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr3:170723098A>C	ENST00000314251.3	-	7	1018	c.939T>G	c.(937-939)gcT>gcG	p.A313A	SLC2A2_ENST00000382808.4_Silent_p.A194A	NM_000340.1	NP_000331.1	P11168	GTR2_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 2	313					carbohydrate metabolic process (GO:0005975)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose transport (GO:0015758)|hexose transmembrane transport (GO:0035428)|hexose transport (GO:0008645)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	brush border (GO:0005903)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	D-glucose transmembrane transporter activity (GO:0055056)|dehydroascorbic acid transporter activity (GO:0033300)|glucose transmembrane transporter activity (GO:0005355)|hexose transmembrane transporter activity (GO:0015149)	p.A313A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24	all_cancers(22;1.41e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.122)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)		Streptozocin(DB00428)	AAAATTGCTGAGCCACATGCA	0.433																																					p.A313A												SLC2A2,central_nervous_system,brain,Substitution - Missense,-2	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T939G	3						.						183.0	169.0	174.0					3																	170723098		2203	4300	6503	172205792	SO:0001819	synonymous_variant	6514	exon7			J03810	CCDS3215.1	3q26.2-q27	2013-05-22			ENSG00000163581	ENSG00000163581		"""Solute carriers"""	11006	protein-coding gene	gene with protein product		138160		GLUT2		1852621	Standard	NM_000340		Approved		uc003fhe.1	P11168	OTTHUMG00000158997	ENST00000314251.3:c.939T>G	3.37:g.170723098A>C			172205792	NM_000340	A8K481|B2R936|B7Z547|F8W8V8|Q9UCW9	Silent	SNP	ENST00000314251.3	37	CCDS3215.1																																																																																				0.433	SLC2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352834.1	NM_000340	
MST1R	4486	hgsc.bcm.edu	37	3	49933985	49933985	+	Silent	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr3:49933985T>A	ENST00000296474.3	-	9	2454	c.2427A>T	c.(2425-2427)gcA>gcT	p.A809A	CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Silent_p.A809A	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	809	IPT/TIG 3.				cellular component movement (GO:0006928)|defense response (GO:0006952)|innate immune response (GO:0045087)|macrophage colony-stimulating factor signaling pathway (GO:0038145)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|response to virus (GO:0009615)|signal transduction (GO:0007165)|single fertilization (GO:0007338)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|macrophage colony-stimulating factor receptor activity (GO:0005011)	p.A809A(2)		cervix(1)|endometrium(5)|large_intestine(3)|lung(17)|ovary(5)|prostate(2)|skin(1)|urinary_tract(3)	37				BRCA - Breast invasive adenocarcinoma(193;4.65e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.00553)|Kidney(197;0.00625)		TGCTTTCCACTGCCCTAAGCC	0.582																																					p.A809A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A2427T	3						.						120.0	103.0	108.0					3																	49933985		2203	4300	6503	49908989	SO:0001819	synonymous_variant	4486	exon9			X70040	CCDS2807.1, CCDS58833.1	3p21	2008-08-18			ENSG00000164078	ENSG00000164078		"""CD molecules"""	7381	protein-coding gene	gene with protein product		600168	"""PTK8 protein tyrosine kinase 8"""	RON, PTK8		8386824	Standard	NM_002447		Approved	CDw136, CD136	uc003cxy.4	Q04912	OTTHUMG00000156709	ENST00000296474.3:c.2427A>T	3.37:g.49933985T>A			49908989	NM_002447	B5A944|B5A945|B5A946|B5A947	Silent	SNP	ENST00000296474.3	37	CCDS2807.1																																																																																				0.582	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1		
HTR3C	170572	hgsc.bcm.edu	37	3	183772635	183772635	+	Missense_Mutation	SNP	G	G	A	rs183919204		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr3:183772635G>A	ENST00000318351.1	+	2	228	c.194G>A	c.(193-195)cGt>cAt	p.R65H		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	65					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)	p.R65H(2)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	ATCCCTACCCGTGTCAACATC	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		20689	0.001		0.0	False		,,,				2504	0.0				p.R65H												.	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G194A	3						.						137.0	111.0	120.0					3																	183772635		2203	4300	6503	185255329	SO:0001583	missense	170572	exon2			AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.194G>A	3.37:g.183772635G>A	ENSP00000322617:p.Arg65His		185255329	NM_130770	A2RRR5	Missense_Mutation	SNP	ENST00000318351.1	37	CCDS3250.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	.	1.781	-0.481841	0.04383	.	.	ENSG00000178084	ENST00000318351	T	0.79454	-1.27	4.43	-6.54	0.01860	Neurotransmitter-gated ion-channel ligand-binding (3);	2.322460	0.01299	N	0.010255	T	0.49304	0.1549	N	0.04686	-0.185	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.45716	-0.9242	10	0.13470	T	0.59	5.3539	2.3097	0.04183	0.255:0.1178:0.3962:0.231	.	65	Q8WXA8	5HT3C_HUMAN	H	65	ENSP00000322617:R65H	ENSP00000322617:R65H	R	+	2	0	HTR3C	185255329	0.000000	0.05858	0.000000	0.03702	0.451000	0.32288	-1.183000	0.03079	-1.188000	0.02705	-1.267000	0.01435	CGT		0.532	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20890176	20890176	+	Silent	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr12:20890176T>C	ENST00000266509.2	+	11	1886	c.1518T>C	c.(1516-1518)tgT>tgC	p.C506C	SLCO1C1_ENST00000545604.1_Silent_p.C506C|SLCO1C1_ENST00000545102.1_Silent_p.C388C|SLCO1C1_ENST00000381552.1_Silent_p.C506C|SLCO1C1_ENST00000540354.1_Silent_p.C457C	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	506	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.C506C(1)		NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TTGCTGGTTGTCAAACCTCCA	0.398																																					p.C506C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1518C	12						.						101.0	94.0	96.0					12																	20890176		2203	4300	6503	20781443	SO:0001819	synonymous_variant	53919	exon11			AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.1518T>C	12.37:g.20890176T>C			20781443	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Silent	SNP	ENST00000266509.2	37	CCDS8683.1																																																																																				0.398	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35T	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val		25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
