#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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
MST1L	11223	broad.mit.edu	37	1	17084961	17084961	+	RNA	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:17084961C>T	ENST00000455405.2	-	0	227							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TGTGCCTCACCGATTCCGCAA	0.622																																						uc010ock.1																			0					0						c.(1513-1515)CGC>CAC		SubName: Full=Hepatocyte growth factor-like protein homolog;																																						11223							g.chr1:17084961C>T	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084961C>T						CROCC_uc009voy.1_Intron|MST1P9_uc001azp.3_Missense_Mutation_p.R79Q	p.R505H	NR_002729						11	1514	-								B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37	c.1514G>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	16.31|16.31	3.086043|3.086043	0.55861|0.55861	.|.	.|.	ENSG00000186715|ENSG00000186715	ENST00000334998|ENST00000389184;ENST00000442552	.|.	.|.	.|.	.|.	.|.	.|.	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000|0.000000	0.37761|0.37761	N|N	0.001957|0.001957	T|T	0.65616|0.65616	0.2708|0.2708	.|.	.|.	.|.	.|.	.|.	.|.	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.87578	0.999|0.998	T|T	0.70182|0.70182	-0.4942|-0.4942	6|6	0.42905|0.87932	T|D	0.14|0	.|.	6.8326|6.8326	0.23919|0.23919	0.0:0.9999:0.0:1.0E-4|0.0:0.9999:0.0:1.0E-4	.|.	505|505	Q2TV78-2|Q2TV78	.|MSTP9_HUMAN	H|Q	505|474;505	.|.	ENSP00000439273:R505H|ENSP00000445850:R474Q	R|R	-|-	2|2	0|0	MST1P9|MST1P9	16957548|16957548	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	4.864000|4.864000	0.62990|0.62990	-0.000000|-0.000000	0.14550|0.14550	0.000000|0.000000	0.15137|0.15137	CGC|CGG		0.622	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
MAGOH	4116	broad.mit.edu	37	1	53692748	53692748	+	Missense_Mutation	SNP	A	A	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:53692748A>G	ENST00000371470.3	-	5	571	c.410T>C	c.(409-411)aTt>aCt	p.I137T	MAGOH_ENST00000371466.4_Missense_Mutation_p.I100T|RP5-1024G6.7_ENST00000569869.1_RNA	NM_002370.3	NP_002361.1	P61326	MGN_HUMAN	mago-nashi homolog, proliferation-associated (Drosophila)	137					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I137T(1)		haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	6						GTGTAATCCAATAAGACTGAA	0.378																																					Colon(150;521 2416 7674 18129)	uc001cvf.1																			1	Substitution - Missense(1)		lung(1)		0						c.(409-411)ATT>ACT		mago-nashi homolog							58.0	56.0	57.0					1																	53692748		2203	4300	6503	SO:0001583	missense	4116				mRNA 3'-end processing|mRNA export from nucleus|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|regulation of translation|termination of RNA polymerase II transcription	catalytic step 2 spliceosome|cytosol|exon-exon junction complex|nuclear speck	protein binding|RNA binding	g.chr1:53692748A>G	AF035940	CCDS577.1	1p32.3	2010-04-16	2001-11-28		ENSG00000162385	ENSG00000162385			6815	protein-coding gene	gene with protein product		602603	"""mago-nashi (Drosophila) homolog, proliferation-associated"""			9479507	Standard	NM_002370		Approved	MAGOHA, MAGOH1	uc001cvf.2	P61326	OTTHUMG00000008932	ENST00000371470.3:c.410T>C	1.37:g.53692748A>G	ENSP00000360525:p.Ile137Thr					MAGOH_uc010ont.1_Missense_Mutation_p.I100T	p.I137T	NM_002370	NP_002361	P61326	MGN_HUMAN			5	498	-			137					B1ARP8|B2R5A2|O35169|P50606|Q5SW69	Missense_Mutation	SNP	ENST00000371470.3	37	c.410T>C	CCDS577.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.259752	0.59321	.	.	ENSG00000162385	ENST00000371470;ENST00000371466	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.86410	0.5926	M	0.80028	2.48	0.80722	D	1	B;B	0.32717	0.051;0.381	B;P	0.61003	0.12;0.882	D	0.84407	0.0563	9	0.42905	T	0.14	-19.5899	16.8222	0.85835	1.0:0.0:0.0:0.0	.	100;137	B1ARP8;P61326	.;MGN_HUMAN	T	137;100	.	ENSP00000360521:I100T	I	-	2	0	MAGOH	53465336	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.802000	0.91910	2.371000	0.80710	0.533000	0.62120	ATT		0.378	MAGOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024730.1	NM_002370	
VPS72	6944	broad.mit.edu	37	1	151149180	151149180	+	Silent	SNP	A	A	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:151149180A>T	ENST00000354473.4	-	6	1104	c.1068T>A	c.(1066-1068)ccT>ccA	p.P356P	TMOD4_ENST00000601585.1_5'Flank|VPS72_ENST00000496809.1_5'Flank|TMOD4_ENST00000416280.2_5'Flank			Q15906	VPS72_HUMAN	vacuolar protein sorting 72 homolog (S. cerevisiae)	345					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	14	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			GGGGCTCAGGAGGTGGCGGGC	0.572																																					Pancreas(109;1131 2287 3209 24201)	uc001exe.1																			0				breast(1)|pancreas(1)	2						c.(1033-1035)CCT>CCA		transcription factor-like 1							72.0	83.0	79.0					1																	151149180		2203	4299	6502	SO:0001819	synonymous_variant	6944				chromatin modification|negative regulation of transcription from RNA polymerase II promoter	nucleus|protein complex	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr1:151149180A>T	D43642	CCDS989.1, CCDS59201.1	1q21	2008-02-05	2006-12-19	2005-09-08	ENSG00000163159	ENSG00000163159			11644	protein-coding gene	gene with protein product		600607	"""transcription factor-like 1"", ""vacuolar protein sorting 72 (yeast)"""	TCFL1		7702631	Standard	NM_001271087		Approved	YL-1, YL1, Swc2	uc001exe.2	Q15906	OTTHUMG00000012345	ENST00000354473.4:c.1068T>A	1.37:g.151149180A>T						TMOD4_uc001exd.2_5'Flank|TMOD4_uc001exc.3_5'Flank|TMOD4_uc010pct.1_5'Flank	p.P345P	NM_005997	NP_005988	Q15906	VPS72_HUMAN	UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)		6	1078	-	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		345			Poly-Pro.|Pro-rich.		A6NLK9|A6PW55|Q53GJ2|Q5U0R4	Silent	SNP	ENST00000354473.4	37	c.1035T>A	CCDS59201.1																																																																																				0.572	VPS72-002	NOVEL	mRNA_start_NF|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000034394.3	NM_005997	
YY1AP1	55249	broad.mit.edu	37	1	155646478	155646478	+	Missense_Mutation	SNP	A	A	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:155646478A>G	ENST00000295566.4	-	5	406	c.383T>C	c.(382-384)tTt>tCt	p.F128S	YY1AP1_ENST00000535662.1_5'Flank|YY1AP1_ENST00000368330.2_Missense_Mutation_p.F62S|YY1AP1_ENST00000438245.2_Missense_Mutation_p.F62S|YY1AP1_ENST00000361831.5_Missense_Mutation_p.F51S|YY1AP1_ENST00000476093.1_5'UTR|YY1AP1_ENST00000359205.5_Missense_Mutation_p.F51S|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000405763.3_Missense_Mutation_p.F200S|YY1AP1_ENST00000368339.5_Missense_Mutation_p.F200S|YY1AP1_ENST00000347088.5_Missense_Mutation_p.F62S|YY1AP1_ENST00000368340.5_Missense_Mutation_p.F200S|YY1AP1_ENST00000407221.1_Missense_Mutation_p.F51S|YY1AP1_ENST00000311573.5_Missense_Mutation_p.F51S|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000404643.1_Missense_Mutation_p.F62S|YY1AP1_ENST00000355499.4_Missense_Mutation_p.F62S	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	128					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CAGCTGTTCAAATAGTTCCTT	0.438																																						uc001fln.2																			0				ovary(2)|skin(1)	3						c.(382-384)TTT>TCT		YY1-associated protein isoform 2							207.0	170.0	182.0					1																	155646478		2203	4300	6503	SO:0001583	missense	55249				regulation of cell cycle|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding	g.chr1:155646478A>G	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.383T>C	1.37:g.155646478A>G	ENSP00000295566:p.Phe128Ser					YY1AP1_uc010pgg.1_5'UTR|YY1AP1_uc010pgh.1_Missense_Mutation_p.F51S|YY1AP1_uc010pgi.1_Missense_Mutation_p.F200S|YY1AP1_uc001flh.2_Missense_Mutation_p.F200S|YY1AP1_uc009wqt.2_Missense_Mutation_p.F51S|YY1AP1_uc001flk.2_Missense_Mutation_p.F51S|YY1AP1_uc001fll.2_Missense_Mutation_p.F62S|YY1AP1_uc009wqv.2_5'UTR|YY1AP1_uc001flm.2_Missense_Mutation_p.F51S|YY1AP1_uc001fli.2_Missense_Mutation_p.F62S|YY1AP1_uc009wqu.2_5'UTR|YY1AP1_uc001flj.2_Missense_Mutation_p.F62S|YY1AP1_uc009wqw.2_Missense_Mutation_p.F51S|YY1AP1_uc001flo.2_5'UTR|YY1AP1_uc001flp.2_Missense_Mutation_p.F62S|YY1AP1_uc010pgj.1_Missense_Mutation_p.F128S|YY1AP1_uc009wqx.2_Missense_Mutation_p.F200S|YY1AP1_uc010pgk.1_Missense_Mutation_p.F200S	p.F128S	NM_139118	NP_620829	Q9H869	YYAP1_HUMAN			5	407	-	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)		128					B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	c.383T>C	CCDS1115.1	.	.	.	.	.	.	.	.	.	.	A	10.56	1.385654	0.25031	.	.	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000405763;ENST00000438245;ENST00000443231;ENST00000454523	T;T;T;T;T;T;T;T;T;T;T	0.22743	1.98;1.99;1.98;1.99;1.98;1.95;1.97;1.99;1.98;1.99;1.94	3.78	3.78	0.43462	.	0.236456	0.35805	N	0.002964	T	0.08714	0.0216	N	0.14661	0.345	0.09310	N	1	P;B;B;P;B;B;P	0.43885	0.755;0.429;0.128;0.82;0.128;0.099;0.604	B;B;B;P;B;B;B	0.47430	0.332;0.247;0.044;0.547;0.044;0.074;0.253	T	0.06232	-1.0838	10	0.87932	D	0	.	12.3301	0.55035	1.0:0.0:0.0:0.0	.	62;128;200;200;128;62;200	B4DZQ4;B4DQQ0;B4DMP2;B0QZ55;Q9H869;Q9H869-2;Q5VYZ1	.;.;.;.;YYAP1_HUMAN;.;.	S	51;62;51;62;51;200;128;62;51;62;200;200;62;51;62	ENSP00000352134:F51S;ENSP00000347686:F62S;ENSP00000311138:F51S;ENSP00000316079:F62S;ENSP00000355298:F51S;ENSP00000357324:F200S;ENSP00000295566:F128S;ENSP00000357314:F62S;ENSP00000385791:F51S;ENSP00000385390:F62S;ENSP00000357323:F200S	ENSP00000295566:F128S	F	-	2	0	YY1AP1	153913102	0.995000	0.38212	0.288000	0.24862	0.118000	0.20060	5.963000	0.70372	1.573000	0.49748	0.374000	0.22700	TTT		0.438	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
PEAR1	375033	broad.mit.edu	37	1	156875138	156875138	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:156875138C>T	ENST00000338302.3	+	5	454	c.229C>T	c.(229-231)Cgt>Tgt	p.R77C	PEAR1_ENST00000292357.7_Missense_Mutation_p.R77C			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	77	EMI. {ECO:0000255|PROSITE- ProRule:PRU00384}.				recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.R77S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GACCGTGTACCGTCAGGTGGT	0.657																																						uc001fqj.1																			1	Substitution - Missense(1)		lung(1)	ovary(2)|central_nervous_system(1)	3						c.(229-231)CGT>TGT		platelet endothelial aggregation receptor 1							65.0	58.0	61.0					1																	156875138		2203	4300	6503	SO:0001583	missense	375033					integral to membrane		g.chr1:156875138C>T	AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.229C>T	1.37:g.156875138C>T	ENSP00000344465:p.Arg77Cys					PEAR1_uc009wsl.1_5'Flank|PEAR1_uc001fqk.1_5'Flank	p.R77C	NM_001080471	NP_001073940	Q5VY43	PEAR1_HUMAN			4	345	+	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)		77			EMI.		Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	c.229C>T	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641052	0.67244	.	.	ENSG00000187800	ENST00000338302;ENST00000455314;ENST00000292357	D;T;D	0.90844	-2.74;0.51;-2.74	3.92	3.92	0.45320	EMI domain (1);	0.180201	0.27035	N	0.021250	D	0.89818	0.6825	L	0.36672	1.1	0.58432	D	0.999997	D	0.89917	1.0	D	0.63488	0.915	D	0.91395	0.5138	10	0.87932	D	0	.	13.4913	0.61397	0.0:1.0:0.0:0.0	.	77	Q5VY43	PEAR1_HUMAN	C	77	ENSP00000344465:R77C;ENSP00000389742:R77C;ENSP00000292357:R77C	ENSP00000292357:R77C	R	+	1	0	PEAR1	155141762	1.000000	0.71417	0.997000	0.53966	0.904000	0.53231	1.860000	0.39428	2.015000	0.59207	0.655000	0.94253	CGT		0.657	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
CD5L	922	broad.mit.edu	37	1	157804444	157804444	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr1:157804444G>A	ENST00000368174.4	-	4	567	c.471C>T	c.(469-471)aaC>aaT	p.N157N	CD5L_ENST00000484609.1_5'Flank	NM_005894.2	NP_005885.1	O43866	CD5L_HUMAN	CD5 molecule-like	157	SRCR 2. {ECO:0000255|PROSITE- ProRule:PRU00196}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	scavenger receptor activity (GO:0005044)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	52	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			TATACCACTGGTTCTGGTGCT	0.622																																						uc001frk.3																			0				ovary(1)	1						c.(469-471)AAC>AAT		CD5 molecule-like precursor							103.0	101.0	102.0					1																	157804444		2203	4300	6503	SO:0001819	synonymous_variant	922				apoptosis|cellular defense response	extracellular space|membrane	scavenger receptor activity	g.chr1:157804444G>A	U82812	CCDS1171.1	1q21-q23	2008-02-05	2006-03-28		ENSG00000073754	ENSG00000073754			1690	protein-coding gene	gene with protein product		602592	"""apoptosis inhibitor 6"", ""CD5 antigen-like (scavenger receptor cysteine rich family)"""	API6		9045627	Standard	NM_005894		Approved	Spalpha	uc001frk.4	O43866	OTTHUMG00000022440	ENST00000368174.4:c.471C>T	1.37:g.157804444G>A							p.N157N	NM_005894	NP_005885	O43866	CD5L_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.24)		4	614	-	all_hematologic(112;0.0378)		157			SRCR 2.		A8K7M5|Q6UX63	Silent	SNP	ENST00000368174.4	37	c.471C>T	CCDS1171.1																																																																																				0.622	CD5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058346.1	NM_005894	
OR4C46	119749	broad.mit.edu	37	11	51516009	51516009	+	Missense_Mutation	SNP	C	C	T	rs137991158		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr11:51516009C>T	ENST00000328188.1	+	1	728	c.728C>T	c.(727-729)aCg>aTg	p.T243M		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	243						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(5)|large_intestine(5)|lung(31)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	48						TCCCACATCACGGTTGTCATC	0.468													.|||	1	0.000199681	0.0	0.0	5008	,	,		19962	0.001		0.0	False		,,,				2504	0.0					uc010ric.1																			0				ovary(1)	1						c.(727-729)ACG>ATG		olfactory receptor, family 4, subfamily C,		C	MET/THR	1,4401		0,1,2200	135.0	114.0	121.0		728	1.4	0.3	11	dbSNP_134	121	0,8592		0,0,4296	no	missense	OR4C46	NM_001004703.1	81	0,1,6496	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	243/310	51516009	1,12993	2201	4296	6497	SO:0001583	missense	119749				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:51516009C>T		CCDS73288.1	11p11.12	2012-08-09			ENSG00000185926	ENSG00000185926		"""GPCR / Class A : Olfactory receptors"""	31271	protein-coding gene	gene with protein product		614273					Standard	NM_001004703		Approved		uc010ric.2	A6NHA9	OTTHUMG00000166705	ENST00000328188.1:c.728C>T	11.37:g.51516009C>T	ENSP00000329056:p.Thr243Met						p.T243M	NM_001004703	NP_001004703	A6NHA9	O4C46_HUMAN			1	728	+			243			Helical; Name=6; (Potential).			Missense_Mutation	SNP	ENST00000328188.1	37	c.728C>T	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	7.494	0.651307	0.14516	2.27E-4	0.0	ENSG00000185926	ENST00000328188	T	0.38401	1.14	2.33	1.38	0.22167	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000249	T	0.40767	0.1130	L	0.60904	1.88	0.09310	N	1	D	0.59357	0.985	P	0.53146	0.719	T	0.19712	-1.0297	10	0.52906	T	0.07	.	6.9475	0.24526	0.0:0.8456:0.0:0.1544	.	243	A6NHA9	O4C46_HUMAN	M	243	ENSP00000329056:T243M	ENSP00000329056:T243M	T	+	2	0	OR4C46	51372585	0.000000	0.05858	0.345000	0.25642	0.051000	0.14879	-0.509000	0.06336	0.340000	0.23745	0.121000	0.15741	ACG		0.468	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703	
