#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ADRB1	153	broad.mit.edu	37	10	115804632	115804633	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:115804632_115804633insT	ENST00000369295.2	+	1	827_828	c.741_742insT	c.(742-744)ttcfs	p.F248fs		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	248					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)	p.R249fs*60(1)		large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	ACCTGCGGGTGTTCCGCGAGGC	0.678																																					p.V247fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.741_742insT	10						.																																			115794623	SO:0001589	frameshift_variant	153	exon1			J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.743dupT	10.37:g.115804634_115804634dupT	ENSP00000358301:p.Phe248fs	Somatic		Capture	Illumina HiSeq	Phase_I	115794622	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Frame_Shift_Ins	INS	ENST00000369295.2	37	CCDS7586.1																																																																																				0.678	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
FAM188A	80013	broad.mit.edu	37	10	15863676	15863676	+	Missense_Mutation	SNP	C	C	T	rs140756231		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:15863676C>T	ENST00000277632.3	-	9	1000	c.780G>A	c.(778-780)atG>atA	p.M260I	FAM188A_ENST00000477891.1_5'UTR	NM_024948.2	NP_079224.1	Q9H8M7	F188A_HUMAN	family with sequence similarity 188, member A	260					apoptotic process (GO:0006915)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.M260I(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(2)	22						TTAAAGCTTCCATTAGTGTTA	0.318																																					p.M260I	Pancreas(159;946 1953 2111 4475 22008)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G780A	10						.	C	ILE/MET	0,4404		0,0,2202	106.0	100.0	102.0		780	5.1	1.0	10	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAM188A	NM_024948.2	10	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	260/446	15863676	1,13003	2202	4300	6502	15903682	SO:0001583	missense	80013	exon9			AK023459	CCDS7110.1	10p13	2009-07-14	2009-07-14	2009-07-14	ENSG00000148481	ENSG00000148481			23578	protein-coding gene	gene with protein product	"""caspase recruitment domain containing pro-apoptotic protein"", ""CARD-containing protein"""	611649	"""chromosome 10 open reading frame 97"""	C10orf97		12054670, 17652099	Standard	XM_005252600		Approved	FLJ13397, CARP, my042, DERP5	uc001iod.1	Q9H8M7	OTTHUMG00000017734	ENST00000277632.3:c.780G>A	10.37:g.15863676C>T	ENSP00000277632:p.Met260Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15903682	NM_024948	Q5SZ68|Q5SZ69|Q5SZ70|Q6IA40|Q6P7P0|Q7Z2S1|Q8WUF1|Q9H3I4	Missense_Mutation	SNP	ENST00000277632.3	37	CCDS7110.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.507622	0.64410	0.0	1.16E-4	ENSG00000148481	ENST00000277632;ENST00000418767;ENST00000436829	T;T;T	0.27890	1.64;1.64;1.64	5.1	5.1	0.69264	.	0.079119	0.85682	D	0.000000	T	0.33876	0.0878	L	0.59436	1.845	0.80722	D	1	B	0.29481	0.245	B	0.31946	0.138	T	0.08186	-1.0734	10	0.22706	T	0.39	-15.0958	17.6489	0.88157	0.0:1.0:0.0:0.0	.	260	Q9H8M7	F188A_HUMAN	I	260;100;113	ENSP00000277632:M260I;ENSP00000388661:M100I;ENSP00000389883:M113I	ENSP00000277632:M260I	M	-	3	0	FAM188A	15903682	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.901000	0.75693	2.537000	0.85549	0.467000	0.42956	ATG		0.318	FAM188A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046990.2	NM_024948	
MLLT10	8028	broad.mit.edu	37	10	21823574	21823574	+	Splice_Site	SNP	A	A	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:21823574A>G	ENST00000307729.7	+	2	179	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	MLLT10_ENST00000377059.3_Start_Codon_SNP_p.M1V|MLLT10_ENST00000495130.1_3'UTR|MLLT10_ENST00000377091.2_Splice_Site_p.M1V|MLLT10_ENST00000377072.3_Splice_Site_p.M1V|MLLT10_ENST00000377100.3_Splice_Site_p.M1V|MLLT10_ENST00000446906.2_Splice_Site_p.M1V			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	1					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.M1V(2)		NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						TCCCTCTTAGATGGTCTCTAG	0.617			T	"""MLL, PICALM, CDK6"""	AL																																p.M1V			Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1G	10						.						107.0	103.0	104.0					10																	21823574		2203	4300	6503	21863580	SO:0001630	splice_region_variant	8028	exon1			U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1-1A>G	10.37:g.21823574A>G		Somatic		Capture	Illumina HiSeq	Phase_I	21863580	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	A	17.36	3.371205	0.61624	.	.	ENSG00000078403	ENST00000377100;ENST00000377072;ENST00000446906;ENST00000307729;ENST00000377091;ENST00000377059	T;T;T;T;T	0.48836	0.8;2.42;2.41;2.41;2.41	3.78	3.78	0.43462	.	0.430453	0.20354	U	0.093988	T	0.62221	0.2410	.	.	.	0.49051	D	0.999746	B;P;B;B;P	0.49447	0.323;0.713;0.323;0.323;0.924	B;P;B;B;P	0.60682	0.267;0.678;0.354;0.354;0.878	T	0.62872	-0.6762	8	.	.	.	.	12.9446	0.58365	1.0:0.0:0.0:0.0	.	1;1;1;1;1	E9PBP4;Q5VX90;P55197;Q66K63;B1ANA8	.;.;AF10_HUMAN;.;.	V	1	ENSP00000366304:M1V;ENSP00000366272:M1V;ENSP00000401406:M1V;ENSP00000307411:M1V;ENSP00000366258:M1V	.	M	+	1	0	MLLT10	21863580	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.709000	0.84645	1.689000	0.51079	0.374000	0.22700	ATG		0.617	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		Missense_Mutation
ZWINT	11130	broad.mit.edu	37	10	58118208	58118208	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:58118208G>T	ENST00000373944.3	-	8	843	c.805C>A	c.(805-807)Caa>Aaa	p.Q269K	ZWINT_ENST00000460654.1_5'UTR|ZWINT_ENST00000318387.2_Missense_Mutation_p.Q149K|ZWINT_ENST00000395405.1_Missense_Mutation_p.Q269K|ZWINT_ENST00000361148.6_Missense_Mutation_p.Q222K			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	269					establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)	p.Q269K(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						CCAGCAGGTTGTAGACCAACA	0.517																																					p.Q269K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C805A	10						.						106.0	99.0	102.0					10																	58118208		2203	4300	6503	57788214	SO:0001583	missense	11130	exon8			AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"""ZW10 interactor"""				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.805C>A	10.37:g.58118208G>T	ENSP00000363055:p.Gln269Lys	Somatic		Capture	Illumina HiSeq	Phase_I	57788214	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.467|6.467	0.454260|0.454260	0.12283|0.12283	.|.	.|.	ENSG00000122952|ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387;ENST00000361148|ENST00000373940	T;T;T;T|.	0.46063|.	0.88;0.88;0.88;0.88|.	3.82|3.82	-0.528|-0.528	0.11905|0.11905	.|.	1.692860|.	0.03833|.	N|.	0.269300|.	T|T	0.19604|0.19604	0.0471|0.0471	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	1|1	B;B|.	0.13145|.	0.007;0.007|.	B;B|.	0.08055|.	0.003;0.003|.	T|T	0.23547|0.23547	-1.0185|-1.0185	10|5	0.87932|.	D|.	0|.	.|.	1.8897|1.8897	0.03245|0.03245	0.1069:0.177:0.3534:0.3627|0.1069:0.177:0.3534:0.3627	.|.	222;269|.	A6NNV6;O95229|.	.;ZWINT_HUMAN|.	K|K	269;269;149;222|82	ENSP00000363055:Q269K;ENSP00000378801:Q269K;ENSP00000322850:Q149K;ENSP00000354921:Q222K|.	ENSP00000322850:Q149K|.	Q|T	-|-	1|2	0|0	ZWINT|ZWINT	57788214|57788214	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.012000|0.012000	0.07955|0.07955	-0.018000|-0.018000	0.12568|0.12568	-0.081000|-0.081000	0.12662|0.12662	0.557000|0.557000	0.71058|0.71058	CAA|ACA		0.517	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		
GLUD1	2746	broad.mit.edu	37	10	88854335	88854335	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:88854335G>A	ENST00000277865.4	-	1	288	c.192C>T	c.(190-192)ccC>ccT	p.P64P	FAM35A_ENST00000298786.4_5'Flank|GLUD1_ENST00000544149.1_5'Flank|GLUD1_ENST00000537649.1_5'Flank|FAM35A_ENST00000298784.1_5'Flank	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	64					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|glutamate catabolic process (GO:0006538)|glutamine metabolic process (GO:0006541)|positive regulation of insulin secretion (GO:0032024)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|tricarboxylic acid metabolic process (GO:0072350)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|glutamate dehydrogenase (NAD+) activity (GO:0004352)|glutamate dehydrogenase [NAD(P)+] activity (GO:0004353)|GTP binding (GO:0005525)|identical protein binding (GO:0042802)|leucine binding (GO:0070728)|NAD+ binding (GO:0070403)	p.P64P(1)		endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	TGAAGAAGTTGGGGTCGTCCT	0.716																																					p.P64P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C192T	10						.						60.0	66.0	64.0					10																	88854335		2202	4300	6502	88844315	SO:0001819	synonymous_variant	2746	exon1			M20867	CCDS7382.1	10q23.2	2010-03-17			ENSG00000148672	ENSG00000148672	1.4.1.3		4335	protein-coding gene	gene with protein product		138130		GLUD		2757358	Standard	NM_005271		Approved	GDH	uc001keh.3	P00367	OTTHUMG00000018666	ENST00000277865.4:c.192C>T	10.37:g.88854335G>A		Somatic		Capture	Illumina HiSeq	Phase_I	88844315	NM_005271	B3KV55|B4DGN5|Q5TBU3	Silent	SNP	ENST00000277865.4	37	CCDS7382.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.557733	0.27827	.	.	ENSG00000148672	ENST00000394415	.	.	.	4.02	3.12	0.35913	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	10.534	0.44994	0.0979:0.0:0.9021:0.0	.	.	.	.	X	38	.	ENSP00000377937:Q38X	Q	-	1	0	GLUD1	88844315	1.000000	0.71417	1.000000	0.80357	0.347000	0.29111	1.240000	0.32731	0.897000	0.36392	-0.339000	0.08088	CAA		0.716	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271	
CYP2C8	1558	broad.mit.edu	37	10	96827408	96827408	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr10:96827408C>T	ENST00000371270.3	-	2	303	c.209G>A	c.(208-210)gGc>gAc	p.G70D	CYP2C8_ENST00000535898.1_Intron|CYP2C8_ENST00000539050.1_5'UTR	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	70					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)	p.G70D(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	GGGATTCATGCCAAAATACAC	0.413																																					p.G70D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G209A	10						.						105.0	97.0	100.0					10																	96827408		2203	4300	6503	96817398	SO:0001583	missense	1558	exon2			M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.209G>A	10.37:g.96827408C>T	ENSP00000360317:p.Gly70Asp	Somatic		Capture	Illumina HiSeq	Phase_I	96817398	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155611	0.57259	.	.	ENSG00000138115	ENST00000371270	T	0.74209	-0.82	4.64	4.64	0.57946	.	0.000000	0.85682	U	0.000000	D	0.89805	0.6821	M	0.94142	3.5	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.92705	0.6178	10	0.87932	D	0	.	16.221	0.82258	0.0:1.0:0.0:0.0	.	70	P10632	CP2C8_HUMAN	D	70	ENSP00000360317:G70D	ENSP00000360317:G70D	G	-	2	0	CYP2C8	96817398	0.997000	0.39634	0.926000	0.36857	0.042000	0.13812	4.858000	0.62947	2.424000	0.82194	0.561000	0.74099	GGC		0.413	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
ZNF214	7761	broad.mit.edu	37	11	7022353	7022353	+	Silent	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr11:7022353C>T	ENST00000278314.4	-	3	876	c.561G>A	c.(559-561)caG>caA	p.Q187Q	ZNF214_ENST00000531083.1_5'Flank|ZNF214_ENST00000536068.1_Silent_p.Q187Q	NM_013249.2	NP_037381.2	Q9UL59	ZN214_HUMAN	zinc finger protein 214	187					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Q187Q(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				Epithelial(150;3.87e-08)|BRCA - Breast invasive adenocarcinoma(625;0.081)		TATAAGAATGCTGAACTATGA	0.438																																					p.Q187Q	Ovarian(22;251 657 736 21522 46864)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G561A	11						.						99.0	100.0	99.0					11																	7022353		2200	4294	6494	6978929	SO:0001819	synonymous_variant	7761	exon3			AF056617	CCDS31418.1	11p15.4	2013-01-08				ENSG00000149050		"""Zinc fingers, C2H2-type"", ""-"""	13006	protein-coding gene	gene with protein product		605015					Standard	NM_013249		Approved		uc001mfa.2	Q9UL59		ENST00000278314.4:c.561G>A	11.37:g.7022353C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6978929	NM_013249	B2R8Q1	Silent	SNP	ENST00000278314.4	37	CCDS31418.1																																																																																				0.438	ZNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385349.1		
TENM4	26011	broad.mit.edu	37	11	78380976	78380976	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr11:78380976delG	ENST00000278550.7	-	32	6876	c.6414delC	c.(6412-6414)gtcfs	p.V2138fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2138					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										TGTGGGTCATGACAGCTGTGG	0.448																																					p.V2138fs												.	.	0			c.6414delC	11						.						69.0	66.0	67.0					11																	78380976		2124	4237	6361	78058624	SO:0001589	frameshift_variant	26011	exon32			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.6414delC	11.37:g.78380976delG	ENSP00000278550:p.Val2138fs	None		Capture	Illumina HiSeq	Phase_I	78058624	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	37	CCDS44688.1																																																																																				0.448	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
IFFO1	25900	broad.mit.edu	37	12	6664617	6664617	+	Silent	SNP	G	G	A	rs530504239		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:6664617G>A	ENST00000396840.2	-	1	620	c.579C>T	c.(577-579)ccC>ccT	p.P193P	NOP2_ENST00000542015.1_5'Flank|IFFO1_ENST00000356896.4_Silent_p.P193P|IFFO1_ENST00000336604.4_Silent_p.P193P			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	193						intermediate filament (GO:0005882)		p.P193P(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						AGATGGTGCCGGGCATGAAGC	0.736													G|||	1	0.000199681	0.0	0.0	5008	,	,		10796	0.0		0.0	False		,,,				2504	0.001				p.P193P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C579T	12						.						25.0	29.0	28.0					12																	6664617		2200	4296	6496	6534878	SO:0001819	synonymous_variant	25900	exon1			AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"""Intermediate filament family orphans"""	24970	protein-coding gene	gene with protein product		610495	"""intermediate filament family orphan"""	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.579C>T	12.37:g.6664617G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6534878	NM_001193457	Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Silent	SNP	ENST00000396840.2	37																																																																																					0.736	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000280428.1	NM_080730	
KRT3	3850	broad.mit.edu	37	12	53185037	53185037	+	Silent	SNP	G	G	A	rs372122010		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:53185037G>A	ENST00000417996.2	-	7	1562	c.1488C>T	c.(1486-1488)gaC>gaT	p.D496D	KRT3_ENST00000309505.3_Silent_p.D496D	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	496	Coil 2.|Rod.				epithelial cell differentiation (GO:0030855)|intermediate filament cytoskeleton organization (GO:0045104)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.D496D(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|skin(1)	23						CGATCTCCACGTCCAGGGCCA	0.617																																					p.D496D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1488T	12						.	A		0,4406		0,0,2203	110.0	102.0	105.0		1488	-8.4	0.7	12		105	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	KRT3	NM_057088.2		0,2,6499	AA,AG,GG		0.0233,0.0,0.0154		496/629	53185037	2,13000	2203	4298	6501	51471304	SO:0001819	synonymous_variant	3850	exon7				CCDS44895.1	12q13.13	2013-01-16			ENSG00000186442	ENSG00000186442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6440	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 3"", ""cytokeratin 3"""	148043				7510223, 16831889	Standard	NM_057088		Approved	CK3, K3	uc001say.3	P12035	OTTHUMG00000169799	ENST00000417996.2:c.1488C>T	12.37:g.53185037G>A		Somatic		Capture	Illumina HiSeq	Phase_I	51471304	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																				0.617	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088	
ITGA7	3679	broad.mit.edu	37	12	56088623	56088623	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:56088623T>A	ENST00000555728.1	-	16	2295	c.2267A>T	c.(2266-2268)cAg>cTg	p.Q756L	ITGA7_ENST00000452168.2_Missense_Mutation_p.Q619L|ITGA7_ENST00000394229.2_Missense_Mutation_p.Q712L|ITGA7_ENST00000257879.6_Missense_Mutation_p.Q712L|ITGA7_ENST00000257880.7_Missense_Mutation_p.Q756L|ITGA7_ENST00000553804.1_Missense_Mutation_p.Q716L|ITGA7_ENST00000394230.2_Missense_Mutation_p.Q716L|ITGA7_ENST00000347027.6_Missense_Mutation_p.Q706L			Q13683	ITA7_HUMAN	integrin, alpha 7	756					blood vessel morphogenesis (GO:0048514)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|regulation of cell shape (GO:0008360)|skeletal muscle tissue development (GO:0007519)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|integrin alpha7-beta1 complex (GO:0034677)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	metal ion binding (GO:0046872)	p.Q712L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(16)|ovary(2)|prostate(2)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						GACCAGGAGCTGGGCTTCATG	0.652																																					p.Q619L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1856T	12						.						65.0	61.0	62.0					12																	56088623		2203	4300	6503	54374890	SO:0001583	missense	3679	exon15				CCDS8888.1, CCDS44914.1, CCDS55832.1	12q13	2014-09-17				ENSG00000135424		"""Integrins"""	6143	protein-coding gene	gene with protein product		600536				7607681	Standard	NM_002206		Approved		uc001shh.3	Q13683		ENST00000555728.1:c.2267A>T	12.37:g.56088623T>A	ENSP00000452387:p.Gln756Leu	Somatic		Capture	Illumina HiSeq	Phase_I	54374890	NM_001144997	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	37		.	.	.	.	.	.	.	.	.	.	T	12.63	1.995557	0.35226	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000452168;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000555728	T;T;T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	4.66	2.2	0.27929	Integrin alpha-2 (1);	0.075225	0.53938	N	0.000052	T	0.26846	0.0657	N	0.16833	0.445	0.49483	D	0.999795	B;B;B;B	0.15473	0.005;0.001;0.002;0.013	B;B;B;B	0.20384	0.029;0.008;0.011;0.02	T	0.04029	-1.0983	10	0.33141	T	0.24	.	5.3242	0.15896	0.1559:0.0901:0.0:0.754	.	619;756;716;775	Q13683-13;Q13683;Q13683-3;Q4LE35	.;ITA7_HUMAN;.;.	L	716;712;706;619;756;716;712;756	ENSP00000452120:Q716L;ENSP00000257879:Q712L;ENSP00000343009:Q706L;ENSP00000393844:Q619L;ENSP00000257880:Q756L;ENSP00000377777:Q716L;ENSP00000377776:Q712L;ENSP00000452387:Q756L	ENSP00000257879:Q712L	Q	-	2	0	ITGA7	54374890	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.013000	0.49582	0.224000	0.20940	0.454000	0.30748	CAG		0.652	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
SUOX	6821	broad.mit.edu	37	12	56397748	56397748	+	Missense_Mutation	SNP	G	G	A	rs535313141	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:56397748G>A	ENST00000394109.3	+	3	1299	c.575G>A	c.(574-576)cGg>cAg	p.R192Q	SUOX_ENST00000266971.3_Missense_Mutation_p.R192Q|SUOX_ENST00000356124.4_Missense_Mutation_p.R192Q|SUOX_ENST00000551841.2_Intron|SUOX_ENST00000548274.1_Missense_Mutation_p.R192Q|SUOX_ENST00000394115.2_Missense_Mutation_p.R192Q			P51687	SUOX_HUMAN	sulfite oxidase	192	Moco domain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)	p.R192Q(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			AACAGCCAGCGGCCCTTTAAT	0.552													G|||	5	0.000998403	0.0015	0.0	5008	,	,		19544	0.0		0.0	False		,,,				2504	0.0031				p.R192Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G575A	12						.						78.0	76.0	76.0					12																	56397748		2203	4300	6503	54684015	SO:0001583	missense	6821	exon6			BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.575G>A	12.37:g.56397748G>A	ENSP00000377668:p.Arg192Gln	Somatic		Capture	Illumina HiSeq	Phase_I	54684015	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	37	CCDS8901.2	.	.	.	.	.	.	.	.	.	.	G	16.23	3.063220	0.55432	.	.	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000394109	D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38	5.12	3.3	0.37823	Oxidoreductase, molybdopterin-binding domain (2);	0.213623	0.40640	N	0.001049	D	0.88610	0.6483	L	0.50333	1.59	0.42406	D	0.992581	B	0.17852	0.024	B	0.15052	0.012	D	0.84421	0.0571	10	0.45353	T	0.12	-0.1337	5.5661	0.17170	0.3311:0.0:0.6689:0.0	.	192	P51687	SUOX_HUMAN	Q	192	ENSP00000348440:R192Q;ENSP00000266971:R192Q;ENSP00000377674:R192Q;ENSP00000450245:R192Q;ENSP00000377668:R192Q	ENSP00000266971:R192Q	R	+	2	0	SUOX	54684015	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.614000	0.61183	1.545000	0.49373	-0.218000	0.12543	CGG		0.552	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456	