KRT75	9119	hgsc.bcm.edu	37	12	52818377	52818377	+	Missense_Mutation	SNP	C	C	T	rs61730614	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr12:52818377C>T	ENST00000252245.5	-	9	1800	c.1580G>A	c.(1579-1581)cGg>cAg	p.R527Q	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	527	Tail.				hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R527Q(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		CCCTAAGCCCCGGTTGCTGGT	0.622													C|||	816	0.162939	0.09	0.2493	5008	,	,		18615	0.1558		0.164	False		,,,				2504	0.2065				p.R527Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1580A	12						.	C	GLN/ARG	495,3911	230.4+/-244.6	28,439,1736	159.0	158.0	158.0		1580	4.8	1.0	12	dbSNP_129	158	1401,7199	270.1+/-288.8	115,1171,3014	yes	missense	KRT75	NM_004693.2	43	143,1610,4750	TT,TC,CC		16.2907,11.2347,14.5779	probably-damaging	527/552	52818377	1896,11110	2203	4300	6503	51104644	SO:0001583	missense	9119	exon9			Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1580G>A	12.37:g.52818377C>T	ENSP00000252245:p.Arg527Gln		51104644	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	346	0.15842490842490842	41	0.08333333333333333	78	0.2154696132596685	95	0.1660839160839161	132	0.1741424802110818	C	15.92	2.976106	0.53720	0.112347	0.162907	ENSG00000170454	ENST00000252245	D	0.87809	-2.3	4.83	4.83	0.62350	.	0.000000	0.40064	N	0.001187	T	0.00328	0.0010	L	0.43152	1.355	0.30791	P	0.7408779999999999	D	0.89917	1.0	D	0.74023	0.982	T	0.18935	-1.0321	9	0.16420	T	0.52	.	13.2889	0.60260	0.0:1.0:0.0:0.0	.	527	O95678	K2C75_HUMAN	Q	527	ENSP00000252245:R527Q	ENSP00000252245:R527Q	R	-	2	0	KRT75	51104644	0.574000	0.26684	0.995000	0.50966	0.493000	0.33554	1.022000	0.30052	2.503000	0.84419	0.561000	0.74099	CGG		0.622	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
ESPL1	9700	hgsc.bcm.edu	37	12	53683296	53683296	+	Silent	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr12:53683296T>C	ENST00000257934.4	+	22	5122	c.5031T>C	c.(5029-5031)ttT>ttC	p.F1677F	ESPL1_ENST00000552462.1_Silent_p.F1677F	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1677					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)	p.F1677F(1)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						AGCGCCTCTTTTCCTTCAGGG	0.592																																					p.F1677F	Colon(53;1069 1201 2587 5382)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5031C	12						.						49.0	52.0	51.0					12																	53683296		2203	4300	6503	51969563	SO:0001819	synonymous_variant	9700	exon22			D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.5031T>C	12.37:g.53683296T>C			51969563	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																				0.592	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
RIMBP2	23504	hgsc.bcm.edu	37	12	130941072	130941072	+	Missense_Mutation	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr12:130941072G>T	ENST00000261655.4	-	4	439	c.276C>A	c.(274-276)ttC>ttA	p.F92L	RIMBP2_ENST00000535703.1_5'UTR|RIMBP2_ENST00000536002.1_5'UTR	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	92					negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.F92L(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GGCCATTCATGAACTGTGGGA	0.642																																					p.F92L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C276A	12						.						58.0	47.0	51.0					12																	130941072		2203	4300	6503	129507025	SO:0001583	missense	23504	exon4			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.276C>A	12.37:g.130941072G>T	ENSP00000261655:p.Phe92Leu		129507025	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	0.020	-1.439898	0.01098	.	.	ENSG00000060709	ENST00000261655	T	0.16073	2.37	4.06	0.628	0.17681	.	0.485666	0.20418	N	0.092726	T	0.06005	0.0156	N	0.13327	0.33	0.25634	N	0.986276	B	0.02656	0.0	B	0.01281	0.0	T	0.29792	-1.0000	10	0.11485	T	0.65	-2.6383	0.2462	0.00199	0.3056:0.1344:0.2423:0.3177	.	92	O15034	RIMB2_HUMAN	L	92	ENSP00000261655:F92L	ENSP00000261655:F92L	F	-	3	2	RIMBP2	129507025	1.000000	0.71417	0.040000	0.18447	0.013000	0.08279	1.249000	0.32839	0.711000	0.32018	-0.123000	0.14984	TTC		0.642	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
FAM219B	57184	hgsc.bcm.edu	37	15	75197510	75197510	+	Missense_Mutation	SNP	G	G	C	rs138405677		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	G	G	G	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr15:75197510G>C	ENST00000357635.5	-	3	685	c.365C>G	c.(364-366)tCc>tGc	p.S122C	FAM219B_ENST00000565772.1_Missense_Mutation_p.S36C|FAM219B_ENST00000563706.1_5'UTR|FAM219B_ENST00000457294.2_Missense_Mutation_p.S122C|FAM219B_ENST00000563119.1_Missense_Mutation_p.S122C	NM_020447.3	NP_065180.1	Q5XKK7	F219B_HUMAN	family with sequence similarity 219, member B	122																	AGAGTCGAGGGACACCAGGTT	0.527																																					p.S122C												.	.	0			c.C365G	15						.						85.0	71.0	76.0					15																	75197510		2197	4295	6492	72984563	SO:0001583	missense	57184	exon3			AK000005	CCDS32295.1	15q23	2012-03-06	2012-03-06	2012-03-06	ENSG00000178761	ENSG00000178761			24695	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 17"""	C15orf17		11214971	Standard	NM_020447		Approved	FLJ00005	uc002azh.4	Q5XKK7	OTTHUMG00000172715	ENST00000357635.5:c.365C>G	15.37:g.75197510G>C	ENSP00000350260:p.Ser122Cys		72984563	NM_020447	A8K4Q5|B4DK57|Q9NXY0	Missense_Mutation	SNP	ENST00000357635.5	37	CCDS32295.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.929113	0.92389	.	.	ENSG00000178761	ENST00000357635;ENST00000457294	.	.	.	5.5	5.5	0.81552	.	0.053881	0.85682	D	0.000000	T	0.77585	0.4152	M	0.66939	2.045	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65874	0.939;0.939	T	0.79543	-0.1760	9	0.87932	D	0	-9.644	18.4438	0.90676	0.0:0.0:1.0:0.0	.	122;122	D3DW69;Q5XKK7	.;CO017_HUMAN	C	122	.	ENSP00000350260:S122C	S	-	2	0	C15orf17	72984563	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.006000	0.93592	2.602000	0.87976	0.555000	0.69702	TCC		0.527	FAM219B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420165.1	NM_020447	
CENPE	1062	hgsc.bcm.edu	37	4	104044047	104044047	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr4:104044047G>A	ENST00000265148.3	-	43	7213	c.7124C>T	c.(7123-7125)gCt>gTt	p.A2375V	CENPE_ENST00000380026.3_Missense_Mutation_p.A2254V	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	2375	Kinetochore-binding domain.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)	p.A2338V(1)		NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TAACTGTGTAGCTCTTGATGT	0.338																																					p.A2375V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7124T	4						.						174.0	179.0	177.0					4																	104044047		2203	4300	6503	104263496	SO:0001583	missense	1062	exon43			Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.7124C>T	4.37:g.104044047G>A	ENSP00000265148:p.Ala2375Val		104263496	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.453218	0.43531	.	.	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.68903	-0.36;-0.35	4.57	2.59	0.31030	.	.	.	.	.	T	0.54565	0.1866	L	0.51422	1.61	0.09310	N	1	B;B	0.33073	0.102;0.396	B;B	0.29785	0.022;0.107	T	0.53236	-0.8467	9	0.66056	D	0.02	.	4.2443	0.10663	0.1212:0.0:0.6328:0.246	.	