LRRC23	10233	broad.mit.edu	37	12	7021983	7021983	+	Missense_Mutation	SNP	C	C	T	rs78482853		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:7021983C>T	ENST00000007969.8	+	7	1068	c.848C>T	c.(847-849)aCg>aTg	p.T283M	LRRC23_ENST00000429740.1_Intron|LRRC23_ENST00000443597.2_Missense_Mutation_p.T283M|LRRC23_ENST00000436789.1_Intron|ENO2_ENST00000544774.1_5'Flank|ENO2_ENST00000538763.1_5'Flank|ENO2_ENST00000229277.1_5'Flank|LRRC23_ENST00000323702.5_Intron|ENO2_ENST00000545045.2_5'Flank|ENO2_ENST00000535366.1_5'Flank|ENO2_ENST00000541477.1_5'Flank	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	283	LRRCT.									NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						AACCCATGCACGGACGAAACC	0.602													C|||	6	0.00119808	0.0	0.0	5008	,	,		-128	0.006		0.0	False		,,,				2504	0.0					uc001qrt.3																			0				ovary(1)	1						c.(847-849)ACG>ATG		leucine rich repeat containing 23 isoform a							119.0	114.0	116.0					12																	7021983		2203	4300	6503	SO:0001583	missense	10233							g.chr12:7021983C>T	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.848C>T	12.37:g.7021983C>T	ENSP00000007969:p.Thr283Met					LRRC23_uc001qrp.2_Missense_Mutation_p.T283M|LRRC23_uc001qrq.2_Intron|LRRC23_uc001qrr.2_Missense_Mutation_p.T232M|LRRC23_uc001qrs.2_Intron|LRRC23_uc009zfh.2_Intron|ENO2_uc001qru.1_5'Flank|ENO2_uc009zfi.1_5'Flank|ENO2_uc010sfq.1_5'Flank|ENO2_uc001qrv.1_5'Flank	p.T283M	NM_001135217	NP_001128689	Q53EV4	LRC23_HUMAN			7	1240	+			283			LRRCT.		A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	c.848C>T	CCDS8569.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	C	9.074	0.997587	0.19043	.	.	ENSG00000010626	ENST00000007969;ENST00000443597	T;T	0.61040	0.14;0.14	5.64	4.74	0.60224	.	.	.	.	.	T	0.44953	0.1318	L	0.52759	1.655	0.22171	N	0.999313	D;D	0.58268	0.977;0.982	P;B	0.45343	0.477;0.365	T	0.43956	-0.9359	9	0.37606	T	0.19	-0.1524	8.9697	0.35899	0.1484:0.7775:0.0:0.0741	.	283;283	A8K8K2;Q53EV4	.;LRC23_HUMAN	M	283	ENSP00000007969:T283M;ENSP00000390932:T283M	ENSP00000007969:T283M	T	+	2	0	LRRC23	6892244	0.000000	0.05858	0.006000	0.13384	0.010000	0.07245	1.156000	0.31712	2.633000	0.89246	0.555000	0.69702	ACG		0.602	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992	
PTPN6	5777	broad.mit.edu	37	12	7061224	7061224	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:7061224G>A	ENST00000318974.9	+	3	454	c.210G>A	c.(208-210)gcG>gcA	p.A70A	PTPN6_ENST00000456013.1_Silent_p.A70A|PTPN6_ENST00000399448.1_Silent_p.A72A|PTPN6_ENST00000447931.2_Silent_p.A31A	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	70	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				abortive mitotic cell cycle (GO:0033277)|apoptotic process (GO:0006915)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|natural killer cell mediated cytotoxicity (GO:0042267)|negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of cell proliferation (GO:0008285)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein dephosphorylation (GO:0006470)|regulation of B cell differentiation (GO:0045577)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|type I interferon signaling pathway (GO:0060337)	alpha-beta T cell receptor complex (GO:0042105)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|prostate(3)	18						AGAAGTTTGCGACTCTGACAG	0.587																																						uc001qsb.2																			0				breast(1)	1						c.(208-210)GCG>GCA		protein tyrosine phosphatase, non-receptor type							102.0	119.0	113.0					12																	7061224		2202	4299	6501	SO:0001819	synonymous_variant	5777				apoptosis|cell junction assembly|G-protein coupled receptor protein signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|negative regulation of peptidyl-tyrosine phosphorylation|platelet activation|positive regulation of cell proliferation|positive regulation of phosphatidylinositol 3-kinase cascade|regulation of G1/S transition of mitotic cell cycle|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol|membrane|nucleus	protein binding|protein tyrosine phosphatase activity	g.chr12:7061224G>A		CCDS41744.1, CCDS44820.1, CCDS44821.1	12p13.31	2013-02-14			ENSG00000111679	ENSG00000111679		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9658	protein-coding gene	gene with protein product		176883				1639416	Standard	NM_080548		Approved	HCP, HCPH, PTP-1C, SHP-1, SHP1	uc001qsa.1	P29350	OTTHUMG00000168518	ENST00000318974.9:c.210G>A	12.37:g.7061224G>A						PTPN6_uc001qsa.1_Silent_p.A72A|PTPN6_uc010sfr.1_Silent_p.A31A|PTPN6_uc009zfl.1_Silent_p.A70A|PTPN6_uc010sfs.1_Silent_p.A58A	p.A70A	NM_002831	NP_002822	P29350	PTN6_HUMAN			3	452	+			70			SH2 1.		A8K306|G3V0F8|Q969V8|Q9UK67	Silent	SNP	ENST00000318974.9	37	c.210G>A	CCDS44820.1																																																																																				0.587	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831	
ADAMTS20	80070	broad.mit.edu	37	12	43823483	43823483	+	Silent	SNP	G	G	A	rs376977266		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:43823483G>A	ENST00000389420.3	-	24	3425	c.3426C>T	c.(3424-3426)acC>acT	p.T1142T	ADAMTS20_ENST00000395541.2_Intron|ADAMTS20_ENST00000553158.1_Silent_p.T1142T	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	1142					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		GTAATAAAGCGGTCTCAAGTT	0.338																																						uc010skx.1																			0				central_nervous_system(5)|ovary(4)|lung(3)|large_intestine(2)|skin(2)|urinary_tract(1)|kidney(1)|pancreas(1)	19						c.(3424-3426)ACC>ACT		a disintegrin-like and metalloprotease with		G		0,4406		0,0,2203	60.0	56.0	57.0		3426	-1.6	0.0	12		57	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ADAMTS20	NM_025003.3		0,1,6500	AA,AG,GG		0.0116,0.0,0.0077		1142/1911	43823483	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	80070					proteinaceous extracellular matrix	zinc ion binding	g.chr12:43823483G>A	AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.3426C>T	12.37:g.43823483G>A						ADAMTS20_uc001rno.1_Intron|ADAMTS20_uc001rnp.1_Silent_p.T296T	p.T1142T	NM_025003	NP_079279	P59510	ATS20_HUMAN		GBM - Glioblastoma multiforme(48;0.0473)	24	3426	-	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)	1142					A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	c.3426C>T	CCDS31778.2																																																																																				0.338	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
GALNT4	8693	broad.mit.edu	37	12	89917757	89917757	+	Silent	SNP	G	G	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:89917757G>T	ENST00000529983.2	-	1	826	c.570C>A	c.(568-570)atC>atA	p.I190I	POC1B_ENST00000549504.1_Intron|GALNT4_ENST00000413530.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Silent_p.I187I|POC1B_ENST00000393179.4_Intron|POC1B_ENST00000313546.3_Intron|POC1B_ENST00000541909.1_Intron|POC1B-GALNT4_ENST00000547474.1_Intron|POC1B_ENST00000549035.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	190	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CAAGATTGCTGATGTAAGTTT	0.458											OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001tbd.2																			0					0						c.(568-570)ATC>ATA		polypeptide N-acetylgalactosaminyltransferase 4							85.0	82.0	83.0					12																	89917757		1911	4120	6031	SO:0001819	synonymous_variant	8693				carbohydrate metabolic process	Golgi membrane|integral to membrane|perinuclear region of cytoplasm	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr12:89917757G>T	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.570C>A	12.37:g.89917757G>T			OREG0022018	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1271	POC1B_uc001tba.2_Intron|POC1B_uc001tbb.2_Intron|POC1B_uc001tbc.2_Intron|POC1B_uc010sun.1_Intron|GALNT4_uc001tbe.2_Silent_p.I187I|GALNT4_uc010suo.1_Intron	p.I190I	NM_003774	NP_003765	Q8N4A0	GALT4_HUMAN			1	779	-			190			Lumenal (Potential).|Catalytic subdomain A.		B2R775|B4DMX6|O00208	Silent	SNP	ENST00000529983.2	37	c.570C>A	CCDS53817.1																																																																																				0.458	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
RIC8B	55188	broad.mit.edu	37	12	107177813	107177814	+	Frame_Shift_Ins	INS	-	-	A	rs376206658		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:107177813_107177814insA	ENST00000392839.2	+	2	229_230	c.123_124insA	c.(124-126)aaafs	p.K42fs	RIC8B_ENST00000392837.4_Frame_Shift_Ins_p.K42fs|RIC8B_ENST00000549643.1_Intron|RIC8B_ENST00000355478.2_5'UTR	NM_018157.2	NP_060627.2	Q9NVN3	RIC8B_HUMAN	RIC8 guanine nucleotide exchange factor B	42					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	G-protein alpha-subunit binding (GO:0001965)|guanyl-nucleotide exchange factor activity (GO:0005085)			kidney(2)|large_intestine(5)|lung(10)|ovary(1)|urinary_tract(1)	19						CAGATGAAGATAAAAGAAAGGT	0.351																																						uc001tlx.2																			0				ovary(1)	1						c.(121-126)GATAAAfs		resistance to inhibitors of cholinesterase 8																																				SO:0001589	frameshift_variant	55188				regulation of G-protein coupled receptor protein signaling pathway	cell cortex|cytosol|plasma membrane	G-protein alpha-subunit binding|guanyl-nucleotide exchange factor activity	g.chr12:107177813_107177814insA	AK128102	CCDS9109.2	12q23.3	2013-08-05	2013-08-05		ENSG00000111785	ENSG00000111785			25555	protein-coding gene	gene with protein product		609147	"""resistance to inhibitors of cholinesterase 8 homolog B (C. elegans)"""				Standard	XM_005268998		Approved	FLJ10620, hSyn, RIC8	uc001tlx.3	Q9NVN3	OTTHUMG00000144188	ENST00000392839.2:c.127dupA	12.37:g.107177817_107177817dupA	ENSP00000376583:p.Lys42fs					RIC8B_uc001tlw.2_Frame_Shift_Ins_p.D41fs|RIC8B_uc001tly.2_5'UTR|RIC8B_uc001tlz.2_RNA	p.D41fs	NM_018157	NP_060627	Q9NVN3	RIC8B_HUMAN			2	248_249	+			41_42					A2RTZ0|Q4G103|Q6ZRN4|Q86WD3	Frame_Shift_Ins	INS	ENST00000392839.2	37	c.123_124insA	CCDS9109.2																																																																																				0.351	RIC8B-006	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000291398.2	NM_018157	
USP30	84749	broad.mit.edu	37	12	109495849	109495849	+	Silent	SNP	C	C	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:109495849C>A	ENST00000257548.5	+	3	405	c.312C>A	c.(310-312)tcC>tcA	p.S104S	RNA5SP372_ENST00000390836.1_RNA|USP30_ENST00000392784.2_Silent_p.S73S	NM_032663.3	NP_116052.2	Q70CQ3	UBP30_HUMAN	ubiquitin specific peptidase 30	104	USP.				mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(7)|kidney(1)|large_intestine(1)|liver(2)|lung(11)|prostate(1)|skin(3)|stomach(2)	28						CCCAGTACTCCAGGGATCAGA	0.478																																						uc010sxi.1																			0				lung(1)	1						c.(310-312)TCC>TCA		ubiquitin specific peptidase 30							257.0	258.0	258.0					12																	109495849		2203	4300	6503	SO:0001819	synonymous_variant	84749				ubiquitin-dependent protein catabolic process	integral to membrane|mitochondrial outer membrane	cysteine-type peptidase activity|ubiquitin thiolesterase activity	g.chr12:109495849C>A	BC022094	CCDS9123.2	12q23.3	2006-01-20	2005-08-08		ENSG00000135093	ENSG00000135093		"""Ubiquitin-specific peptidases"""	20065	protein-coding gene	gene with protein product		612492	"""ubiquitin specific protease 30"""			12838346	Standard	XM_005253962		Approved	MGC10702, FLJ40511	uc010sxi.2	Q70CQ3	OTTHUMG00000133613	ENST00000257548.5:c.312C>A	12.37:g.109495849C>A						USP30_uc001tnu.3_Silent_p.S73S	p.S104S	NM_032663	NP_116052	Q70CQ3	UBP30_HUMAN			3	416	+			104			Cytoplasmic (Potential).		Q8WTU7|Q96JX4|Q9BSS3	Silent	SNP	ENST00000257548.5	37	c.312C>A	CCDS9123.2																																																																																				0.478	USP30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257733.2	NM_032663	
CCDC60	160777	broad.mit.edu	37	12	119773039	119773039	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr12:119773039C>T	ENST00000327554.2	+	1	523	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	CCDC60_ENST00000546345.1_3'UTR|CCDC60_ENST00000536742.1_Missense_Mutation_p.R20W|CCDC60_ENST00000539847.1_Missense_Mutation_p.R20W	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	20										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		GGGGGCTGTCCGGCCCTTTTA	0.502																																						uc001txe.2																			0				ovary(2)|upper_aerodigestive_tract(1)	3						c.(58-60)CGG>TGG		coiled-coil domain containing 60							69.0	77.0	74.0					12																	119773039		2203	4300	6503	SO:0001583	missense	160777							g.chr12:119773039C>T	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.58C>T	12.37:g.119773039C>T	ENSP00000333374:p.Arg20Trp						p.R20W	NM_178499	NP_848594	Q8IWA6	CCD60_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.207)	1	523	+	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)		20						Missense_Mutation	SNP	ENST00000327554.2	37	c.58C>T	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	C	6.197	0.404573	0.11754	.	.	ENSG00000183273	ENST00000536742;ENST00000327554;ENST00000539847	T;T;T	0.48836	0.8;1.83;0.95	4.42	-3.66	0.04489	.	1.591660	0.03532	N	0.222527	T	0.17492	0.0420	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09773	-1.0659	9	.	.	.	0.016	3.2878	0.06937	0.3849:0.3158:0.0:0.2993	.	20	Q8IWA6	CCD60_HUMAN	W	20	ENSP00000445505:R20W;ENSP00000333374:R20W;ENSP00000443403:R20W	.	R	+	1	2	CCDC60	118257422	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.894000	0.04123	-0.330000	0.08514	-0.377000	0.06932	CGG		0.502	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
EXD1	161829	broad.mit.edu	37	15	41501708	41501708	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr15:41501708G>A	ENST00000314992.5	-	5	541	c.351C>T	c.(349-351)tgC>tgT	p.C117C	EXD1_ENST00000458580.2_Silent_p.C175C	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	117	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						CCTGCAGCCAGCACAGTTTGC	0.373																																						uc001znk.2																			0				ovary(1)	1						c.(349-351)TGC>TGT		exonuclease 3'-5' domain containing 1							62.0	57.0	59.0					15																	41501708		2203	4300	6503	SO:0001819	synonymous_variant	161829				nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	intracellular	3'-5' exonuclease activity|nucleic acid binding	g.chr15:41501708G>A	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.351C>T	15.37:g.41501708G>A						EXD1_uc010ucv.1_Silent_p.C175C	p.C117C	NM_152596	NP_689809	Q8NHP7	EXD1_HUMAN			5	542	-			117			3'-5' exonuclease.		A8K909|B7Z839|Q6ZW94	Silent	SNP	ENST00000314992.5	37	c.351C>T	CCDS10072.1																																																																																				0.373	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
PKD1L2	114780	broad.mit.edu	37	16	81175094	81175094	+	RNA	SNP	C	C	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr16:81175094C>G	ENST00000525539.1	-	0	5224				PKD1L2_ENST00000533478.1_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCAGGGGCCACTCCGTGCCGC	0.587																																						uc002fgh.1																			0				ovary(1)|central_nervous_system(1)|pancreas(1)	3						c.(5224-5226)AGT>ACT		polycystin 1-like 2 isoform a							19.0	22.0	21.0					16																	81175094		1979	4151	6130			114780				neuropeptide signaling pathway	integral to membrane	calcium ion binding|ion channel activity|sugar binding	g.chr16:81175094C>G	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81175094C>G						PKD1L2_uc002fgg.1_RNA	p.S1742T	NM_052892	NP_443124	Q7Z442	PK1L2_HUMAN			31	5225	-			1742			Cytoplasmic (Potential).		Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37	c.5225G>C																																																																																					0.587	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
POLR2A	5430	broad.mit.edu	37	17	7417217	7417217	+	Frame_Shift_Del	DEL	T	T	-			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr17:7417217delT	ENST00000322644.6	+	29	6033	c.5634delT	c.(5632-5634)agtfs	p.S1878fs		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1878	C-terminal domain (CTD); 52 X 7 AA approximate tandem repeats of Y-[ST]-P- [STQ]-[ST]-P-[SRTEVKGN].				7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CGCCTACCAGTcccacctatt	0.527																																						uc002ghf.3																			0				pancreas(1)	1						c.(5632-5634)AGTfs		DNA-directed RNA polymerase II A							224.0	234.0	231.0					17																	7417217		2203	4300	6503	SO:0001589	frameshift_variant	5430				mRNA capping|nuclear mRNA splicing, via spliceosome|positive regulation of viral transcription|protein phosphorylation|regulation of transcription, DNA-dependent|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	DNA-directed RNA polymerase II, core complex	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|RNA-directed RNA polymerase activity|ubiquitin protein ligase binding	g.chr17:7417217delT			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.5634delT	17.37:g.7417217delT	ENSP00000314949:p.Ser1878fs						p.S1878fs	NM_000937	NP_000928	P24928	RPB1_HUMAN			29	5868	+		Prostate(122;0.173)	1878			41.|52 X 7 AA approximate tandem repeats of Y-[ST]-P-[STQ]-[ST]-P-[SRTEVKGN].		A6NN93|B9EH88|Q6NX41	Frame_Shift_Del	DEL	ENST00000322644.6	37	c.5634delT	CCDS32548.1																																																																																				0.527	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