NTN4	59277	broad.mit.edu	37	12	96107055	96107055	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:96107055G>A	ENST00000343702.4	-	4	1374	c.926C>T	c.(925-927)cCg>cTg	p.P309L	NTN4_ENST00000538383.1_Missense_Mutation_p.P272L|NTN4_ENST00000552603.1_5'Flank|NTN4_ENST00000344911.4_Missense_Mutation_p.P272L|NTN4_ENST00000553059.1_Missense_Mutation_p.P309L	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4	309	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|extracellular matrix organization (GO:0030198)|neuron remodeling (GO:0016322)|regulation of branching involved in salivary gland morphogenesis by extracellular matrix-epithelial cell signaling (GO:0060668)	basement membrane (GO:0005604)|plasma membrane (GO:0005886)				NS(2)|breast(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	25						ATTGTATAACGGGGCACAGTG	0.512																																					p.P309L												.	.	0			c.C926T	12						.						105.0	93.0	97.0					12																	96107055		2203	4300	6503	94631186	SO:0001583	missense	59277	exon4			AF119916	CCDS9054.1	12q22	2013-03-01			ENSG00000074527	ENSG00000074527		"""Netrins"""	13658	protein-coding gene	gene with protein product	"""beta-netrin"", ""Netrin-4"""	610401				11038171	Standard	NM_021229		Approved		uc001tei.3	Q9HB63	OTTHUMG00000170290	ENST00000343702.4:c.926C>T	12.37:g.96107055G>A	ENSP00000340998:p.Pro309Leu	None		Capture	Illumina HiSeq	Phase_I	94631186	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Missense_Mutation	SNP	ENST00000343702.4	37	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546358	0.65198	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	4.99	4.99	0.66335	EGF-like, laminin (3);	0.052214	0.85682	D	0.000000	D	0.82388	0.5026	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.991	D	0.85923	0.1447	10	0.72032	D	0.01	.	18.2809	0.90097	0.0:0.0:1.0:0.0	.	309;309	Q9HB63-2;Q9HB63	.;NET4_HUMAN	L	309;272;272;309	ENSP00000340998:P309L;ENSP00000339436:P272L;ENSP00000444432:P272L;ENSP00000447292:P309L	ENSP00000340998:P309L	P	-	2	0	NTN4	94631186	1.000000	0.71417	0.764000	0.31436	0.052000	0.14988	7.500000	0.81588	2.323000	0.78572	0.491000	0.48974	CCG		0.512	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	
BTBD11	121551	broad.mit.edu	37	12	108013823	108013823	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr12:108013823G>A	ENST00000280758.5	+	11	3041	c.2513G>A	c.(2512-2514)cGc>cAc	p.R838H	BTBD11_ENST00000420571.2_Missense_Mutation_p.R719H|RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000357167.4_Missense_Mutation_p.R375H|BTBD11_ENST00000490090.2_Missense_Mutation_p.R838H	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	838						integral component of membrane (GO:0016021)		p.R838H(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(18)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	53						CAGCAGCACCGCAGGCCTCTC	0.602																																					p.R375H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1124A	12						.						54.0	52.0	53.0					12																	108013823		2203	4300	6503	106537953	SO:0001583	missense	121551	exon9			AK091276	CCDS31893.1, CCDS41827.1	12q24.11	2013-10-02			ENSG00000151136	ENSG00000151136		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23844	protein-coding gene	gene with protein product							Standard	XM_005268645		Approved	FLJ33957, ABTB2B	uc001tmk.1	A6QL63	OTTHUMG00000150413	ENST00000280758.5:c.2513G>A	12.37:g.108013823G>A	ENSP00000280758:p.Arg838His	Somatic		Capture	Illumina HiSeq	Phase_I	106537953	NM_001017523	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.846832	0.91277	.	.	ENSG00000151136	ENST00000280758;ENST00000420571;ENST00000490090;ENST00000357167	T;T;T;T	0.50001	1.02;0.76;1.05;0.84	5.04	5.04	0.67666	.	0.103648	0.64402	D	0.000002	T	0.65883	0.2734	L	0.60455	1.87	0.80722	D	1	D;P;D;P	0.76494	0.999;0.796;0.998;0.954	D;B;P;P	0.80764	0.994;0.165;0.7;0.481	T	0.65043	-0.6264	10	0.41790	T	0.15	.	18.4012	0.90516	0.0:0.0:1.0:0.0	.	719;375;838;838	A6QL63-2;E9PHS4;A6QL63;A6QL63-3	.;.;BTBDB_HUMAN;.	H	838;719;838;375	ENSP00000280758:R838H;ENSP00000413889:R719H;ENSP00000447319:R838H;ENSP00000349690:R375H	ENSP00000280758:R838H	R	+	2	0	BTBD11	106537953	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.819000	0.99357	2.326000	0.78906	0.650000	0.86243	CGC		0.602	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322	
POSTN	10631	broad.mit.edu	37	13	38154705	38154705	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr13:38154705G>A	ENST00000379747.4	-	11	1639	c.1522C>T	c.(1522-1524)Cgc>Tgc	p.R508C	POSTN_ENST00000379743.4_Missense_Mutation_p.R508C|POSTN_ENST00000541179.1_Missense_Mutation_p.R508C|POSTN_ENST00000379742.4_Missense_Mutation_p.R508C|POSTN_ENST00000541481.1_Missense_Mutation_p.R508C|POSTN_ENST00000379749.4_Missense_Mutation_p.R508C	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	508	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of Notch signaling pathway (GO:0008593)|skeletal system development (GO:0001501)|tissue development (GO:0009888)	proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network (GO:0005802)	heparin binding (GO:0008201)	p.R508C(3)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(16)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	59		Lung NSC(96;2.09e-05)|Prostate(109;0.0513)|Breast(139;0.0538)|Lung SC(185;0.0743)		all cancers(112;2.48e-08)|Epithelial(112;2.78e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000853)|BRCA - Breast invasive adenocarcinoma(63;0.013)|GBM - Glioblastoma multiforme(144;0.0154)		TACCTAAAGCGCTTATCTTGT	0.438																																					p.R508C												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.C1522T	13						.						279.0	267.0	271.0					13																	38154705		2203	4300	6503	37052705	SO:0001583	missense	10631	exon11			D13665	CCDS9364.1, CCDS45034.1, CCDS53864.1, CCDS66530.1, CCDS66531.1	13q13.3	2008-02-05			ENSG00000133110	ENSG00000133110			16953	protein-coding gene	gene with protein product		608777				8363580, 12235007	Standard	NM_006475		Approved	OSF-2, PN, periostin	uc001uwo.4	Q15063	OTTHUMG00000016751	ENST00000379747.4:c.1522C>T	13.37:g.38154705G>A	ENSP00000369071:p.Arg508Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37052705	NM_001135934	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.047403	0.75846	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.91996	-2.95;-2.95;-2.95;-2.95;-2.95;-2.95	5.02	5.02	0.67125	FAS1 domain (4);	0.290945	0.39475	N	0.001349	D	0.95758	0.8620	M	0.70275	2.135	0.54753	D	0.999982	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.993;0.999;0.996;0.975;0.993	D	0.95922	0.8931	10	0.62326	D	0.03	-9.2511	18.6988	0.91613	0.0:0.0:1.0:0.0	.	508;508;508;508;508;508;508	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	C	508	ENSP00000437959:R508C;ENSP00000369073:R508C;ENSP00000369071:R508C;ENSP00000369067:R508C;ENSP00000369066:R508C;ENSP00000437953:R508C	ENSP00000369066:R508C	R	-	1	0	POSTN	37052705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.653000	0.61462	2.472000	0.83506	0.557000	0.71058	CGC		0.438	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475	
MRPS31	10240	broad.mit.edu	37	13	41345272	41345273	+	Start_Codon_SNP	DNP	TC	TC	GA			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	TC	TC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr13:41345272_41345273TC>GA	ENST00000323563.6	-	1	36_37	c.0_1GA>TC	c.(-2-3)gcGAtg>gcTCtg	p.0_1insAL		NM_005830.3	NP_005821.2	Q92665	RT31_HUMAN	mitochondrial ribosomal protein S31	0						mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|structural constituent of ribosome (GO:0003735)	p.?(2)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00394)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(188;0.194)		all cancers(112;1.52e-08)|Epithelial(112;7.63e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000192)|GBM - Glioblastoma multiforme(144;0.00233)|BRCA - Breast invasive adenocarcinoma(63;0.0706)		CTAGGAAACATCGCCGAGACAC	0.589																																					.												.	.	2	Unknown(2)	large_intestine(2)	c.0_1TC	13						.																																			40243273	SO:0001582	initiator_codon_variant	10240	exon1			Z68747	CCDS9372.1	13q14.11	2012-09-13			ENSG00000102738	ENSG00000102738		"""Mitochondrial ribosomal proteins / small subunits"""	16632	protein-coding gene	gene with protein product		611992				11279123, 8567980	Standard	NM_005830		Approved	IMOGN38	uc001uxm.4	Q92665	OTTHUMG00000016777	ENST00000323563.6:c.1_1delinsGA	13.37:g.41345272_41345273delinsGA	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	40243272	NM_005830	B2RCS3|Q5VYC8|Q8WTV8	Translation_Start_Site	DNP	ENST00000323563.6	37	CCDS9372.1																																																																																				0.589	MRPS31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044640.2		Missense_Mutation
SLITRK1	114798	broad.mit.edu	37	13	84454595	84454595	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr13:84454595T>A	ENST00000377084.2	-	1	1933	c.1048A>T	c.(1048-1050)Atc>Ttc	p.I350F		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	350	LRRNT 2.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.I350F(1)		NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		GACCCTGGGATGTGGTCGCAG	0.537																																					p.I350F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1048T	13						.						72.0	69.0	70.0					13																	84454595		2203	4300	6503	83352596	SO:0001583	missense	114798	exon1			AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1048A>T	13.37:g.84454595T>A	ENSP00000366288:p.Ile350Phe	Somatic		Capture	Illumina HiSeq	Phase_I	83352596	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	T	9.615	1.132273	0.21041	.	.	ENSG00000178235	ENST00000377084	T	0.52057	0.68	5.38	4.2	0.49525	Leucine-rich repeat-containing N-terminal (1);	0.116357	0.64402	D	0.000015	T	0.38612	0.1047	N	0.14661	0.345	0.58432	D	0.999994	D	0.54964	0.969	P	0.55667	0.781	T	0.12293	-1.0553	10	0.10111	T	0.7	-8.8179	9.901	0.41348	0.0:0.081:0.0:0.919	.	350	Q96PX8	SLIK1_HUMAN	F	350	ENSP00000366288:I350F	ENSP00000366288:I350F	I	-	1	0	SLITRK1	83352596	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.165000	0.42396	0.895000	0.36342	0.454000	0.30748	ATC		0.537	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
POTEG	404785	broad.mit.edu	37	14	19553707	19553707	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr14:19553707G>C	ENST00000409832.3	+	1	343	c.291G>C	c.(289-291)aaG>aaC	p.K97N		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	97								p.K97N(1)		cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						TCAGGAGCAAGATGGGCAAGT	0.622																																					p.K97N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G291C	14						.						61.0	75.0	70.0					14																	19553707		1569	3284	4853	18623707	SO:0001583	missense	404785	exon1				CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.291G>C	14.37:g.19553707G>C	ENSP00000386971:p.Lys97Asn	Somatic		Capture	Illumina HiSeq	Phase_I	18623707	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	5.551	0.286597	0.10513	.	.	ENSG00000222036	ENST00000409832	T	0.30448	1.53	0.535	0.535	0.17133	.	.	.	.	.	T	0.27798	0.0684	L	0.58101	1.795	0.09310	N	1	B	0.17852	0.024	B	0.16722	0.016	T	0.30268	-0.9984	8	0.54805	T	0.06	.	.	.	.	.	97	Q6S5H5	POTEG_HUMAN	N	97	ENSP00000386971:K97N	ENSP00000386971:K97N	K	+	3	2	POTEG	18623707	0.050000	0.20438	0.049000	0.19019	0.021000	0.10359	0.488000	0.22371	0.560000	0.29169	0.403000	0.27427	AAG		0.622	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
FAM179B	23116	broad.mit.edu	37	14	45494986	45494986	+	Splice_Site	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr14:45494986G>A	ENST00000361577.3	+	8	3453	c.3239G>A	c.(3238-3240)gGg>gAg	p.G1080E	FAM179B_ENST00000382233.2_3'UTR|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000361462.2_Splice_Site_p.G1080E	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1080	Ser-rich.							p.G1080E(1)		endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						GGATTTACAGGGTCATCATCA	0.308																																					p.G1080E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3239A	14						.						107.0	104.0	105.0					14																	45494986		2203	4299	6502	44564736	SO:0001630	splice_region_variant	23116	exon8			AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.3239-1G>A	14.37:g.45494986G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44564736	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	G	10.32	1.317671	0.23994	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462	T;T	0.03772	3.81;3.81	5.48	3.64	0.41730	Armadillo-type fold (1);	0.673329	0.14409	N	0.321390	T	0.03695	0.0105	L	0.27053	0.805	0.80722	D	1	B;B	0.27416	0.178;0.078	B;B	0.24541	0.054;0.034	T	0.49163	-0.8968	9	.	.	.	.	7.5978	0.28058	0.0773:0.0:0.6317:0.291	.	1080;1080	G3XAE9;Q9Y4F4	.;F179B_HUMAN	E	1080	ENSP00000355045:G1080E;ENSP00000354917:G1080E	.	G	+	2	0	FAM179B	44564736	1.000000	0.71417	0.983000	0.44433	0.344000	0.29017	3.013000	0.49582	0.683000	0.31428	0.579000	0.79373	GGG		0.308	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	Missense_Mutation
CCDC88C	440193	broad.mit.edu	37	14	91744333	91744334	+	Missense_Mutation	DNP	GA	GA	AT			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	GA	GA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr14:91744333_91744334GA>AT	ENST00000389857.6	-	29	5076_5077	c.4990_4991TC>AT	c.(4990-4992)TCc>ATc	p.S1664I	CCDC88C_ENST00000331194.7_Missense_Mutation_p.S188I	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1664					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.S1664>?(2)|p.S188>?(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				ACTGCTGGGGGAGGCCGAGCAG	0.668																																					.												.	.	3	Complex(3)	large_intestine(3)	c.4990_4991AT	14						.																																			90814087	SO:0001583	missense	440193	exon29				CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.4990_4991delinsAT	14.37:g.91744333_91744334delinsAT	ENSP00000374507:p.Ser1664Ile	Somatic		Capture	Illumina HiSeq	Phase_I	90814086	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	DNP	ENST00000389857.6	37	CCDS45151.1																																																																																				0.668	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
RYR3	6263	broad.mit.edu	37	15	34113537	34113537	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:34113537G>T	ENST00000389232.4	+	79	10952	c.10882G>T	c.(10882-10884)Gag>Tag	p.E3628*	RYR3_ENST00000415757.3_Nonsense_Mutation_p.E3623*	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3628					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.E3627*(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TGGTGCTGCAGAGATGGTCCT	0.463																																					p.E3628X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G10882T	15						.						33.0	34.0	33.0					15																	34113537		1988	4190	6178	31900829	SO:0001587	stop_gained	6263	exon79				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10882G>T	15.37:g.34113537G>T	ENSP00000373884:p.Glu3628*	Somatic		Capture	Illumina HiSeq	Phase_I	31900829	NM_001036	O15175|Q15412	Nonsense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	G	52	18.954125	0.99913	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	18.6774	0.91534	0.0:0.0:1.0:0.0	.	.	.	.	X	3628;3627;3623	.	ENSP00000354735:E3623X	E	+	1	0	RYR3	31900829	1.000000	0.71417	0.958000	0.39756	0.416000	0.31233	9.657000	0.98554	2.650000	0.89964	0.655000	0.94253	GAG		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
ZNF106	64397	broad.mit.edu	37	15	42742900	42742900	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:42742900G>A	ENST00000263805.4	-	2	1827	c.1501C>T	c.(1501-1503)Cct>Tct	p.P501S	ZNF106_ENST00000565380.1_Intron|ZNF106_ENST00000565611.1_Intron	NM_001284306.1|NM_001284307.1|NM_022473.1	NP_001271235.1|NP_001271236.1|NP_071918.1	Q9H2Y7	ZN106_HUMAN	zinc finger protein 106	501					insulin receptor signaling pathway (GO:0008286)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P501S(1)									GATATGTAAGGACCATGGTTA	0.363																																					p.P501S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1501T	15						.						217.0	213.0	214.0					15																	42742900		2203	4299	6502	40530192	SO:0001583	missense	64397	exon2			AF205632	CCDS32208.1, CCDS61602.1, CCDS61603.1	15q15.1	2012-11-27	2012-11-27		ENSG00000103994	ENSG00000103994		"""Zinc fingers, C2H2-type"""	12886	protein-coding gene	gene with protein product	"""SH3-domain binding protein 3"""		"""zinc finger protein 106 homolog (mouse)"""	ZFP106			Standard	XM_005254591		Approved	ZNF474, SH3BP3	uc001zpw.3	Q9H2Y7	OTTHUMG00000173244	ENST00000263805.4:c.1501C>T	15.37:g.42742900G>A	ENSP00000263805:p.Pro501Ser	Somatic		Capture	Illumina HiSeq	Phase_I	40530192	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.818185	0.00072	.	.	ENSG00000103994	ENST00000263805	T	0.44083	0.93	4.99	3.77	0.43336	.	0.332965	0.32769	N	0.005676	T	0.12518	0.0304	N	0.01188	-0.97	0.19775	N	0.999953	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32107	-0.9919	10	0.02654	T	1	-0.7096	8.3204	0.32126	0.7733:0.0:0.2267:0.0	.	284;501	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	S	501	ENSP00000263805:P501S	ENSP00000263805:P501S	P	-	1	0	ZFP106	40530192	0.990000	0.36364	0.312000	0.25196	0.174000	0.22865	1.984000	0.40658	1.014000	0.39417	-0.504000	0.04507	CCT		0.363	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
HERC1	8925	broad.mit.edu	37	15	64046726	64046726	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:64046726C>A	ENST00000443617.2	-	7	1839	c.1752G>T	c.(1750-1752)tgG>tgT	p.W584C		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	584					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.W584C(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTCCAAAAGACCATACAGTTC	0.328																																					p.W584C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1752T	15						.						133.0	118.0	123.0					15																	64046726		1867	4084	5951	61833779	SO:0001583	missense	8925	exon7			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.1752G>T	15.37:g.64046726C>A	ENSP00000390158:p.Trp584Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61833779	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.399340	0.83120	.	.	ENSG00000103657	ENST00000443617	D	0.85258	-1.96	5.25	5.25	0.73442	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.64402	U	0.000001	D	0.93782	0.8012	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94743	0.7920	10	0.87932	D	0	.	18.846	0.92208	0.0:1.0:0.0:0.0	.	584;584	C9JUT5;Q15751	.;HERC1_HUMAN	C	584	ENSP00000390158:W584C	ENSP00000390158:W584C	W	-	3	0	HERC1	61833779	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.818000	0.86416	2.466000	0.83321	0.467000	0.42956	TGG		0.328	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