2254;2375	Q02224-3;Q02224	.;CENPE_HUMAN	V	2375;2339;2254	ENSP00000265148:A2375V;ENSP00000369365:A2254V	ENSP00000265148:A2375V	A	-	2	0	CENPE	104263496	0.000000	0.05858	0.075000	0.20258	0.367000	0.29736	0.544000	0.23253	2.070000	0.61991	0.467000	0.42956	GCT		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ANXA10	11199	hgsc.bcm.edu	37	4	169060676	169060676	+	Missense_Mutation	SNP	G	G	A	rs202148101		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr4:169060676G>A	ENST00000359299.3	+	3	326	c.140G>A	c.(139-141)cGc>cAc	p.R47H		NM_007193.4	NP_009124.2	Q9UJ72	ANX10_HUMAN	annexin A10	47						mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)	p.R47H(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(2)	16		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0325)		CTGACTCAGCGCTGCAATGCA	0.418																																					p.R47H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G140A	4						.	G	HIS/ARG	0,4406		0,0,2203	107.0	101.0	103.0		140	3.2	0.7	4		103	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ANXA10	NM_007193.4	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	47/325	169060676	2,13004	2203	4300	6503	169297251	SO:0001583	missense	11199	exon3			AJ238979	CCDS34096.1	4q32.3	2008-02-05			ENSG00000109511	ENSG00000109511		"""Annexins"""	534	protein-coding gene	gene with protein product		608008				10458909	Standard	NM_007193		Approved	ANX14	uc003irm.3	Q9UJ72	OTTHUMG00000161275	ENST00000359299.3:c.140G>A	4.37:g.169060676G>A	ENSP00000352248:p.Arg47His		169297251	NM_007193	Q96IQ5|Q9UJV4	Missense_Mutation	SNP	ENST00000359299.3	37	CCDS34096.1	.	.	.	.	.	.	.	.	.	.	G	9.801	1.180530	0.21787	0.0	2.33E-4	ENSG00000109511	ENST00000359299;ENST00000393751	T	0.12774	2.65	5.82	3.19	0.36642	.	0.211827	0.40385	N	0.001107	T	0.18841	0.0452	M	0.81179	2.53	0.43149	D	0.994913	B	0.25719	0.132	B	0.22386	0.039	T	0.03863	-1.0997	10	0.72032	D	0.01	.	10.1456	0.42762	0.2196:0.0:0.7804:0.0	.	47	Q9UJ72	ANX10_HUMAN	H	47	ENSP00000352248:R47H	ENSP00000352248:R47H	R	+	2	0	ANXA10	169297251	1.000000	0.71417	0.701000	0.30321	0.008000	0.06430	3.810000	0.55613	0.833000	0.34828	-0.742000	0.03525	CGC		0.418	ANXA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364348.2	NM_007193	
DOCK11	139818	hgsc.bcm.edu	37	X	117739300	117739300	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chrX:117739300G>A	ENST00000276202.7	+	24	2725	c.2662G>A	c.(2662-2664)Gtt>Att	p.V888I	DOCK11_ENST00000276204.6_Missense_Mutation_p.V888I	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	888					blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V888I(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						TGAAGATGACGTTCCTATCAA	0.348																																					p.V888I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2662A	X						.						139.0	121.0	127.0					X																	117739300		2203	4300	6503	117623328	SO:0001583	missense	139818	exon24			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.2662G>A	X.37:g.117739300G>A	ENSP00000276202:p.Val888Ile		117623328	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Missense_Mutation	SNP	ENST00000276202.7	37	CCDS35373.1	.	.	.	.	.	.	.	.	.	.	G	11.09	1.535761	0.27475	.	.	ENSG00000147251	ENST00000276204;ENST00000276202	T;T	0.69806	-0.43;-0.43	5.43	5.43	0.79202	.	0.119735	0.56097	D	0.000022	T	0.47358	0.1441	N	0.25060	0.705	0.47374	D	0.999409	P;P	0.40266	0.71;0.71	B;B	0.28385	0.089;0.089	T	0.49643	-0.8918	10	0.13470	T	0.59	-7.932	17.4229	0.87519	0.0:0.0:1.0:0.0	.	888;888	A6NIW2;Q5JSL3	.;DOC11_HUMAN	I	888	ENSP00000276204:V888I;ENSP00000276202:V888I	ENSP00000276202:V888I	V	+	1	0	DOCK11	117623328	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	4.283000	0.58977	2.415000	0.81967	0.600000	0.82982	GTT		0.348	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
XAGE3	170626	hgsc.bcm.edu	37	X	52891653	52891653	+	Silent	SNP	C	C	T	rs73206488		TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chrX:52891653C>T	ENST00000346279.3	-	5	400	c.330G>A	c.(328-330)caG>caA	p.Q110Q	XAGE3_ENST00000375491.3_Silent_p.Q110Q	NM_133179.2	NP_573440.1	Q8WTP9	XAGE3_HUMAN	X antigen family, member 3	110								p.Q110Q(1)		kidney(1)|large_intestine(1)|lung(2)	4						TCATTTAAACCTGTGGTTGCC	0.338																																					p.Q110Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G330A	X						.																																			52908378	SO:0001819	synonymous_variant	170626	exon5			BG354572	CCDS14347.1	Xp11.22	2010-09-27	2004-06-07	2005-01-27	ENSG00000171402	ENSG00000171402			14618	protein-coding gene	gene with protein product	"""cancer/testis antigen family 12, member 3a"", ""cancer/testis antigen family 12, member 3b"""	300740	"""placenta-specific 6; G antigen, family D, 4"""	PLAC6, GAGED4			Standard	NM_133179		Approved	XAGE-3, pp9012, CT12.3a, CT12.3b	uc004dre.3	Q8WTP9	OTTHUMG00000021587	ENST00000346279.3:c.330G>A	X.37:g.52891653C>T			52908378	NM_133179	Q5JS82|Q8WYS9	Silent	SNP	ENST00000346279.3	37	CCDS14347.1																																																																																				0.338	XAGE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056686.1	NM_133179	
ATP7A	538	hgsc.bcm.edu	37	X	77284880	77284880	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chrX:77284880G>C	ENST00000341514.6	+	15	3205	c.3050G>C	c.(3049-3051)gGa>gCa	p.G1017A	ATP7A_ENST00000343533.5_Missense_Mutation_p.G939A|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	1017					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)	p.G1017A(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	GTGGGTACAGGAGTAGGTGCT	0.463																																					p.G1017A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3050C	X						.						139.0	121.0	127.0					X																	77284880		2203	4296	6499	77171536	SO:0001583	missense	538	exon15			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.3050G>C	X.37:g.77284880G>C	ENSP00000345728:p.Gly1017Ala		77171536	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	37	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.926982	0.92319	.	.	ENSG00000165240	ENST00000343533;ENST00000341514	D;D	0.90133	-2.62;-2.62	5.94	5.94	0.96194	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.95382	0.8501	M	0.74647	2.275	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95406	0.8494	10	0.72032	D	0.01	1.3434	19.2446	0.93896	0.0:0.0:1.0:0.0	.	1017	Q04656	ATP7A_HUMAN	A	939;1017	ENSP00000343026:G939A;ENSP00000345728:G1017A	ENSP00000345728:G1017A	G	+	2	0	ATP7A	77171536	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.869000	0.99810	2.497000	0.84241	0.506000	0.49869	GGA		0.463	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