CEP131	22994	broad.mit.edu	37	17	79164553	79164553	+	Missense_Mutation	SNP	C	C	T	rs537921227		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr17:79164553C>T	ENST00000269392.4	-	24	3249	c.3002G>A	c.(3001-3003)cGc>cAc	p.R1001H	AZI1_ENST00000575907.1_Missense_Mutation_p.R965H|AZI1_ENST00000450824.2_Missense_Mutation_p.R998H|AZI1_ENST00000374782.3_Missense_Mutation_p.R962H	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		1001					cell differentiation (GO:0030154)|G2/M transition of mitotic cell cycle (GO:0000086)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular protein transport (GO:0090316)|regulation of centrosome duplication (GO:0010824)|spermatogenesis (GO:0007283)	BBSome (GO:0034464)|cell projection (GO:0042995)|centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(1)|lung(12)|ovary(2)|prostate(3)|urinary_tract(5)	36	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)			GAACTCCTGGCGGATCACCTG	0.692																																						uc002jzp.1																			0				central_nervous_system(2)|large_intestine(1)|ovary(1)	4						c.(3001-3003)CGC>CAC		5-azacytidine induced 1 isoform a							22.0	23.0	22.0					17																	79164553		2202	4296	6498	SO:0001583	missense	22994				cell differentiation|G2/M transition of mitotic cell cycle|multicellular organismal development|spermatogenesis	centrosome|cytosol|intracellular membrane-bounded organelle		g.chr17:79164553C>T																												ENST00000269392.4:c.3002G>A	17.37:g.79164553C>T	ENSP00000269392:p.Arg1001His					AZI1_uc002jzm.1_Missense_Mutation_p.R433H|AZI1_uc002jzn.1_Missense_Mutation_p.R998H|AZI1_uc002jzo.1_Missense_Mutation_p.R962H|AZI1_uc010wum.1_Missense_Mutation_p.R965H|AZI1_uc002jzq.2_Missense_Mutation_p.R149H	p.R1001H	NM_014984	NP_055799	Q9UPN4	AZI1_HUMAN	BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.117)		24	3202	-	all_neural(118;0.0804)|Melanoma(429;0.242)		1001					A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37	c.3002G>A		.	.	.	.	.	.	.	.	.	.	C	23.7	4.448895	0.84101	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.20332	2.25;2.08;2.25	4.33	3.35	0.38373	.	0.066568	0.64402	N	0.000014	T	0.41259	0.1151	M	0.66939	2.045	0.47153	D	0.999337	D;D;P;P	0.89917	1.0;1.0;0.788;0.788	D;D;B;B	0.68765	0.96;0.96;0.244;0.244	T	0.33214	-0.9877	10	0.66056	D	0.02	-16.9427	12.083	0.53682	0.0:0.9152:0.0:0.0848	.	998;1001;962;998	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	H	998;962;1001	ENSP00000393583:R998H;ENSP00000363914:R962H;ENSP00000269392:R1001H	ENSP00000269392:R1001H	R	-	2	0	AZI1	76779148	1.000000	0.71417	0.998000	0.56505	0.788000	0.44548	3.021000	0.49651	1.037000	0.40024	0.591000	0.81541	CGC		0.692	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1		
DSG4	147409	broad.mit.edu	37	18	28989414	28989414	+	Splice_Site	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr18:28989414G>A	ENST00000308128.4	+	13	2068		c.e13-1		RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Splice_Site|RP11-534N16.1_ENST00000581856.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4						anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TTCTTGGGCAGTGGCTCCACT	0.498																																						uc002kwq.2																			0				central_nervous_system(5)|ovary(3)	8						c.e13-1		desmoglein 4 isoform 2 preproprotein							119.0	125.0	123.0					18																	28989414		2203	4300	6503	SO:0001630	splice_region_variant	147409				homophilic cell adhesion	desmosome|integral to membrane	calcium ion binding	g.chr18:28989414G>A	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.1934-1G>A	18.37:g.28989414G>A						DSG4_uc002kwr.2_Splice_Site_p.L645_splice	p.L645_splice	NM_177986	NP_817123	Q86SJ6	DSG4_HUMAN	OV - Ovarian serous cystadenocarcinoma(10;0.00504)		13	2069	+								A2RUI1|Q6Y9L9|Q8IXV4	Splice_Site	SNP	ENST00000308128.4	37	c.1934_splice	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	G	15.47	2.844417	0.51164	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	.	.	.	5.55	5.55	0.83447	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4765	0.94991	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DSG4	27243412	1.000000	0.71417	0.675000	0.29917	0.021000	0.10359	6.309000	0.72825	2.760000	0.94817	0.655000	0.94253	.		0.498	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	Intron
CCDC178	374864	broad.mit.edu	37	18	30950074	30950074	+	Silent	SNP	G	G	C			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr18:30950074G>C	ENST00000383096.3	-	6	470	c.288C>G	c.(286-288)gtC>gtG	p.V96V	CCDC178_ENST00000579947.1_Silent_p.V96V|CCDC178_ENST00000406524.2_Silent_p.V96V|CCDC178_ENST00000579916.1_Silent_p.V96V|CCDC178_ENST00000402325.1_Silent_p.V96V|CCDC178_ENST00000300227.8_Silent_p.V96V|CCDC178_ENST00000583930.1_Silent_p.V96V|CCDC178_ENST00000403303.1_Silent_p.V96V			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	96																	TCATTTTGTTGACACAAGGTG	0.378																																						uc002kxn.2																			0				ovary(1)	1						c.(286-288)GTC>GTG		hypothetical protein LOC374864 isoform 1							95.0	86.0	89.0					18																	30950074		2203	4300	6503	SO:0001819	synonymous_variant	374864							g.chr18:30950074G>C	AK126038	CCDS11906.1, CCDS42424.1	18q12.1	2012-10-15	2012-10-15	2012-10-15	ENSG00000166960	ENSG00000166960			29588	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 34"""	C18orf34			Standard	NM_198995		Approved	FLJ44050	uc002kxn.2	Q5BJE1	OTTHUMG00000132279	ENST00000383096.3:c.288C>G	18.37:g.30950074G>C						C18orf34_uc010xbr.1_Silent_p.V96V|C18orf34_uc010dmf.1_Silent_p.V96V|C18orf34_uc002kxo.2_Silent_p.V96V|C18orf34_uc002kxp.2_Silent_p.V96V	p.V96V	NM_001105528	NP_001098998	Q5BJE1	CR034_HUMAN			5	430	-			96					A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Silent	SNP	ENST00000383096.3	37	c.288C>G	CCDS42424.1																																																																																				0.378	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	
SERPINB13	5275	broad.mit.edu	37	18	61262397	61262397	+	Silent	SNP	C	C	T	rs368658099		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr18:61262397C>T	ENST00000344731.5	+	7	852	c.750C>T	c.(748-750)aaC>aaT	p.N250N	SERPINB13_ENST00000269489.5_Intron	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	250					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.N250N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|urinary_tract(1)	25						TTCTGCCCAACGACATCGATG	0.458																																						uc002ljc.2																			1	Substitution - coding silent(1)		lung(1)	ovary(1)	1						c.(748-750)AAC>AAT		serine (or cysteine) proteinase inhibitor, clade		C		0,4406		0,0,2203	152.0	140.0	144.0		750	1.5	1.0	18		144	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SERPINB13	NM_012397.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		250/392	61262397	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5275				regulation of proteolysis|response to UV	cytoplasm|extracellular region	serine-type endopeptidase inhibitor activity	g.chr18:61262397C>T	AF169949, BC101821	CCDS11985.1	18q21.33	2014-02-18	2005-08-18		ENSG00000197641	ENSG00000197641		"""Serine (or cysteine) peptidase inhibitors"""	8944	protein-coding gene	gene with protein product		604445	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 13"""	PI13		9297979, 10512713, 24172014	Standard	NM_012397		Approved	HUR7, hurpin, headpin	uc002ljc.3	Q9UIV8	OTTHUMG00000060406	ENST00000344731.5:c.750C>T	18.37:g.61262397C>T						SERPINB13_uc002ljd.2_Silent_p.N114N|SERPINB13_uc010xep.1_Silent_p.N259N|SERPINB13_uc010xeq.1_Silent_p.N71N|SERPINB13_uc010xer.1_Silent_p.N71N	p.N250N	NM_012397	NP_036529	Q9UIV8	SPB13_HUMAN			7	918	+			250					A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Silent	SNP	ENST00000344731.5	37	c.750C>T	CCDS11985.1																																																																																				0.458	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397	
TJP3	27134	broad.mit.edu	37	19	3728405	3728405	+	Intron	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:3728405C>T	ENST00000541714.2	+	2	453				TJP3_ENST00000539908.2_Intron|TJP3_ENST00000589378.1_Intron|TJP3_ENST00000587686.1_Missense_Mutation_p.P11L|TJP3_ENST00000382008.3_Intron|TJP3_ENST00000262968.9_Missense_Mutation_p.P11L	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3						regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCATCTTCCCCGCTCCCCTC	0.627																																						uc010xhv.1																			0				ovary(1)|central_nervous_system(1)|skin(1)	3						c.(31-33)CCC>CTC		tight junction protein 3							63.0	48.0	53.0					19																	3728405		2203	4300	6503	SO:0001627	intron_variant	27134					tight junction	protein binding	g.chr19:3728405C>T	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.-9-17C>T	19.37:g.3728405C>T						TJP3_uc010xhs.1_Intron|TJP3_uc010xht.1_Intron|TJP3_uc010xhu.1_Intron|TJP3_uc010xhw.1_Missense_Mutation_p.P11L	p.P11L	NM_014428	NP_055243	O95049	ZO3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)	1	32	+			Error:Variant_position_missing_in_O95049_after_alignment					A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	c.32C>T	CCDS32873.2	.	.	.	.	.	.	.	.	.	.	C	3.169	-0.170513	0.06461	.	.	ENSG00000105289	ENST00000262968	T	0.15603	2.41	3.81	-2.81	0.05805	.	0.369626	0.19574	N	0.111029	T	0.08537	0.0212	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.18808	-1.0325	9	0.66056	D	0.02	.	1.4122	0.02294	0.1512:0.3254:0.3158:0.2076	.	11;11	O95049-3;O95049-2	.;.	L	11	ENSP00000262968:P11L	ENSP00000262968:P11L	P	+	2	0	TJP3	3679405	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.026000	0.13599	-0.293000	0.08986	0.456000	0.33151	CCC		0.627	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
CD70	970	broad.mit.edu	37	19	6586314	6586314	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:6586314C>T	ENST00000245903.3	-	3	448	c.299G>A	c.(298-300)cGt>cAt	p.R100H	CD70_ENST00000423145.3_Missense_Mutation_p.R100H	NM_001252.3	NP_001243.1	P32970	CD70_HUMAN	CD70 molecule	100					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	protease binding (GO:0002020)|receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|skin(1)	11						GATGCCATCACGATGGATACG	0.642																																					Pancreas(183;2617 2876 10173 34193)	uc002mfi.2																			0					0						c.(298-300)CGT>CAT		tumor necrosis factor ligand superfamily, member							112.0	79.0	90.0					19																	6586314		2203	4300	6503	SO:0001583	missense	970				cell proliferation|cell-cell signaling|immune response|induction of apoptosis|signal transduction	extracellular space|integral to membrane of membrane fraction|integral to plasma membrane	cytokine activity|protease binding|tumor necrosis factor receptor binding	g.chr19:6586314C>T	L08096	CCDS12170.1	19p13	2013-05-22	2006-10-27	2006-10-27		ENSG00000125726		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11937	protein-coding gene	gene with protein product		602840	"""tumor necrosis factor (ligand) superfamily, member 7"""	CD27LG, TNFSF7		8387892, 8120384	Standard	NM_001252		Approved	CD27L	uc002mfi.3	P32970		ENST00000245903.3:c.299G>A	19.37:g.6586314C>T	ENSP00000245903:p.Arg100His					CD70_uc010xjf.1_Missense_Mutation_p.R100H	p.R100H	NM_001252	NP_001243	P32970	CD70_HUMAN			3	449	-			100			Extracellular (Potential).		B4DPR8|Q53XX4|Q96J57	Missense_Mutation	SNP	ENST00000245903.3	37	c.299G>A	CCDS12170.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099502	0.56183	.	.	ENSG00000125726	ENST00000423145;ENST00000245903	D;D	0.94758	-3.51;-3.51	4.32	-1.95	0.07548	Tumour necrosis factor (3);Tumour necrosis factor-like (2);Tumour necrosis factor, conserved site (1);	0.505078	0.16813	N	0.198478	D	0.83078	0.5176	N	0.19112	0.55	0.09310	N	1	P;B	0.37985	0.613;0.073	B;B	0.29267	0.1;0.013	T	0.76271	-0.3020	10	0.42905	T	0.14	-12.4533	3.3193	0.07044	0.1864:0.3737:0.0:0.4399	.	100;100	B4DPR8;P32970	.;CD70_HUMAN	H	100	ENSP00000395294:R100H;ENSP00000245903:R100H	ENSP00000245903:R100H	R	-	2	0	CD70	6537314	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.578000	0.05841	-0.201000	0.10284	0.556000	0.70494	CGT		0.642	CD70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457860.1		
RETN	56729	broad.mit.edu	37	19	7734784	7734784	+	Splice_Site	SNP	G	G	A	rs566843624		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:7734784G>A	ENST00000221515.2	+	3	284	c.196G>A	c.(196-198)Ggc>Agc	p.G66S	RETN_ENST00000381324.2_Intron	NM_001193374.1|NM_020415.3	NP_001180303.1|NP_065148.1	Q9HD89	RETN_HUMAN	resistin	66					aging (GO:0007568)|fat cell differentiation (GO:0045444)|negative regulation of feeding behavior (GO:2000252)|positive regulation of collagen metabolic process (GO:0010714)|positive regulation of progesterone secretion (GO:2000872)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				ovary(1)	1						TTGCCCCCGAGGTGAGTGCAG	0.627																																						uc002mhf.1																			0				ovary(1)	1						c.(196-198)GGC>AGC		resistin							47.0	48.0	48.0					19																	7734784		2203	4300	6503	SO:0001630	splice_region_variant	56729						hormone activity	g.chr19:7734784G>A	AF205952	CCDS12182.1	19p13.2	2008-02-05				ENSG00000104918			20389	protein-coding gene	gene with protein product		605565				12050208	Standard	NM_020415		Approved	FIZZ3, ADSF, RETN1	uc002mhf.1	Q9HD89		ENST00000221515.2:c.196+1G>A	19.37:g.7734784G>A						RETN_uc002mhg.1_Missense_Mutation_p.G66S|RETN_uc010dvm.1_Intron	p.G66S	NM_020415	NP_065148	Q9HD89	RETN_HUMAN			3	242	+			66					D6W649|Q540D9|Q76B53	Missense_Mutation	SNP	ENST00000221515.2	37	c.196G>A	CCDS12182.1	.	.	.	.	.	.	.	.	.	.	g	16.15	3.042232	0.55003	.	.	ENSG00000104918	ENST00000221515	T	0.57436	0.4	4.72	3.68	0.42216	.	0.134047	0.33834	N	0.004505	T	0.51176	0.1659	M	0.64676	1.99	0.80722	D	1	P	0.34934	0.476	B	0.39840	0.311	T	0.51403	-0.8710	10	0.49607	T	0.09	-19.4623	9.1079	0.36710	0.1025:0.0:0.8975:0.0	.	66	Q9HD89	RETN_HUMAN	S	66	ENSP00000221515:G66S	ENSP00000221515:G66S	G	+	1	0	RETN	7640784	1.000000	0.71417	0.839000	0.33178	0.036000	0.12997	2.348000	0.44045	1.000000	0.39049	-0.270000	0.10280	GGC		0.627	RETN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461731.1	NM_020415	Missense_Mutation
PODNL1	79883	broad.mit.edu	37	19	14046601	14046601	+	Missense_Mutation	SNP	C	C	T	rs147712582	byFrequency	TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:14046601C>T	ENST00000339560.5	-	5	721	c.448G>A	c.(448-450)Gcg>Acg	p.A150T	PODNL1_ENST00000254320.3_Missense_Mutation_p.A68T|PODNL1_ENST00000538371.2_Missense_Mutation_p.A148T|PODNL1_ENST00000538517.2_Intron	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	150	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			GCCAGATCCGCGACACGGAGG	0.667																																						uc002mxr.2																			0				central_nervous_system(1)	1						c.(448-450)GCG>ACG		podocan-like 1 isoform 1			THR/ALA,,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	26.0	28.0	28.0		442,,448	3.9	0.0	19	dbSNP_134	28	0,8600		0,0,4300	no	missense,intron,missense	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	58,,58	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	possibly-damaging,,possibly-damaging	148/511,,150/513	14046601	4,13002	2203	4300	6503	SO:0001583	missense	79883					proteinaceous extracellular matrix		g.chr19:14046601C>T	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.448G>A	19.37:g.14046601C>T	ENSP00000345175:p.Ala150Thr					PODNL1_uc010xni.1_Missense_Mutation_p.A68T|PODNL1_uc010xnj.1_Missense_Mutation_p.A148T|PODNL1_uc002mxs.2_Intron	p.A150T	NM_024825	NP_079101	Q6PEZ8	PONL1_HUMAN	OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)		5	722	-			150			Leu-rich.|LRR 4.		B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	c.448G>A	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.282377	0.40394	9.08E-4	0.0	ENSG00000132000	ENST00000538371;ENST00000339560;ENST00000254320	T;T;T	0.24538	1.85;5.5;1.85	4.97	3.92	0.45320	.	0.272209	0.25836	N	0.027983	T	0.36496	0.0969	L	0.44542	1.39	0.09310	N	1	D;D;D	0.69078	0.997;0.975;0.995	P;P;P	0.59948	0.848;0.586;0.866	T	0.10706	-1.0618	10	0.87932	D	0	.	10.7284	0.46083	0.0:0.9077:0.0:0.0923	.	148;68;150	F5H7F9;B7Z3M0;Q6PEZ8	.;.;PONL1_HUMAN	T	148;150;68	ENSP00000442553:A148T;ENSP00000345175:A150T;ENSP00000254320:A68T	ENSP00000254320:A68T	A	-	1	0	PODNL1	13907601	0.065000	0.20965	0.004000	0.12327	0.219000	0.24729	3.572000	0.53849	1.080000	0.41073	0.479000	0.44913	GCG		0.667	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