SHC4	399694	broad.mit.edu	37	15	49118177	49118177	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:49118177delG	ENST00000332408.4	-	12	2312	c.1884delC	c.(1882-1884)tccfs	p.S628fs	SHC4_ENST00000537958.1_Frame_Shift_Del_p.S342fs|SHC4_ENST00000396535.3_Frame_Shift_Del_p.S385fs	NM_203349.3	NP_976224.3	Q6S5L8	SHC4_HUMAN	SHC (Src homology 2 domain containing) family, member 4	628					apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of cell proliferation (GO:0008284)|regulation of gene expression (GO:0010468)|stem cell differentiation (GO:0048863)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)		p.N629fs*>2(1)		breast(1)|endometrium(2)|large_intestine(8)|lung(11)|ovary(3)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	29		all_lung(180;0.00466)		all cancers(107;9.4e-08)|GBM - Glioblastoma multiforme(94;5.94e-07)		GTCATTTGTTGGAATGCAAAA	0.343																																					p.S628fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1884delC	15						.						229.0	218.0	222.0					15																	49118177		2197	4295	6492	46905469	SO:0001589	frameshift_variant	399694	exon12			AY358250	CCDS10130.1	15q21.1-q21.2	2013-02-14			ENSG00000185634	ENSG00000185634		"""SH2 domain containing"""	16743	protein-coding gene	gene with protein product	"""rai-like protein"""						Standard	NM_203349		Approved	RaLP	uc001zxb.1	Q6S5L8	OTTHUMG00000131513	ENST00000332408.4:c.1884delC	15.37:g.49118177delG	ENSP00000329668:p.Ser628fs	Somatic		Capture	Illumina HiSeq	Phase_I	46905469	NM_203349	Q6UXQ3|Q8IYW3	Frame_Shift_Del	DEL	ENST00000332408.4	37	CCDS10130.1																																																																																				0.343	SHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254371.1	NM_203349	
ACSBG1	23205	broad.mit.edu	37	15	78486312	78486312	+	Silent	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:78486312C>T	ENST00000258873.4	-	4	709	c.504G>A	c.(502-504)ccG>ccA	p.P168P	ACSBG1_ENST00000541759.1_Intron|ACSBG1_ENST00000560817.1_Intron|ACSBG1_ENST00000558828.1_5'Flank	NM_001199377.1|NM_015162.4	NP_001186306.1|NP_055977.3	Q96GR2	ACBG1_HUMAN	acyl-CoA synthetase bubblegum family member 1	168					long-chain fatty acid metabolic process (GO:0001676)|myelination (GO:0042552)|ovarian follicle atresia (GO:0001552)|response to glucocorticoid (GO:0051384)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.P168P(1)		endometrium(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	37						AGAACCACTCCGGGGAGTTGA	0.667																																					p.P164P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G492A	15						.						45.0	43.0	44.0					15																	78486312		2196	4293	6489	76273367	SO:0001819	synonymous_variant	23205	exon4			AB014531	CCDS10298.1	15q23-q24	2006-02-09			ENSG00000103740	ENSG00000103740		"""Acyl-CoA synthetase family"""	29567	protein-coding gene	gene with protein product	"""bubblegum"", ""very long-chain acyl-CoA synthetase"", ""lipidosin"""	614362				9734811, 10954726	Standard	NM_015162		Approved	BGM, FLJ30320, MGC14352, BG1, KIAA0631, hBG1, hsBG	uc002bdh.3	Q96GR2	OTTHUMG00000143734	ENST00000258873.4:c.504G>A	15.37:g.78486312C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76273367	NM_001199377	B2RB61|O75126|Q76N27|Q9HC26	Silent	SNP	ENST00000258873.4	37	CCDS10298.1																																																																																				0.667	ACSBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289802.2	NM_015162	
LINC00052	145978	broad.mit.edu	37	15	88121557	88121558	+	lincRNA	DEL	CA	CA	-	rs147007133|rs368572077		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	CA	CA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr15:88121557_88121558delCA	ENST00000560153.1	+	0	426_427				RP11-648K4.2_ENST00000560439.1_lincRNA	NR_026869.1		Q96N35	TMM83_HUMAN	long intergenic non-protein coding RNA 52							integral component of membrane (GO:0016021)											gtttctctctcACACACACACA	0.406																																					.												.	.	0			.	15						.																																			85922562			145978	.			AK056023		15q25.3	2012-10-12	2011-08-10	2011-08-10		ENSG00000259527		"""Long non-coding RNAs"""	26455	non-coding RNA	RNA, long non-coding			"""transmembrane protein 83"", ""non-protein coding RNA 52"""	TMEM83, NCRNA00052			Standard	NR_026869		Approved	FLJ31461	uc002bmc.1	Q96N35			15.37:g.88121567_88121568delCA		Somatic		Capture	Illumina HiSeq	Phase_I	85922561	.		Frame_Shift_Del	DEL	ENST00000560153.1	37																																																																																					0.406	LINC00052-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000416151.1	XR_017978	
ABCA3	21	broad.mit.edu	37	16	2345597	2345597	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr16:2345597G>A	ENST00000301732.5	-	18	3108	c.2408C>T	c.(2407-2409)aCg>aTg	p.T803M	ABCA3_ENST00000382381.3_Missense_Mutation_p.T745M	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	803					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.T803M(1)		breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GTACCTGTGCGTGCTCTCTCT	0.632																																					p.T803M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2408T	16						.						148.0	151.0	150.0					16																	2345597		2198	4300	6498	2285598	SO:0001583	missense	21	exon18			U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.2408C>T	16.37:g.2345597G>A	ENSP00000301732:p.Thr803Met	Somatic		Capture	Illumina HiSeq	Phase_I	2285598	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148139	0.37923	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.82984	-1.67	5.65	4.67	0.58626	.	0.228442	0.44483	N	0.000454	D	0.82305	0.5008	M	0.77313	2.365	0.80722	D	1	P;D;P	0.55800	0.801;0.973;0.801	B;B;B	0.39299	0.279;0.296;0.296	D	0.85090	0.0951	10	0.56958	D	0.05	.	15.2494	0.73532	0.0:0.1409:0.859:0.0	.	803;807;803	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	M	803;807	ENSP00000301732:T803M	ENSP00000301732:T803M	T	-	2	0	ABCA3	2285598	1.000000	0.71417	0.890000	0.34922	0.838000	0.47535	7.409000	0.80053	1.565000	0.49641	0.655000	0.94253	ACG		0.632	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
ATF7IP2	80063	broad.mit.edu	37	16	10534248	10534248	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr16:10534248A>G	ENST00000396560.2	+	6	1350	c.1123A>G	c.(1123-1125)Att>Gtt	p.I375V	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.I375V|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.I375V|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.I375V	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.I375V(1)		large_intestine(3)	3						TCAAAGACGTATTAAAACAGT	0.294																																					p.I375V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1123G	16						.						38.0	40.0	39.0					16																	10534248		2190	4293	6483	10441749	SO:0001583	missense	80063	exon5			AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.1123A>G	16.37:g.10534248A>G	ENSP00000379808:p.Ile375Val	Somatic		Capture	Illumina HiSeq	Phase_I	10441749	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	.	.	.	.	.	.	.	.	.	.	A	5.959	0.360844	0.11296	.	.	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13	4.42	2.14	0.27477	.	0.236755	0.29565	N	0.011795	T	0.25005	0.0607	L	0.31065	0.9	0.23859	N	0.996645	B;B	0.31705	0.336;0.021	B;B	0.27796	0.083;0.022	T	0.10776	-1.0615	10	0.36615	T	0.2	-3.6356	6.1972	0.20555	0.7866:0.0:0.2134:0.0	.	375;375	Q5U623-2;Q5U623	.;MCAF2_HUMAN	V	375	ENSP00000379807:I375V;ENSP00000379808:I375V;ENSP00000440791:I375V;ENSP00000348799:I375V;ENSP00000322811:I375V	ENSP00000322811:I375V	I	+	1	0	ATF7IP2	10441749	1.000000	0.71417	0.917000	0.36280	0.475000	0.33008	0.519000	0.22862	0.193000	0.20303	-0.353000	0.07706	ATT		0.294	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
ATXN2L	11273	broad.mit.edu	37	16	28841955	28841955	+	Silent	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr16:28841955C>T	ENST00000336783.4	+	9	1221	c.1054C>T	c.(1054-1056)Ctg>Ttg	p.L352L	RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000382686.4_Silent_p.L352L|ATXN2L_ENST00000325215.6_Silent_p.L352L|ATXN2L_ENST00000395547.2_Silent_p.L352L|ATXN2L_ENST00000564304.1_Silent_p.L352L|ATXN2L_ENST00000570200.1_Silent_p.L352L|ATXN2L_ENST00000340394.8_Silent_p.L352L	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	352					regulation of cytoplasmic mRNA processing body assembly (GO:0010603)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|membrane (GO:0016020)|nuclear speck (GO:0016607)	poly(A) RNA binding (GO:0044822)	p.L352L(2)		breast(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36						GTATATCCCTCTGCCTCAACG	0.557																																					p.L352L												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1054T	16						.						41.0	40.0	40.0					16																	28841955		2197	4300	6497	28749456	SO:0001819	synonymous_variant	11273	exon9				CCDS10639.1, CCDS10640.1, CCDS10641.1, CCDS32423.1, CCDS45451.1, CCDS58443.1	16p11	2008-02-05			ENSG00000168488	ENSG00000168488			31326	protein-coding gene	gene with protein product		607931				11784712, 14769358	Standard	NM_007245		Approved	A2lp, A2D	uc002dqy.4	Q8WWM7	OTTHUMG00000097038	ENST00000336783.4:c.1054C>T	16.37:g.28841955C>T		Somatic		Capture	Illumina HiSeq	Phase_I	28749456	NM_148415	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Silent	SNP	ENST00000336783.4	37	CCDS10641.1																																																																																				0.557	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245	
CD2BP2	10421	broad.mit.edu	37	16	30365289	30365289	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr16:30365289G>T	ENST00000305596.3	-	4	483	c.308C>A	c.(307-309)gCc>gAc	p.A103D	CD2BP2_ENST00000569466.1_Missense_Mutation_p.A103D|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	103					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)	p.A103D(1)		breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						GTTGCCATCGGCATCAAAGTG	0.617																																					p.A103D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C308A	16						.						86.0	84.0	84.0					16																	30365289		2197	4300	6497	30272790	SO:0001583	missense	10421	exon4			AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 59"""	604470	"""CD2 antigen (cytoplasmic tail)-binding protein 2"""			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.308C>A	16.37:g.30365289G>T	ENSP00000304903:p.Ala103Asp	Somatic		Capture	Illumina HiSeq	Phase_I	30272790	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	37	CCDS10675.1	.	.	.	.	.	.	.	.	.	.	g	17.62	3.434997	0.62955	.	.	ENSG00000169217	ENST00000305596	T	0.32023	1.47	5.39	5.39	0.77823	.	0.052285	0.85682	D	0.000000	T	0.21103	0.0508	N	0.25789	0.76	0.54753	D	0.999989	B	0.32302	0.363	B	0.22386	0.039	T	0.05225	-1.0898	10	0.15499	T	0.54	1.6863	17.9376	0.89017	0.0:0.0:1.0:0.0	.	103	O95400	CD2B2_HUMAN	D	103	ENSP00000304903:A103D	ENSP00000304903:A103D	A	-	2	0	CD2BP2	30272790	1.000000	0.71417	0.982000	0.44146	0.844000	0.47949	8.517000	0.90555	2.523000	0.85059	0.558000	0.71614	GCC		0.617	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110	
FN3KRP	79672	broad.mit.edu	37	17	80674690	80674691	+	Frame_Shift_Ins	INS	-	-	G	rs200977511		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr17:80674690_80674691insG	ENST00000269373.6	+	1	132_133	c.59_60insG	c.(58-63)tcggggfs	p.SG20fs	FN3KRP_ENST00000535965.1_5'UTR|RP11-388C12.1_ENST00000574471.1_lincRNA	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	20							kinase activity (GO:0016301)	p.G23fs*31(1)		breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			ACGGGCCACTCGGGGGGCGGGT	0.708																																					p.S20fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.59_60insG	17						.			12,4222		1,10,2106						4.3	0.2			22	4,8204		0,4,4100	no	frameshift	FN3KRP	NM_024619.3		1,14,6206	A1A1,A1R,RR		0.0487,0.2834,0.1286				16,12426				78267980	SO:0001589	frameshift_variant	79672	exon1			AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.65dupG	17.37:g.80674696_80674696dupG	ENSP00000269373:p.Ser20fs	Somatic		Capture	Illumina HiSeq	Phase_I	78267979	NM_024619	Q969F4|Q9H0U7	Frame_Shift_Ins	INS	ENST00000269373.6	37	CCDS11817.1																																																																																				0.708	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
SMG6	23293	broad.mit.edu	37	17	2196186	2196186	+	Missense_Mutation	SNP	G	G	A	rs371760718		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr17:2196186G>A	ENST00000263073.6	-	5	2287	c.2237C>T	c.(2236-2238)gCg>gTg	p.A746V	SMG6_ENST00000544865.1_Missense_Mutation_p.A715V	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	746					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)	p.A746V(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CCCATAATTCGCTGTATCACT	0.458																																					p.A715V	Melanoma(59;28 1088 11621 25887 46638 50814)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2144T	17						.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	139.0	130.0	133.0		2144,2237	5.3	1.0	17		133	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	SMG6	NM_001170957.1,NM_017575.4	64,64	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	715/1389,746/1420	2196186	2,13004	2203	4300	6503	2142936	SO:0001583	missense	23293	exon5			AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.2237C>T	17.37:g.2196186G>A	ENSP00000263073:p.Ala746Val	Somatic		Capture	Illumina HiSeq	Phase_I	2142936	NM_001170957	B7Z874|O94837|Q86VH6|Q9UF60	Missense_Mutation	SNP	ENST00000263073.6	37	CCDS11016.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.405571	0.42715	0.0	2.33E-4	ENSG00000070366	ENST00000263073;ENST00000544865	T;T	0.17528	2.27;2.27	5.26	5.26	0.73747	Tetratricopeptide-like helical (1);	0.185206	0.47852	D	0.000216	T	0.14743	0.0356	L	0.44542	1.39	0.44316	D	0.997192	P	0.36944	0.574	B	0.31245	0.126	T	0.04752	-1.0929	10	0.29301	T	0.29	-1.4572	14.4731	0.67529	0.0:0.147:0.853:0.0	.	746	Q86US8	EST1A_HUMAN	V	746;715	ENSP00000263073:A746V;ENSP00000443920:A715V	ENSP00000263073:A746V	A	-	2	0	SMG6	2142936	1.000000	0.71417	1.000000	0.80357	0.354000	0.29330	5.375000	0.66173	2.469000	0.83416	0.467000	0.42956	GCG		0.458	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
MAP2K4	6416	broad.mit.edu	37	17	12028657	12028657	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr17:12028657G>A	ENST00000353533.5	+	8	923	c.860G>A	c.(859-861)cGc>cAc	p.R287H	MAP2K4_ENST00000415385.3_Missense_Mutation_p.R298H	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	287	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(3)|p.R287H(2)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		TATGATGTCCGCTCTGATGTC	0.398			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																p.R287H			Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	.	15	Whole gene deletion(10)|Unknown(3)|Substitution - Missense(2)	breast(4)|ovary(4)|large_intestine(3)|lung(2)|biliary_tract(1)|pancreas(1)	c.G860A	17						.						251.0	196.0	215.0					17																	12028657		2203	4300	6503	11969382	SO:0001583	missense	6416	exon8			L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.860G>A	17.37:g.12028657G>A	ENSP00000262445:p.Arg287His	Somatic		Capture	Illumina HiSeq	Phase_I	11969382	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244669	0.59103	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.21191	2.02;2.02	5.1	5.1	0.69264	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48768	0.1518	M	0.73753	2.245	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.998	T	0.49051	-0.8979	10	0.87932	D	0	.	17.8064	0.88602	0.0:0.0:1.0:0.0	.	159;298;287	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	H	287;298;264;159	ENSP00000262445:R287H;ENSP00000410402:R298H	ENSP00000262445:R287H	R	+	2	0	MAP2K4	11969382	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.561000	0.98142	2.814000	0.96858	0.563000	0.77884	CGC		0.398	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1		
ZNF536	9745	broad.mit.edu	37	19	31040301	31040302	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr19:31040301_31040302insA	ENST00000355537.3	+	4	3922_3923	c.3775_3776insA	c.(3775-3777)gacfs	p.D1259fs		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1259					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CCAGAGCCTGGACAAGCCGATG	0.594																																					p.D1259fs												.	.	0			c.3775_3776insA	19						.																																			35732142	SO:0001589	frameshift_variant	9745	exon4				CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3776dupA	19.37:g.31040302_31040302dupA	ENSP00000347730:p.Asp1259fs	None		Capture	Illumina HiSeq	Phase_I	35732141	NM_014717	A2RU18	Frame_Shift_Ins	INS	ENST00000355537.3	37	CCDS32984.1																																																																																				0.594	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
THEG	51298	broad.mit.edu	37	19	375839	375839	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr19:375839G>A	ENST00000342640.4	-	1	174	c.132C>T	c.(130-132)gaC>gaT	p.D44D	THEG_ENST00000346878.2_Silent_p.D44D	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	44					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)		p.D44D(1)		NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGTTCGGGGTCTGTGACCC	0.682																																					p.D44D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C132T	19						.						43.0	49.0	47.0					19																	375839		2203	4300	6503	326839	SO:0001819	synonymous_variant	51298	exon1			AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"""cancer/testis antigen 56"""	609503	"""Theg homolog (mouse)"""			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.132C>T	19.37:g.375839G>A		Somatic		Capture	Illumina HiSeq	Phase_I	326839	NM_199202	A6NMJ8	Silent	SNP	ENST00000342640.4	37	CCDS12025.1																																																																																				0.682	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		
CLEC4M	10332	broad.mit.edu	37	19	7830936	7830937	+	Missense_Mutation	DNP	GG	GG	CC	rs59003279|rs59002457	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr19:7830936_7830937GG>CC	ENST00000327325.5	+	4	745_746	c.627_628GG>CC	c.(625-630)acGGag>acCCag	p.E210Q	CLEC4M_ENST00000597522.1_Intron|CLEC4M_ENST00000595496.1_Intron|CLEC4M_ENST00000334806.5_Missense_Mutation_p.E159Q|CLEC4M_ENST00000248228.4_Missense_Mutation_p.E188Q|CLEC4M_ENST00000357361.2_Missense_Mutation_p.E210Q|CLEC4M_ENST00000394122.2_Missense_Mutation_p.E198Q|CLEC4M_ENST00000596707.1_Missense_Mutation_p.E189Q|CLEC4M_ENST00000359059.5_Missense_Mutation_p.E166Q|CLEC4M_ENST00000596363.1_Missense_Mutation_p.E182Q	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	210	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.T209T(2)|p.T209>?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						AGGAGCTGACGGAGCTGAAGGC	0.579																																					.												.	.	3	Substitution - coding silent(2)|Complex(1)	large_intestine(2)|endometrium(1)	c.474_475CC	19						.																																			7736937	SO:0001583	missense	10332	exon4			AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		Exception_encountered	19.37:g.7830936_7830937delinsCC	ENSP00000316228:p.Glu210Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7736936	NM_001144904	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	DNP	ENST00000327325.5	37	CCDS12187.1																																																																																				0.579	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
PRPF31	26121	broad.mit.edu	37	19	54634776	54634777	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr19:54634776_54634777delGG	ENST00000321030.4	+	14	1762_1763	c.1413_1414delGG	c.(1411-1416)aaggtgfs	p.KV471fs	PRPF31_ENST00000419967.1_Frame_Shift_Del_p.G450fs|PRPF31_ENST00000391755.1_Frame_Shift_Del_p.KV465fs	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	471					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)	p.K471fs*3(1)		breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CAGAGAAGAAGGTGGCTGAGGC	0.564																																					p.471_472del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1413_1414del	19						.																																			59326589	SO:0001589	frameshift_variant	26121	exon14			AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"""PRP31 pre-mRNA processing factor 31 homolog (yeast)"", ""PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"""	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.1413_1414delGG	19.37:g.54634776_54634777delGG	ENSP00000324122:p.Lys471fs	Somatic		Capture	Illumina HiSeq	Phase_I	59326588	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Frame_Shift_Del	DEL	ENST00000321030.4	37	CCDS12879.1																																																																																				0.564	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