KLHL4	56062	hgsc.bcm.edu	37	X	86772949	86772949	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chrX:86772949G>A	ENST00000373119.4	+	1	198	c.53G>A	c.(52-54)cGc>cAc	p.R18H	KLHL4_ENST00000373114.4_Missense_Mutation_p.R18H	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	18						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R18H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						CTAAGGCTACGCTGGAGGTGG	0.493																																					p.R18H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G53A	X						.						116.0	106.0	110.0					X																	86772949		2203	4300	6503	86659605	SO:0001583	missense	56062	exon1			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.53G>A	X.37:g.86772949G>A	ENSP00000362211:p.Arg18His		86659605	NM_057162	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902316	0.52227	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.86769	-2.17;-2.15	5.05	4.16	0.48862	.	0.000000	0.64402	D	0.000003	D	0.83613	0.5292	L	0.47016	1.485	0.58432	D	0.999996	B;B	0.28933	0.157;0.228	B;B	0.33846	0.081;0.171	T	0.81346	-0.0974	10	0.59425	D	0.04	.	10.9597	0.47379	0.0963:0.0:0.9037:0.0	.	18;18	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	H	18	ENSP00000362211:R18H;ENSP00000362206:R18H	ENSP00000362206:R18H	R	+	2	0	KLHL4	86659605	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.672000	0.68102	1.047000	0.40274	0.513000	0.50165	CGC		0.493	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
SLITRK2	84631	hgsc.bcm.edu	37	X	144904519	144904519	+	Silent	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chrX:144904519G>A	ENST00000370490.1	+	1	4831	c.576G>A	c.(574-576)agG>agA	p.R192R	SLITRK2_ENST00000428560.2_Silent_p.R192R|SLITRK2_ENST00000413937.2_Silent_p.R192R|SLITRK2_ENST00000447897.2_Silent_p.R192R|SLITRK2_ENST00000434188.2_Silent_p.R192R			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	192					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.R192S(1)|p.R192R(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GGGGGAATAGGCTAAAAGTAA	0.473																																					p.R192R												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.G576A	X						.						146.0	125.0	132.0					X																	144904519		2203	4300	6503	144712211	SO:0001819	synonymous_variant	84631	exon3			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.576G>A	X.37:g.144904519G>A			144712211	NM_001144006	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																				0.473	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
CCDC93	54520	hgsc.bcm.edu	37	2	118704387	118704387	+	Splice_Site	SNP	C	C	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr2:118704387C>G	ENST00000376300.2	-	16	1433	c.1296G>C	c.(1294-1296)aaG>aaC	p.K432N	CCDC93_ENST00000319432.5_Splice_Site_p.K431N	NM_019044.4	NP_061917.3	Q567U6	CCD93_HUMAN	coiled-coil domain containing 93	432								p.K432N(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(2)	29						GAGCCTTTACCTTTTCATCTC	0.418																																					p.K432N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1296C	2						.						164.0	139.0	147.0					2																	118704387		2203	4300	6503	118420857	SO:0001630	splice_region_variant	54520	exon16			BC028609	CCDS2121.2	2q14.1	2008-02-05			ENSG00000125633	ENSG00000125633			25611	protein-coding gene	gene with protein product						12477932	Standard	NM_019044		Approved	FLJ10996	uc002tlj.3	Q567U6	OTTHUMG00000058517	ENST00000376300.2:c.1296+1G>C	2.37:g.118704387C>G			118420857	NM_019044	A8K3V7|Q4LE78|Q53TJ2|Q8TBX5|Q9H6R5|Q9NV15	Missense_Mutation	SNP	ENST00000376300.2	37	CCDS2121.2	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450299	0.43531	.	.	ENSG00000125633	ENST00000376300;ENST00000319432	T;T	0.18174	2.23;2.23	5.39	5.39	0.77823	.	0.245137	0.42294	D	0.000731	T	0.13372	0.0324	L	0.44542	1.39	0.50632	D	0.999884	P	0.40000	0.698	B	0.21546	0.035	T	0.07102	-1.0790	9	.	.	.	-24.1956	17.5251	0.87798	0.0:1.0:0.0:0.0	.	432	Q567U6	CCD93_HUMAN	N	432;431	ENSP00000365477:K432N;ENSP00000324135:K431N	.	K	-	3	2	CCDC93	118420857	1.000000	0.71417	0.998000	0.56505	0.564000	0.35744	5.024000	0.64090	2.804000	0.96469	0.655000	0.94253	AAG		0.418	CCDC93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000129615.1	NM_019044	Missense_Mutation
MARCH7	64844	hgsc.bcm.edu	37	2	160599695	160599695	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr2:160599695A>G	ENST00000259050.4	+	3	399	c.277A>G	c.(277-279)Aaa>Gaa	p.K93E	MARCH7_ENST00000409591.1_Missense_Mutation_p.K55E|MARCH7_ENST00000409175.1_Missense_Mutation_p.K93E|MARCH7_ENST00000473749.1_3'UTR|MARCH7_ENST00000539065.1_Missense_Mutation_p.K93E	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	93	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.K93E(1)		breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						AAAAAGACCTAAACTTTCCTG	0.403																																					p.K93E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A277G	2						.						135.0	130.0	132.0					2																	160599695		2203	4300	6503	160307941	SO:0001583	missense	64844	exon3			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.277A>G	2.37:g.160599695A>G	ENSP00000259050:p.Lys93Glu		160307941	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	A	18.51	3.639934	0.67244	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000421037;ENST00000409591	T;T;T;T;T	0.59638	2.13;2.42;2.13;0.25;2.13	5.54	5.54	0.83059	.	0.046653	0.85682	D	0.000000	T	0.72653	0.3487	M	0.62723	1.935	0.45307	D	0.998305	D;D;D	0.69078	0.974;0.997;0.997	P;D;D	0.73380	0.655;0.98;0.98	T	0.75548	-0.3279	10	0.72032	D	0.01	-5.003	14.2554	0.66048	1.0:0.0:0.0:0.0	.	93;55;93	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	E	93;93;93;93;55	ENSP00000386830:K93E;ENSP00000442992:K93E;ENSP00000259050:K93E;ENSP00000392862:K93E;ENSP00000387238:K55E	ENSP00000259050:K93E	K	+	1	0	MARCH7	160307941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.766000	0.74970	2.107000	0.64212	0.528000	0.53228	AAA		0.403	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
SLC5A6	8884	hgsc.bcm.edu	37	2	27423971	27423971	+	Silent	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr2:27423971T>C	ENST00000310574.3	-	16	2132	c.1659A>G	c.(1657-1659)cgA>cgG	p.R553R	SLC5A6_ENST00000408041.1_Silent_p.R553R|SLC5A6_ENST00000461319.1_5'UTR	NM_021095.2	NP_066918.2	Q9Y289	SC5A6_HUMAN	solute carrier family 5 (sodium/multivitamin and iodide cotransporter), member 6	553					biotin metabolic process (GO:0006768)|biotin transport (GO:0015878)|pantothenate metabolic process (GO:0015939)|pantothenate transmembrane transport (GO:0015887)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.R553R(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(8)|ovary(3)|prostate(1)|skin(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Biotin(DB00121)|gabapentin enacarbil(DB08872)|Lipoic Acid(DB00166)	GGGACCGGCCTCGCATTCTCC	0.607																																					p.R553R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1659G	2						.						92.0	90.0	91.0					2																	27423971		2203	4300	6503	27277475	SO:0001819	synonymous_variant	8884	exon16			AF069307	CCDS1740.1	2p23	2013-07-19	2013-07-19		ENSG00000138074	ENSG00000138074		"""Solute carriers"""	11041	protein-coding gene	gene with protein product		604024	"""solute carrier family 5 (sodium-dependent vitamin transporter), member 6"""			9516450, 10329687	Standard	NM_021095		Approved	SMVT	uc002rjd.3	Q9Y289	OTTHUMG00000097075	ENST00000310574.3:c.1659A>G	2.37:g.27423971T>C			27277475	NM_021095	B2RB85|D6W549|Q969Y5	Silent	SNP	ENST00000310574.3	37	CCDS1740.1																																																																																				0.607	SLC5A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214194.1	NM_021095	