FCGBP	8857	broad.mit.edu	37	19	40395990	40395990	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:40395990G>A	ENST00000221347.6	-	15	7414	c.7407C>T	c.(7405-7407)ttC>ttT	p.F2469F		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2469	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCATGAAGTCGAAGCGGCGGC	0.672																																						uc002omp.3																			0				ovary(4)|skin(4)|central_nervous_system(1)	9						c.(7405-7407)TTC>TTT		Fc fragment of IgG binding protein precursor							117.0	88.0	98.0					19																	40395990		2181	3910	6091	SO:0001819	synonymous_variant	8857					extracellular region	protein binding	g.chr19:40395990G>A	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.7407C>T	19.37:g.40395990G>A							p.F2469F	NM_003890	NP_003881	Q9Y6R7	FCGBP_HUMAN	Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)		15	7415	-	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		2469			VWFD 6.		O95784	Silent	SNP	ENST00000221347.6	37	c.7407C>T	CCDS12546.1																																																																																				0.672	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PRR12	57479	broad.mit.edu	37	19	50105110	50105110	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr19:50105110G>A	ENST00000418929.2	+	6	4720	c.4708G>A	c.(4708-4710)Gga>Aga	p.G1570R		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	749							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CGAGAGTGGCGGAGAGGGCAT	0.647																																						uc002poo.3																			0				central_nervous_system(1)|pancreas(1)	2						c.(4708-4710)GGA>AGA		proline rich 12							23.0	32.0	29.0					19																	50105110		2038	4161	6199	SO:0001583	missense	57479						DNA binding	g.chr19:50105110G>A	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4708G>A	19.37:g.50105110G>A	ENSP00000394510:p.Gly1570Arg						p.G1570R	NM_020719	NP_065770	Q9ULL5	PRR12_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	6	4708	+		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)	749					E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	37	c.4708G>A	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	9.571	1.121058	0.20877	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	3.72	3.72	0.42706	.	0.407398	0.17771	N	0.162569	T	0.75302	0.3831	L	0.60455	1.87	0.49483	D	0.999796	D	0.89917	1.0	D	0.91635	0.999	T	0.78254	-0.2275	9	0.87932	D	0	-11.6601	14.4198	0.67175	0.0:0.0:1.0:0.0	.	1570	Q9ULL5-3	.	R	1570;750;750	.	ENSP00000246798:G750R	G	+	1	0	PRR12	54796922	1.000000	0.71417	0.998000	0.56505	0.270000	0.26580	7.834000	0.86773	1.902000	0.55061	0.305000	0.20034	GGA		0.647	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
MYT1L	23040	broad.mit.edu	37	2	1926965	1926965	+	Silent	SNP	G	G	A	rs370624330		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr2:1926965G>A	ENST00000399161.2	-	10	1323	c.576C>T	c.(574-576)gaC>gaT	p.D192D	MYT1L_ENST00000428368.2_Silent_p.D192D	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	192					cell differentiation (GO:0030154)|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)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(16)|lung(50)|ovary(5)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	97	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)		TGTCATATTCGTCATTATTGT	0.388																																						uc002qxe.2																			0				ovary(5)|central_nervous_system(1)	6						c.(574-576)GAC>GAT		myelin transcription factor 1-like							85.0	80.0	82.0					2																	1926965		1927	4137	6064	SO:0001819	synonymous_variant	23040				cell differentiation|nervous system development	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr2:1926965G>A	AF036943	CCDS46222.1	2p25.3	2013-01-10			ENSG00000186487	ENSG00000186487		"""Zinc fingers, C2HC-type containing"""	7623	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 1"""	613084				9373037	Standard	XM_006711862		Approved	KIAA1106, NZF1, ZC2HC4B	uc002qxd.3	Q9UL68	OTTHUMG00000151407	ENST00000399161.2:c.576C>T	2.37:g.1926965G>A						MYT1L_uc002qxd.2_Silent_p.D192D|MYT1L_uc010ewl.1_RNA	p.D192D	NM_015025	NP_055840	Q9UL68	MYT1L_HUMAN		OV - Ovarian serous cystadenocarcinoma(76;0.169)|all cancers(51;0.244)	10	1403	-	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.037)|all_epithelial(98;0.241)	192					A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37	c.576C>T																																																																																					0.388	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025	
XDH	7498	broad.mit.edu	37	2	31620554	31620554	+	Missense_Mutation	SNP	C	C	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr2:31620554C>A	ENST00000379416.3	-	6	523	c.475G>T	c.(475-477)Ggc>Tgc	p.G159C		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	159					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	GTCCGGAAGCCCTGGAGGATG	0.552																																					Colon(66;682 1445 30109 40147)	uc002rnv.1																			0				skin(4)|breast(2)|ovary(1)|central_nervous_system(1)	8						c.(475-477)GGC>TGC		xanthine dehydrogenase	Allopurinol(DB00437)|Carvedilol(DB01136)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Desflurane(DB01189)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|NADH(DB00157)|Nitrofurazone(DB00336)|Papaverine(DB01113)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Rasburicase(DB00049)|Spermine(DB00127)|Trifluoperazine(DB00831)|Vitamin E(DB00163)						118.0	125.0	123.0					2																	31620554		2203	4300	6503	SO:0001583	missense	7498				purine nucleotide catabolic process|xanthine catabolic process	cytosol|extracellular region|peroxisome	2 iron, 2 sulfur cluster binding|electron carrier activity|flavin adenine dinucleotide binding|iron ion binding|molybdopterin cofactor binding|protein homodimerization activity|xanthine dehydrogenase activity|xanthine oxidase activity	g.chr2:31620554C>A	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.475G>T	2.37:g.31620554C>A	ENSP00000368727:p.Gly159Cys						p.G159C	NM_000379	NP_000370	P47989	XDH_HUMAN			6	554	-	Acute lymphoblastic leukemia(172;0.155)		159					Q16681|Q16712|Q4PJ16	Missense_Mutation	SNP	ENST00000379416.3	37	c.475G>T	CCDS1775.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.762375	0.49468	.	.	ENSG00000158125	ENST00000379416	T	0.63417	-0.04	6.07	4.29	0.51040	[2Fe-2S]-binding (3);Xanthine dehydrogenase, small subunit (1);	0.000000	0.85682	D	0.000000	T	0.80994	0.4731	M	0.89414	3.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83490	0.0069	10	0.87932	D	0	.	12.0704	0.53613	0.0:0.8592:0.0:0.1408	.	159	P47989	XDH_HUMAN	C	159	ENSP00000368727:G159C	ENSP00000368727:G159C	G	-	1	0	XDH	31474058	1.000000	0.71417	0.998000	0.56505	0.010000	0.07245	7.175000	0.77632	0.912000	0.36772	-0.136000	0.14681	GGC		0.552	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
TMPRSS6	164656	broad.mit.edu	37	22	37482392	37482392	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr22:37482392C>T	ENST00000346753.3	-	8	1047	c.931G>A	c.(931-933)Gtc>Atc	p.V311I	TMPRSS6_ENST00000442782.2_Missense_Mutation_p.V311I|TMPRSS6_ENST00000406856.1_Missense_Mutation_p.V302I|TMPRSS6_ENST00000381792.2_Missense_Mutation_p.V302I|TMPRSS6_ENST00000406725.1_Missense_Mutation_p.V302I	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	311	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				angiogenesis (GO:0001525)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|intracellular signal transduction (GO:0035556)|iron ion homeostasis (GO:0055072)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(5)|central_nervous_system(4)|endometrium(4)|kidney(4)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)	40						TTCTTCCAGACGACCGCCATG	0.667																																						uc003aqs.1																			0				breast(4)|ovary(1)|skin(1)	6						c.(931-933)GTC>ATC		transmembrane protease, serine 6							28.0	27.0	27.0					22																	37482392		2202	4299	6501	SO:0001583	missense	164656				angiogenesis|extracellular matrix organization|fibrinolysis|intracellular signal transduction|proteolysis	integral to membrane|intracellular|plasma membrane	serine-type endopeptidase activity	g.chr22:37482392C>T	AY055383	CCDS13941.1, CCDS74856.1, CCDS74857.1	22q13.1	2010-04-13			ENSG00000187045	ENSG00000187045		"""Serine peptidases / Transmembrane"""	16517	protein-coding gene	gene with protein product		609862					Standard	NM_001289000		Approved	FLJ30744	uc003aqs.1	Q8IU80	OTTHUMG00000150541	ENST00000346753.3:c.931G>A	22.37:g.37482392C>T	ENSP00000334962:p.Val311Ile					TMPRSS6_uc003aqt.1_Missense_Mutation_p.V302I|TMPRSS6_uc003aqu.2_Missense_Mutation_p.V302I	p.V311I	NM_153609	NP_705837	Q8IU80	TMPS6_HUMAN			8	1045	-			311			CUB 1.|Extracellular (Potential).		B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Missense_Mutation	SNP	ENST00000346753.3	37	c.931G>A	CCDS13941.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.972292	0.74246	.	.	ENSG00000187045	ENST00000381792;ENST00000346753;ENST00000406725;ENST00000406856;ENST00000442782	T;T;T;T;T	0.59502	0.26;0.26;0.26;0.26;0.26	4.55	4.55	0.56014	CUB (1);	0.181737	0.37219	N	0.002199	T	0.64327	0.2588	L	0.34521	1.04	0.43304	D	0.9953	D;D;D	0.76494	0.999;0.995;0.991	P;P;P	0.62089	0.898;0.654;0.452	T	0.67952	-0.5537	10	0.56958	D	0.05	.	16.3113	0.82872	0.0:1.0:0.0:0.0	.	311;302;311	Q8IU80-2;Q8IU80-5;Q8IU80	.;.;TMPS6_HUMAN	I	302;311;302;302;311	ENSP00000371211:V302I;ENSP00000334962:V311I;ENSP00000385453:V302I;ENSP00000384964:V302I;ENSP00000397691:V311I	ENSP00000334962:V311I	V	-	1	0	TMPRSS6	35812338	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.185000	0.58330	2.071000	0.62044	0.655000	0.94253	GTC		0.667	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609	
CHL1	10752	broad.mit.edu	37	3	440026	440026	+	Missense_Mutation	SNP	A	A	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:440026A>T	ENST00000256509.2	+	25	3853	c.3211A>T	c.(3211-3213)Aat>Tat	p.N1071Y	CHL1_ENST00000397491.2_Missense_Mutation_p.N1055Y	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		TTGGGGCGATAATGATAGCAT	0.383																																						uc003bou.2																			0				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12						c.(3163-3165)AAT>TAT		cell adhesion molecule with homology to L1CAM							88.0	86.0	87.0					3																	440026		2203	4300	6503	SO:0001583	missense	10752				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix		g.chr3:440026A>T	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.3211A>T	3.37:g.440026A>T	ENSP00000256509:p.Asn1071Tyr					CHL1_uc003bot.2_Missense_Mutation_p.N1071Y|CHL1_uc003bow.1_Missense_Mutation_p.N1055Y|CHL1_uc011asi.1_Intron	p.N1055Y	NM_006614	NP_006605	O00533	CHL1_HUMAN		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)	24	3434	+		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)	1055			Extracellular (Potential).		Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	c.3163A>T	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	16.98	3.272095	0.59649	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.61040	0.14;0.16	5.72	5.72	0.89469	.	0.102592	0.64402	D	0.000005	T	0.66117	0.2757	L	0.29908	0.895	0.54753	D	0.999988	P;D	0.89917	0.565;1.0	P;D	0.83275	0.531;0.996	T	0.69580	-0.5107	10	0.72032	D	0.01	.	14.557	0.68106	1.0:0.0:0.0:0.0	.	1055;1071	O00533;O00533-2	CHL1_HUMAN;.	Y	1071;1055	ENSP00000256509:N1071Y;ENSP00000380628:N1055Y	ENSP00000256509:N1071Y	N	+	1	0	CHL1	415026	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.828000	0.86729	2.189000	0.69895	0.528000	0.53228	AAT		0.383	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
FGD5	152273	broad.mit.edu	37	3	14861539	14861539	+	Missense_Mutation	SNP	G	G	A	rs546389054		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:14861539G>A	ENST00000285046.5	+	1	1071	c.961G>A	c.(961-963)Gcc>Acc	p.A321T	FGD5_ENST00000543601.1_Missense_Mutation_p.A80T	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	321	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GGATGAGTCCGCCGAGGAGAG	0.552																																						uc003bzc.2																			0				ovary(3)|kidney(1)|pancreas(1)	5						c.(961-963)GCC>ACC		FYVE, RhoGEF and PH domain containing 5							66.0	72.0	70.0					3																	14861539		2002	4182	6184	SO:0001583	missense	152273				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding	g.chr3:14861539G>A	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.961G>A	3.37:g.14861539G>A	ENSP00000285046:p.Ala321Thr					FGD5_uc011avk.1_Missense_Mutation_p.A321T	p.A321T	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN			1	1071	+			321			Glu-rich.		B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	c.961G>A	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	11.46	1.646552	0.29246	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.77750	-1.12;-0.91	5.34	-1.16	0.09678	.	0.749106	0.12161	N	0.493987	T	0.57242	0.2040	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.35724	-0.9777	10	0.16420	T	0.52	-4.4292	0.8015	0.01076	0.2781:0.1919:0.3321:0.1979	.	80;321	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	T	321;80	ENSP00000285046:A321T;ENSP00000445949:A80T	ENSP00000285046:A321T	A	+	1	0	FGD5	14836543	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.231000	0.17872	-0.966000	0.03587	-0.797000	0.03246	GCC		0.552	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
VILL	50853	broad.mit.edu	37	3	38035909	38035909	+	Missense_Mutation	SNP	A	A	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:38035909A>G	ENST00000283713.6	+	4	559	c.293A>G	c.(292-294)cAg>cGg	p.Q98R	VILL_ENST00000383759.2_Missense_Mutation_p.Q98R|VILL_ENST00000465644.1_Intron			O15195	VILL_HUMAN	villin-like	98					actin filament capping (GO:0051693)|cytoskeleton organization (GO:0007010)	actin cytoskeleton (GO:0015629)	structural constituent of cytoskeleton (GO:0005200)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|stomach(3)|urinary_tract(2)	28				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		CGCGAGGCGCAGGGCCACGAG	0.721																																						uc003chj.2																			0					0						c.(292-294)CAG>CGG		villin-like protein							18.0	24.0	22.0					3																	38035909		2183	4283	6466	SO:0001583	missense	50853				actin filament capping|cytoskeleton organization	actin cytoskeleton	actin binding|structural constituent of cytoskeleton	g.chr3:38035909A>G		CCDS2670.2	3p21	2004-07-28			ENSG00000136059	ENSG00000136059			30906	protein-coding gene	gene with protein product						9179494	Standard	XM_005265191		Approved		uc003chl.3	O15195	OTTHUMG00000130814	ENST00000283713.6:c.293A>G	3.37:g.38035909A>G	ENSP00000283713:p.Gln98Arg					VILL_uc003chk.1_Missense_Mutation_p.Q98R|VILL_uc003chl.2_Missense_Mutation_p.Q98R|VILL_uc010hgu.2_5'UTR	p.Q98R	NM_015873	NP_056957	O15195	VILL_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)	4	579	+			98					A8MZP1|Q9BT80|Q9BWH7	Missense_Mutation	SNP	ENST00000283713.6	37	c.293A>G	CCDS2670.2	.	.	.	.	.	.	.	.	.	.	A	23.3	4.394178	0.83011	.	.	ENSG00000136059	ENST00000283713;ENST00000416303;ENST00000492491;ENST00000383759;ENST00000356246	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	3.89	3.89	0.44902	Gelsolin domain (1);	0.118865	0.64402	D	0.000015	T	0.58779	0.2146	M	0.94101	3.495	0.48830	D	0.999712	D	0.76494	0.999	D	0.81914	0.995	T	0.69884	-0.5024	10	0.72032	D	0.01	-20.1753	12.1281	0.53928	1.0:0.0:0.0:0.0	.	98	O15195	VILL_HUMAN	R	98	ENSP00000283713:Q98R;ENSP00000393661:Q98R;ENSP00000427355:Q98R;ENSP00000373266:Q98R	ENSP00000283713:Q98R	Q	+	2	0	VILL	38010913	1.000000	0.71417	0.983000	0.44433	0.707000	0.40811	8.909000	0.92647	1.769000	0.52152	0.460000	0.39030	CAG		0.721	VILL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253360.3	NM_015873	