LILRB1	10859	broad.mit.edu	37	19	55146728	55146728	+	Silent	SNP	T	T	C	rs139400692		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr19:55146728T>C	ENST00000396331.1	+	13	1935	c.1578T>C	c.(1576-1578)gaT>gaC	p.D526D	LILRB1_ENST00000324602.7_Silent_p.D527D|LILRB1_ENST00000462628.1_3'UTR|LILRB1_ENST00000427581.2_Silent_p.D576D|LILRB1_ENST00000448689.1_Missense_Mutation_p.M501T|LILRB1_ENST00000396327.3_Silent_p.D527D|LILRB1_ENST00000396332.4_Silent_p.D526D|LILRB1_ENST00000396317.1_Silent_p.D510D|LILRB1_ENST00000434867.2_Silent_p.D526D|LILRB1_ENST00000396321.2_Silent_p.D526D|LILRB1_ENST00000418536.2_Silent_p.D510D|LILRB1_ENST00000396315.1_Silent_p.D527D	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	526					cellular response to lipopolysaccharide (GO:0071222)|defense response to virus (GO:0051607)|dendritic cell differentiation (GO:0097028)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|interferon-gamma production (GO:0032609)|interferon-gamma secretion (GO:0072643)|negative regulation of alpha-beta T cell activation (GO:0046636)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of CD8-positive, alpha-beta T cell activation (GO:2001186)|negative regulation of cell cycle (GO:0045786)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of endocytosis (GO:0045806)|negative regulation of interferon-beta secretion (GO:0035548)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-12 secretion (GO:2001183)|negative regulation of mononuclear cell proliferation (GO:0032945)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|negative regulation of osteoclast development (GO:2001205)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001189)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transforming growth factor-beta secretion (GO:2001202)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytolysis (GO:0045919)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of gamma-delta T cell activation involved in immune response (GO:2001193)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor internalization (GO:0031623)|regulation of immune response (GO:0050776)|response to virus (GO:0009615)|signal transduction (GO:0007165)|T cell proliferation involved in immune response (GO:0002309)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	HLA-A specific inhibitory MHC class I receptor activity (GO:0030107)|HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)|MHC class I protein binding (GO:0042288)|MHC class I receptor activity (GO:0032393)|protein homodimerization activity (GO:0042803)|protein phosphatase 1 binding (GO:0008157)|SH2 domain binding (GO:0042169)	p.D526D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(38)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	74				GBM - Glioblastoma multiforme(193;0.0188)		CAGCTGCCGATGCCCAGGAAG	0.612										HNSCC(37;0.09)																											p.D526D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1578C	19						.	T	,,,	3,4403	4.2+/-10.8	0,3,2200	65.0	72.0	70.0		1581,1581,1578,1578	0.2	0.0	19	dbSNP_134	70	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	,,,	0,9,6490	CC,CT,TT		0.0698,0.0681,0.0692	,,,	527/653,527/652,526/652,526/651	55146728	9,12989	2203	4296	6499	59838540	SO:0001819	synonymous_variant	10859	exon12			AF009220	CCDS42614.1, CCDS42615.1, CCDS42616.1, CCDS42617.1, CCDS62803.1	19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6605	protein-coding gene	gene with protein product		604811				9285411, 9382880	Standard	XM_006726246		Approved	LIR-1, ILT2, MIR-7, CD85, LIR1, CD85j	uc002qgm.3	Q8NHL6		ENST00000396331.1:c.1578T>C	19.37:g.55146728T>C		Somatic		Capture	Illumina HiSeq	Phase_I	59838540	NM_001081639	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Silent	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	T	0.001	-2.934463	0.00053	6.81E-4	6.98E-4	ENSG00000104972	ENST00000448689	T	0.00484	7.08	1.35	0.234	0.15390	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.16217	-1.0410	6	0.10636	T	0.68	.	3.9581	0.09399	0.0:0.7519:0.0:0.2481	.	.	.	.	T	501	ENSP00000409968:M501T	ENSP00000410165:M501T	M	+	2	0	LILRB1	59838540	0.000000	0.05858	0.001000	0.08648	0.024000	0.10985	-1.014000	0.03641	0.124000	0.18369	-1.216000	0.01612	ATG		0.612	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4		
ADAMTSL4	54507	broad.mit.edu	37	1	150530505	150530506	+	Frame_Shift_Ins	INS	-	-	GG	rs149280379		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:150530505_150530506insGG	ENST00000369038.2	+	12	2463_2464	c.2262_2263insGG	c.(2263-2265)gggfs	p.G755fs	ADAMTSL4_ENST00000369039.5_Frame_Shift_Ins_p.G778fs|RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Frame_Shift_Ins_p.G755fs|ADAMTSL4_ENST00000369041.5_Frame_Shift_Ins_p.G755fs			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	755	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)	p.F754L(1)		breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGCAGGAATTTGGGGGGGGTGG	0.693																																					p.F754fs												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.2262_2263insGG	1						.																																			148797130	SO:0001589	frameshift_variant	54507	exon14			BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.2269_2270dupGG	1.37:g.150530512_150530513dupGG	ENSP00000358034:p.Gly755fs	None		Capture	Illumina HiSeq	Phase_I	148797129	NM_025008	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Frame_Shift_Ins	INS	ENST00000369038.2	37	CCDS955.1																																																																																				0.693	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
RPRD2	23248	broad.mit.edu	37	1	150381476	150381477	+	Intron	INS	-	-	TA	rs201753698|rs3037594|rs5777726	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:150381476_150381477insTA	ENST00000369068.4	+	2	209				RPRD2_ENST00000369067.3_Intron|RPRD2_ENST00000539519.1_Intron|RPRD2_ENST00000401000.4_Intron|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2							DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ATTGAAAACACTGTATCAGCTG	0.371														2516	0.502396	0.7012	0.4942	5008	,	,		19863	0.2827		0.5934	False		,,,				2504	0.3722				.												.	.	0			.	1						.																																			148648101	SO:0001627	intron_variant	23248	.			BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.206-8595->TA	1.37:g.150381476_150381477insTA		Somatic		Capture	Illumina HiSeq	Phase_I	148648100	.	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	De_novo_Start_OutOfFrame	INS	ENST00000369068.4	37	CCDS44216.1																																																																																				0.371	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
ZNF687	57592	broad.mit.edu	37	1	151260053	151260053	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:151260053G>A	ENST00000368879.2	+	2	1384	c.1286G>A	c.(1285-1287)gGg>gAg	p.G429E		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	429					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G429E(1)		breast(2)|central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(2)	32	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			CTGCCTGGGGGGACTGCCACC	0.642																																					p.G429E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1286A	1						.						40.0	41.0	41.0					1																	151260053		2203	4300	6503	149526677	SO:0001583	missense	57592	exon2				CCDS992.1	1q21.2	2008-05-02			ENSG00000143373	ENSG00000143373			29277	protein-coding gene	gene with protein product		610568				10718198	Standard	NM_020832		Approved	KIAA1441	uc001exq.3	Q8N1G0	OTTHUMG00000012347	ENST00000368879.2:c.1286G>A	1.37:g.151260053G>A	ENSP00000357874:p.Gly429Glu	Somatic		Capture	Illumina HiSeq	Phase_I	149526677	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Missense_Mutation	SNP	ENST00000368879.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.62|11.62	1.692849|1.692849	0.30052|0.30052	.|.	.|.	ENSG00000143373|ENSG00000143373	ENST00000336715;ENST00000324048;ENST00000368879|ENST00000426871	T;T;T|T	0.00792|0.00637	5.69;5.69;6.02|6.05	4.35|4.35	2.37|2.37	0.29283|0.29283	.|.	0.519865|0.519865	0.14517|0.14517	N|N	0.314735|0.314735	T|T	0.00356|0.00356	0.0011|0.0011	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	D;D;D|.	0.76494|.	0.993;0.995;0.999|.	D;P;D|.	0.74023|.	0.915;0.791;0.982|.	T|T	0.48811|0.48811	-0.9002|-0.9002	10|8	0.51188|0.56958	T|D	0.08|0.05	.|.	5.5134|5.5134	0.16894|0.16894	0.16:0.4637:0.3763:0.0|0.16:0.4637:0.3763:0.0	.|.	429;429;429|.	Q8N1G0-2;Q8N1G0;F8WCX2|.	.;ZN687_HUMAN;.|.	E|R	429|32	ENSP00000336620:G429E;ENSP00000319829:G429E;ENSP00000357874:G429E|ENSP00000398821:G32R	ENSP00000319829:G429E|ENSP00000398821:G32R	G|G	+|+	2|1	0|0	ZNF687|ZNF687	149526677|149526677	0.924000|0.924000	0.31332|0.31332	0.613000|0.613000	0.29037|0.29037	0.922000|0.922000	0.55478|0.55478	3.327000|3.327000	0.52045|0.52045	0.686000|0.686000	0.31488|0.31488	0.511000|0.511000	0.50034|0.50034	GGG|GGA		0.642	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
FLG	2312	broad.mit.edu	37	1	152279018	152279018	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:152279018C>T	ENST00000368799.1	-	3	8379	c.8344G>A	c.(8344-8346)Ggt>Agt	p.G2782S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2782	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.G2782C(1)|p.G2782S(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGTCCTGACCGTCTTGGGAT	0.602									Ichthyosis																												p.G2782S												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G8344A	1						.						452.0	589.0	542.0					1																	152279018		2197	4300	6497	150545642	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.8344G>A	1.37:g.152279018C>T	ENSP00000357789:p.Gly2782Ser	Somatic		Capture	Illumina HiSeq	Phase_I	150545642	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.796142	0.31777	.	.	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.07327	3.2	3.43	-3.86	0.04230	.	.	.	.	.	T	0.02156	0.0067	M	0.66506	2.035	0.09310	N	1	B	0.34349	0.45	B	0.16289	0.015	T	0.31475	-0.9942	9	0.66056	D	0.02	7.8015	4.5156	0.11934	0.0:0.2616:0.3148:0.4236	.	2782	P20930	FILA_HUMAN	S	2782;44	ENSP00000357789:G2782S	ENSP00000357786:G44S	G	-	1	0	FLG	150545642	0.250000	0.23951	0.000000	0.03702	0.036000	0.12997	0.628000	0.24522	-0.841000	0.04200	0.306000	0.20318	GGT		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EPHA2	1969	broad.mit.edu	37	1	16477403	16477403	+	Silent	SNP	C	C	T	rs370213656		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:16477403C>T	ENST00000358432.5	-	2	295	c.141G>A	c.(139-141)ccG>ccA	p.P47P	EPHA2_ENST00000461614.1_Intron	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	47	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.|Mediates interaction with CLDN4.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P47P(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	CTTTGCCATACGGGTGTGTGA	0.612																																					p.P47P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G141A	1						.	C		0,4406		0,0,2203	109.0	104.0	106.0		141	-11.7	0.3	1		106	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	EPHA2	NM_004431.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		47/977	16477403	2,13004	2203	4300	6503	16349990	SO:0001819	synonymous_variant	1969	exon2			BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.141G>A	1.37:g.16477403C>T		Somatic		Capture	Illumina HiSeq	Phase_I	16349990	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																				0.612	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
CRNN	49860	broad.mit.edu	37	1	152383218	152383218	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:152383218C>T	ENST00000271835.3	-	3	402	c.340G>A	c.(340-342)Ggc>Agc	p.G114S	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	114					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)	p.G114S(1)		breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTCCTTCGCCCAGCTCCTGC	0.617																																					p.G114S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G340A	1						.						142.0	159.0	153.0					1																	152383218		2203	4300	6503	150649842	SO:0001583	missense	49860	exon3			AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"""EF-hand domain containing"""	1230	protein-coding gene	gene with protein product		611312	"""chromosome 1 open reading frame 10"""	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.340G>A	1.37:g.152383218C>T	ENSP00000271835:p.Gly114Ser	Somatic		Capture	Illumina HiSeq	Phase_I	150649842	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.832|9.832	1.188686|1.188686	0.21954|0.21954	.|.	.|.	ENSG00000143536|ENSG00000143536	ENST00000451038|ENST00000271835	.|T	.|0.04234	.|3.67	4.63|4.63	-1.43|-1.43	0.08884|0.08884	.|.	0.848072|0.848072	0.10168|0.10168	N|N	0.707539|0.707539	T|T	0.01320|0.01320	0.0043|0.0043	L|L	0.58810|0.58810	1.83|1.83	0.09310|0.09310	N|N	1|1	.|B	.|0.10296	.|0.003	.|B	.|0.12156	.|0.007	T|T	0.47749|0.47749	-0.9093|-0.9093	7|10	0.13470|0.13853	T|T	0.59|0.58	.|.	5.4689|5.4689	0.16658|0.16658	0.0:0.4159:0.1446:0.4395|0.0:0.4159:0.1446:0.4395	.|.	.|114	.|Q9UBG3	.|CRNN_HUMAN	R|S	114|114	.|ENSP00000271835:G114S	ENSP00000402565:G114R|ENSP00000271835:G114S	G|G	-|-	1|1	0|0	CRNN|CRNN	150649842|150649842	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	-0.141000|-0.141000	0.10327|0.10327	-0.379000|-0.379000	0.07906|0.07906	-1.842000|-1.842000	0.00583|0.00583	GGG|GGC		0.617	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
AXDND1	126859	broad.mit.edu	37	1	179478463	179478463	+	Silent	SNP	T	T	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:179478463T>C	ENST00000367618.3	+	21	2808	c.2421T>C	c.(2419-2421)tcT>tcC	p.S807S		NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	807								p.S807S(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						ACACATGCTCTTGCCTCCTTT	0.368																																					p.S807S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2421C	1						.						87.0	82.0	83.0					1																	179478463		2203	4300	6503	177745086	SO:0001819	synonymous_variant	126859	exon21			BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.2421T>C	1.37:g.179478463T>C		Somatic		Capture	Illumina HiSeq	Phase_I	177745086	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Silent	SNP	ENST00000367618.3	37	CCDS30948.1																																																																																				0.368	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
CACNA1E	777	broad.mit.edu	37	1	181741306	181741306	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:181741306G>A	ENST00000367573.2	+	37	5078	c.5078G>A	c.(5077-5079)cGc>cAc	p.R1693H	CACNA1E_ENST00000358338.5_Missense_Mutation_p.R1625H|CACNA1E_ENST00000357570.5_Missense_Mutation_p.R1644H|CACNA1E_ENST00000367567.4_Missense_Mutation_p.R1300H|CACNA1E_ENST00000360108.3_Missense_Mutation_p.R1674H|CACNA1E_ENST00000526775.1_Missense_Mutation_p.R1674H|RNA5SP70_ENST00000517168.1_RNA|CACNA1E_ENST00000367570.1_Missense_Mutation_p.R1693H	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1693					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)	p.R1693H(1)		NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						GAGAACGAACGCTGCGGCACC	0.557																																					p.R1693H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5078A	1						.						201.0	202.0	202.0					1																	181741306		2190	4281	6471	180007929	SO:0001583	missense	777	exon37			AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.5078G>A	1.37:g.181741306G>A	ENSP00000356545:p.Arg1693His	Somatic		Capture	Illumina HiSeq	Phase_I	180007929	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.197467	0.79015	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98701	-5.08;-5.08;-5.08;-5.08;-5.08;-5.08;-5.08	5.5	5.5	0.81552	Ion transport (1);	0.098253	0.64402	D	0.000001	D	0.98400	0.9468	L	0.49571	1.57	0.50467	D	0.999876	D;P;P	0.59767	0.986;0.938;0.938	P;P;P	0.61874	0.895;0.626;0.511	D	0.98572	1.0646	10	0.66056	D	0.02	.	13.3362	0.60518	0.0762:0.0:0.9238:0.0	.	1674;1693;1693	Q15878-2;Q15878;Q15878-3	.;CAC1E_HUMAN;.	H	1693;1674;1644;1625;1300;1674;1693	ENSP00000356542:R1693H;ENSP00000434814:R1674H;ENSP00000350183:R1644H;ENSP00000351101:R1625H;ENSP00000356539:R1300H;ENSP00000353222:R1674H;ENSP00000356545:R1693H	ENSP00000350183:R1644H	R	+	2	0	CACNA1E	180007929	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.841000	0.55850	2.588000	0.87417	0.643000	0.83706	CGC		0.557	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
NAV1	89796	broad.mit.edu	37	1	201750299	201750299	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:201750299G>A	ENST00000367296.4	+	5	1945	c.1525G>A	c.(1525-1527)Gat>Aat	p.D509N	NAV1_ENST00000367297.4_Missense_Mutation_p.D509N|NAV1_ENST00000367295.1_Missense_Mutation_p.D118N|NAV1_ENST00000367302.1_Missense_Mutation_p.D522N|IPO9-AS1_ENST00000413035.1_RNA|NAV1_ENST00000295624.6_Missense_Mutation_p.D509N|NAV1_ENST00000367300.3_Missense_Mutation_p.D509N	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	509					microtubule bundle formation (GO:0001578)|neuron migration (GO:0001764)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.D509N(1)		breast(5)|central_nervous_system(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(10)|lung(29)|ovary(4)|prostate(3)|skin(1)|stomach(2)	70						TGAGAGCTGTGATGATTCATC	0.552																																					p.D118N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G352A	1						.						90.0	95.0	93.0					1																	201750299		2203	4300	6503	200016922	SO:0001583	missense	89796	exon3			AF086348	CCDS1414.1, CCDS1414.2, CCDS53456.1	1q32.3	2008-07-18			ENSG00000134369	ENSG00000134369			15989	protein-coding gene	gene with protein product	"""neuron navigator-1"", ""pore membrane and/or filament interacting like protein 3"""	611628				12079279, 12062803	Standard	NM_020443		Approved	FLJ12560, FLJ14203, KIAA1151, MGC14961, POMFIL3, steerin-1, DKFZp781D0314	uc001gwu.3	Q8NEY1	OTTHUMG00000035766	ENST00000367296.4:c.1525G>A	1.37:g.201750299G>A	ENSP00000356265:p.Asp509Asn	Somatic		Capture	Illumina HiSeq	Phase_I	200016922	NM_001167738	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	G	24.3	4.519159	0.85495	.	.	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000391966;ENST00000367295	T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29	5.78	5.78	0.91487	.	0.291916	0.37304	N	0.002143	T	0.38612	0.1047	L	0.43923	1.385	0.53688	D	0.999979	B;B;B;B	0.30361	0.152;0.137;0.277;0.241	B;B;B;B	0.33042	0.051;0.133;0.157;0.051	T	0.23833	-1.0177	10	0.87932	D	0	-16.4422	19.619	0.95647	0.0:0.0:1.0:0.0	.	118;509;17;509	Q8NEY1-5;Q8NEY1;A8MYI2;Q8NEY1-3	.;NAV1_HUMAN;.;.	N	522;509;509;509;509;17;118	ENSP00000356271:D522N;ENSP00000356265:D509N;ENSP00000295624:D509N;ENSP00000356266:D509N;ENSP00000356269:D509N;ENSP00000356264:D118N	ENSP00000295624:D509N	D	+	1	0	NAV1	200016922	1.000000	0.71417	0.811000	0.32455	0.989000	0.77384	6.454000	0.73493	2.717000	0.92951	0.655000	0.94253	GAT		0.552	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443	
CASZ1	54897	broad.mit.edu	37	1	10699141	10699146	+	In_Frame_Del	DEL	TCGTCG	TCGTCG	-	rs201089181	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	TCGTCG	TCGTCG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:10699141_10699146delTCGTCG	ENST00000377022.3	-	21	5450_5455	c.5133_5138delCGACGA	c.(5131-5139)gacgacgag>gag	p.DD1711del	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1711	Asp-rich.|Glu-rich.				multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D1711_D1712delDD(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		GCGCAGgtcctcgtcgtcgtcgtcct	0.752														356	0.0710863	0.0696	0.036	5008	,	,		2110	0.0804		0.0348	False		,,,				2504	0.1258				p.1711_1713del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.5133_5138del	1						.			213,13,2916		50,0,113,2,9,1397						3.1	1.0		dbSNP_131	3	215,29,6202		36,0,143,0,29,3015	no	codingComplex	CASZ1	NM_001079843.1		86,0,256,2,38,4412	A1A1,A1A2,A1R,A2A2,A2R,RR		3.7853,7.1929,4.902				428,42,9118				10621733	SO:0001651	inframe_deletion	54897	exon21			AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.5133_5138delCGACGA	1.37:g.10699147_10699152delTCGTCG	ENSP00000366221:p.Asp1711_Asp1712del	Somatic		Capture	Illumina HiSeq	Phase_I	10621728	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	In_Frame_Del	DEL	ENST00000377022.3	37	CCDS41246.1																																																																																				0.752	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