B3GNT2	10678	hgsc.bcm.edu	37	2	62449423	62449423	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr2:62449423T>A	ENST00000301998.4	+	2	320	c.68T>A	c.(67-69)tTt>tAt	p.F23Y	B3GNT2_ENST00000405767.1_Missense_Mutation_p.F23Y	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	23					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.F23Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			TTCATTTATTTTATTATGGAA	0.388																																					p.F23Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T68A	2						.						66.0	72.0	70.0					2																	62449423		2203	4300	6503	62302927	SO:0001583	missense	10678	exon2			AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"""Beta 3-glycosyltransferases"""	15629	protein-coding gene	gene with protein product		605581	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"""	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.68T>A	2.37:g.62449423T>A	ENSP00000305595:p.Phe23Tyr		62302927	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Missense_Mutation	SNP	ENST00000301998.4	37	CCDS1870.1	.	.	.	.	.	.	.	.	.	.	T	16.07	3.017327	0.54576	.	.	ENSG00000170340	ENST00000301998;ENST00000405767	T;T	0.27402	1.67;1.67	6.02	6.02	0.97574	.	0.559141	0.18375	N	0.143144	T	0.20901	0.0503	N	0.08118	0	0.21325	N	0.999722	B	0.15473	0.013	B	0.16722	0.016	T	0.26916	-1.0089	10	0.72032	D	0.01	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	23	Q9NY97	B3GN2_HUMAN	Y	23	ENSP00000305595:F23Y;ENSP00000384692:F23Y	ENSP00000305595:F23Y	F	+	2	0	B3GNT2	62302927	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.698000	0.84413	2.311000	0.77944	0.533000	0.62120	TTT		0.388	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577	
ECEL1	9427	hgsc.bcm.edu	37	2	233347830	233347830	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr2:233347830C>T	ENST00000304546.1	-	9	1776	c.1566G>A	c.(1564-1566)gtG>gtA	p.V522V	ECEL1_ENST00000409941.1_Silent_p.V522V	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	522					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)	p.V522V(1)		breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		ACTCCTTGTCCACAGCATCGG	0.652																																					p.V522V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1566A	2						.						55.0	35.0	42.0					2																	233347830		2203	4300	6503	233056074	SO:0001819	synonymous_variant	9427	exon9			Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"""damage induced neuronal endopeptidase"""	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1566G>A	2.37:g.233347830C>T			233056074	NM_004826	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Silent	SNP	ENST00000304546.1	37	CCDS2493.1																																																																																				0.652	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826	
CYLC2	1539	hgsc.bcm.edu	37	9	105767934	105767934	+	Missense_Mutation	SNP	A	A	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr9:105767934A>C	ENST00000374798.3	+	5	1091	c.1021A>C	c.(1021-1023)Aag>Cag	p.K341Q	CYLC2_ENST00000487798.1_Missense_Mutation_p.K341Q	NM_001340.3	NP_001331.1	Q14093	CYLC2_HUMAN	cylicin, basic protein of sperm head cytoskeleton 2	341	31 X 3 AA repeats of K-K-X.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)	p.K341Q(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(14)|ovary(1)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)	41		all_hematologic(171;0.125)				ggatgaaaagaaggatgcaaa	0.368																																					p.K341Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1021C	9						.						51.0	54.0	53.0					9																	105767934		2202	4299	6501	104807755	SO:0001583	missense	1539	exon5			Z46788	CCDS35085.1	9q31.2	2008-07-21			ENSG00000155833	ENSG00000155833			2583	protein-coding gene	gene with protein product		604035				7737358	Standard	NM_001340		Approved		uc004bbs.2	Q14093	OTTHUMG00000020396	ENST00000374798.3:c.1021A>C	9.37:g.105767934A>C	ENSP00000420256:p.Lys341Gln		104807755	NM_001340	B2R8F4|Q5VVJ9	Missense_Mutation	SNP	ENST00000374798.3	37	CCDS35085.1	.	.	.	.	.	.	.	.	.	.	a	4.983	0.182600	0.09495	.	.	ENSG00000155833	ENST00000374798;ENST00000487798	T;T	0.23754	1.89;1.89	2.26	1.12	0.20585	.	.	.	.	.	T	0.16811	0.0404	N	0.14661	0.345	0.26485	N	0.975049	D	0.65815	0.995	P	0.52598	0.703	T	0.12553	-1.0543	9	0.14252	T	0.57	.	3.4745	0.07579	0.7886:0.0:0.2114:0.0	.	341	Q14093	CYLC2_HUMAN	Q	341	ENSP00000420256:K341Q;ENSP00000417674:K341Q	ENSP00000420256:K341Q	K	+	1	0	CYLC2	104807755	0.535000	0.26370	0.993000	0.49108	0.203000	0.24098	0.708000	0.25719	1.039000	0.40074	0.392000	0.25879	AAG		0.368	CYLC2-001	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053463.3	NM_001340	
RBM18	92400	hgsc.bcm.edu	37	9	125014165	125014165	+	Silent	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr9:125014165C>T	ENST00000417201.3	-	3	341	c.201G>A	c.(199-201)caG>caA	p.Q67Q	RBM18_ENST00000483428.1_5'UTR	NM_033117.3	NP_149108.1	Q96H35	RBM18_HUMAN	RNA binding motif protein 18	67	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.Q67Q(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	7						AGCCTCGAGGCTGTCCCTCCA	0.413																																					p.Q67Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G201A	9						.						82.0	86.0	85.0					9																	125014165		2203	4300	6503	124053986	SO:0001819	synonymous_variant	92400	exon3			AK057676	CCDS6839.1	9q34.11	2013-02-12			ENSG00000119446	ENSG00000119446		"""RNA binding motif (RRM) containing"""	28413	protein-coding gene	gene with protein product						12477932	Standard	NM_033117		Approved	MGC2734	uc004bma.2	Q96H35	OTTHUMG00000020602	ENST00000417201.3:c.201G>A	9.37:g.125014165C>T			124053986	NM_033117	B3KQ89	Silent	SNP	ENST00000417201.3	37	CCDS6839.1																																																																																				0.413	RBM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053928.2	NM_033117	