NPRL2	10641	broad.mit.edu	37	3	50385755	50385755	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:50385755G>A	ENST00000232501.3	-	8	1245	c.807C>T	c.(805-807)acC>acT	p.T269T	CYB561D2_ENST00000232508.5_5'Flank|CYB561D2_ENST00000424512.1_5'Flank|ZMYND10-AS1_ENST00000440013.1_RNA|CYB561D2_ENST00000418577.1_5'Flank|XXcos-LUCA11.5_ENST00000606589.1_5'Flank|NPRL2_ENST00000493465.1_Intron|ZMYND10_ENST00000231749.3_5'Flank|CYB561D2_ENST00000425346.1_5'Flank|ZMYND10_ENST00000360165.3_5'Flank	NM_006545.4	NP_006536.3	Q8WTW4	NPRL2_HUMAN	nitrogen permease regulator-like 2 (S. cerevisiae)	269					negative regulation of kinase activity (GO:0033673)|protein phosphorylation (GO:0006468)		GTPase activator activity (GO:0005096)|protein kinase activity (GO:0004672)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|urinary_tract(1)	11						TACCTTGCTTGGTCACGTAGG	0.577																																						uc003daj.1																			0				lung(1)	1						c.(805-807)ACC>ACT		tumor suppressor candidate 4							76.0	68.0	71.0					3																	50385755		2203	4300	6503	SO:0001819	synonymous_variant	10641				negative regulation of kinase activity		protein binding|protein kinase activity	g.chr3:50385755G>A	AF040708	CCDS2826.1	3p21.3	2010-03-30	2010-03-30	2010-03-30	ENSG00000114388	ENSG00000114388			24969	protein-coding gene	gene with protein product		607072	"""tumor suppressor candidate 4"""	TUSC4		11085536	Standard	NM_006545		Approved	NPR2L, NPR2	uc003daj.1	Q8WTW4	OTTHUMG00000156864	ENST00000232501.3:c.807C>T	3.37:g.50385755G>A						ZMYND10_uc003dag.1_5'Flank|ZMYND10_uc010hll.1_5'Flank|ZMYND10_uc003dah.1_5'Flank|ZMYND10_uc010hlm.1_5'Flank|NPRL2_uc003dai.1_Silent_p.T149T|CYB561D2_uc003dak.2_5'Flank|CYB561D2_uc003dal.2_5'Flank|CYB561D2_uc003dam.2_5'Flank	p.T269T	NM_006545	NP_006536	Q8WTW4	NPRL2_HUMAN			8	1210	-			269					A8K831|Q6FGS2|Q9Y249|Q9Y497	Silent	SNP	ENST00000232501.3	37	c.807C>T	CCDS2826.1																																																																																				0.577	NPRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346299.1	NM_006545	
STXBP5L	9515	broad.mit.edu	37	3	120833881	120833881	+	Missense_Mutation	SNP	A	A	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:120833881A>G	ENST00000273666.6	+	6	851	c.580A>G	c.(580-582)Atc>Gtc	p.I194V	STXBP5L_ENST00000492541.1_Missense_Mutation_p.I194V|STXBP5L_ENST00000472879.1_Missense_Mutation_p.I194V|STXBP5L_ENST00000471454.1_Missense_Mutation_p.I194V|STXBP5L_ENST00000497029.1_Missense_Mutation_p.I194V	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	194					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		TGGATATGTTATCATGTGGAA	0.318																																						uc003eec.3																			0				ovary(7)|skin(2)	9						c.(580-582)ATC>GTC		syntaxin binding protein 5-like							100.0	93.0	96.0					3																	120833881		1826	4069	5895	SO:0001583	missense	9515				exocytosis|protein transport	cytoplasm|integral to membrane|plasma membrane		g.chr3:120833881A>G	AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.580A>G	3.37:g.120833881A>G	ENSP00000273666:p.Ile194Val					STXBP5L_uc011bji.1_Missense_Mutation_p.I194V	p.I194V	NM_014980	NP_055795	Q9Y2K9	STB5L_HUMAN		GBM - Glioblastoma multiforme(114;0.0694)	6	720	+			194			WD 3.		Q4G1B4|Q6PIC3	Missense_Mutation	SNP	ENST00000273666.6	37	c.580A>G	CCDS43137.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.800816	0.50315	.	.	ENSG00000145087	ENST00000273666;ENST00000471454;ENST00000472879;ENST00000497029;ENST00000492541;ENST00000471262	T;T;T;T;T;T	0.53206	0.63;1.52;0.63;0.63;1.31;1.52	5.56	5.56	0.83823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.63943	0.2554	M	0.77103	2.36	0.58432	D	0.999999	B;P	0.48640	0.005;0.913	B;P	0.61592	0.007;0.891	T	0.63721	-0.6573	10	0.33141	T	0.24	-21.4244	10.1198	0.42614	0.9254:0.0:0.0746:0.0	.	194;194	E9PFI2;Q9Y2K9	.;STB5L_HUMAN	V	194	ENSP00000273666:I194V;ENSP00000420019:I194V;ENSP00000419627:I194V;ENSP00000420287:I194V;ENSP00000420666:I194V;ENSP00000420167:I194V	ENSP00000273666:I194V	I	+	1	0	STXBP5L	122316571	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.574000	0.82434	2.116000	0.64780	0.402000	0.26972	ATC		0.318	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
SI	6476	broad.mit.edu	37	3	164730787	164730787	+	Missense_Mutation	SNP	G	G	A	rs192640245		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr3:164730787G>A	ENST00000264382.3	-	34	4105	c.4043C>T	c.(4042-4044)aCg>aTg	p.T1348M		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1348	Sucrase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TTCATCTTCCGTTAGAGTTTT	0.323										HNSCC(35;0.089)			G|||	1	0.000199681	0.0	0.0	5008	,	,		15219	0.001		0.0	False		,,,				2504	0.0					uc003fei.2																			0				ovary(7)|upper_aerodigestive_tract(4)|skin(2)|pancreas(1)	14						c.(4042-4044)ACG>ATG		sucrase-isomaltase	Acarbose(DB00284)	G	MET/THR	0,4406		0,0,2203	133.0	130.0	131.0		4043	3.5	0.8	3		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	SI	NM_001041.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1348/1828	164730787	1,13005	2203	4300	6503	SO:0001583	missense	6476				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|brush border|Golgi apparatus|integral to membrane	carbohydrate binding|oligo-1,6-glucosidase activity|sucrose alpha-glucosidase activity	g.chr3:164730787G>A	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.4043C>T	3.37:g.164730787G>A	ENSP00000264382:p.Thr1348Met	HNSCC(35;0.089)					p.T1348M	NM_001041	NP_001032	P14410	SUIS_HUMAN			34	4105	-		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)	1348			Sucrase.|Lumenal.		A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	c.4043C>T	CCDS3196.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.76	2.033840	0.35893	0.0	1.16E-4	ENSG00000090402	ENST00000264382	D	0.88975	-2.45	4.35	3.48	0.39840	Glycoside hydrolase, superfamily (1);	0.278355	0.36234	N	0.002713	D	0.91284	0.7252	L	0.57536	1.79	0.09310	N	0.999999	D	0.76494	0.999	D	0.68621	0.959	T	0.83237	-0.0060	10	0.62326	D	0.03	.	8.1342	0.31046	0.1896:0.0:0.8104:0.0	.	1348	P14410	SUIS_HUMAN	M	1348	ENSP00000264382:T1348M	ENSP00000264382:T1348M	T	-	2	0	SI	166213481	0.357000	0.24938	0.764000	0.31436	0.689000	0.40095	-0.370000	0.07523	1.015000	0.39444	0.585000	0.79938	ACG		0.323	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
DGKQ	1609	broad.mit.edu	37	4	956666	956666	+	Silent	SNP	C	C	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:956666C>A	ENST00000273814.3	-	17	2002	c.1929G>T	c.(1927-1929)gtG>gtT	p.V643V	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	643	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|protein kinase C signaling (GO:0070528)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to ATP (GO:0033198)|thrombin receptor signaling pathway (GO:0070493)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|kinase binding (GO:0019900)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|phospholipase binding (GO:0043274)			breast(1)|endometrium(2)|kidney(2)|lung(2)|prostate(2)	9			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CGCCACCACACACCAGCACCC	0.682																																					Esophageal Squamous(17;537 645 4447 26373)	uc003gbw.2																			0				kidney(1)	1						c.(1927-1929)GTG>GTT		diacylglycerol kinase, theta							42.0	33.0	36.0					4																	956666		2178	4292	6470	SO:0001819	synonymous_variant	1609				activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway|platelet activation|protein kinase C signaling cascade|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to ATP|thrombin receptor signaling pathway	cytoskeleton|cytosol|nuclear speck|plasma membrane	activating transcription factor binding|ATP binding|diacylglycerol kinase activity|kinase binding|metal ion binding|phospholipase binding	g.chr4:956666C>A	L38707	CCDS3342.1	4p16.3	2008-08-29	2002-08-29		ENSG00000145214	ENSG00000145214			2856	protein-coding gene	gene with protein product		601207	"""diacylglycerol kinase, theta (110kD)"""	DAGK4		8617502, 9099683	Standard	NM_001347		Approved	DAGK, DAGK7	uc003gbw.4	P52824	OTTHUMG00000088629	ENST00000273814.3:c.1929G>T	4.37:g.956666C>A						DGKQ_uc010ibn.2_Silent_p.V630V	p.V643V	NM_001347	NP_001338	P52824	DGKQ_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.0158)		17	2003	-			643			DAGKc.		Q6P3W4	Silent	SNP	ENST00000273814.3	37	c.1929G>T	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	C	9.463	1.093516	0.20471	.	.	ENSG00000145214	ENST00000509465	.	.	.	4.85	-0.0284	0.13922	.	.	.	.	.	T	0.41419	0.1158	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20806	-1.0264	4	.	.	.	.	1.3677	0.02205	0.1391:0.3942:0.1358:0.3309	.	.	.	.	F	577	.	.	C	-	2	0	DGKQ	946666	0.590000	0.26815	0.976000	0.42696	0.783000	0.44284	-0.132000	0.10467	-0.316000	0.08690	-0.140000	0.14226	TGT		0.682	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1		
PRKG2	5593	broad.mit.edu	37	4	82056416	82056416	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:82056416C>T	ENST00000395578.1	-	14	1785	c.1669G>A	c.(1669-1671)Gtt>Att	p.V557I	PRKG2_ENST00000264399.1_Missense_Mutation_p.V557I|PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000418486.2_Missense_Mutation_p.V528I|PRKG2_ENST00000545647.1_Missense_Mutation_p.V137I			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	557	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						ACACAAGCAACGCAGAATTTG	0.413																																						uc003hmh.2																			0				breast(3)|central_nervous_system(2)|ovary(1)|large_intestine(1)	7						c.(1669-1671)GTT>ATT		protein kinase, cGMP-dependent, type II							132.0	126.0	128.0					4																	82056416		2203	4300	6503	SO:0001583	missense	5593				platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity	g.chr4:82056416C>T	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.1669G>A	4.37:g.82056416C>T	ENSP00000378945:p.Val557Ile					PRKG2_uc011ccf.1_Missense_Mutation_p.V137I|PRKG2_uc011ccg.1_Missense_Mutation_p.V137I|PRKG2_uc011cch.1_Missense_Mutation_p.V528I	p.V557I	NM_006259	NP_006250	Q13237	KGP2_HUMAN			13	1683	-			557			Protein kinase.		B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	37	c.1669G>A	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.580916	0.46006	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486;ENST00000545647	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.77	5.77	0.91146	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.286388	0.39274	N	0.001415	T	0.38134	0.1029	N	0.05306	-0.075	0.46798	D	0.999204	B;B	0.29037	0.231;0.049	B;B	0.28784	0.064;0.094	T	0.36407	-0.9749	10	0.10902	T	0.67	-22.7833	12.8838	0.58032	0.0:0.9252:0.0:0.0748	.	528;557	E7EPE6;Q13237	.;KGP2_HUMAN	I	557;557;528;137	ENSP00000378945:V557I;ENSP00000264399:V557I;ENSP00000389038:V528I;ENSP00000439967:V137I	ENSP00000264399:V557I	V	-	1	0	PRKG2	82275440	0.916000	0.31088	0.700000	0.30305	0.989000	0.77384	1.688000	0.37690	2.720000	0.93068	0.650000	0.86243	GTT		0.413	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
FAT4	79633	broad.mit.edu	37	4	126372061	126372061	+	Missense_Mutation	SNP	G	G	A	rs370611770		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:126372061G>A	ENST00000394329.3	+	9	9903	c.9890G>A	c.(9889-9891)cGt>cAt	p.R3297H	FAT4_ENST00000335110.5_Missense_Mutation_p.R1595H	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3297	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TATGTGCCCCGTTTTGTTTCC	0.403																																						uc003ifj.3																			0				ovary(9)|skin(5)|upper_aerodigestive_tract(2)|pancreas(2)	18						c.(9889-9891)CGT>CAT		FAT tumor suppressor homolog 4 precursor		G	HIS/ARG	0,4406		0,0,2203	57.0	59.0	58.0		9890	5.4	1.0	4		58	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAT4	NM_024582.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	3297/4982	126372061	1,13005	2203	4300	6503	SO:0001583	missense	79633				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr4:126372061G>A	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9890G>A	4.37:g.126372061G>A	ENSP00000377862:p.Arg3297His					FAT4_uc011cgp.1_Missense_Mutation_p.R1595H|FAT4_uc003ifi.1_Missense_Mutation_p.R775H	p.R3297H	NM_024582	NP_078858	Q6V0I7	FAT4_HUMAN			9	9890	+			3297			Cadherin 31.|Extracellular (Potential).		A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	c.9890G>A	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.48	3.398961	0.62177	0.0	1.16E-4	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01745	4.66;4.66	5.42	5.42	0.78866	Cadherin (2);Cadherin-like (1);	0.000000	0.35262	U	0.003335	T	0.07234	0.0183	L	0.40543	1.245	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.988;0.998	T	0.48758	-0.9007	10	0.36615	T	0.2	.	19.2521	0.93929	0.0:0.0:1.0:0.0	.	1595;3297;3297	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	H	3297;1595	ENSP00000377862:R3297H;ENSP00000335169:R1595H	ENSP00000335169:R1595H	R	+	2	0	FAT4	126591511	1.000000	0.71417	0.996000	0.52242	0.511000	0.34104	9.666000	0.98612	2.542000	0.85734	0.655000	0.94253	CGT		0.403	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
DCHS2	54798	broad.mit.edu	37	4	155241880	155241880	+	Silent	SNP	C	C	T	rs372810438		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:155241880C>T	ENST00000357232.4	-	14	3305	c.3306G>A	c.(3304-3306)acG>acA	p.T1102T		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1102	Cadherin 9. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GAAATGGATTCGTGCCAGGGT	0.453																																						uc003inw.2																			0				ovary(3)|pancreas(1)	4						c.(3304-3306)ACG>ACA		dachsous 2 isoform 1							363.0	391.0	381.0					4																	155241880		2203	4300	6503	SO:0001819	synonymous_variant	54798				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr4:155241880C>T	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3306G>A	4.37:g.155241880C>T							p.T1102T	NM_017639	NP_060109	Q6V1P9	PCD23_HUMAN		LUSC - Lung squamous cell carcinoma(193;0.107)	14	3306	-	all_hematologic(180;0.208)	Renal(120;0.0854)	1102			Cadherin 9.		B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	c.3306G>A	CCDS3785.1																																																																																				0.453	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
CFAP97	57587	broad.mit.edu	37	4	186111564	186111564	+	Missense_Mutation	SNP	T	T	C			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:186111564T>C	ENST00000458385.2	-	2	906	c.787A>G	c.(787-789)Att>Gtt	p.I263V	KIAA1430_ENST00000514798.1_Missense_Mutation_p.I263V|KIAA1430_ENST00000296775.6_Missense_Mutation_p.I263V	NM_020827.1	NP_065878.1	Q9P2B7	K1430_HUMAN		263										endometrium(3)|kidney(2)|large_intestine(5)|upper_aerodigestive_tract(1)	11		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)		AGAGGGCTAATGTCTGGAGTT	0.398																																						uc003ixf.3																			0					0						c.(787-789)ATT>GTT		hypothetical protein LOC57587							104.0	89.0	94.0					4																	186111564		1880	4105	5985	SO:0001583	missense	57587							g.chr4:186111564T>C																												ENST00000458385.2:c.787A>G	4.37:g.186111564T>C	ENSP00000409964:p.Ile263Val					KIAA1430_uc003ixg.2_Missense_Mutation_p.I263V	p.I263V	NM_020827	NP_065878	Q9P2B7	K1430_HUMAN		all cancers(43;9.44e-26)|Epithelial(43;2.64e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.66e-11)|Colorectal(24;6.03e-05)|BRCA - Breast invasive adenocarcinoma(30;8.01e-05)|GBM - Glioblastoma multiforme(59;0.000331)|COAD - Colon adenocarcinoma(29;0.000427)|STAD - Stomach adenocarcinoma(60;0.000777)|LUSC - Lung squamous cell carcinoma(40;0.00924)|READ - Rectum adenocarcinoma(43;0.165)	2	934	-		all_lung(41;1.19e-13)|Lung NSC(41;3.16e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00872)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)	263					B3KRP7|D3DP60|Q05CU1|Q4W5M4|Q8N6E7|Q9UF45	Missense_Mutation	SNP	ENST00000458385.2	37	c.787A>G	CCDS47168.1	.	.	.	.	.	.	.	.	.	.	T	11.04	1.521011	0.27211	.	.	ENSG00000164323	ENST00000458385;ENST00000514798;ENST00000296775	T;T;T	0.46819	1.44;0.86;0.86	5.55	3.05	0.35203	.	0.134406	0.47093	N	0.000241	T	0.36880	0.0983	L	0.48642	1.525	0.27324	N	0.956962	B;B	0.26081	0.141;0.087	B;B	0.22753	0.041;0.018	T	0.19549	-1.0302	10	0.25751	T	0.34	-2.5019	9.971	0.41754	0.0:0.1401:0.0:0.8599	.	263;263	Q9P2B7-2;Q9P2B7	.;K1430_HUMAN	V	263	ENSP00000409964:I263V;ENSP00000423312:I263V;ENSP00000296775:I263V	ENSP00000296775:I263V	I	-	1	0	KIAA1430	186348558	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	3.719000	0.54926	0.993000	0.38866	0.533000	0.62120	ATT		0.398	KIAA1430-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000360717.2		