FOXJ3	22887	broad.mit.edu	37	1	42647652	42647652	+	Silent	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:42647652C>T	ENST00000372572.1	-	14	2000	c.1689G>A	c.(1687-1689)gtG>gtA	p.V563V	FOXJ3_ENST00000361776.1_Silent_p.V529V|FOXJ3_ENST00000372573.1_Silent_p.V563V|FOXJ3_ENST00000545068.1_Silent_p.V563V|FOXJ3_ENST00000361346.1_Silent_p.V563V|FOXJ3_ENST00000372571.1_Silent_p.V77V	NM_001198851.1	NP_001185780.1	Q9UPW0	FOXJ3_HUMAN	forkhead box J3	563					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V563V(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18	Ovarian(52;0.01)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGTGGCATCACTGAAGGAG	0.438																																					p.V563V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1689A	1						.						93.0	86.0	88.0					1																	42647652		2203	4300	6503	42420239	SO:0001819	synonymous_variant	22887	exon14			AB028964	CCDS30689.1, CCDS55594.1	1p34.2	2008-04-10			ENSG00000198815	ENSG00000198815		"""Forkhead boxes"""	29178	protein-coding gene	gene with protein product							Standard	NM_014947		Approved	KIAA1041	uc001chf.3	Q9UPW0	OTTHUMG00000007026	ENST00000372572.1:c.1689G>A	1.37:g.42647652C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42420239	NM_001198851	A7MBL7|A7MD18|D3DPW2|Q9NSS7	Silent	SNP	ENST00000372572.1	37	CCDS30689.1																																																																																				0.438	FOXJ3-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000018310.1	NM_014947	
CPT2	1376	broad.mit.edu	37	1	53676799	53676799	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:53676799A>C	ENST00000371486.3	+	4	1968	c.1453A>C	c.(1453-1455)Acc>Ccc	p.T485P	RP5-1024G6.2_ENST00000452466.1_RNA	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	485					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	15					L-Carnitine(DB00583)|Perhexiline(DB01074)	GACAGTGGCCACCTACGAGTC	0.587																																					p.T485P												.	.	0			c.A1453C	1						.						39.0	37.0	38.0					1																	53676799		2203	4300	6503	53449387	SO:0001583	missense	1376	exon4			BC002445	CCDS575.1	1p32.3	2014-01-09	2009-03-04		ENSG00000157184	ENSG00000157184	2.3.1.21		2330	protein-coding gene	gene with protein product		600650	"""carnitine palmitoyltransferase II"""	CPT1		1339389	Standard	NM_000098		Approved	CPTASE	uc001cvb.4	P23786	OTTHUMG00000008942	ENST00000371486.3:c.1453A>C	1.37:g.53676799A>C	ENSP00000360541:p.Thr485Pro	None		Capture	Illumina HiSeq	Phase_I	53449387	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357597	0.82243	.	.	ENSG00000157184	ENST00000371486	D	0.93019	-3.15	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.97467	0.9171	M	0.92833	3.35	0.80722	D	1	D	0.63046	0.992	D	0.77004	0.989	D	0.98415	1.0574	10	0.87932	D	0	-23.8723	16.1205	0.81351	1.0:0.0:0.0:0.0	.	485	P23786	CPT2_HUMAN	P	485	ENSP00000360541:T485P	ENSP00000360541:T485P	T	+	1	0	CPT2	53449387	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	9.339000	0.96797	2.205000	0.71048	0.533000	0.62120	ACC		0.587	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098	
USH2A	7399	broad.mit.edu	37	1	216040453	216040453	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr1:216040453C>T	ENST00000307340.3	-	44	9127	c.8741G>A	c.(8740-8742)cGa>cAa	p.R2914Q	USH2A_ENST00000366943.2_Missense_Mutation_p.R2914Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2914	Fibronectin type-III 15. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)	p.R2914Q(1)		NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		AGTCACTTCTCGGCTCGGTGT	0.428										HNSCC(13;0.011)																											p.R2914Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8741A	1						.						126.0	107.0	113.0					1																	216040453		2203	4300	6503	214107076	SO:0001583	missense	7399	exon44			AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.8741G>A	1.37:g.216040453C>T	ENSP00000305941:p.Arg2914Gln	Somatic		Capture	Illumina HiSeq	Phase_I	214107076	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	5.711	0.315717	0.10789	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.52983	0.64;0.64	5.72	-9.62	0.00547	Fibronectin, type III (2);Immunoglobulin-like fold (1);	1.379900	0.05579	N	0.572596	T	0.20659	0.0497	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20907	-1.0261	10	0.12103	T	0.63	.	10.0839	0.42406	0.0:0.2298:0.5232:0.247	.	2914	O75445	USH2A_HUMAN	Q	2914	ENSP00000305941:R2914Q;ENSP00000355910:R2914Q	ENSP00000305941:R2914Q	R	-	2	0	USH2A	214107076	0.027000	0.19231	0.000000	0.03702	0.038000	0.13279	-0.077000	0.11394	-2.123000	0.00823	-2.049000	0.00408	CGA		0.428	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
SEL1L2	80343	broad.mit.edu	37	20	13830200	13830200	+	Missense_Mutation	SNP	G	G	T	rs200162045		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr20:13830200G>T	ENST00000284951.5	-	20	2072	c.1998C>A	c.(1996-1998)caC>caA	p.H666Q	SEL1L2_ENST00000378072.5_Missense_Mutation_p.H553Q|SEL1L2_ENST00000486903.1_5'UTR			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	666						integral component of membrane (GO:0016021)		p.H666Q(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|lung(25)|ovary(2)|skin(3)|urinary_tract(1)	51						ATAAGTCCCAGTGTGGTCCAA	0.483																																					p.H666Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1998A	20						.						164.0	164.0	164.0					20																	13830200		1968	4158	6126	13778200	SO:0001583	missense	80343	exon20			AL137678	CCDS59443.1	20p12.1	2011-03-31	2006-11-24	2006-11-24	ENSG00000101251	ENSG00000101251			15897	protein-coding gene	gene with protein product		614289	"""chromosome 20 open reading frame 50"""	C20orf50			Standard	NM_001271539		Approved	DKFZp434C1826	uc010zrl.3	Q5TEA6	OTTHUMG00000031910	ENST00000284951.5:c.1998C>A	20.37:g.13830200G>T	ENSP00000284951:p.His666Gln	Somatic		Capture	Illumina HiSeq	Phase_I	13778200	NM_025229	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	G	7.142	0.582078	0.13749	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.21734	1.99;2.35	5.54	4.6	0.57074	.	0.350142	0.24856	N	0.035044	T	0.09949	0.0244	N	0.08118	0	0.27485	N	0.95246	B;B	0.24675	0.109;0.013	B;B	0.19666	0.026;0.012	T	0.25572	-1.0128	10	0.17832	T	0.49	-0.3648	10.079	0.42377	0.0915:0.0:0.9085:0.0	.	553;666	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	Q	553;666	ENSP00000367312:H553Q;ENSP00000284951:H666Q	ENSP00000284951:H666Q	H	-	3	2	SEL1L2	13778200	1.000000	0.71417	1.000000	0.80357	0.149000	0.21700	1.213000	0.32407	1.352000	0.45808	0.638000	0.83543	CAC		0.483	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229	
ZNF831	128611	broad.mit.edu	37	20	57829119	57829119	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr20:57829119C>T	ENST00000371030.2	+	5	4355	c.4355C>T	c.(4354-4356)gCc>gTc	p.A1452V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1452							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A1452V(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGCTGCTGGCCTCCCAGGAT	0.517																																					p.A1452V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4355T	20						.						69.0	73.0	72.0					20																	57829119		2010	4184	6194	57262514	SO:0001583	missense	128611	exon5			AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4355C>T	20.37:g.57829119C>T	ENSP00000360069:p.Ala1452Val	Somatic		Capture	Illumina HiSeq	Phase_I	57262514	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381928	0.42207	.	.	ENSG00000124203	ENST00000371030	T	0.04758	3.56	5.74	4.69	0.59074	.	0.654924	0.14050	N	0.344838	T	0.04227	0.0117	L	0.29908	0.895	0.09310	N	1	B	0.22003	0.063	B	0.19666	0.026	T	0.44003	-0.9356	10	0.15952	T	0.53	-4.2115	9.1784	0.37127	0.0:0.8849:0.0:0.1151	.	1452	Q5JPB2	ZN831_HUMAN	V	1452	ENSP00000360069:A1452V	ENSP00000360069:A1452V	A	+	2	0	ZNF831	57262514	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	0.552000	0.23376	1.340000	0.45581	0.650000	0.86243	GCC		0.517	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
COL20A1	57642	broad.mit.edu	37	20	61959790	61959790	+	Missense_Mutation	SNP	C	C	T	rs371016549		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr20:61959790C>T	ENST00000358894.6	+	34	3821	c.3721C>T	c.(3721-3723)Cgc>Tgc	p.R1241C	COL20A1_ENST00000326996.6_Missense_Mutation_p.R1273C|COL20A1_ENST00000435874.1_Missense_Mutation_p.R1254C|COL20A1_ENST00000422202.1_Missense_Mutation_p.R1254C	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1241					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)		p.R1240C(1)		NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					CCCTGGCACCCGCAGCAAGGC	0.667																																					p.P1240P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3720T	20						.	C	CYS/ARG	0,3838		0,0,1919	20.0	25.0	23.0		3721	0.8	0.0	20		23	1,8213		0,1,4106	no	missense	COL20A1	NM_020882.2	180	0,1,6025	TT,TC,CC		0.0122,0.0,0.0083	possibly-damaging	1241/1285	61959790	1,12051	1919	4107	6026	61430234	SO:0001583	missense	57642	exon34			BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3721C>T	20.37:g.61959790C>T	ENSP00000351767:p.Arg1241Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61430234	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.065107	0.36470	0.0	1.22E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202;ENST00000415763;ENST00000455906	D;D;D;D;D;D	0.91464	-2.2;-2.19;-2.19;-2.19;-2.85;-2.7	3.13	0.783	0.18572	.	0.688712	0.12868	U	0.432527	D	0.83298	0.5224	N	0.08118	0	0.09310	N	1	P;P	0.39831	0.69;0.564	P;B	0.47075	0.536;0.075	T	0.75263	-0.3379	10	0.72032	D	0.01	.	7.8728	0.29576	0.429:0.571:0.0:0.0	.	1254;1241	Q9P218-2;Q9P218	.;COKA1_HUMAN	C	1241;1273;1254;1254;382;237	ENSP00000351767:R1241C;ENSP00000323077:R1273C;ENSP00000408690:R1254C;ENSP00000414753:R1254C;ENSP00000410799:R382C;ENSP00000406345:R237C	ENSP00000323077:R1273C	R	+	1	0	COL20A1	61430234	0.003000	0.15002	0.005000	0.12908	0.475000	0.33008	0.556000	0.23438	0.408000	0.25621	0.313000	0.20887	CGC		0.667	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
DSCAM	1826	broad.mit.edu	37	21	41385141	41385141	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr21:41385141G>A	ENST00000400454.1	-	33	6336	c.5859C>T	c.(5857-5859)tcC>tcT	p.S1953S		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1953				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.S1953S(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				TGGAGGAGGCGGAGGAGGCGG	0.637																																					p.S1953S	Melanoma(134;970 1778 1785 21664 32388)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5859T	21						.						32.0	34.0	34.0					21																	41385141		1959	4132	6091	40307011	SO:0001819	synonymous_variant	1826	exon33			AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.5859C>T	21.37:g.41385141G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40307011	NM_001389	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																				0.637	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
RIPK4	54101	broad.mit.edu	37	21	43164174	43164174	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr21:43164174G>A	ENST00000352483.2	-	8	1271	c.1207C>T	c.(1207-1209)Cgc>Tgc	p.R403C	AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Missense_Mutation_p.R355C|RIPK4_ENST00000542057.1_Missense_Mutation_p.R292C|RIPK4_ENST00000544709.1_Missense_Mutation_p.R292C			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	403					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R403C(1)|p.R355C(1)		NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GAGGAGCTGCGGCTGAGCTCC	0.632																																					p.R355C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1063T	21						.						33.0	36.0	35.0					21																	43164174		2203	4300	6503	42037243	SO:0001583	missense	54101	exon7			AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"""Ankyrin repeat domain containing"""	496	protein-coding gene	gene with protein product	"""protein kinase C-associated kinase"", ""PKC-delta-interacting protein kinase"""	605706	"""ankyrin repeat domain 3"""	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.1207C>T	21.37:g.43164174G>A	ENSP00000330161:p.Arg403Cys	Somatic		Capture	Illumina HiSeq	Phase_I	42037243	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		.	.	.	.	.	.	.	.	.	.	G	24.0	4.482727	0.84747	.	.	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057;ENST00000330470	T;T;T;T	0.79141	-1.01;-1.01;-1.24;-1.24	5.06	5.06	0.68205	.	0.092177	0.47093	D	0.000252	T	0.73513	0.3596	N	0.08118	0	0.46774	D	0.999196	D	0.71674	0.998	P	0.56916	0.809	T	0.78713	-0.2097	10	0.48119	T	0.1	-37.6766	17.4187	0.87508	0.0:0.0:1.0:0.0	.	355	P57078-2	.	C	355;403;292;292;94	ENSP00000332454:R355C;ENSP00000330161:R403C;ENSP00000441754:R292C;ENSP00000442901:R292C	ENSP00000330975:R94C	R	-	1	0	RIPK4	42037243	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	3.822000	0.55708	2.340000	0.79590	0.655000	0.94253	CGC		0.632	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
SREBF2	6721	broad.mit.edu	37	22	42299029	42299030	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr22:42299029_42299030insT	ENST00000361204.4	+	17	3129_3130	c.2963_2964insT	c.(2962-2967)caaaaafs	p.Q988fs	MIR33A_ENST00000385197.1_RNA|SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	988					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						GCGCTCTGGCAAAAACAGGCCA	0.658																																					p.Q988fs												.	.	0			c.2963_2964insT	22						.																																			40628976	SO:0001589	frameshift_variant	6721	exon17			U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	Exception_encountered	22.37:g.42299029_42299030insT	ENSP00000354476:p.Gln988fs	None		Capture	Illumina HiSeq	Phase_I	40628975	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Frame_Shift_Ins	INS	ENST00000361204.4	37	CCDS14023.1																																																																																				0.658	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
SCUBE1	80274	broad.mit.edu	37	22	43617229	43617229	+	Missense_Mutation	SNP	C	C	T	rs150431448	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr22:43617229C>T	ENST00000360835.4	-	13	1625	c.1499G>A	c.(1498-1500)cGg>cAg	p.R500Q		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	500					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)	p.R500Q(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				GCTGTGGGGCCGGAGGTGGCA	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		12935	0.0		0.002	False		,,,				2504	0.0				p.R500Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1499A	22						.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	34.0	39.0	37.0		1499	-2.7	0.1	22	dbSNP_134	37	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SCUBE1	NM_173050.3	43	0,3,6499	TT,TC,CC		0.0233,0.0227,0.0231	benign	500/989	43617229	3,13001	2203	4299	6502	41947173	SO:0001583	missense	80274	exon13				CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.1499G>A	22.37:g.43617229C>T	ENSP00000354080:p.Arg500Gln	Somatic		Capture	Illumina HiSeq	Phase_I	41947173	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	C	5.847	0.340400	0.11069	2.27E-4	2.33E-4	ENSG00000159307	ENST00000360835	D	0.85171	-1.95	4.68	-2.66	0.06077	.	0.372012	0.28834	N	0.014000	T	0.68118	0.2966	N	0.17723	0.515	0.58432	D	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.49312	-0.8953	10	0.13853	T	0.58	.	10.4102	0.44289	0.0:0.5805:0.0:0.4195	.	500	Q8IWY4	SCUB1_HUMAN	Q	500	ENSP00000354080:R500Q	ENSP00000354080:R500Q	R	-	2	0	SCUBE1	41947173	0.000000	0.05858	0.050000	0.19076	0.094000	0.18550	-0.613000	0.05610	-0.269000	0.09298	-0.137000	0.14449	CGG		0.647	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
NEB	4703	broad.mit.edu	37	2	152342437	152342437	+	Missense_Mutation	SNP	C	C	T	rs368346105		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr2:152342437C>T	ENST00000172853.10	-	149	19994	c.19847G>A	c.(19846-19848)cGt>cAt	p.R6616H	NEB_ENST00000604864.1_Missense_Mutation_p.R8472H|NEB_ENST00000509223.2_Missense_Mutation_p.R385H|NEB_ENST00000409198.1_Missense_Mutation_p.R6616H|NEB_ENST00000427231.2_Missense_Mutation_p.R8472H|NEB_ENST00000603639.1_Missense_Mutation_p.R8472H|NEB_ENST00000397345.3_Missense_Mutation_p.R8472H|NEB_ENST00000397336.2_Missense_Mutation_p.R447H			P20929	NEBU_HUMAN	nebulin	6616	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.R6616H(1)		NS(5)|autonomic_ganglia(3)|breast(9)|central_nervous_system(5)|cervix(3)|endometrium(35)|kidney(16)|large_intestine(77)|liver(1)|lung(99)|ovary(9)|pancreas(3)|prostate(13)|skin(7)|stomach(8)|upper_aerodigestive_tract(6)|urinary_tract(2)	301				BRCA - Breast invasive adenocarcinoma(221;0.219)		ATACATGGCACGGAAGATTTT	0.398																																					p.R8472H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G25415A	2						.	C	HIS/ARG,HIS/ARG,HIS/ARG	0,3872		0,0,1936	88.0	84.0	85.0		25415,25415,19847	5.4	1.0	2		85	1,8301		0,1,4150	no	missense,missense,missense	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	29,29,29	0,1,6086	TT,TC,CC		0.012,0.0,0.0082	possibly-damaging,possibly-damaging,possibly-damaging	8472/8526,8472/8526,6616/6670	152342437	1,12173	1936	4151	6087	152050683	SO:0001583	missense	4703	exon182			X83957	CCDS46424.1, CCDS54407.1, CCDS54408.1, CCDS74588.1	2q22	2014-09-17			ENSG00000183091	ENSG00000183091			7720	protein-coding gene	gene with protein product	"""nemaline myopathy type 2"""	161650		NEM2		10051637, 9359044	Standard	NM_001164507		Approved	NEB177D	uc010fnx.3	P20929	OTTHUMG00000153784	ENST00000172853.10:c.19847G>A	2.37:g.152342437C>T	ENSP00000172853:p.Arg6616His	Somatic		Capture	Illumina HiSeq	Phase_I	152050683	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.4|27.4	4.826696|4.826696	0.90955|0.90955	0.0|0.0	1.2E-4|1.2E-4	ENSG00000183091|ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853;ENST00000397336;ENST00000509223|ENST00000397337;ENST00000434685	T;T;T;T;T;T;T|.	0.34667|.	1.35;1.35;1.35;1.35;1.35;1.35;1.35|.	5.36|5.36	5.36|5.36	0.76844|0.76844	Src homology-3 domain (4);|.	0.053412|.	0.85682|.	D|.	0.000000|.	D|D	0.84647|0.84647	0.5518|0.5518	M|M	0.93978|0.93978	3.48|3.48	0.80722|0.80722	D|D	1|1	D;D;D;P;D;D|.	0.89917|.	0.999;1.0;0.999;0.503;0.999;0.999|.	D;D;D;B;D;D|.	0.77557|.	0.938;0.99;0.973;0.034;0.966;0.966|.	D|D	0.87960|0.87960	0.2729|0.2729	10|5	0.72032|.	D|.	0.01|.	.|.	12.1116|12.1116	0.53842|0.53842	0.0:0.9206:0.0:0.0794|0.0:0.9206:0.0:0.0794	.|.	385;447;385;6616;2954;8472|.	B7Z6B9;B7Z6P9;B7Z6N8;P20929;Q14215;F8WCL5|.	.;.;.;NEBU_HUMAN;.;.|.	H|M	6616;8472;8472;2572;2954;6616;447;385|606;713	ENSP00000386259:R6616H;ENSP00000380505:R8472H;ENSP00000416578:R8472H;ENSP00000410961:R2954H;ENSP00000172853:R6616H;ENSP00000380497:R447H;ENSP00000427083:R385H|.	ENSP00000172853:R6616H|.	R|V	-|-	2|1	0|0	NEB|NEB	152050683|152050683	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	6.091000|6.091000	0.71406|0.71406	2.516000|2.516000	0.84829|0.84829	0.462000|0.462000	0.41574|0.41574	CGT|GTG		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
SESTD1	91404	broad.mit.edu	37	2	179977458	179977458	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr2:179977458G>C	ENST00000428443.3	-	17	2270	c.1954C>G	c.(1954-1956)Cct>Gct	p.P652A		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	652							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.P652A(1)		breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			TACCCATCAGGATAAACTACT	0.333																																					p.P652A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1954G	2						.						93.0	93.0	93.0					2																	179977458		2203	4300	6503	179685703	SO:0001583	missense	91404	exon17			AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1954C>G	2.37:g.179977458G>C	ENSP00000415332:p.Pro652Ala	Somatic		Capture	Illumina HiSeq	Phase_I	179685703	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Missense_Mutation	SNP	ENST00000428443.3	37	CCDS33338.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.706785	0.89018	.	.	ENSG00000187231	ENST00000428443	T	0.19806	2.12	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.30854	0.0778	N	0.14661	0.345	0.80722	D	1	D;D	0.76494	0.993;0.999	D;D	0.80764	0.971;0.994	T	0.13308	-1.0514	9	.	.	.	-4.3863	19.245	0.93898	0.0:0.0:1.0:0.0	.	652;652	Q86VW0;B3KTX3	SESD1_HUMAN;.	A	652	ENSP00000415332:P652A	.	P	-	1	0	SESTD1	179685703	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.230000	0.95299	2.534000	0.85438	0.467000	0.42956	CCT		0.333	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