TPM2	7169	hgsc.bcm.edu	37	9	35689790	35689790	+	Missense_Mutation	SNP	G	G	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr9:35689790G>C	ENST00000360958.2	-	1	129	c.25C>G	c.(25-27)Cag>Gag	p.Q9E	TPM2_ENST00000329305.2_Missense_Mutation_p.Q9E|TPM2_ENST00000378300.5_Missense_Mutation_p.Q9E|TPM2_ENST00000378292.3_Missense_Mutation_p.Q9E	NM_003289.3	NP_003280.2	P07951	TPM2_HUMAN	tropomyosin 2 (beta)	9					muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of ATPase activity (GO:0043462)	cytosol (GO:0005829)|muscle thin filament tropomyosin (GO:0005862)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)	p.Q9E(2)		NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_epithelial(49;0.121)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TTCAGCATCTGCATCTTCTTC	0.667																																					p.Q9E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C25G	9						.						204.0	195.0	198.0					9																	35689790		2203	4300	6503	35679790	SO:0001583	missense	7169	exon1				CCDS6586.1, CCDS6587.1	9p13	2014-09-17	2003-12-02		ENSG00000198467	ENSG00000198467		"""Tropomyosins"""	12011	protein-coding gene	gene with protein product	"""nemaline myopathy type 4"""	190990	"""arthrogryposis multiplex congenital, distal, type 1"""	AMCD1		7606936	Standard	NM_003289		Approved	DA1, NEM4	uc003zxq.3	P07951	OTTHUMG00000019878	ENST00000360958.2:c.25C>G	9.37:g.35689790G>C	ENSP00000354219:p.Gln9Glu		35679790	NM_213674	A6NM85|P06468|Q13894|Q53FM4|Q5TCU4|Q5TCU7|Q9UH67	Missense_Mutation	SNP	ENST00000360958.2	37	CCDS6587.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.355778	0.82243	.	.	ENSG00000198467	ENST00000378300;ENST00000378292;ENST00000329305;ENST00000360958	D;D;D;D	0.87966	-2.32;-2.32;-2.32;-2.32	4.62	4.62	0.57501	.	.	.	.	.	D	0.94427	0.8207	M	0.90252	3.1	0.52501	D	0.99995	P;P;P;B;B	0.51653	0.526;0.72;0.947;0.202;0.023	P;P;D;B;B	0.71656	0.539;0.528;0.974;0.105;0.442	D	0.95490	0.8568	9	0.87932	D	0	-8.3255	16.185	0.81946	0.0:0.0:1.0:0.0	.	9;9;9;9;9	B4DGC2;A7XZE4;P07951;Q5TCU8;P07951-2	.;.;TPM2_HUMAN;.;.	E	9	ENSP00000367550:Q9E;ENSP00000367542:Q9E;ENSP00000367541:Q9E;ENSP00000354219:Q9E	ENSP00000367541:Q9E	Q	-	1	0	TPM2	35679790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.546000	0.98097	2.384000	0.81235	0.561000	0.74099	CAG		0.667	TPM2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052376.1	NM_003289	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88247631	88247631	+	Missense_Mutation	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr9:88247631T>A	ENST00000357081.3	-	14	2105	c.1961A>T	c.(1960-1962)cAc>cTc	p.H654L	AGTPBP1_ENST00000376083.3_Missense_Mutation_p.H614L|AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000376109.3_Missense_Mutation_p.H666L|AGTPBP1_ENST00000432218.1_Missense_Mutation_p.H492L			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	654					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.H614L(1)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						AGGCGGAATGTGACCAAAATA	0.413																																					p.H614L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1841T	9						.						82.0	80.0	80.0					9																	88247631		2203	4300	6503	87437451	SO:0001583	missense	23287	exon14			AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1961A>T	9.37:g.88247631T>A	ENSP00000349592:p.His654Leu		87437451	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Missense_Mutation	SNP	ENST00000357081.3	37		.	.	.	.	.	.	.	.	.	.	T	22.5	4.298759	0.81025	.	.	ENSG00000135049	ENST00000357081;ENST00000376083;ENST00000376109;ENST00000432218	T;T;T;T	0.54479	2.05;2.06;2.03;0.57	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.72993	0.3530	M	0.76574	2.34	0.80722	D	1	D;D;D;D	0.89917	0.97;1.0;1.0;0.995	P;D;D;D	0.83275	0.885;0.988;0.996;0.964	T	0.75425	-0.3322	10	0.59425	D	0.04	-17.5333	16.3015	0.82820	0.0:0.0:0.0:1.0	.	666;654;492;614	Q9UPW5-3;Q9UPW5;B4DHX2;Q9UPW5-2	.;CBPC1_HUMAN;.;.	L	654;614;666;492	ENSP00000349592:H654L;ENSP00000365251:H614L;ENSP00000365277:H666L;ENSP00000402804:H492L	ENSP00000349592:H654L	H	-	2	0	AGTPBP1	87437451	1.000000	0.71417	0.988000	0.46212	0.803000	0.45373	7.374000	0.79633	2.239000	0.73571	0.533000	0.62120	CAC		0.413	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
SH2D3C	10044	hgsc.bcm.edu	37	9	130540871	130540871	+	Splice_Site	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr9:130540871G>A	ENST00000314830.8	-	1	149	c.36C>T	c.(34-36)ttC>ttT	p.F12F		NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	12					JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CACACTCACTGAACTTTTTGC	0.527																																					p.F12F												.	.	0			c.C36T	9						.						423.0	353.0	377.0					9																	130540871		2203	4300	6503	129580692	SO:0001630	splice_region_variant	10044	exon1			AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.37+1C>T	9.37:g.130540871G>A			129580692	NM_170600	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Silent	SNP	ENST00000314830.8	37	CCDS6877.1																																																																																				0.527	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489	Silent
FREM2	341640	hgsc.bcm.edu	37	13	39266024	39266024	+	Missense_Mutation	SNP	C	C	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr13:39266024C>T	ENST00000280481.7	+	1	4759	c.4543C>T	c.(4543-4545)Cgt>Tgt	p.R1515C		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1515					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.R1515C(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)		CACCGATGGACGTAACCCTGT	0.438																																					p.R1515C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4543T	13						.						141.0	127.0	132.0					13																	39266024		2203	4300	6503	38164024	SO:0001583	missense	341640	exon1			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.4543C>T	13.37:g.39266024C>T	ENSP00000280481:p.Arg1515Cys		38164024	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025214	0.35701	.	.	ENSG00000150893	ENST00000280481	T	0.26518	1.73	6.07	6.07	0.98685	.	0.471167	0.26237	N	0.025532	T	0.19327	0.0464	L	0.40543	1.245	0.41873	D	0.990288	P	0.44659	0.84	B	0.38562	0.276	T	0.01630	-1.1308	10	0.38643	T	0.18	.	7.9903	0.30237	0.0:0.816:0.0:0.184	.	1515	Q5SZK8	FREM2_HUMAN	C	1515	ENSP00000280481:R1515C	ENSP00000280481:R1515C	R	+	1	0	FREM2	38164024	0.947000	0.32204	0.176000	0.23000	0.988000	0.76386	6.120000	0.71596	2.890000	0.99128	0.650000	0.86243	CGT		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ARMC4	55130	hgsc.bcm.edu	37	10	28257853	28257853	+	Splice_Site	SNP	G	G	C	rs57067036	byFrequency	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr10:28257853G>C	ENST00000305242.5	-	9	1329	c.1237C>G	c.(1237-1239)Cgg>Ggg	p.R413G	ARMC4_ENST00000537576.1_Splice_Site_p.R105G|ARMC4_ENST00000545014.1_Intron|ARMC4_ENST00000480504.1_5'UTR|ARMC4_ENST00000239715.3_Splice_Site_p.R270G	NM_018076.2	NP_060546.2	Q5T2S8	ARMC4_HUMAN	armadillo repeat containing 4	413					cell projection organization (GO:0030030)|cilium movement (GO:0003341)|left/right axis specification (GO:0070986)|outer dynein arm assembly (GO:0036158)|ventricular system development (GO:0021591)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)		p.R413G(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(17)|liver(1)|lung(17)|ovary(5)|prostate(3)|skin(8)|stomach(2)|urinary_tract(3)	75						GAAACATACCGAAGTAATTGT	0.453													G|||	402	0.0802716	0.1082	0.1037	5008	,	,		17999	0.0099		0.0845	False		,,,				2504	0.0941				p.R413G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1237G	10						.						