TUBB7P	56604	broad.mit.edu	37	4	190904404	190904404	+	IGR	SNP	T	T	C			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr4:190904404T>C								FRG1 (20045 upstream) : RNA5SP174 (31888 downstream)																							CTGCGTTTTCTATGAGCTGGT	0.507																																						uc011clg.1																			0					0						c.(574-576)ATA>ATG		tubulin, beta polypeptide 4, member Q							22.0	35.0	31.0					4																	190904404		1840	3964	5804	SO:0001628	intergenic_variant	56604				'de novo' posttranslational protein folding|microtubule-based movement|protein polymerization	cytoplasm|microtubule	GTP binding|GTPase activity|structural molecule activity	g.chr4:190904404T>C																													4.37:g.190904404T>C							p.I192M	NM_020040	NP_064424	Q99867	TBB4Q_HUMAN		all cancers(3;4.1e-31)|Epithelial(3;1.44e-30)|OV - Ovarian serous cystadenocarcinoma(60;2.03e-15)|BRCA - Breast invasive adenocarcinoma(30;8.54e-06)|Lung(3;3.23e-05)|STAD - Stomach adenocarcinoma(60;8.24e-05)|LUSC - Lung squamous cell carcinoma(40;0.000184)|GBM - Glioblastoma multiforme(59;0.00839)|READ - Rectum adenocarcinoma(43;0.155)	4	579	-		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)	193						Missense_Mutation	SNP		37	c.576A>G																																																																																				0	0.507								
CDH18	1016	broad.mit.edu	37	5	19544032	19544032	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr5:19544032G>A	ENST00000507958.1	-	11	2326	c.1336C>T	c.(1336-1338)Ctc>Ttc	p.L446F	CDH18_ENST00000274170.4_Missense_Mutation_p.L446F|CDH18_ENST00000511273.1_Missense_Mutation_p.L446F|CDH18_ENST00000506372.1_Missense_Mutation_p.L446F|CDH18_ENST00000502796.1_Missense_Mutation_p.L446F|CDH18_ENST00000382275.1_Missense_Mutation_p.L446F			Q13634	CAD18_HUMAN	cadherin 18, type 2	446	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					TCTCTGTCGAGAACCTTTGTA	0.363																																						uc003jgc.2																			0				ovary(5)|large_intestine(1)|skin(1)	7						c.(1336-1338)CTC>TTC		cadherin 18, type 2 preproprotein							146.0	137.0	140.0					5																	19544032		2203	4300	6503	SO:0001583	missense	1016				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:19544032G>A	U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1336C>T	5.37:g.19544032G>A	ENSP00000425093:p.Leu446Phe					CDH18_uc003jgd.2_Missense_Mutation_p.L446F|CDH18_uc011cnm.1_Missense_Mutation_p.L446F	p.L446F	NM_004934	NP_004925	Q13634	CAD18_HUMAN			8	1713	-	Lung NSC(1;0.00734)|all_lung(1;0.0197)		446			Extracellular (Potential).|Cadherin 4.		A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	c.1336C>T	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	16.90	3.250457	0.59212	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	5.14	4.27	0.50696	Cadherin (4);Cadherin-like (1);	0.074244	0.56097	D	0.000036	T	0.79569	0.4468	M	0.86740	2.835	0.39258	D	0.964158	B;B	0.29481	0.154;0.245	B;B	0.39771	0.309;0.211	T	0.78265	-0.2271	9	.	.	.	.	9.5957	0.39573	0.1716:0.0:0.8284:0.0	.	446;446	B4DHG6;Q13634	.;CAD18_HUMAN	F	446;446;446;446;446;446;392;446	ENSP00000371710:L446F;ENSP00000425093:L446F;ENSP00000274170:L446F;ENSP00000424931:L446F;ENSP00000422138:L446F;ENSP00000427383:L392F;ENSP00000425854:L446F	.	L	-	1	0	CDH18	19579789	1.000000	0.71417	0.938000	0.37757	0.832000	0.47134	4.938000	0.63519	1.178000	0.42870	0.313000	0.20887	CTC		0.363	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
PIK3R1	5295	broad.mit.edu	37	5	67591247	67591249	+	Splice_Site	DEL	GGT	GGT	-			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr5:67591247_67591249delGGT	ENST00000521381.1	+	14	2361_2363	c.1745_1747delGGT	c.(1744-1749)aggtgg>agg	p.W583del	PIK3R1_ENST00000336483.5_Splice_Site_p.W313del|PIK3R1_ENST00000396611.1_Splice_Site_p.W583del|PIK3R1_ENST00000523872.1_Splice_Site_p.W220del|PIK3R1_ENST00000320694.8_Splice_Site_p.W283del|PIK3R1_ENST00000521657.1_Splice_Site_p.W583del|PIK3R1_ENST00000274335.5_Splice_Site_p.W583del	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	583					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.M582_D605>I(4)|p.?(4)|p.Y580fs*1(1)|p.0?(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	CTGTTTTTCAGGTGGTTGACTCA	0.365			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																												uc003jva.2				Rec	yes		5	5q13.1	5295	Mis|F|O	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""			"""E, O"""			gliobastoma|ovarian|colorectal		10	Complex - deletion inframe(4)|Unknown(4)|Whole gene deletion(1)|Deletion - Frameshift(1)	p.M582_D605>I(4)|p.?(3)|p.Y580fs*1(1)	large_intestine(4)|ovary(2)|central_nervous_system(2)|lung(1)|breast(1)	endometrium(34)|central_nervous_system(27)|large_intestine(20)|breast(7)|ovary(5)|haematopoietic_and_lymphoid_tissue(3)|lung(2)|urinary_tract(1)|skin(1)|pancreas(1)	101						c.e14-1		phosphoinositide-3-kinase, regulatory subunit 1	Isoproterenol(DB01064)																																			SO:0001630	splice_region_variant	5295				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|growth hormone receptor signaling pathway|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|interspecies interaction between organisms|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol 3-kinase cascade|phosphatidylinositol phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of establishment of protein localization in plasma membrane|positive regulation of glucose import|T cell costimulation|T cell receptor signaling pathway	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex	1-phosphatidylinositol binding|ErbB-3 class receptor binding|insulin binding|insulin receptor binding|insulin receptor substrate binding|insulin-like growth factor receptor binding|phosphatidylinositol 3-kinase regulator activity|protein phosphatase binding	g.chr5:67591247_67591249delGGT	M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1746-1GGT>-	5.37:g.67591250_67591252delGGT		TCGA GBM(4;<1E-08)				PIK3R1_uc003jvb.2_Splice_Site_p.M582_splice|PIK3R1_uc003jvc.2_Splice_Site_p.M282_splice|PIK3R1_uc003jvd.2_Splice_Site_p.M312_splice|PIK3R1_uc003jve.2_Splice_Site_p.M261_splice|PIK3R1_uc011crb.1_Splice_Site_p.M252_splice	p.M582_splice	NM_181523	NP_852664	P27986	P85A_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	14	2306	+		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)						B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Splice_Site	DEL	ENST00000521381.1	37	c.1746_splice	CCDS3993.1																																																																																				0.365	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2	NM_181504	In_Frame_Del
CDK7	1022	broad.mit.edu	37	5	68555711	68555711	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr5:68555711G>A	ENST00000256443.3	+	7	578	c.475G>A	c.(475-477)Gcc>Acc	p.A159T	CDK7_ENST00000513629.1_Intron|CDK7_ENST00000502604.1_Missense_Mutation_p.A66T|CDK7_ENST00000514676.1_Missense_Mutation_p.A122T	NM_001799.3	NP_001790.1	P50613	CDK7_HUMAN	cyclin-dependent kinase 7	159	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				7-methylguanosine mRNA capping (GO:0006370)|androgen receptor signaling pathway (GO:0030521)|ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|cell division (GO:0051301)|cell proliferation (GO:0008283)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA-dependent ATPase activity (GO:0008094)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription coactivator activity (GO:0003713)			endometrium(1)|lung(2)	3		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)		TTTTGGCCTGGCCAAATCTTT	0.388								Nucleotide excision repair (NER)																														uc003jvs.3																			0				lung(1)	1						c.(475-477)GCC>ACC	NER	cyclin-dependent kinase 7							68.0	71.0	70.0					5																	68555711		2203	4300	6503	SO:0001583	missense	1022				androgen receptor signaling pathway|cell division|cell proliferation|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|G2/M transition of mitotic cell cycle|mRNA capping|nucleotide-excision repair, DNA damage removal|positive regulation of transcription from RNA polymerase II promoter|positive regulation of viral transcription|regulation of cyclin-dependent protein kinase activity|S phase of mitotic cell cycle|termination of RNA polymerase I transcription|transcription elongation from RNA polymerase I promoter|transcription elongation from RNA polymerase II promoter|transcription initiation from RNA polymerase I promoter|transcription initiation from RNA polymerase II promoter|transcription-coupled nucleotide-excision repair|viral reproduction	holo TFIIH complex|mitochondrion	androgen receptor binding|ATP binding|cyclin-dependent protein kinase activity|DNA-dependent ATPase activity|protein C-terminus binding|RNA polymerase II carboxy-terminal domain kinase activity|transcription coactivator activity	g.chr5:68555711G>A		CCDS3999.1	5q12.1	2012-11-05	2007-11-21		ENSG00000134058	ENSG00000134058		"""Cyclin-dependent kinases"", ""General transcription factor IIH complex subunits"""	1778	protein-coding gene	gene with protein product		601955	"""cyclin-dependent kinase 7 (homolog of Xenopus MO15 cdk-activating kinase)"", ""cyclin-dependent kinase 7 (MO15 homolog, Xenopus laevis, cdk-activating kinase)"""			8069918	Standard	NM_001799		Approved	CAK1, CDKN7, MO15, STK1, CAK	uc003jvs.4	P50613	OTTHUMG00000099358	ENST00000256443.3:c.475G>A	5.37:g.68555711G>A	ENSP00000256443:p.Ala159Thr					CDK7_uc003jvt.3_Missense_Mutation_p.A118T|CDK7_uc003jvu.3_Missense_Mutation_p.A66T	p.A159T	NM_001799	NP_001790	P50613	CDK7_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;2.98e-56)|Epithelial(20;3.54e-52)|all cancers(19;9.11e-48)|Lung(70;0.0185)	7	656	+		Lung NSC(167;7.26e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)	159			Protein kinase.		Q9BS60|Q9UE19	Missense_Mutation	SNP	ENST00000256443.3	37	c.475G>A	CCDS3999.1	.	.	.	.	.	.	.	.	.	.	G	35	5.591339	0.96590	.	.	ENSG00000134058	ENST00000506563;ENST00000256443;ENST00000514676;ENST00000502604	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	5.52	5.52	0.82312	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.84074	0.5392	M	0.90870	3.155	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87120	0.2190	10	0.87932	D	0	.	18.5748	0.91150	0.0:0.0:1.0:0.0	.	122;159	D6RAD4;P50613	.;CDK7_HUMAN	T	66;159;122;66	ENSP00000425043:A66T;ENSP00000256443:A159T;ENSP00000422737:A122T;ENSP00000422121:A66T	ENSP00000256443:A159T	A	+	1	0	CDK7	68591467	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.473000	0.97714	2.764000	0.94973	0.491000	0.48974	GCC		0.388	CDK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216802.3	NM_001799	
FAM13B	51306	broad.mit.edu	37	5	137275998	137275998	+	Silent	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr5:137275998C>T	ENST00000033079.3	-	23	3115	c.2664G>A	c.(2662-2664)gaG>gaA	p.E888E	PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000502810.1_3'UTR|FAM13B_ENST00000420893.2_Silent_p.E860E|PKD2L2_ENST00000290431.5_3'UTR|FAM13B_ENST00000425075.2_Silent_p.E764E|PKD2L2_ENST00000508638.1_3'UTR	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	888					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						ACTCTCTGTACTCCTCAAGCA	0.353																																						uc003lbz.2																			0					0						c.(2662-2664)GAG>GAA		hypothetical protein LOC51306 isoform 1							107.0	103.0	104.0					5																	137275998		2203	4300	6503	SO:0001819	synonymous_variant	51306				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr5:137275998C>T	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.2664G>A	5.37:g.137275998C>T						FAM13B_uc003lcb.2_Silent_p.E764E|FAM13B_uc003lca.2_Silent_p.E860E|PKD2L2_uc003lbw.1_3'UTR|PKD2L2_uc003lbx.2_3'UTR|PKD2L2_uc003lby.2_Intron|PKD2L2_uc011cyi.1_3'UTR	p.E888E	NM_016603	NP_057687	Q9NYF5	FA13B_HUMAN			23	3198	-			888					D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Silent	SNP	ENST00000033079.3	37	c.2664G>A	CCDS4195.1																																																																																				0.353	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
PREP	5550	broad.mit.edu	37	6	105800946	105800946	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr6:105800946C>T	ENST00000369110.3	-	7	916	c.724G>A	c.(724-726)Gat>Aat	p.D242N		NM_002726.4	NP_002717.3	P48147	PPCE_HUMAN	prolyl endopeptidase	242					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(2)|large_intestine(7)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)			Oxytocin(DB00107)	CGGCCATCATCAGATAACTAA	0.353																																						uc003prc.2																			0				ovary(3)	3						c.(724-726)GAT>AAT		prolyl endopeptidase	Oxytocin(DB00107)						111.0	116.0	115.0					6																	105800946		2203	4300	6503	SO:0001583	missense	5550				proteolysis		serine-type endopeptidase activity	g.chr6:105800946C>T		CCDS5053.1	6q22	2008-02-05			ENSG00000085377	ENSG00000085377	3.4.21.26		9358	protein-coding gene	gene with protein product		600400				7959018	Standard	NM_002726		Approved		uc003prc.3	P48147	OTTHUMG00000015297	ENST00000369110.3:c.724G>A	6.37:g.105800946C>T	ENSP00000358106:p.Asp242Asn						p.D242N	NM_002726	NP_002717	P48147	PPCE_HUMAN			7	927	-		all_cancers(87;0.000128)|Acute lymphoblastic leukemia(125;1.9e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0344)|Lung NSC(302;0.191)|Colorectal(196;0.202)	242					Q8N6D4	Missense_Mutation	SNP	ENST00000369110.3	37	c.724G>A	CCDS5053.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621367	0.66787	.	.	ENSG00000085377	ENST00000369110	T	0.42900	0.96	5.56	4.68	0.58851	Peptidase S9A, oligopeptidase, N-terminal (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.124969	0.64402	D	0.000001	T	0.37919	0.1021	M	0.77406	2.37	0.54753	D	0.999982	B	0.33022	0.394	B	0.38225	0.268	T	0.42716	-0.9435	10	0.56958	D	0.05	-29.3639	13.1292	0.59371	0.0:0.9212:0.0:0.0788	.	242	P48147	PPCE_HUMAN	N	242	ENSP00000358106:D242N	ENSP00000358106:D242N	D	-	1	0	PREP	105907639	0.999000	0.42202	0.955000	0.39395	0.896000	0.52359	4.630000	0.61297	2.775000	0.95449	0.655000	0.94253	GAT		0.353	PREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041658.1		
SLC29A4	222962	broad.mit.edu	37	7	5340251	5340251	+	Silent	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr7:5340251C>T	ENST00000396872.3	+	10	1569	c.1408C>T	c.(1408-1410)Ctg>Ttg	p.L470L	SLC29A4_ENST00000297195.4_Silent_p.L470L|SLC29A4_ENST00000439491.2_3'UTR|SLC29A4_ENST00000406453.3_Silent_p.L456L			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	470					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	GCCCATGATCCTGGCGGCAGG	0.706																																						uc003sod.2																			0				liver(1)	1						c.(1408-1410)CTG>TTG		solute carrier family 29 (nucleoside							50.0	48.0	49.0					7																	5340251		2203	4300	6503	SO:0001819	synonymous_variant	222962				nucleobase, nucleoside and nucleotide metabolic process	apical plasma membrane|integral to membrane	nucleoside transmembrane transporter activity	g.chr7:5340251C>T	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"""Solute carriers"""	23097	protein-coding gene	gene with protein product		609149	"""solute carrier family 29 (nucleoside transporters), member 4"""			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.1408C>T	7.37:g.5340251C>T						SLC29A4_uc003soc.2_Silent_p.L470L|SLC29A4_uc003soe.2_Silent_p.L456L|SLC29A4_uc010ksw.2_Intron	p.L470L	NM_153247	NP_694979	Q7RTT9	S29A4_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	10	1569	+		Ovarian(82;0.0175)	470			Helical; (Potential).		Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	c.1408C>T	CCDS5340.1																																																																																				0.706	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247	