FAM161A	84140	broad.mit.edu	37	2	62081176	62081176	+	Start_Codon_SNP	SNP	T	T	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr2:62081176T>A	ENST00000405894.3	-	1	102	c.1A>T	c.(1-3)Atg>Ttg	p.M1L	FAM161A_ENST00000404929.1_Start_Codon_SNP_p.M1L	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	1					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GAGGTGGCCATCGCCCCGCCT	0.706																																					p.M1L												.	.	0			c.A1T	2						.						10.0	11.0	11.0					2																	62081176		1566	3576	5142	61934680	SO:0001582	initiator_codon_variant	84140	exon1				CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1A>T	2.37:g.62081176T>A	ENSP00000385893:p.Met1Leu	None		Capture	Illumina HiSeq	Phase_I	61934680	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	.	.	.	.	.	.	.	.	.	.	T	18.76	3.693678	0.68386	.	.	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.30182	2.37;1.54	4.45	3.26	0.37387	.	.	.	.	.	T	0.49932	0.1586	.	.	.	0.80722	D	1	B;D	0.61697	0.123;0.99	B;D	0.73380	0.037;0.98	T	0.49808	-0.8900	8	0.87932	D	0	.	7.1288	0.25488	0.0:0.1015:0.0:0.8985	.	1;1	Q3B820;Q3B820-3	F161A_HUMAN;.	L	1	ENSP00000385158:M1L;ENSP00000385893:M1L	ENSP00000303170:M1L	M	-	1	0	FAM161A	61934680	0.987000	0.35691	0.776000	0.31678	0.255000	0.26057	1.856000	0.39389	0.993000	0.38866	0.528000	0.53228	ATG		0.706	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	Missense_Mutation
ZNF385B	151126	broad.mit.edu	37	2	180309623	180309623	+	Missense_Mutation	SNP	G	G	A	rs200150920		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr2:180309623G>A	ENST00000410066.1	-	9	1780	c.1177C>T	c.(1177-1179)Cgg>Tgg	p.R393W	ZNF385B_ENST00000466398.1_5'UTR|ZNF385B_ENST00000409343.1_Missense_Mutation_p.R317W|ZNF385B_ENST00000409692.1_Missense_Mutation_p.R291W|ZNF385B_ENST00000336917.5_Missense_Mutation_p.R291W	NM_152520.4	NP_689733.3	Q569K4	Z385B_HUMAN	zinc finger protein 385B	393	Interaction with p53/TP53.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|p53 binding (GO:0002039)|zinc ion binding (GO:0008270)	p.R393W(1)		breast(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	26			Epithelial(96;0.174)|OV - Ovarian serous cystadenocarcinoma(117;0.201)			CTCGGGCTCCGCTGGAGTTTG	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		17884	0.0		0.001	False		,,,				2504	0.0				p.R317W	Colon(155;204 2491 32774 51842)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C949T	2						.						238.0	232.0	234.0					2																	180309623		2203	4300	6503	180017868	SO:0001583	missense	151126	exon7			AK057999	CCDS33339.1, CCDS46463.1, CCDS46464.1	2q31.3-q32.1	2012-10-05	2007-12-06	2007-12-06	ENSG00000144331	ENSG00000144331			26332	protein-coding gene	gene with protein product		612344	"""zinc finger protein 533"""	ZNF533		12477932	Standard	NM_152520		Approved	FLJ25270	uc002unn.4	Q569K4	OTTHUMG00000154559	ENST00000410066.1:c.1177C>T	2.37:g.180309623G>A	ENSP00000386845:p.Arg393Trp	Somatic		Capture	Illumina HiSeq	Phase_I	180017868	NM_001113397	Q49A04|Q6ZMZ7|Q8IY01|Q8N8H2|Q96DK4	Missense_Mutation	SNP	ENST00000410066.1	37	CCDS33339.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.0	4.081001	0.76528	.	.	ENSG00000144331	ENST00000410066;ENST00000336917;ENST00000409343;ENST00000409692	T;T;T;T	0.35236	1.32;1.34;1.33;1.34	5.53	0.0343	0.14183	.	0.000000	0.85682	D	0.000000	T	0.46833	0.1413	L	0.42245	1.32	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.32214	-0.9915	10	0.87932	D	0	-13.0643	10.2829	0.43550	0.062:0.0:0.4307:0.5072	.	393;317	Q569K4;Q569K4-2	Z385B_HUMAN;.	W	393;291;317;291	ENSP00000386845:R393W;ENSP00000338225:R291W;ENSP00000386379:R317W;ENSP00000386507:R291W	ENSP00000338225:R291W	R	-	1	2	ZNF385B	180017868	1.000000	0.71417	0.989000	0.46669	0.923000	0.55619	1.810000	0.38932	-0.333000	0.08476	-0.259000	0.10710	CGG		0.498	ZNF385B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335972.1	NM_152520	
SEMA5B	54437	broad.mit.edu	37	3	122667472	122667472	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr3:122667472A>G	ENST00000357599.3	-	3	595	c.209T>C	c.(208-210)tTg>tCg	p.L70S	SEMA5B_ENST00000195173.4_Missense_Mutation_p.L70S|SEMA5B_ENST00000465147.1_5'UTR|SEMA5B_ENST00000451055.2_Missense_Mutation_p.L124S	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	70					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.L70S(1)|p.L124S(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GCTGGGCAGCAACAGCGAGAC	0.622																																					p.L70S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T209C	3						.						49.0	46.0	47.0					3																	122667472		2203	4300	6503	124150162	SO:0001583	missense	54437	exon3			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.209T>C	3.37:g.122667472A>G	ENSP00000350215:p.Leu70Ser	Somatic		Capture	Illumina HiSeq	Phase_I	124150162	NM_001031702	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065957	0.55539	.	.	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583;ENST00000421053;ENST00000449546	T;T;T;T	0.36157	1.3;1.27;1.34;1.4	4.93	3.79	0.43588	.	0.210897	0.24508	N	0.037905	T	0.16514	0.0397	N	0.08118	0	0.28670	N	0.905652	B;B;B	0.10296	0.002;0.003;0.003	B;B;B	0.08055	0.003;0.002;0.002	T	0.06552	-1.0820	10	0.29301	T	0.29	.	6.7509	0.23487	0.8976:0.0:0.1024:0.0	.	12;70;70	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	S	70;70;12;124;70;70;70	ENSP00000350215:L70S;ENSP00000195173:L70S;ENSP00000389588:L124S;ENSP00000377208:L70S	ENSP00000195173:L70S	L	-	2	0	SEMA5B	124150162	0.995000	0.38212	0.967000	0.41034	0.973000	0.67179	3.138000	0.50570	2.192000	0.70111	0.528000	0.53228	TTG		0.622	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
SLC41A3	54946	broad.mit.edu	37	3	125725960	125725960	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr3:125725960G>T	ENST00000315891.6	-	11	1601	c.1363C>A	c.(1363-1365)Ctc>Atc	p.L455I	SLC41A3_ENST00000346785.5_Missense_Mutation_p.L419I|SLC41A3_ENST00000383598.2_Missense_Mutation_p.L429I|SLC41A3_ENST00000360370.4_Missense_Mutation_p.L455I|SLC41A3_ENST00000508835.1_Missense_Mutation_p.L338I	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	455						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)	p.L429I(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		CCAGTACCGAGCAGGTCCCCC	0.587																																					p.L455I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1363A	3						.						85.0	78.0	80.0					3																	125725960		2203	4300	6503	127208650	SO:0001583	missense	54946	exon11				CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1363C>A	3.37:g.125725960G>T	ENSP00000326070:p.Leu455Ile	Somatic		Capture	Illumina HiSeq	Phase_I	127208650	NM_001008485	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.519252	0.64634	.	.	ENSG00000114544	ENST00000360370;ENST00000346785;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000508835	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.52	2.75	0.32379	MgtE magnesium transporter, integral membrane (1);	0.064455	0.64402	D	0.000005	T	0.43590	0.1254	L	0.55834	1.745	0.58432	D	0.99999	D;D;D;D;D	0.89917	0.999;1.0;0.986;0.989;1.0	D;D;P;P;D	0.87578	0.983;0.998;0.833;0.896;0.998	T	0.19745	-1.0296	10	0.22109	T	0.4	.	8.5114	0.33220	0.2562:0.0:0.7438:0.0	.	338;455;419;455;429	B7Z4Y2;E7ENY4;Q96GZ6-3;Q96GZ6;Q96GZ6-7	.;.;.;S41A3_HUMAN;.	I	455;419;429;446;455;338	ENSP00000353533:L455I;ENSP00000264471:L419I;ENSP00000373092:L429I;ENSP00000326070:L455I;ENSP00000427409:L338I	ENSP00000326070:L455I	L	-	1	0	SLC41A3	127208650	1.000000	0.71417	0.753000	0.31225	0.569000	0.35902	4.954000	0.63631	0.694000	0.31654	0.591000	0.81541	CTC		0.587	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836	
CP	1356	broad.mit.edu	37	3	148939523	148939523	+	Silent	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr3:148939523C>T	ENST00000264613.6	-	1	319	c.57G>A	c.(55-57)gcG>gcA	p.A19A		NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	19					cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)	p.A19A(1)		breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	GCTTTTCTTTCGCCCAGGCTG	0.363																																					p.A19A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G57A	3						.						64.0	66.0	65.0					3																	148939523		2203	4299	6502	150422213	SO:0001819	synonymous_variant	1356	exon1			M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.57G>A	3.37:g.148939523C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150422213	NM_000096	Q14063|Q2PP18|Q9UKS4	Silent	SNP	ENST00000264613.6	37	CCDS3141.1																																																																																				0.363	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
GRM2	2912	broad.mit.edu	37	3	51749942	51749942	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr3:51749942delC	ENST00000395052.3	+	4	2387	c.2153delC	c.(2152-2154)acafs	p.T718fs	GRM2_ENST00000475478.1_3'UTR|GRM2_ENST00000442933.2_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	718					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|glutamate secretion (GO:0014047)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.T718fs*>155(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GAGGTGGTGACACTGCGCTGC	0.627																																					p.T100fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.299delC	3						.						78.0	58.0	65.0					3																	51749942		2203	4300	6503	51724982	SO:0001589	frameshift_variant	2912	exon2			L35318	CCDS2834.1	3p21.2	2013-09-20			ENSG00000164082	ENSG00000164082		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4594	protein-coding gene	gene with protein product		604099				7620613	Standard	NM_000839		Approved	GPRC1B, mGlu2, MGLUR2	uc010hlv.3	Q14416	OTTHUMG00000156902	ENST00000395052.3:c.2153delC	3.37:g.51749942delC	ENSP00000378492:p.Thr718fs	Somatic		Capture	Illumina HiSeq	Phase_I	51724982	NM_001130063	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Frame_Shift_Del	DEL	ENST00000395052.3	37	CCDS2834.1																																																																																				0.627	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1		
MCF2L2	23101	broad.mit.edu	37	3	183059345	183059345	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr3:183059345A>G	ENST00000328913.3	-	4	646	c.349T>C	c.(349-351)Tcc>Ccc	p.S117P	MCF2L2_ENST00000414362.2_Missense_Mutation_p.S117P|MCF2L2_ENST00000473233.1_Missense_Mutation_p.S117P|MCF2L2_ENST00000447025.2_Missense_Mutation_p.S117P	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	117	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.						Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.S117P(1)		breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			CGTGTCAAGGATGCCTTTACG	0.388																																					p.S117P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T349C	3						.						121.0	115.0	117.0					3																	183059345		2203	4300	6503	184542039	SO:0001583	missense	23101	exon4			AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.349T>C	3.37:g.183059345A>G	ENSP00000328118:p.Ser117Pro	Somatic		Capture	Illumina HiSeq	Phase_I	184542039	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.902535	0.52227	.	.	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000414362;ENST00000482017	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	5.43	5.43	0.79202	Cellular retinaldehyde-binding/triple function, C-terminal (2);	0.200860	0.44688	D	0.000422	T	0.76054	0.3934	M	0.64404	1.975	0.43338	D	0.995386	D;D;D	0.89917	0.993;0.997;1.0	D;D;D	0.91635	0.947;0.968;0.999	T	0.78119	-0.2328	10	0.62326	D	0.03	.	13.72	0.62720	1.0:0.0:0.0:0.0	.	117;117;117	Q86YR7-3;Q86YR7-2;Q86YR7	.;.;MF2L2_HUMAN	P	117;117;117;117;89	ENSP00000328118:S117P;ENSP00000420070:S117P;ENSP00000388190:S117P;ENSP00000414131:S117P;ENSP00000417345:S89P	ENSP00000328118:S117P	S	-	1	0	MCF2L2	184542039	1.000000	0.71417	0.998000	0.56505	0.141000	0.21300	6.908000	0.75730	2.063000	0.61619	0.533000	0.62120	TCC		0.388	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	
ARHGEF38	54848	broad.mit.edu	37	4	106552167	106552168	+	Frame_Shift_Ins	INS	-	-	A	rs61757395|rs200163297	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr4:106552167_106552168insA	ENST00000420470.2	+	4	765_766	c.621_622insA	c.(622-624)aagfs	p.K208fs	ARHGEF38_ENST00000265154.2_Frame_Shift_Ins_p.K208fs	NM_001242729.1	NP_001229658.1	Q9NXL2	ARH38_HUMAN	Rho guanine nucleotide exchange factor (GEF) 38	208	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.					cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.E209fs*>12(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(3)	11						AAGAAGAGCTGAAGGAACATTT	0.401																																					p.L207fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.621_622insA	4						.																																			106771617	SO:0001589	frameshift_variant	54848	exon4			AK000191	CCDS3670.1, CCDS56338.1	4q24	2012-07-24			ENSG00000236699	ENSG00000236699		"""Rho guanine nucleotide exchange factors"""	25968	protein-coding gene	gene with protein product							Standard	NM_001242729		Approved	FLJ20184	uc003hxv.2	Q9NXL2	OTTHUMG00000154752	ENST00000420470.2:c.623dupA	4.37:g.106552169_106552169dupA	ENSP00000416125:p.Lys208fs	Somatic		Capture	Illumina HiSeq	Phase_I	106771616	NM_017700	C9JIB4	Frame_Shift_Ins	INS	ENST00000420470.2	37	CCDS56338.1																																																																																				0.401	ARHGEF38-001	PUTATIVE	basic|appris_principal|readthrough_transcript|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000336934.3	NM_017700	
PDGFRA	5156	broad.mit.edu	37	4	55141054	55141054	+	Missense_Mutation	SNP	C	C	T	rs587778595|rs201503614|rs121913270|rs121913271		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr4:55141054C>T	ENST00000257290.5	+	12	2031	c.1700C>T	c.(1699-1701)cCa>cTa	p.P567L	FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	567					adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.S566_E571>R(39)|p.S566_E571>K(7)|p.P567L(1)|p.S566_Y572>RIDDL(1)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TCAATCAGCCCAGATGGACAT	0.458			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											p.P567L	Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	PDGFRA,central_nervous_system,brain,Substitution - coding silent,-1 	.	48	Complex - deletion inframe(47)|Substitution - Missense(1)	small_intestine(37)|soft_tissue(6)|stomach(4)|large_intestine(1)	c.C1700T	4						.						87.0	89.0	88.0					4																	55141054		2203	4300	6503	54835811	SO:0001583	missense	5156	exon12	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1700C>T	4.37:g.55141054C>T	ENSP00000257290:p.Pro567Leu	Somatic		Capture	Illumina HiSeq	Phase_I	54835811	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315590	0.81469	.	.	ENSG00000134853	ENST00000257290	D	0.95588	-3.75	5.78	5.78	0.91487	Protein kinase-like domain (1);	0.000000	0.31949	U	0.006811	D	0.96984	0.9015	L	0.60012	1.86	0.80722	D	1	P;D	0.89917	0.663;1.0	P;D	0.87578	0.55;0.998	D	0.94980	0.8125	10	0.18710	T	0.47	.	20.0109	0.97448	0.0:1.0:0.0:0.0	.	567;567	P16234-3;P16234	.;PGFRA_HUMAN	L	567	ENSP00000257290:P567L	ENSP00000257290:P567L	P	+	2	0	PDGFRA	54835811	1.000000	0.71417	0.965000	0.40720	0.441000	0.31987	4.586000	0.60984	2.738000	0.93877	0.591000	0.81541	CCA		0.458	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
UGT2A1	10941	broad.mit.edu	37	4	70455232	70455232	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr4:70455232A>C	ENST00000503640.1	-	6	1497	c.1442T>G	c.(1441-1443)cTc>cGc	p.L481R	UGT2A1_ENST00000514019.1_Missense_Mutation_p.L647R|UGT2A1_ENST00000286604.4_Missense_Mutation_p.L481R|UGT2A1_ENST00000502343.1_5'Flank|UGT2A2_ENST00000457664.2_Missense_Mutation_p.L490R|UGT2A1_ENST00000512704.1_Missense_Mutation_p.L437R	NM_006798.3	NP_006789.2	Q9Y4X1	UD2A1_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide A1, complex locus	481					cellular glucuronidation (GO:0052695)|detection of chemical stimulus (GO:0009593)|metabolic process (GO:0008152)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)	p.L481R(1)|p.L490R(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(11)|ovary(2)|prostate(1)|skin(2)	30						GAACCAGGTGAGGTCATGGGC	0.483																																					p.L481R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1442G	4						.						134.0	130.0	131.0					4																	70455232		2203	4300	6503	70489821	SO:0001583	missense	10941	exon6			AJ006054	CCDS3529.1, CCDS58901.1, CCDS58902.1	4q13	2013-03-28	2010-12-02					"""UDP glucuronosyltransferases"""	12542	protein-coding gene	gene with protein product		604716	"""UDP glycosyltransferase 2 family, polypeptide A1"", ""UDP glucuronosyltransferase 2 family, polypeptide A1"""			10359671	Standard	NM_001252274		Approved		uc011caq.2	Q9Y4X1	OTTHUMG00000184942	ENST00000503640.1:c.1442T>G	4.37:g.70455232A>C	ENSP00000424478:p.Leu481Arg	Somatic		Capture	Illumina HiSeq	Phase_I	70489821	NM_006798	B4E2F4|D3GER1|D3GER2|E9PDM7|J3KNA3	Missense_Mutation	SNP	ENST00000503640.1	37	CCDS3529.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.357786	0.61403	.	.	ENSG00000173610	ENST00000457664;ENST00000503640;ENST00000512704;ENST00000514019;ENST00000286604	T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	D	0.88808	0.6537	M	0.93594	3.435	.	.	.	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.996;0.999	D;D;D;D;D	0.91635	0.99;0.999;0.982;0.919;0.972	D	0.92951	0.6380	9	0.87932	D	0	.	12.7146	0.57107	1.0:0.0:0.0:0.0	.	647;647;437;490;481	E9PDM7;B4E2F4;D6RFW5;Q9Y4X1-2;Q9Y4X1	.;.;.;.;UD2A1_HUMAN	R	490;481;437;647;481	ENSP00000387888:L490R;ENSP00000424478:L481R;ENSP00000421432:L437R;ENSP00000425497:L647R;ENSP00000286604:L481R	ENSP00000286604:L481R	L	-	2	0	UGT2A1	70489821	1.000000	0.71417	1.000000	0.80357	0.325000	0.28411	8.975000	0.93437	2.043000	0.60533	0.472000	0.43445	CTC		0.483	UGT2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251554.3	NM_006798	
APC	324	broad.mit.edu	37	5	112116592	112116592	+	Nonsense_Mutation	SNP	C	C	T	rs587781392		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:112116592C>T	ENST00000457016.1	+	6	1017	c.637C>T	c.(637-639)Cga>Tga	p.R213*	APC_ENST00000257430.4_Nonsense_Mutation_p.R213*|RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000508376.2_Nonsense_Mutation_p.R213*			P25054	APC_HUMAN	adenomatous polyposis coli	213	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R213*(20)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TATGGAAAAACGAGCACAGGT	0.348		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											p.R223X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,rectum,Substitution - Nonsense,0 	.	20	Substitution - Nonsense(20)	large_intestine(19)|lung(1)	c.C667T	5	GRCh37	CM920027	APC	M		.						58.0	57.0	58.0					5																	112116592		2202	4300	6502	112144491	SO:0001587	stop_gained	324	exon5	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.637C>T	5.37:g.112116592C>T	ENSP00000413133:p.Arg213*	Somatic		Capture	Illumina HiSeq	Phase_I	112144491	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	37	6.046788	0.97231	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.56	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.0079	14.2561	0.66053	0.4075:0.5925:0.0:0.0	.	.	.	.	X	213;223;213;213;213	.	ENSP00000257430:R213X	R	+	1	2	APC	112144491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.672000	0.46850	0.659000	0.30945	0.655000	0.94253	CGA		0.348	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