4.0	3.0	3.0					10																	28257853		1476	3114	4590	28297859	SO:0001630	splice_region_variant	55130	exon9			AL136859	CCDS7157.1	10p12.1-p11.23	2014-02-03			ENSG00000169126	ENSG00000169126		"""Armadillo repeat containing"""	25583	protein-coding gene	gene with protein product		615408				11230166	Standard	XM_005252485		Approved	FLJ10817, FLJ10376, DKFZP434P1735, CILD23	uc001itz.3	Q5T2S8	OTTHUMG00000017867	ENST00000305242.5:c.1238+1C>G	10.37:g.28257853G>C			28297859	NM_018076	A8K906|B7Z7I1|Q9H0C0	Missense_Mutation	SNP	ENST00000305242.5	37	CCDS7157.1	.	.	.	.	.	.	.	.	.	.	G	1.710	-0.499285	0.04291	.	.	ENSG00000169126	ENST00000537576;ENST00000305242;ENST00000537573;ENST00000434029;ENST00000239715	T;T;T;T	0.35789	1.29;1.29;1.29;1.29	3.89	2.01	0.26516	.	1.074070	0.07060	N	0.833582	T	0.32645	0.0836	L	0.54323	1.7	0.09310	N	1	B	0.23650	0.089	B	0.20184	0.028	T	0.29761	-1.0001	10	0.42905	T	0.14	-2.5181	5.8125	0.18473	0.1073:0.1956:0.6971:0.0	.	413	Q5T2S8	ARMC4_HUMAN	G	105;413;105;307;270	ENSP00000443208:R105G;ENSP00000306410:R413G;ENSP00000398155:R307G;ENSP00000239715:R270G	ENSP00000239715:R270G	R	-	1	2	ARMC4	28297859	0.264000	0.24093	0.040000	0.18447	0.005000	0.04900	0.581000	0.23819	0.598000	0.29829	-0.232000	0.12228	CGG		0.453	ARMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047339.1	NM_018076	Missense_Mutation
PRKG1	5592	hgsc.bcm.edu	37	10	54042069	54042069	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr10:54042069A>G	ENST00000401604.2	+	14	1851	c.1657A>G	c.(1657-1659)Act>Gct	p.T553A	PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373985.1_Missense_Mutation_p.T541A|PRKG1-AS1_ENST00000426785.2_RNA|PRKG1_ENST00000373975.2_Missense_Mutation_p.T271A|PRKG1_ENST00000373980.4_Missense_Mutation_p.T568A			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	553	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)	p.T568A(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		TGAACTCCTGACTGGCAGGTA	0.453																																					p.T568A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1702G	10						.						89.0	77.0	81.0					10																	54042069		2203	4300	6503	53712075	SO:0001583	missense	5592	exon14				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.1657A>G	10.37:g.54042069A>G	ENSP00000384200:p.Thr553Ala		53712075	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.274858	0.80580	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.10192	2.9;2.9;2.9	5.63	5.63	0.86233	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.15869	0.0382	L	0.31207	0.915	0.80722	D	1	B;P;P	0.44344	0.044;0.582;0.833	B;P;P	0.53760	0.034;0.477;0.734	T	0.12319	-1.0552	10	0.13853	T	0.58	-16.7666	15.791	0.78364	1.0:0.0:0.0:0.0	.	271;568;553	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	A	553;541;568;271;165	ENSP00000384200:T553A;ENSP00000363097:T541A;ENSP00000363092:T568A	ENSP00000327642:T271A	T	+	1	0	PRKG1	53712075	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.518000	0.81795	2.270000	0.75569	0.460000	0.39030	ACT		0.453	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
BICC1	80114	hgsc.bcm.edu	37	10	60588615	60588615	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr10:60588615T>A	ENST00000373886.3	+	21	2893	c.2889T>A	c.(2887-2889)taT>taA	p.Y963*		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	963					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.Y963*(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						CCCGTCAGTATCACTCAGACA	0.498																																					p.Y963X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T2889A	10						.						113.0	101.0	105.0					10																	60588615		2203	4300	6503	60258621	SO:0001587	stop_gained	80114	exon21			AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.2889T>A	10.37:g.60588615T>A	ENSP00000362993:p.Tyr963*		60258621	NM_001080512		Nonsense_Mutation	SNP	ENST00000373886.3	37	CCDS31206.1	.	.	.	.	.	.	.	.	.	.	T	37	6.378379	0.97520	.	.	ENSG00000122870	ENST00000373886	.	.	.	5.87	-0.463	0.12164	.	0.290182	0.39759	N	0.001270	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.5457	10.2871	0.43573	0.0:0.3085:0.0:0.6915	.	.	.	.	X	963	.	ENSP00000362993:Y963X	Y	+	3	2	BICC1	60258621	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	0.829000	0.27449	-0.235000	0.09767	0.533000	0.62120	TAT		0.498	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	
APC	324	hgsc.bcm.edu	37	5	112173600	112173600	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:112173600C>A	ENST00000457016.1	+	16	2689	c.2309C>A	c.(2308-2310)tCa>tAa	p.S770*	APC_ENST00000508376.2_Nonsense_Mutation_p.S770*|APC_ENST00000257430.4_Nonsense_Mutation_p.S770*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	770	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.S770*(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)		CAGCACTTATCAGAAACTTTT	0.393		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.S752X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	c.C2255A	5	GRCh37	CD941579|CM035803	APC	D|M		.						56.0	57.0	57.0					5																	112173600		2202	4300	6502	112201499	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.2309C>A	5.37:g.112173600C>A	ENSP00000413133:p.Ser770*		112201499	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.220596	0.97390	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.3781	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	770;752;770;770;770	.	ENSP00000257430:S770X	S	+	2	0	APC	112201499	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	TCA		0.393	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
APC	324	hgsc.bcm.edu	37	5	112174158	112174158	+	Missense_Mutation	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:112174158A>G	ENST00000457016.1	+	16	3247	c.2867A>G	c.(2866-2868)tAc>tGc	p.Y956C	APC_ENST00000508376.2_Missense_Mutation_p.Y956C|APC_ENST00000257430.4_Missense_Mutation_p.Y956C|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	956	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)|p.Y956C(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)		AAATTAGAATACAAGAGATCT	0.348		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.Y938C	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|skin(1)	c.A2813G	5						.						68.0	68.0	68.0					5																	112174158		2202	4300	6502	112202057	SO:0001583	missense	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.2867A>G	5.37:g.112174158A>G	ENSP00000413133:p.Tyr956Cys		112202057	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	A	14.17	2.455127	0.43634	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	D;D;D;D;D	0.93906	-2.59;-3.31;-2.59;-2.59;-2.77	5.77	4.61	0.57282	.	0.200690	0.44688	N	0.000428	D	0.95017	0.8387	L	0.55481	1.735	0.49687	D	0.999818	P;D	0.89917	0.66;1.0	B;D	0.75484	0.154;0.986	D	0.94156	0.7410	10	0.49607	T	0.09	-5.9424	11.6284	0.51160	0.9305:0.0:0.0695:0.0	.	958;956	Q4LE70;P25054	.;APC_HUMAN	C	956;938;956;956;956	ENSP00000413133:Y956C;ENSP00000423224:Y938C;ENSP00000257430:Y956C;ENSP00000427089:Y956C;ENSP00000423828:Y956C	ENSP00000257430:Y956C	Y	+	2	0	APC	112202057	1.000000	0.71417	0.998000	0.56505	0.933000	0.57130	4.760000	0.62235	1.012000	0.39366	0.455000	0.32223	TAC		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