DNAH11	8701	broad.mit.edu	37	7	21641054	21641054	+	Missense_Mutation	SNP	G	G	A	rs183521702	byFrequency	TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr7:21641054G>A	ENST00000409508.3	+	18	3497	c.3466G>A	c.(3466-3468)Gga>Aga	p.G1156R	DNAH11_ENST00000328843.6_Missense_Mutation_p.G1156R	NM_001277115.1	NP_001264044.1	Q96DT5	DYH11_HUMAN	dynein, axonemal, heavy chain 11	1156	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(13)|central_nervous_system(3)|cervix(4)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(50)|lung(101)|ovary(10)|pancreas(4)|prostate(7)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	230						GACAGATTCCGGACTTCAGAG	0.343									Kartagener syndrome				G|||	5	0.000998403	0.0038	0.0	5008	,	,		18088	0.0		0.0	False		,,,				2504	0.0					uc003svc.2																			0				ovary(8)|large_intestine(3)|pancreas(3)|central_nervous_system(1)	15						c.(3466-3468)GGA>AGA		dynein, axonemal, heavy chain 11		G	ARG/GLY	21,3613		0,21,1796	80.0	79.0	79.0		3466	5.7	1.0	7		79	1,8155		0,1,4077	yes	missense	DNAH11	NM_003777.3	125	0,22,5873	AA,AG,GG		0.0123,0.5779,0.1866	possibly-damaging	1156/4524	21641054	22,11768	1817	4078	5895	SO:0001583	missense	8701	Kartagener_syndrome	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	microtubule-based movement	axonemal dynein complex|cilium axoneme|cytoplasm|microtubule	ATP binding|ATPase activity|microtubule motor activity	g.chr7:21641054G>A	U83569	CCDS64602.1	7p21	2008-07-18	2006-09-04					"""Axonemal dyneins"""	2942	protein-coding gene	gene with protein product	"""dynein, ciliary, heavy chain 11"", ""dynein, heavy chain beta-like"""	603339	"""dynein, axonemal, heavy polypeptide 11"""			9256245	Standard	NM_001277115		Approved	Dnahc11, DPL11, CILD7, DNAHC11, DNAHBL, DNHBL	uc031swp.1	Q96DT5		ENST00000409508.3:c.3466G>A	7.37:g.21641054G>A	ENSP00000475939:p.Gly1156Arg						p.G1156R	NM_003777	NP_003768	Q96DT5	DYH11_HUMAN			18	3497	+			1156			Stem (By similarity).		Q9UJ82	Missense_Mutation	SNP	ENST00000409508.3	37	c.3466G>A		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.57	2.873196	0.51695	0.005779	1.23E-4	ENSG00000105877	ENST00000328843	T	0.23147	1.92	5.7	5.7	0.88788	.	0.058880	0.64402	D	0.000002	T	0.11537	0.0281	.	.	.	0.49687	D	0.999819	P	0.38788	0.647	B	0.30495	0.116	T	0.05767	-1.0865	9	0.23302	T	0.38	.	12.7537	0.57321	0.0753:0.0:0.9247:0.0	.	1156	Q96DT5	DYH11_HUMAN	R	1156	ENSP00000330671:G1156R	ENSP00000330671:G1156R	G	+	1	0	DNAH11	21607579	1.000000	0.71417	0.957000	0.39632	0.598000	0.36846	6.313000	0.72844	2.705000	0.92388	0.650000	0.86243	GGA		0.343	DNAH11-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000326582.6	NM_003777	
EGFR	1956	broad.mit.edu	37	7	55220278	55220278	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr7:55220278G>A	ENST00000275493.2	+	6	845	c.668G>A	c.(667-669)tGc>tAc	p.C223Y	EGFR_ENST00000342916.3_Missense_Mutation_p.C223Y|EGFR_ENST00000454757.2_Missense_Mutation_p.C170Y|EGFR_ENST00000455089.1_Missense_Mutation_p.C178Y|EGFR_ENST00000442591.1_Missense_Mutation_p.C223Y|EGFR_ENST00000344576.2_Missense_Mutation_p.C223Y|EGFR_ENST00000420316.2_Missense_Mutation_p.C223Y	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	223			Missing (variant EGFR vIII; found in a lung cancer sample; somatic mutation; induces lung cancer when exogenously expressed). {ECO:0000269|PubMed:16672372}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCCGGGCGCTGCCGTGGCAAG	0.602		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	A|O|Mis	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	glioma|NSCLC		0		p.V30_R297>G(5)		lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(667-669)TGC>TAC		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						84.0	96.0	92.0					7																	55220278		2203	4300	6503	SO:0001583	missense	1956	Lung_Cancer_Familial_Clustering_of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55220278G>A		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.668G>A	7.37:g.55220278G>A	ENSP00000275493:p.Cys223Tyr	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc003tqh.2_Missense_Mutation_p.C223Y|EGFR_uc003tqi.2_Missense_Mutation_p.C223Y|EGFR_uc003tqj.2_Missense_Mutation_p.C223Y|EGFR_uc010kzg.1_Missense_Mutation_p.C178Y|EGFR_uc011kco.1_Missense_Mutation_p.C170Y|EGFR_uc003tql.1_RNA	p.C223Y	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		6	914	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		223			Approximate.|Extracellular (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.668G>A	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.783058	0.90282	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	D;D;D;D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18;-3.18;-3.18;-3.18	5.3	5.3	0.74995	Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	0.000000	0.85682	D	0.000000	D	0.97216	0.9090	M	0.88979	2.995	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.998;1.0;1.0;1.0;1.0	D	0.97976	1.0346	10	0.87932	D	0	.	17.5084	0.87753	0.0:0.0:1.0:0.0	.	178;223;223;223;223	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	Y	178;223;93;223;223;223;223;170;17	ENSP00000415559:C178Y;ENSP00000342376:C223Y;ENSP00000345973:C223Y;ENSP00000413843:C223Y;ENSP00000275493:C223Y;ENSP00000410031:C223Y;ENSP00000395243:C170Y	ENSP00000275493:C223Y	C	+	2	0	EGFR	55187772	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	9.778000	0.99011	2.448000	0.82819	0.655000	0.94253	TGC		0.602	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
EGFR	1956	broad.mit.edu	37	7	55238870	55238870	+	Missense_Mutation	SNP	G	G	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr7:55238870G>T	ENST00000275493.2	+	16	2060	c.1883G>T	c.(1882-1884)tGc>tTc	p.C628F	EGFR_ENST00000454757.2_Missense_Mutation_p.C575F|EGFR_ENST00000455089.1_Missense_Mutation_p.C583F|EGFR_ENST00000442591.1_Missense_Mutation_p.C628F	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	628					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCCTACAGATGCACTGGGCCA	0.393		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	A|O|Mis	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	glioma|NSCLC		0				lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(1882-1884)TGC>TTC		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						134.0	119.0	124.0					7																	55238870		2203	4300	6503	SO:0001583	missense	1956	Lung_Cancer_Familial_Clustering_of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55238870G>T		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1883G>T	7.37:g.55238870G>T	ENSP00000275493:p.Cys628Phe	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc010kzg.1_Missense_Mutation_p.C583F|EGFR_uc011kco.1_Missense_Mutation_p.C575F|EGFR_uc011kcp.1_RNA|EGFR_uc011kcq.1_RNA	p.C628F	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		16	2129	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		628			Extracellular (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.1883G>T	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996769	0.54147	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.54	5.54	0.83059	Growth factor, receptor (1);	0.087063	0.85682	D	0.000000	T	0.78991	0.4371	H	0.97635	4.045	0.80722	D	1	D;D	0.59767	0.986;0.969	P;P	0.55455	0.746;0.776	D	0.86469	0.1784	10	0.87932	D	0	.	16.5484	0.84457	0.0:0.0:1.0:0.0	.	583;628	Q504U8;P00533	.;EGFR_HUMAN	F	583;498;628;628;575;422	ENSP00000415559:C583F;ENSP00000275493:C628F;ENSP00000410031:C628F;ENSP00000395243:C575F	ENSP00000275493:C628F	C	+	2	0	EGFR	55206364	1.000000	0.71417	0.970000	0.41538	0.066000	0.16364	7.285000	0.78660	2.768000	0.95171	0.561000	0.74099	TGC		0.393	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
POM121C	100101267	broad.mit.edu	37	7	75068439	75068439	+	Silent	SNP	G	G	T	rs587689353		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr7:75068439G>T	ENST00000257665.5	-	4	1016	c.1017C>A	c.(1015-1017)ccC>ccA	p.P339P	POM121C_ENST00000453279.2_Silent_p.P97P|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	339	Pore side. {ECO:0000255}.|Required for targeting to the nucleus and nuclear pore complex.|Ser-rich.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						CAAAAGAAGCGGGGACTCCAC	0.468																																						uc010lde.1																			0					0						c.(1015-1017)CCC>CCA		Homo sapiens POM121-2 mRNA for nuclear pore membrane protein 121-2, partial cds.							168.0	167.0	167.0					7																	75068439		2203	4300	6503	SO:0001819	synonymous_variant	100101267				mRNA transport|protein transport|transmembrane transport	endoplasmic reticulum membrane|nuclear membrane|nuclear pore	protein binding	g.chr7:75068439G>T		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"""POM121 membrane glycoprotein C"""			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.1017C>A	7.37:g.75068439G>T						POM121C_uc003udk.3_Silent_p.P97P	p.P339P			A8CG34	P121C_HUMAN			4	1017	-			339			Required for targeting to the nucleus and nuclear pore complex.|Pore side (Potential).|Ser-rich.		O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37	c.1017C>A																																																																																					0.468	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415	
MYOM2	9172	broad.mit.edu	37	8	2005570	2005570	+	Missense_Mutation	SNP	G	G	A	rs147661043		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr8:2005570G>A	ENST00000262113.4	+	4	509	c.368G>A	c.(367-369)cGc>cAc	p.R123H	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	123					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R123H(2)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TCCCAGGCCCGCGACAAGCTG	0.617																																						uc003wpx.3																			2	Substitution - Missense(2)		large_intestine(1)|endometrium(1)	ovary(4)|central_nervous_system(1)|skin(1)	6						c.(367-369)CGC>CAC		myomesin 2							29.0	30.0	30.0					8																	2005570		2203	4300	6503	SO:0001583	missense	9172				muscle contraction	myosin filament	structural constituent of muscle	g.chr8:2005570G>A		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.368G>A	8.37:g.2005570G>A	ENSP00000262113:p.Arg123His					MYOM2_uc011kwi.1_Intron	p.R123H	NM_003970	NP_003961	P54296	MYOM2_HUMAN		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)	4	506	+		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)	123					Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	c.368G>A	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	G	11.45	1.641288	0.29157	.	.	ENSG00000036448	ENST00000262113	T	0.56611	0.45	4.71	-0.21	0.13176	.	0.326897	0.26792	N	0.022472	T	0.47544	0.1451	M	0.63843	1.955	0.09310	N	1	P	0.43662	0.814	B	0.41374	0.355	T	0.46992	-0.9151	10	0.72032	D	0.01	.	10.4822	0.44700	0.1944:0.0:0.8056:0.0	.	123	P54296	MYOM2_HUMAN	H	123	ENSP00000262113:R123H	ENSP00000262113:R123H	R	+	2	0	MYOM2	1992977	0.034000	0.19679	0.000000	0.03702	0.015000	0.08874	0.763000	0.26517	-0.346000	0.08312	-0.258000	0.10820	CGC		0.617	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
CHRNB3	1142	broad.mit.edu	37	8	42587374	42587374	+	Silent	SNP	C	C	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr8:42587374C>A	ENST00000289957.2	+	5	1052	c.924C>A	c.(922-924)acC>acA	p.T308T		NM_000749.3	NP_000740.1	Q05901	ACHB3_HUMAN	cholinergic receptor, nicotinic, beta 3 (neuronal)	308					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|drug binding (GO:0008144)			endometrium(4)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	25	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		Galantamine(DB00674)|Nicotine(DB00184)	TTTTTGTGACCCTGTCCATCA	0.448																																						uc003xpi.1																			0				ovary(1)	1						c.(922-924)ACC>ACA		cholinergic receptor, nicotinic, beta							311.0	269.0	283.0					8																	42587374		2203	4300	6503	SO:0001819	synonymous_variant	1142				synaptic transmission, cholinergic	cell junction|nicotinic acetylcholine-gated receptor-channel complex|postsynaptic membrane	nicotinic acetylcholine-activated cation-selective channel activity|receptor activity	g.chr8:42587374C>A	U62438	CCDS6134.1	8p11.21	2012-02-11	2012-02-07		ENSG00000147432	ENSG00000147432		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1963	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 3 (neuronal)"""	118508	"""cholinergic receptor, nicotinic, beta polypeptide 3"""			1505988	Standard	NM_000749		Approved		uc003xpi.1	Q05901	OTTHUMG00000165262	ENST00000289957.2:c.924C>A	8.37:g.42587374C>A							p.T308T	NM_000749	NP_000740	Q05901	ACHB3_HUMAN	Lung(22;0.0199)|LUSC - Lung squamous cell carcinoma(45;0.0869)		5	1052	+	all_lung(13;5.7e-12)|Lung NSC(13;1.6e-10)|Ovarian(28;0.00579)|Prostate(17;0.0119)|Lung SC(25;0.184)	all_lung(54;0.00026)|Lung NSC(58;0.000992)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.0954)	308			Helical; (Potential).		Q15827	Silent	SNP	ENST00000289957.2	37	c.924C>A	CCDS6134.1																																																																																				0.448	CHRNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383055.1		
KCNV1	27012	broad.mit.edu	37	8	110984560	110984560	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr8:110984560G>A	ENST00000524391.1	-	3	1950	c.918C>T	c.(916-918)aaC>aaT	p.N306N	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Silent_p.N306N			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	306					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			TGCGCCCCACGTTCTCCAGCT	0.532																																						uc003ynr.3																			0				lung(1)|kidney(1)	2						c.(916-918)AAC>AAT		potassium channel, subfamily V, member 1							92.0	77.0	82.0					8																	110984560		2203	4300	6503	SO:0001819	synonymous_variant	27012					voltage-gated potassium channel complex	ion channel inhibitor activity|potassium channel regulator activity|voltage-gated potassium channel activity	g.chr8:110984560G>A	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.918C>T	8.37:g.110984560G>A						KCNV1_uc010mcw.2_Silent_p.N306N	p.N306N	NM_014379	NP_055194	Q6PIU1	KCNV1_HUMAN	OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)		2	1260	-	all_neural(195;0.219)		306			Extracellular (Potential).		Q9UHJ4	Silent	SNP	ENST00000524391.1	37	c.918C>T	CCDS6314.1																																																																																				0.532	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379	
GCNT1	2650	broad.mit.edu	37	9	79117571	79117571	+	Missense_Mutation	SNP	G	G	A	rs368814183		TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chr9:79117571G>A	ENST00000376730.4	+	4	757	c.274G>A	c.(274-276)Gac>Aac	p.D92N	GCNT1_ENST00000536223.1_Missense_Mutation_p.D92N|GCNT1_ENST00000442371.1_Missense_Mutation_p.D92N|GCNT1_ENST00000444201.2_Missense_Mutation_p.D92N	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	92	Stem region. {ECO:0000250}.				cell adhesion molecule production (GO:0060352)|cellular protein metabolic process (GO:0044267)|glycoprotein biosynthetic process (GO:0009101)|kidney morphogenesis (GO:0060993)|leukocyte tethering or rolling (GO:0050901)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to insulin (GO:0032868)|tissue morphogenesis (GO:0048729)	extracellular space (GO:0005615)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(6)|lung(11)|prostate(2)|urinary_tract(1)	30						GACACCTGACGACTATATAAA	0.393																																						uc010mpf.2																			0					0						c.(274-276)GAC>AAC		beta-1,3-galactosyl-O-glycosyl-glycoprotein		A	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	0,4406		0,0,2203	105.0	110.0	108.0		274,274,274,274,274	4.0	0.7	9		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	23,23,23,23,23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	92/429,92/429,92/429,92/429,92/429	79117571	1,13005	2203	4300	6503	SO:0001583	missense	2650				protein O-linked glycosylation	Golgi membrane|integral to membrane	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity	g.chr9:79117571G>A	L41415	CCDS6653.1	9q13	2013-02-25	2010-03-16		ENSG00000187210	ENSG00000187210	2.4.1.102	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4203	protein-coding gene	gene with protein product	"""core 2 beta1,6 N-acetylglucosaminyltransferase-I"", ""beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N--acetylglucosaminyltransferase"""	600391	"""glucosaminyl (N-acetyl) transferase 1, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"""	NACGT2		8449405, 9915862	Standard	NM_001490		Approved	C2GNT, NAGCT2	uc004akf.4	Q02742	OTTHUMG00000020044	ENST00000376730.4:c.274G>A	9.37:g.79117571G>A	ENSP00000365920:p.Asp92Asn					GCNT1_uc010mpg.2_Missense_Mutation_p.D92N|GCNT1_uc010mph.2_Missense_Mutation_p.D92N|GCNT1_uc004akf.3_Missense_Mutation_p.D92N|GCNT1_uc010mpi.2_Missense_Mutation_p.D92N|GCNT1_uc004akh.3_Missense_Mutation_p.D92N	p.D92N	NM_001490	NP_001481	Q02742	GCNT1_HUMAN			3	615	+			92			Lumenal (Potential).|Stem region (By similarity).		Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	c.274G>A	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	g	9.809	1.182515	0.21870	0.0	1.16E-4	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.84	4.03	0.46877	.	0.108515	0.64402	N	0.000007	T	0.49864	0.1582	M	0.80183	2.485	0.32525	N	0.535763	P	0.45672	0.864	B	0.39771	0.309	T	0.65401	-0.6177	9	.	.	.	.	12.8565	0.57888	0.1317:0.0:0.8683:0.0	.	92	Q02742	GCNT1_HUMAN	N	92	ENSP00000440883:D92N;ENSP00000415454:D92N;ENSP00000390703:D92N;ENSP00000365920:D92N	.	D	+	1	0	GCNT1	78307391	1.000000	0.71417	0.672000	0.29872	0.038000	0.13279	5.334000	0.65923	0.837000	0.34925	-0.127000	0.14921	GAC		0.393	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634	