CDC23	8697	broad.mit.edu	37	5	137542257	137542257	+	Silent	SNP	C	C	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:137542257C>G	ENST00000394886.2	-	3	381	c.351G>C	c.(349-351)ctG>ctC	p.L117L	CDC23_ENST00000394884.3_Silent_p.L117L|CDC23_ENST00000505120.1_Missense_Mutation_p.C116S	NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	117					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of exit from mitosis (GO:0007096)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|ubiquitin-dependent protein catabolic process (GO:0006511)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ubiquitin-protein transferase activity (GO:0004842)	p.L111L(2)		autonomic_ganglia(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(6)|prostate(2)|skin(1)	23			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			AATACATATACAGAAAATAGG	0.393																																					p.L117L												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.G351C	5						.						71.0	71.0	71.0					5																	137542257		2203	4300	6503	137570156	SO:0001819	synonymous_variant	8697	exon3			AF053977	CCDS4200.2	5q31	2013-01-17	2013-01-17		ENSG00000094880	ENSG00000094880		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1724	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 8"""	603462	"""CDC23 (cell division cycle 23, yeast, homolog)"", ""cell division cycle 23 homolog (S. cerevisiae)"""			9790767	Standard	NM_004661		Approved	APC8, ANAPC8, CUT23	uc003lcl.3	Q9UJX2	OTTHUMG00000129198	ENST00000394886.2:c.351G>C	5.37:g.137542257C>G		Somatic		Capture	Illumina HiSeq	Phase_I	137570156	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	37	CCDS4200.2	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620655	0.46736	.	.	ENSG00000094880	ENST00000505120	T	0.35236	1.32	5.96	0.881	0.19166	.	.	.	.	.	T	0.41213	0.1149	.	.	.	0.24644	N	0.99356	.	.	.	.	.	.	T	0.37888	-0.9686	6	0.87932	D	0	-10.1168	10.3983	0.44214	0.0:0.5917:0.0:0.4083	.	.	.	.	S	116	ENSP00000423704:C116S	ENSP00000422505:C93S	C	-	2	0	CDC23	137570156	0.803000	0.28956	0.989000	0.46669	0.975000	0.68041	-0.059000	0.11731	-0.127000	0.11661	-0.312000	0.09012	TGT		0.393	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2		
GRM6	2916	broad.mit.edu	37	5	178413190	178413190	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:178413190G>T	ENST00000517717.1	-	9	2103	c.2065C>A	c.(2065-2067)Cct>Act	p.P689T	GRM6_ENST00000231188.5_Missense_Mutation_p.P689T|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	689					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.P689T(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		ATGAAGGGAGGGGGTGTGACC	0.642																																					p.P689T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2065A	5						.						55.0	64.0	61.0					5																	178413190		2203	4300	6503	178345796	SO:0001583	missense	2916	exon8			U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.2065C>A	5.37:g.178413190G>T	ENSP00000430767:p.Pro689Thr	Somatic		Capture	Illumina HiSeq	Phase_I	178345796	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.360278	0.82353	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.88509	-2.39;-2.39	5.02	5.02	0.67125	GPCR, family 3, C-terminal (2);	.	.	.	.	D	0.95529	0.8547	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.98	D	0.96207	0.9150	9	0.66056	D	0.02	.	16.2011	0.82078	0.0:0.0:1.0:0.0	.	845;689	E7EX65;O15303	.;GRM6_HUMAN	T	845;689;689	ENSP00000231188:P689T;ENSP00000430767:P689T	ENSP00000231188:P689T	P	-	1	0	GRM6	178345796	1.000000	0.71417	0.937000	0.37676	0.971000	0.66376	9.661000	0.98601	2.495000	0.84180	0.462000	0.41574	CCT		0.642	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
UGT3A1	133688	broad.mit.edu	37	5	35954451	35954451	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:35954451G>A	ENST00000274278.3	-	7	1782	c.1425C>T	c.(1423-1425)gcC>gcT	p.A475A	UGT3A1_ENST00000513233.1_5'Flank	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	475				A -> V (in Ref. 1; BAB71358). {ECO:0000305}.		integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)	p.A475A(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			GCTGCTGGAAGGCATAGGGCT	0.602																																					p.A475A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1425T	5						.						106.0	80.0	89.0					5																	35954451		2203	4300	6503	35990208	SO:0001819	synonymous_variant	133688	exon7				CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"""UDP glucuronosyltransferases"""	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.1425C>T	5.37:g.35954451G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35990208	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																				0.602	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
ITGA2	3673	broad.mit.edu	37	5	52379277	52379277	+	Missense_Mutation	SNP	C	C	A	rs2303122	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:52379277C>A	ENST00000296585.5	+	27	3395	c.3252C>A	c.(3250-3252)ttC>ttA	p.F1084L		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	1084					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cellular response to hormone stimulus (GO:0032870)|collagen-activated signaling pathway (GO:0038065)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|hepatocyte differentiation (GO:0070365)|hypotonic response (GO:0006971)|integrin-mediated signaling pathway (GO:0007229)|mammary gland development (GO:0030879)|mesodermal cell differentiation (GO:0048333)|organ morphogenesis (GO:0009887)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell projection organization (GO:0031346)|positive regulation of collagen binding (GO:0033343)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA binding (GO:0043388)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|response to amine (GO:0014075)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to L-ascorbic acid (GO:0033591)|response to muscle activity (GO:0014850)|response to organic cyclic compound (GO:0014070)|skin morphogenesis (GO:0043589)|substrate-dependent cell migration (GO:0006929)|tissue homeostasis (GO:0001894)|viral process (GO:0016032)	axon terminus (GO:0043679)|basal part of cell (GO:0045178)|cell outer membrane (GO:0009279)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|focal adhesion (GO:0005925)|integrin alpha2-beta1 complex (GO:0034666)|integrin complex (GO:0008305)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)	p.F1084L(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(8)|liver(1)|lung(18)|pancreas(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	47		Lung NSC(810;3.11e-05)|Breast(144;0.014)|Prostate(461;0.0181)				ACGGGACTTTCGCATCAGTAA	0.368																																					p.F1084L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3252A	5						.						103.0	96.0	98.0					5																	52379277		2203	4300	6503	52415034	SO:0001583	missense	3673	exon27				CCDS3957.1	5q11.2	2010-03-23			ENSG00000164171	ENSG00000164171		"""CD molecules"", ""Integrins"""	6137	protein-coding gene	gene with protein product		192974		CD49B			Standard	NM_002203		Approved	CD49b	uc003joy.3	P17301	OTTHUMG00000131165	ENST00000296585.5:c.3252C>A	5.37:g.52379277C>A	ENSP00000296585:p.Phe1084Leu	Somatic		Capture	Illumina HiSeq	Phase_I	52415034	NM_002203	Q14595	Missense_Mutation	SNP	ENST00000296585.5	37	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.330299	0.41297	.	.	ENSG00000164171	ENST00000296585	T	0.39997	1.05	5.89	-2.52	0.06346	.	0.051975	0.85682	D	0.000000	T	0.26376	0.0644	L	0.41079	1.255	0.25033	P	0.99125234	B	0.32302	0.363	B	0.27380	0.079	T	0.26950	-1.0088	9	0.22706	T	0.39	.	11.2635	0.49097	0.0:0.4392:0.0:0.5608	.	1084	P17301	ITA2_HUMAN	L	1084	ENSP00000296585:F1084L	ENSP00000296585:F1084L	F	+	3	2	ITGA2	52415034	0.994000	0.37717	0.973000	0.42090	0.440000	0.31957	0.114000	0.15520	-0.667000	0.05303	-0.247000	0.11927	TTC		0.368	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	
PDE4D	5144	broad.mit.edu	37	5	59189238	59189238	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:59189238delC	ENST00000340635.6	-	1	387	c.212delG	c.(211-213)tgtfs	p.C71fs	PDE4D_ENST00000502484.2_Intron|PDE4D_ENST00000546160.1_Intron	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	71	Pro-rich.				adrenergic receptor signaling pathway (GO:0071875)|adrenergic receptor signaling pathway involved in positive regulation of heart rate (GO:0086024)|aging (GO:0007568)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cAMP (GO:0071320)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|establishment of endothelial barrier (GO:0061028)|multicellular organism growth (GO:0035264)|negative regulation of heart contraction (GO:0045822)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-5 production (GO:0032754)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of receptor activity (GO:0010469)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|smooth muscle contraction (GO:0006939)|T cell receptor signaling pathway (GO:0050852)	calcium channel complex (GO:0034704)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|ATPase binding (GO:0051117)|beta-2 adrenergic receptor binding (GO:0031698)|cAMP binding (GO:0030552)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)	p.C71fs*66(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|pancreas(1)	15		all_cancers(5;6.5e-58)|all_epithelial(5;1.75e-57)|all_lung(5;6.84e-18)|Lung NSC(5;1.29e-17)|Melanoma(5;0.00168)|Prostate(74;0.00234)|Colorectal(97;0.00629)|Ovarian(174;0.00832)|Breast(144;0.00996)|all_hematologic(6;0.0344)|Hepatocellular(6;0.0742)|Esophageal squamous(6;0.0954)		Epithelial(2;2.6e-55)|all cancers(2;2.66e-49)|OV - Ovarian serous cystadenocarcinoma(10;1.48e-39)|Colorectal(2;8.29e-08)|Lung(2;4.47e-07)|STAD - Stomach adenocarcinoma(2;1.11e-05)|COAD - Colon adenocarcinoma(2;0.00012)|LUSC - Lung squamous cell carcinoma(2;0.000775)|LUAD - Lung adenocarcinoma(3;0.0173)|READ - Rectum adenocarcinoma(2;0.0276)	Adenosine monophosphate(DB00131)|Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	cTGTAgcggacactggggctg	0.816																																					p.C71fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.212delG	5						.						1.0	2.0	2.0					5																	59189238		659	1664	2323	59224995	SO:0001589	frameshift_variant	5144	exon1				CCDS47213.1, CCDS54858.1, CCDS54859.1, CCDS56369.1, CCDS56370.1, CCDS56371.1, CCDS56372.1, CCDS56373.1	5q12	2010-06-24	2010-06-24				3.1.4.17	"""Phosphodiesterases"""	8783	protein-coding gene	gene with protein product	"""phosphodiesterase E3 dunce homolog (Drosophila)"""	600129	"""phosphodiesterase 4D, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E3)"""	DPDE3			Standard	NM_006203		Approved		uc003jsa.2	Q08499		ENST00000340635.6:c.212delG	5.37:g.59189238delC	ENSP00000345502:p.Cys71fs	Somatic		Capture	Illumina HiSeq	Phase_I	59224995	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Frame_Shift_Del	DEL	ENST00000340635.6	37	CCDS47213.1																																																																																				0.816	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3		
GFPT2	9945	broad.mit.edu	37	5	179743769	179743769	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr5:179743769C>T	ENST00000253778.8	-	12	1316	c.1147G>A	c.(1147-1149)Gtg>Atg	p.V383M	GFPT2_ENST00000520165.1_5'UTR	NM_005110.2	NP_005101.1	O94808	GFPT2_HUMAN	glutamine-fructose-6-phosphate transaminase 2	383	SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|energy reserve metabolic process (GO:0006112)|fructose 6-phosphate metabolic process (GO:0006002)|glutamine metabolic process (GO:0006541)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|glutamine-fructose-6-phosphate transaminase (isomerizing) activity (GO:0004360)	p.V383M(1)		breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34	all_cancers(89;4.97e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	Medulloblastoma(196;0.0392)|all_neural(177;0.0529)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		L-Glutamine(DB00130)	CTTACAGCCACGGCAGCGTGG	0.562																																					p.V383M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1147A	5						.						34.0	36.0	35.0					5																	179743769		2118	4231	6349	179676375	SO:0001583	missense	9945	exon12			AB016789	CCDS43411.1	5q	2008-07-18			ENSG00000131459	ENSG00000131459			4242	protein-coding gene	gene with protein product	"""glutamine: fructose-6-phosphate aminotransferase 2"""	603865				10198162	Standard	NM_005110		Approved	GFAT2	uc003mlw.1	O94808	OTTHUMG00000163442	ENST00000253778.8:c.1147G>A	5.37:g.179743769C>T	ENSP00000253778:p.Val383Met	Somatic		Capture	Illumina HiSeq	Phase_I	179676375	NM_005110	Q53XM2|Q9BWS4	Missense_Mutation	SNP	ENST00000253778.8	37	CCDS43411.1	.	.	.	.	.	.	.	.	.	.	C	19.06	3.753671	0.69648	.	.	ENSG00000131459	ENST00000253778	T	0.62941	-0.01	5.89	5.02	0.67125	Sugar isomerase (SIS) (2);	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	N	0.21583	0.68	0.80722	D	1	D	0.57899	0.981	B	0.43225	0.412	T	0.49466	-0.8937	9	.	.	.	-25.9777	16.4872	0.84188	0.1321:0.8679:0.0:0.0	.	383	O94808	GFPT2_HUMAN	M	383	ENSP00000253778:V383M	.	V	-	1	0	GFPT2	179676375	0.999000	0.42202	0.890000	0.34922	0.851000	0.48451	3.961000	0.56759	1.475000	0.48197	0.561000	0.74099	GTG		0.562	GFPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373444.4	NM_005110	
MCM3	4172	broad.mit.edu	37	6	52129555	52129556	+	Frame_Shift_Ins	INS	-	-	TC	rs150087575	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:52129555_52129556insTC	ENST00000229854.7	-	17	2333_2334	c.2257_2258insGA	c.(2257-2259)gatfs	p.D753fs	MCM3_ENST00000596288.1_Frame_Shift_Ins_p.D798fs|MCM3_ENST00000419835.2_Frame_Shift_Ins_p.D707fs			P25205	MCM3_HUMAN	minichromosome maintenance complex component 3	753					DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	alpha DNA polymerase:primase complex (GO:0005658)|centrosome (GO:0005813)|intracellular membrane-bounded organelle (GO:0043231)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	20	Lung NSC(77;0.0931)					CCGGAACACATCCAAGAGGGCC	0.52																																					p.D753fs												.	.	0			c.2258_2259insGA	6						.																																			52237515	SO:0001589	frameshift_variant	4172	exon17			X62153	CCDS4940.1, CCDS4940.2, CCDS75468.1	6p12	2008-02-05	2007-04-04		ENSG00000112118	ENSG00000112118			6945	protein-coding gene	gene with protein product		602693	"""minichromosome maintenance deficient (S. cerevisiae) 3"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae)"""			1549468	Standard	NM_002388		Approved		uc011dwu.2	P25205	OTTHUMG00000014844	ENST00000229854.7:c.2257_2258insGA	6.37:g.52129555_52129556insTC	ENSP00000229854:p.Asp753fs	None		Capture	Illumina HiSeq	Phase_I	52237514	NM_002388	B4DWW4|Q92660|Q9BTR3|Q9NUE7	Frame_Shift_Ins	INS	ENST00000229854.7	37																																																																																					0.520	MCM3-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470784.1		
PHF3	23469	broad.mit.edu	37	6	64395792	64395793	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:64395792_64395793insA	ENST00000262043.3	+	4	2509_2510	c.2169_2170insA	c.(2170-2172)aaafs	p.K724fs	PHF3_ENST00000393387.1_Frame_Shift_Ins_p.K724fs|PHF3_ENST00000509330.1_Frame_Shift_Ins_p.K724fs			Q92576	PHF3_HUMAN	PHD finger protein 3	724					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(7)|cervix(2)|endometrium(8)|kidney(7)|large_intestine(18)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(6)	75	all_cancers(3;0.0241)|all_epithelial(2;0.00306)|Lung NSC(77;0.121)		LUSC - Lung squamous cell carcinoma(74;0.0644)|Lung(124;0.148)			GTGGGTTTTGCAAAAAACCACA	0.396																																					p.C723fs	GBM(135;136 1820 29512 34071 46235)											.	.	0			c.2169_2170insA	6						.																																			64453752	SO:0001589	frameshift_variant	23469	exon3			AF091622	CCDS4966.1	6q12	2013-09-24			ENSG00000118482	ENSG00000118482		"""Zinc fingers, PHD-type"""	8921	protein-coding gene	gene with protein product		607789				11856869	Standard	XM_005248701		Approved		uc003pep.1	Q92576	OTTHUMG00000014952	ENST00000262043.3:c.2175dupA	6.37:g.64395798_64395798dupA	ENSP00000262043:p.Lys724fs	None		Capture	Illumina HiSeq	Phase_I	64453751	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Ins	INS	ENST00000262043.3	37	CCDS4966.1																																																																																				0.396	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
TFAP2A	7020	broad.mit.edu	37	6	10407063	10407063	+	Silent	SNP	C	C	G			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:10407063C>G	ENST00000482890.1	-	4	847	c.495G>C	c.(493-495)ccG>ccC	p.P165P	TFAP2A_ENST00000379613.3_Silent_p.P167P|TFAP2A_ENST00000379608.3_Silent_p.P159P|TFAP2A_ENST00000319516.4_Silent_p.P161P|TFAP2A_ENST00000497266.1_5'UTR|TFAP2A-AS1_ENST00000420777.1_RNA|TFAP2A_ENST00000379604.2_Silent_p.P165P			P05549	AP2A_HUMAN	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)	165					anterior neuropore closure (GO:0021506)|basement membrane organization (GO:0071711)|bone morphogenesis (GO:0060349)|cellular response to iron ion (GO:0071281)|cornea development in camera-type eye (GO:0061303)|embryonic body morphogenesis (GO:0010172)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic forelimb morphogenesis (GO:0035115)|embryonic pattern specification (GO:0009880)|epidermis morphogenesis (GO:0048730)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|keratinocyte development (GO:0003334)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell development (GO:0014032)|oculomotor nerve formation (GO:0021623)|optic cup structural organization (GO:0003409)|optic vesicle morphogenesis (GO:0003404)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of bone mineralization (GO:0030501)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell differentiation (GO:0045595)|regulation of neuron differentiation (GO:0045664)|retina layer formation (GO:0010842)|sensory perception of sound (GO:0007605)|sympathetic nervous system development (GO:0048485)|transcription from RNA polymerase II promoter (GO:0006366)|trigeminal nerve development (GO:0021559)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.P165P(1)|p.P159P(1)		breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)	13	Breast(50;0.0427)|Ovarian(93;0.0991)	all_hematologic(90;0.107)				TGTTAATACCCGGGTCTTCTA	0.403																																					p.P165P												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G495C	6						.						168.0	154.0	159.0					6																	10407063		2203	4300	6503	10515049	SO:0001819	synonymous_variant	7020	exon3			X52611	CCDS4510.1, CCDS34337.1, CCDS43422.1	6p24.3	2013-09-19	2001-11-28		ENSG00000137203	ENSG00000137203			11742	protein-coding gene	gene with protein product		107580	"""transcription factor AP-2 alpha (activating enhancer-binding protein 2 alpha)"""	TFAP2, AP2TF		1916817, 3063603	Standard	NM_001032280		Approved	AP-2	uc003myr.3	P05549	OTTHUMG00000014235	ENST00000482890.1:c.495G>C	6.37:g.10407063C>G		Somatic		Capture	Illumina HiSeq	Phase_I	10515049	NM_003220	Q13777|Q5TAV5|Q8N1C6	Silent	SNP	ENST00000482890.1	37	CCDS4510.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.503920	0.26949	.	.	ENSG00000137203	ENST00000475264	.	.	.	5.61	2.7	0.31948	.	.	.	.	.	T	0.50222	0.1603	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49925	-0.8887	4	.	.	.	-11.8004	12.3583	0.55188	0.0:0.6202:0.3071:0.0727	.	.	.	.	P	70	.	.	R	-	2	0	TFAP2A	10515049	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	0.550000	0.23345	0.830000	0.34757	-0.140000	0.14226	CGG		0.403	TFAP2A-007	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353619.2	NM_003220	
HIVEP1	3096	broad.mit.edu	37	6	12131039	12131039	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:12131039G>A	ENST00000379388.2	+	6	6581	c.6249G>A	c.(6247-6249)agG>agA	p.R2083R	HIVEP1_ENST00000541134.1_5'UTR	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2083					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R2083R(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				TCCGAGGCAGGGGAAGAGGAA	0.368																																					p.R2083R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6249A	6						.						116.0	106.0	110.0					6																	12131039		1875	4104	5979	12239025	SO:0001819	synonymous_variant	3096	exon6			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.6249G>A	6.37:g.12131039G>A		Somatic		Capture	Illumina HiSeq	Phase_I	12239025	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Silent	SNP	ENST00000379388.2	37	CCDS43426.1																																																																																				0.368	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