ZNF608	57507	hgsc.bcm.edu	37	5	123984478	123984478	+	Silent	SNP	G	G	T			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:123984478G>T	ENST00000306315.5	-	4	2034	c.1599C>A	c.(1597-1599)acC>acA	p.T533T	ZNF608_ENST00000504926.1_Silent_p.T106T	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	533							metal ion binding (GO:0046872)	p.T533T(1)		breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(12)|ovary(3)|skin(6)|urinary_tract(1)	46		all_cancers(142;0.186)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.159)|Kidney(363;0.221)	OV - Ovarian serous cystadenocarcinoma(64;0.00126)|Epithelial(69;0.00238)|all cancers(49;0.00783)		TCCCTTGAGGGGTAGTGGGAG	0.498																																					p.T533T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1599A	5						.						140.0	134.0	136.0					5																	123984478		2203	4300	6503	124012377	SO:0001819	synonymous_variant	57507	exon4			AB033107	CCDS34219.1	5q23.2	2008-05-02			ENSG00000168916	ENSG00000168916		"""Zinc fingers, C2H2-type"""	29238	protein-coding gene	gene with protein product						10574462, 10508479	Standard	NM_020747		Approved	KIAA1281, DKFZp434M098, NY-REN-36	uc003ktq.1	Q9ULD9	OTTHUMG00000162999	ENST00000306315.5:c.1599C>A	5.37:g.123984478G>T			124012377	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Silent	SNP	ENST00000306315.5	37	CCDS34219.1																																																																																				0.498	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432	
LARP1	23367	hgsc.bcm.edu	37	5	154181722	154181722	+	Silent	SNP	T	T	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:154181722T>G	ENST00000336314.4	+	11	1665	c.1641T>G	c.(1639-1641)acT>acG	p.T547T		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	624					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)	p.T624T(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			ACACCTTCACTGCCTGGTCTG	0.512																																					p.T547T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1641G	5						.						162.0	143.0	150.0					5																	154181722		2203	4300	6503	154161915	SO:0001819	synonymous_variant	23367	exon11			AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.1641T>G	5.37:g.154181722T>G			154161915	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Silent	SNP	ENST00000336314.4	37	CCDS4328.1																																																																																				0.512	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
MAP1B	4131	hgsc.bcm.edu	37	5	71495396	71495396	+	Missense_Mutation	SNP	T	T	C			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:71495396T>C	ENST00000296755.7	+	5	6512	c.6214T>C	c.(6214-6216)Tcc>Ccc	p.S2072P		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2072					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.S2072P(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AGAAAAGAAGTCCCCCTCAGA	0.473																																					p.S2072P	Melanoma(17;367 822 11631 31730 47712)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T6214C	5						.						125.0	134.0	131.0					5																	71495396		2203	4300	6503	71531152	SO:0001583	missense	4131	exon5			L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6214T>C	5.37:g.71495396T>C	ENSP00000296755:p.Ser2072Pro		71531152	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.803411	0.31869	.	.	ENSG00000131711	ENST00000296755	T	0.03496	3.91	5.52	5.52	0.82312	.	0.000000	0.64402	D	0.000007	T	0.02807	0.0084	N	0.08118	0	0.42349	D	0.992366	B;B	0.23442	0.085;0.029	B;B	0.19391	0.025;0.018	T	0.56848	-0.7911	10	0.41790	T	0.15	-16.9263	14.8253	0.70107	0.0:0.0:0.0:1.0	.	1946;2072	A2BDK6;P46821	.;MAP1B_HUMAN	P	2072	ENSP00000296755:S2072P	ENSP00000296755:S2072P	S	+	1	0	MAP1B	71531152	0.997000	0.39634	1.000000	0.80357	0.987000	0.75469	1.685000	0.37659	2.104000	0.64026	0.533000	0.62120	TCC		0.473	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
TNPO1	3842	hgsc.bcm.edu	37	5	72157665	72157665	+	Missense_Mutation	SNP	G	G	A			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:72157665G>A	ENST00000337273.5	+	5	812	c.386G>A	c.(385-387)gGa>gAa	p.G129E	TNPO1_ENST00000523768.1_Missense_Mutation_p.G79E|TNPO1_ENST00000506351.2_Missense_Mutation_p.G121E|TNPO1_ENST00000447967.2_Intron|TNPO1_ENST00000454282.1_Missense_Mutation_p.G79E|TNPO1_ENST00000513944.1_3'UTR	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	129					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)	p.G121E(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		GCCTCCAAGGGAGAATTGCAG	0.388																																					p.G121E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G362A	5						.						132.0	123.0	126.0					5																	72157665		2203	4300	6503	72193421	SO:0001583	missense	3842	exon5			U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"""Importins"""	6401	protein-coding gene	gene with protein product	"""importin 2"""	602901	"""karyopherin (importin) beta 2"""	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.386G>A	5.37:g.72157665G>A	ENSP00000336712:p.Gly129Glu		72193421	NM_153188	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.411142	0.25465	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06	5.79	5.79	0.91817	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.62563	0.2438	M	0.64676	1.99	0.80722	D	1	B;B	0.17038	0.014;0.02	B;B	0.17979	0.02;0.012	T	0.56685	-0.7938	10	0.23302	T	0.38	-14.2435	20.0349	0.97554	0.0:0.0:1.0:0.0	.	79;129	Q92973-3;Q92973	.;TNPO1_HUMAN	E	129;79;79;121	ENSP00000336712:G129E;ENSP00000398524:G79E;ENSP00000428899:G79E;ENSP00000425118:G121E	ENSP00000336712:G129E	G	+	2	0	TNPO1	72193421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.452000	0.97615	2.741000	0.93983	0.585000	0.79938	GGA		0.388	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	
DOCK2	1794	hgsc.bcm.edu	37	5	169145673	169145673	+	Silent	SNP	A	A	G			TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AG-3586-01A-02W-0831-10	TCGA-AG-3586-10A-01W-0831-10	g.chr5:169145673A>G	ENST00000256935.8	+	22	2225	c.2145A>G	c.(2143-2145)acA>acG	p.T715T	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000520908.1_Silent_p.T207T	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	715					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)	p.T715T(1)		NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATTGATGACAGTGCTGAAGA	0.373																																					p.T715T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2145G	5						.						111.0	98.0	102.0					5																	169145673		2203	4300	6503	169078251	SO:0001819	synonymous_variant	1794	exon22			BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2145A>G	5.37:g.169145673A>G			169078251	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																				0.373	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