FAM47B	170062	broad.mit.edu	37	X	34962542	34962542	+	Missense_Mutation	SNP	C	C	T			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:34962542C>T	ENST00000329357.5	+	1	1630	c.1594C>T	c.(1594-1596)Cgc>Tgc	p.R532C		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	532								p.R532C(2)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						GGACAGGAGACGCCGGGCGGC	0.498																																						uc004ddi.1																			2	Substitution - Missense(2)		large_intestine(1)|endometrium(1)	ovary(3)|breast(1)	4						c.(1594-1596)CGC>TGC		hypothetical protein LOC170062							94.0	84.0	87.0					X																	34962542		2202	4300	6502	SO:0001583	missense	170062							g.chrX:34962542C>T	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.1594C>T	X.37:g.34962542C>T	ENSP00000328307:p.Arg532Cys						p.R532C	NM_152631	NP_689844	Q8NA70	FA47B_HUMAN			1	1612	+			532					Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	c.1594C>T	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	5.656	0.305749	0.10733	.	.	ENSG00000189132	ENST00000329357	T	0.41758	0.99	0.602	0.602	0.17535	.	.	.	.	.	T	0.18718	0.0449	N	0.14661	0.345	0.09310	N	1	P	0.36768	0.569	B	0.14023	0.01	T	0.11179	-1.0598	8	0.72032	D	0.01	.	.	.	.	.	532	Q8NA70	FA47B_HUMAN	C	532	ENSP00000328307:R532C	ENSP00000328307:R532C	R	+	1	0	FAM47B	34872463	0.002000	0.14202	0.003000	0.11579	0.002000	0.02628	0.279000	0.18771	0.543000	0.28864	0.292000	0.19580	CGC		0.498	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
WNK3	65267	broad.mit.edu	37	X	54319681	54319681	+	Silent	SNP	T	T	C			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:54319681T>C	ENST00000375159.2	-	8	1772	c.1773A>G	c.(1771-1773)tcA>tcG	p.S591S	WNK3_ENST00000375169.3_Silent_p.S591S|WNK3_ENST00000354646.2_Silent_p.S591S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	591					intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of ion transmembrane transporter activity (GO:0032414)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of rubidium ion transmembrane transporter activity (GO:2000688)|positive regulation of rubidium ion transport (GO:2000682)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(24)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80						TCGTTTGATTTGAGGAATAGG	0.398																																						uc004dtd.1																			0				lung(4)|ovary(3)|kidney(2)|central_nervous_system(2)	11						c.(1771-1773)TCA>TCG		WNK lysine deficient protein kinase 3 isoform 2							92.0	82.0	85.0					X																	54319681		2203	4300	6503	SO:0001819	synonymous_variant	65267				intracellular protein kinase cascade|positive regulation of establishment of protein localization in plasma membrane|positive regulation of peptidyl-threonine phosphorylation|positive regulation of rubidium ion transmembrane transporter activity|positive regulation of rubidium ion transport|positive regulation of sodium ion transmembrane transporter activity|positive regulation of sodium ion transport|protein autophosphorylation	adherens junction|tight junction	ATP binding|protein binding|protein serine/threonine kinase activity|rubidium ion transmembrane transporter activity|sodium ion transmembrane transporter activity	g.chrX:54319681T>C	AJ409088	CCDS14357.1, CCDS35302.1	Xp11.22	2008-05-14	2005-01-19	2005-01-22	ENSG00000196632	ENSG00000196632			14543	protein-coding gene	gene with protein product		300358	"""protein kinase, lysine deficient 3"""	PRKWNK3			Standard	NM_020922		Approved		uc004dtc.2	Q9BYP7	OTTHUMG00000021626	ENST00000375159.2:c.1773A>G	X.37:g.54319681T>C						WNK3_uc004dtc.1_Silent_p.S591S	p.S591S	NM_001002838	NP_001002838	Q9BYP7	WNK3_HUMAN			9	2212	-			591					B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Silent	SNP	ENST00000375159.2	37	c.1773A>G	CCDS14357.1																																																																																				0.398	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922	
LAS1L	81887	broad.mit.edu	37	X	64744052	64744052	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:64744052G>A	ENST00000374811.3	-	10	1224	c.1184C>T	c.(1183-1185)aCg>aTg	p.T395M	LAS1L_ENST00000312391.8_3'UTR|LAS1L_ENST00000374807.5_Missense_Mutation_p.T378M|LAS1L_ENST00000374804.5_Missense_Mutation_p.T336M	NM_031206.4	NP_112483.1	Q9Y4W2	LAS1L_HUMAN	LAS1-like (S. cerevisiae)	395					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(3)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	33						TAGGGCCTGCGTGAAGTTCTG	0.567																																						uc004dwa.1																			0		p.T395T(1)		ovary(3)|large_intestine(1)	4						c.(1183-1185)ACG>ATG		LAS1-like							43.0	37.0	39.0					X																	64744052		2203	4300	6503	SO:0001583	missense	81887					MLL1 complex|nucleolus	protein binding	g.chrX:64744052G>A	BC014545	CCDS14381.1, CCDS55433.1, CCDS55434.1	Xq12	2008-02-05			ENSG00000001497	ENSG00000001497			25726	protein-coding gene	gene with protein product						12477932	Standard	NM_031206		Approved	FLJ12525	uc004dwa.2	Q9Y4W2	OTTHUMG00000021720	ENST00000374811.3:c.1184C>T	X.37:g.64744052G>A	ENSP00000363944:p.Thr395Met					LAS1L_uc004dwc.1_Missense_Mutation_p.T378M|LAS1L_uc004dwd.1_Missense_Mutation_p.T336M	p.T395M	NM_031206	NP_112483	Q9Y4W2	LAS1L_HUMAN			10	1256	-			395					A9X410|Q5JXQ0|Q8TEN5|Q9H9V5	Missense_Mutation	SNP	ENST00000374811.3	37	c.1184C>T	CCDS14381.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.454962	0.26161	.	.	ENSG00000001497	ENST00000374807;ENST00000374811;ENST00000374804	.	.	.	4.55	3.45	0.39498	.	0.256321	0.37437	N	0.002093	T	0.65302	0.2678	L	0.55481	1.735	0.80722	D	1	D;B;B	0.89917	1.0;0.362;0.205	D;B;B	0.71870	0.975;0.094;0.015	T	0.63193	-0.6692	9	0.37606	T	0.19	.	7.6283	0.28224	0.1479:0.0:0.8521:0.0	.	336;378;395	Q9Y4W2-3;Q9Y4W2-2;Q9Y4W2	.;.;LAS1L_HUMAN	M	378;395;336	.	ENSP00000363937:T336M	T	-	2	0	LAS1L	64660777	0.989000	0.36119	0.998000	0.56505	0.970000	0.65996	2.088000	0.41663	1.875000	0.54330	0.287000	0.19450	ACG		0.567	LAS1L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056974.1	NM_031206	
BTK	695	broad.mit.edu	37	X	100611220	100611220	+	Silent	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:100611220G>A	ENST00000308731.7	-	15	1549	c.1386C>T	c.(1384-1386)ggC>ggT	p.G462G	BTK_ENST00000372880.1_Intron	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	462	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		G -> D (in XLA).|G -> V (in XLA).		adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						TGGTGCAGACGCCATACAACT	0.522									Agammaglobulinemia, X-linked																													uc004ehg.2																			0				lung(3)|central_nervous_system(2)|ovary(1)	6						c.(1384-1386)GGC>GGT		Bruton agammaglobulinemia tyrosine kinase							59.0	48.0	52.0					X																	100611220		2203	4300	6503	SO:0001819	synonymous_variant	695	Agammaglobulinemia_X-linked	Familial Cancer Database	Bruton Type Agammaglobulinemia	calcium-mediated signaling|induction of apoptosis by extracellular signals|mesoderm development	cytosol|membrane raft|nucleus|plasma membrane	ATP binding|identical protein binding|metal ion binding|non-membrane spanning protein tyrosine kinase activity|phosphatidylinositol-3,4,5-trisphosphate binding	g.chrX:100611220G>A	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1386C>T	X.37:g.100611220G>A						BTK_uc004ehf.2_Intron|BTK_uc010nnh.2_Intron|BTK_uc010nni.2_Intron|BTK_uc004ehe.2_Intron|BTK_uc010nnj.2_RNA|BTK_uc010nnk.2_Intron|BTK_uc010nnl.2_Intron|BTK_uc010nnm.2_Silent_p.G32G|BTK_uc010nnn.2_Intron|BTK_uc010nno.2_Silent_p.G496G|BTK_uc004ehh.1_Intron|BTK_uc004ehi.2_Silent_p.G462G	p.G462G	NM_000061	NP_000052	Q06187	BTK_HUMAN			15	1579	-			462		G -> D (in XLA).|G -> V (in XLA).	Protein kinase.		B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	c.1386C>T	CCDS14482.1																																																																																				0.522	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
SOX3	6658	broad.mit.edu	37	X	139586734	139586734	+	Missense_Mutation	SNP	C	C	G			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:139586734C>G	ENST00000370536.2	-	1	491	c.492G>C	c.(490-492)atG>atC	p.M164I		NM_005634.2	NP_005625.2	P41225	SOX3_HUMAN	SRY (sex determining region Y)-box 3	164					central nervous system development (GO:0007417)|face development (GO:0060324)|hypothalamus development (GO:0021854)|negative regulation of neuron differentiation (GO:0045665)|neuron development (GO:0048666)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|sensory organ development (GO:0007423)|Sertoli cell development (GO:0060009)|sex determination (GO:0007530)|spermatid differentiation (GO:0048515)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|pancreas(1)|skin(1)	10	Acute lymphoblastic leukemia(192;7.65e-05)					CAGAATTGTGCATCTTGGGGT	0.622																																						uc004fbd.1																			0				pancreas(1)	1						c.(490-492)ATG>ATC		SRY (sex determining region Y)-box 3							65.0	64.0	64.0					X																	139586734		2203	4300	6503	SO:0001583	missense	6658				face development|hypothalamus development|negative regulation of neuron differentiation|pituitary gland development|regulation of transcription, DNA-dependent|sensory organ development|sex determination|transcription, DNA-dependent	nucleus	DNA binding	g.chrX:139586734C>G		CCDS14669.1	Xq27.1	2013-10-17			ENSG00000134595	ENSG00000134595		"""SRY (sex determining region Y)-boxes"""	11199	protein-coding gene	gene with protein product		313430	"""panhypopituitarism"""	PHP		15800844	Standard	NM_005634		Approved		uc004fbd.1	P41225	OTTHUMG00000022544	ENST00000370536.2:c.492G>C	X.37:g.139586734C>G	ENSP00000359567:p.Met164Ile						p.M164I	NM_005634	NP_005625	P41225	SOX3_HUMAN			1	492	-	Acute lymphoblastic leukemia(192;7.65e-05)		164			HMG box.		P35714|Q5JWI3|Q9NP49	Missense_Mutation	SNP	ENST00000370536.2	37	c.492G>C	CCDS14669.1	.	.	.	.	.	.	.	.	.	.	c	21.7	4.191916	0.78902	.	.	ENSG00000134595	ENST00000370536	D	0.97710	-4.5	4.12	4.12	0.48240	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	0.000000	0.85682	U	0.000000	D	0.98112	0.9377	M	0.63169	1.94	0.80722	D	1	D	0.65815	0.995	D	0.74023	0.982	D	0.98196	1.0465	9	.	.	.	.	14.7169	0.69275	0.0:1.0:0.0:0.0	.	164	P41225	SOX3_HUMAN	I	164	ENSP00000359567:M164I	.	M	-	3	0	SOX3	139414400	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.231000	0.78106	1.638000	0.50547	0.525000	0.51046	ATG		0.622	SOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058577.1		
PNMA5	114824	broad.mit.edu	37	X	152159506	152159506	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:152159506G>A	ENST00000439251.1	-	2	1075	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W	PNMA5_ENST00000361887.5_Missense_Mutation_p.R213W|PNMA5_ENST00000535214.1_Missense_Mutation_p.R213W|PNMA5_ENST00000452693.1_Missense_Mutation_p.R213W	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	213					positive regulation of apoptotic process (GO:0043065)					breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					TGGAGCACCCGCATGATTGAC	0.527																																						uc010ntw.2																			0				ovary(1)|skin(1)	2						c.(637-639)CGG>TGG		paraneoplastic antigen like 5							76.0	71.0	73.0					X																	152159506		2203	4300	6503	SO:0001583	missense	114824				apoptosis			g.chrX:152159506G>A	AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"""Paraneoplastic Ma antigens"""	18743	protein-coding gene	gene with protein product	"""paraneoplastic antigen family 5"""	300916	"""paraneoplastic antigen like 5"""			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.637C>T	X.37:g.152159506G>A	ENSP00000388850:p.Arg213Trp					PNMA5_uc004fha.3_Missense_Mutation_p.R213W|PNMA5_uc010ntx.2_Missense_Mutation_p.R213W|PNMA5_uc004fgy.3_Missense_Mutation_p.R213W	p.R213W	NM_001103151	NP_001096621	Q96PV4	PNMA5_HUMAN			3	976	-	Acute lymphoblastic leukemia(192;6.56e-05)		213					B4DI72|B7Z9Y9|Q495L5|Q8NET3	Missense_Mutation	SNP	ENST00000439251.1	37	c.637C>T	CCDS14718.1	.	.	.	.	.	.	.	.	.	.	G	14.61	2.586277	0.46110	.	.	ENSG00000198883	ENST00000361887;ENST00000535214;ENST00000439251;ENST00000452693	T;T;T;T	0.11821	2.74;2.74;2.74;2.74	3.31	0.12	0.14691	.	.	.	.	.	T	0.23572	0.0570	M	0.67397	2.05	0.09310	N	1	D	0.89917	1.0	D	0.66084	0.941	T	0.15954	-1.0419	9	0.30078	T	0.28	.	1.0492	0.01576	0.1528:0.2187:0.402:0.2266	.	213	Q96PV4	PNMA5_HUMAN	W	213	ENSP00000354834:R213W;ENSP00000445775:R213W;ENSP00000388850:R213W;ENSP00000392342:R213W	ENSP00000354834:R213W	R	-	1	2	PNMA5	151910162	0.000000	0.05858	0.000000	0.03702	0.261000	0.26267	-0.167000	0.09940	-0.076000	0.12775	-0.542000	0.04241	CGG		0.527	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1	NM_052926	
F8	2157	broad.mit.edu	37	X	154185438	154185438	+	Missense_Mutation	SNP	G	G	A			TCGA-26-5139-01A-01D-1486-08	TCGA-26-5139-10A-01D-1486-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	8199001b-a3c9-47e1-97cf-943fa8030f46	0be951d5-b639-4125-996c-c1245d7750ee	g.chrX:154185438G>A	ENST00000360256.4	-	11	1746	c.1546C>T	c.(1546-1548)Cat>Tat	p.H516Y		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	516	F5/8 type A 2.|Plastocyanin-like 3.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TCCTTCAAATGTTTTACACCT	0.378																																						uc004fmt.2																			0				ovary(5)|large_intestine(2)|pancreas(2)|upper_aerodigestive_tract(1)|skin(1)	11						c.(1546-1548)CAT>TAT		coagulation factor VIII isoform a precursor	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)						107.0	102.0	103.0					X																	154185438		2203	4300	6503	SO:0001583	missense	2157				acute-phase response|blood coagulation, intrinsic pathway|cell adhesion|platelet activation|platelet degranulation	extracellular space|plasma membrane|platelet alpha granule lumen	copper ion binding|oxidoreductase activity|protein binding	g.chrX:154185438G>A	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.1546C>T	X.37:g.154185438G>A	ENSP00000353393:p.His516Tyr						p.H516Y	NM_000132	NP_000123	P00451	FA8_HUMAN			11	1717	-	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)		516			F5/8 type A 2.|Plastocyanin-like 3.		Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	c.1546C>T	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	G	15.56	2.871075	0.51695	.	.	ENSG00000185010	ENST00000360256	D	0.99413	-5.86	5.19	4.31	0.51392	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.294665	0.35838	N	0.002952	D	0.98021	0.9348	N	0.03930	-0.32	0.32362	N	0.557047	D	0.71674	0.998	D	0.63488	0.915	D	0.97409	1.0001	10	0.46703	T	0.11	-20.6562	12.2631	0.54661	0.0:0.2591:0.7409:0.0	.	516	P00451	FA8_HUMAN	Y	516	ENSP00000353393:H516Y	ENSP00000353393:H516Y	H	-	1	0	F8	153838632	0.972000	0.33761	0.996000	0.52242	0.933000	0.57130	1.551000	0.36233	2.155000	0.67459	0.600000	0.82982	CAT		0.378	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