VARS2	57176	broad.mit.edu	37	6	30883004	30883004	+	Silent	SNP	T	T	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:30883004T>A	ENST00000321897.5	+	2	905	c.273T>A	c.(271-273)ggT>ggA	p.G91G	VARS2_ENST00000541562.1_Silent_p.G121G|VARS2_ENST00000416670.2_Silent_p.G91G|VARS2_ENST00000542001.1_5'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)	p.G91G(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						CGAAACCCGGTGAAAAGAAAG	0.458																																					p.G91G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T273A	6						.						87.0	91.0	90.0					6																	30883004		2203	4300	6503	30990983	SO:0001819	synonymous_variant	57176	exon3			AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	21642	protein-coding gene	gene with protein product	"""valine tRNA ligase 2, mitochondrial"""	612802	"""valyl-tRNA synthetase 2-like"", ""valyl-tRNA synthetase like"", ""valyl-tRNA synthetase 2, mitochondrial (putative)"""	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.273T>A	6.37:g.30883004T>A		Somatic		Capture	Illumina HiSeq	Phase_I	30990983	NM_020442	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Silent	SNP	ENST00000321897.5	37	CCDS34387.1																																																																																				0.458	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
KHDC3L	154288	broad.mit.edu	37	6	74073363	74073363	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:74073363C>T	ENST00000370367.3	+	3	487	c.434C>T	c.(433-435)aCg>aTg	p.T145M		NM_001017361.2	NP_001017361.1	Q587J8	KHD3L_HUMAN	KH domain containing 3-like, subcortical maternal complex member	145							RNA binding (GO:0003723)	p.T145M(1)									GAGGCCGGGACGCAGCGTTCG	0.667																																					p.T145M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C434T	6						.						30.0	36.0	34.0					6																	74073363		2202	4300	6502	74130084	SO:0001583	missense	154288	exon3			AB211062	CCDS34484.1	6q13	2012-06-25	2012-06-25	2012-06-25	ENSG00000203908	ENSG00000203908			33699	protein-coding gene	gene with protein product	"""ES cell associated transcript 1"""	611687	"""chromosome 6 open reading frame 221"""	C6orf221		21885028	Standard	NM_001017361		Approved	ECAT1	uc003pgt.4	Q587J8	OTTHUMG00000015024	ENST00000370367.3:c.434C>T	6.37:g.74073363C>T	ENSP00000359392:p.Thr145Met	Somatic		Capture	Illumina HiSeq	Phase_I	74130084	NM_001017361	B2RNW7	Missense_Mutation	SNP	ENST00000370367.3	37	CCDS34484.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.439113	0.43326	.	.	ENSG00000203908	ENST00000370367	T	0.63580	-0.05	2.8	0.861	0.19048	.	0.349521	0.21009	N	0.081708	T	0.54515	0.1863	L	0.54323	1.7	0.09310	N	1	D	0.89917	1.0	D	0.74023	0.982	T	0.45920	-0.9228	10	0.34782	T	0.22	-10.0884	7.1918	0.25831	0.4829:0.5171:0.0:0.0	.	145	Q587J8	ECAT1_HUMAN	M	145	ENSP00000359392:T145M	ENSP00000359392:T145M	T	+	2	0	C6orf221	74130084	0.000000	0.05858	0.002000	0.10522	0.200000	0.23975	-0.608000	0.05641	0.208000	0.20626	-0.181000	0.13052	ACG		0.667	KHDC3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041202.3	NM_001017361	
MYO6	4646	broad.mit.edu	37	6	76576654	76576654	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:76576654G>A	ENST00000369977.3	+	18	1915	c.1776G>A	c.(1774-1776)caG>caA	p.Q592Q	MYO6_ENST00000369981.3_Silent_p.Q592Q|snoU13_ENST00000459013.1_RNA|MYO6_ENST00000369985.4_Silent_p.Q592Q|RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369975.1_Silent_p.Q592Q	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	592	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)	p.Q592Q(1)		breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		TTCAGACCCAGTTTGTGGAGA	0.338																																					p.Q592Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1776A	6						.						67.0	69.0	68.0					6																	76576654		2202	4300	6502	76633374	SO:0001819	synonymous_variant	4646	exon18			U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.1776G>A	6.37:g.76576654G>A		Somatic		Capture	Illumina HiSeq	Phase_I	76633374	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Silent	SNP	ENST00000369977.3	37	CCDS34487.1																																																																																				0.338	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
ASCC3	10973	broad.mit.edu	37	6	101094534	101094534	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr6:101094534C>T	ENST00000369162.2	-	22	3934	c.3590G>A	c.(3589-3591)cGa>cAa	p.R1197Q		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1197	SEC63 1.				cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.R1197Q(2)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		GAGTGTCACTCGGAGGACAGT	0.403																																					p.R1197Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3590A	6						.						122.0	106.0	111.0					6																	101094534		2203	4300	6503	101201255	SO:0001583	missense	10973	exon22			AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.3590G>A	6.37:g.101094534C>T	ENSP00000358159:p.Arg1197Gln	Somatic		Capture	Illumina HiSeq	Phase_I	101201255	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	32	5.137057	0.94517	.	.	ENSG00000112249	ENST00000369162	T	0.61158	0.13	5.39	5.39	0.77823	Sec63 domain (3);	0.000000	0.64402	D	0.000001	T	0.67785	0.2930	M	0.65677	2.01	0.80722	D	1	D	0.71674	0.998	P	0.62184	0.899	T	0.67987	-0.5528	10	0.48119	T	0.1	.	19.1383	0.93436	0.0:1.0:0.0:0.0	.	1197	Q8N3C0	HELC1_HUMAN	Q	1197	ENSP00000358159:R1197Q	ENSP00000358159:R1197Q	R	-	2	0	ASCC3	101201255	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	7.775000	0.85489	2.511000	0.84671	0.591000	0.81541	CGA		0.403	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
GIGYF1	64599	broad.mit.edu	37	7	100285169	100285170	+	Frame_Shift_Ins	INS	-	-	G	rs553150910		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:100285169_100285170insG	ENST00000275732.5	-	4	1540_1541	c.331_332insC	c.(331-333)ctgfs	p.L111fs	GIGYF1_ENST00000471340.2_5'UTR	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	111					insulin-like growth factor receptor signaling pathway (GO:0048009)			p.L111fs*234(1)		central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GGTGCCAGCCAGGGGGGGGCCA	0.673																																					p.L111fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.332_333insC	7						.																																			100123106	SO:0001589	frameshift_variant	64599	exon4			AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.332dupC	7.37:g.100285177_100285177dupG	ENSP00000275732:p.Leu111fs	None		Capture	Illumina HiSeq	Phase_I	100123105	NM_022574	Q6Y7W7|Q8WZ38	Frame_Shift_Ins	INS	ENST00000275732.5	37	CCDS34708.1																																																																																				0.673	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
CREB3L2	64764	broad.mit.edu	37	7	137686449	137686449	+	Start_Codon_SNP	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:137686449C>T	ENST00000330387.6	-	1	354	c.3G>A	c.(1-3)atG>atA	p.M1I	CREB3L2_ENST00000456390.1_Start_Codon_SNP_p.M1I|CREB3L2_ENST00000452463.1_Start_Codon_SNP_p.M1I|CREB3L2_ENST00000468127.1_5'UTR	NM_194071.3	NP_919047.2	Q70SY1	CR3L2_HUMAN	cAMP responsive element binding protein 3-like 2	1					cartilage development (GO:0051216)|chondrocyte differentiation (GO:0002062)|ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of transcription, DNA-templated (GO:0045893)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	cAMP response element binding (GO:0035497)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|transcription regulatory region DNA binding (GO:0044212)	p.M1I(1)	FUS/CREB3L2(158)	breast(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						CCAGCACCTCCATGGCGGTGC	0.701			T	FUS	fibromyxoid sarcoma																																p.M1I			Dom	yes		7	7q34	64764	cAMP responsive element binding protein 3-like 2		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3A	7						.						21.0	21.0	21.0					7																	137686449		2202	4296	6498	137336989	SO:0001582	initiator_codon_variant	64764	exon1			AJ549092	CCDS34760.1, CCDS59083.1	7q34	2013-01-10			ENSG00000182158	ENSG00000182158		"""basic leucine zipper proteins"""	23720	protein-coding gene	gene with protein product		608834					Standard	NM_194071		Approved	BBF2H7, TCAG_1951439	uc003vtw.3	Q70SY1	OTTHUMG00000155744	ENST00000330387.6:c.3G>A	7.37:g.137686449C>T	ENSP00000329140:p.Met1Ile	Somatic		Capture	Illumina HiSeq	Phase_I	137336989	NM_194071	Q6P454|Q6ZMR6	Missense_Mutation	SNP	ENST00000330387.6	37	CCDS34760.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.965121	0.74131	.	.	ENSG00000182158	ENST00000330387;ENST00000544877;ENST00000417785;ENST00000456390;ENST00000452463	T;T;T	0.69306	0.04;-0.39;0.55	5.97	5.97	0.96955	.	0.073106	0.64402	D	0.000012	T	0.60560	0.2278	.	.	.	0.80722	D	1	B;B;B	0.32101	0.356;0.005;0.012	B;B;B	0.26770	0.073;0.014;0.01	T	0.62895	-0.6757	9	0.87932	D	0	.	15.9281	0.79635	0.0:1.0:0.0:0.0	.	1;1;1	Q70SY1-3;Q70SY1-2;Q70SY1	.;.;CR3L2_HUMAN	I	1	ENSP00000329140:M1I;ENSP00000403550:M1I;ENSP00000410314:M1I	ENSP00000329140:M1I	M	-	3	0	CREB3L2	137336989	1.000000	0.71417	1.000000	0.80357	0.851000	0.48451	4.272000	0.58908	2.837000	0.97791	0.655000	0.94253	ATG		0.701	CREB3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341462.1	NM_194071	Missense_Mutation
ZC3HAV1	56829	broad.mit.edu	37	7	138739999	138739999	+	Silent	SNP	G	G	A	rs533214079		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:138739999G>A	ENST00000242351.5	-	10	2455	c.2139C>T	c.(2137-2139)acC>acT	p.T713T	ZC3HAV1_ENST00000464606.1_Silent_p.T835T	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	713					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)	p.T713T(1)		cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						GAGGACGAAAGGTCGCAGTTA	0.408																																					p.T713T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2139T	7						.						119.0	118.0	118.0					7																	138739999		2203	4300	6503	138390539	SO:0001819	synonymous_variant	56829	exon10			BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.2139C>T	7.37:g.138739999G>A		Somatic		Capture	Illumina HiSeq	Phase_I	138390539	NM_020119	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Silent	SNP	ENST00000242351.5	37	CCDS5851.1																																																																																				0.408	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
MGAM	8972	broad.mit.edu	37	7	141754649	141754649	+	Silent	SNP	G	G	C	rs200667889	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:141754649G>C	ENST00000549489.2	+	27	3350	c.3255G>C	c.(3253-3255)gtG>gtC	p.V1085V	MGAM_ENST00000475668.2_Silent_p.V1085V	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1085	Glucoamylase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)	p.V1085V(2)		cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCTATGATGTGCTCATTAAGA	0.463													g|||	2	0.000399361	0.0008	0.0	5008	,	,		18528	0.001		0.0	False		,,,				2504	0.0				p.V1085V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3255C	7						.																																			141401118	SO:0001819	synonymous_variant	8972	exon27			AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.3255G>C	7.37:g.141754649G>C		Somatic		Capture	Illumina HiSeq	Phase_I	141401118	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																				0.463	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
POM121	9883	broad.mit.edu	37	7	72420448	72420448	+	3'UTR	SNP	C	C	G	rs400282	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:72420448C>G	ENST00000395270.1	+	0	5480				NSUN5P2_ENST00000388955.4_RNA	NM_001257190.1	NP_001244119.1	Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin						carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)		p.W47S(3)		NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				CACAGGCATCCATGACATGGG	0.612													.|||	11	0.00219649	0.0015	0.0014	5008	,	,		17883	0.0		0.004	False		,,,				2504	0.0041				.												.	.	3	Substitution - Missense(3)	large_intestine(1)|lung(1)|kidney(1)	.	7						.						40.0	44.0	43.0					7																	72420448		2199	4300	6499	72058384	SO:0001624	3_prime_UTR_variant	260294	.			AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000395270.1:c.*1439C>G	7.37:g.72420448C>G		Somatic		Capture	Illumina HiSeq	Phase_I	72058384	.	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000395270.1	37	CCDS59059.1																																																																																				0.612	POM121-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252020.1		
PPP1R35	221908	broad.mit.edu	37	7	100033079	100033079	+	Silent	SNP	G	G	A	rs569808693		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:100033079G>A	ENST00000292330.2	-	4	856	c.666C>T	c.(664-666)acC>acT	p.T222T	RP11-758P17.2_ENST00000492523.1_RNA|PPP1R35_ENST00000476185.1_5'UTR|RP11-758P17.3_ENST00000475250.1_RNA	NM_145030.2	NP_659467.1	Q8TAP8	PPR35_HUMAN	protein phosphatase 1, regulatory subunit 35	222					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.T222T(1)									GACCGTCCAGGGTCAGGTGTG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		16002	0.0		0.001	False		,,,				2504	0.0				p.T222T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C666T	7						.						87.0	83.0	84.0					7																	100033079		2203	4300	6503	99871015	SO:0001819	synonymous_variant	221908	exon4			BC026269	CCDS5694.1	7q22.1	2012-04-17	2011-10-11	2011-10-11	ENSG00000160813	ENSG00000160813		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28320	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 47"""	C7orf47		12477932	Standard	NM_145030		Approved	MGC22793	uc003uuy.1	Q8TAP8	OTTHUMG00000159540	ENST00000292330.2:c.666C>T	7.37:g.100033079G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99871015	NM_145030	A4D2C5	Silent	SNP	ENST00000292330.2	37	CCDS5694.1																																																																																				0.602	PPP1R35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356095.2	NM_145030	
ZNF862	643641	broad.mit.edu	37	7	149561289	149561289	+	Silent	SNP	G	G	A	rs139787517	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr7:149561289G>A	ENST00000223210.4	+	8	3671	c.3426G>A	c.(3424-3426)gcG>gcA	p.A1142A	RP4-751H13.7_ENST00000608963.1_RNA	NM_001099220.1	NP_001092690.1	O60290	ZN862_HUMAN	zinc finger protein 862	1142					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A1142A(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(1)	34						GGGAAGCAGCGGAGGTTCTGA	0.642													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17280	0.0		0.001	False		,,,				2504	0.0				p.A1142A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3426A	7						.						31.0	35.0	34.0					7																	149561289		1906	4125	6031	149192222	SO:0001819	synonymous_variant	643641	exon8			AB011115	CCDS47741.1	7q36.1	2013-01-11			ENSG00000106479	ENSG00000106479		"""Zinc fingers, C2H2-type"", ""-"""	34519	protein-coding gene	gene with protein product							Standard	NM_001099220		Approved		uc010lpn.3	O60290	OTTHUMG00000158093	ENST00000223210.4:c.3426G>A	7.37:g.149561289G>A		Somatic		Capture	Illumina HiSeq	Phase_I	149192222	NM_001099220	A0AUL8	Silent	SNP	ENST00000223210.4	37	CCDS47741.1																																																																																				0.642	ZNF862-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350165.1	NM_001099220	
RAD54B	25788	broad.mit.edu	37	8	95411726	95411726	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr8:95411726C>A	ENST00000336148.5	-	8	1418	c.1294G>T	c.(1294-1296)Gag>Tag	p.E432*		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	432	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)	p.E432*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			CGATGCCCCTCGTCACAGATT	0.338								Direct reversal of damage;Homologous recombination																													p.E432X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1294T	8						.						81.0	78.0	79.0					8																	95411726		2203	4300	6503	95480902	SO:0001587	stop_gained	25788	exon8			AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1294G>T	8.37:g.95411726C>A	ENSP00000336606:p.Glu432*	Somatic		Capture	Illumina HiSeq	Phase_I	95480902	NM_012415	F6WBS8	Nonsense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	C	40	8.129793	0.98667	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	.	.	.	5.44	4.55	0.56014	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-10.4252	16.0677	0.80897	0.0:0.8654:0.1346:0.0	.	.	.	.	X	432;105	.	ENSP00000336606:E432X	E	-	1	0	RAD54B	95480902	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.757000	0.85209	1.258000	0.44101	0.585000	0.79938	GAG		0.338	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
GRHL2	79977	broad.mit.edu	37	8	102611358	102611358	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr8:102611358G>A	ENST00000251808.3	+	8	1415	c.1077G>A	c.(1075-1077)tgG>tgA	p.W359*	GRHL2_ENST00000395927.1_Nonsense_Mutation_p.W343*	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	359					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.W359*(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			CCTTTACCTGGGACGTGAATG	0.363																																					p.W359X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1077A	8						.						106.0	98.0	101.0					8																	102611358		2203	4300	6503	102680534	SO:0001587	stop_gained	79977	exon8			AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.1077G>A	8.37:g.102611358G>A	ENSP00000251808:p.Trp359*	Somatic		Capture	Illumina HiSeq	Phase_I	102680534	NM_024915	A1L303|Q6NT03|Q9H8B8	Nonsense_Mutation	SNP	ENST00000251808.3	37	CCDS34931.1	.	.	.	.	.	.	.	.	.	.	G	42	9.433395	0.99169	.	.	ENSG00000083307	ENST00000251808;ENST00000395927;ENST00000395928	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.6933	20.5827	0.99408	0.0:0.0:1.0:0.0	.	.	.	.	X	359;343;359	.	ENSP00000251808:W359X	W	+	3	0	GRHL2	102680534	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.725000	0.98778	2.941000	0.99782	0.655000	0.94253	TGG		0.363	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
TBC1D2	55357	broad.mit.edu	37	9	100963835	100963835	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr9:100963835C>T	ENST00000375064.1	-	11	2421	c.2383G>A	c.(2383-2385)Gtg>Atg	p.V795M	TBC1D2_ENST00000342112.5_Missense_Mutation_p.V577M|TBC1D2_ENST00000375063.1_Missense_Mutation_p.V335M|TBC1D2_ENST00000375066.5_Missense_Mutation_p.V795M	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	795	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)	p.V795M(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GCAAAGACCACGAGGAACCAG	0.612																																					p.V795M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2383A	9						.						143.0	106.0	119.0					9																	100963835		2203	4300	6503	100003656	SO:0001583	missense	55357	exon11			AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"""prostate antigen recognized and identified by SEREX"""	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.2383G>A	9.37:g.100963835C>T	ENSP00000364205:p.Val795Met	Somatic		Capture	Illumina HiSeq	Phase_I	100003656	NM_018421	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375064.1	37		.	.	.	.	.	.	.	.	.	.	C	24.5	4.534861	0.85812	.	.	ENSG00000095383	ENST00000375064;ENST00000375066;ENST00000342112;ENST00000375063	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.85	4.85	0.62838	Rab-GAP/TBC domain (4);	0.000000	0.85682	D	0.000000	T	0.34542	0.0901	M	0.77406	2.37	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.70227	0.957;0.968	T	0.15665	-1.0429	10	0.66056	D	0.02	.	16.7564	0.85501	0.0:1.0:0.0:0.0	.	795;795	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	M	795;795;577;335	ENSP00000364205:V795M;ENSP00000364207:V795M;ENSP00000341567:V577M;ENSP00000364203:V335M	ENSP00000341567:V577M	V	-	1	0	TBC1D2	100003656	1.000000	0.71417	0.992000	0.48379	0.923000	0.55619	6.060000	0.71141	2.245000	0.73994	0.555000	0.69702	GTG		0.612	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421	
DDX58	23586	broad.mit.edu	37	9	32480268	32480268	+	Nonsense_Mutation	SNP	G	G	A	rs371404578		TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr9:32480268G>A	ENST00000379883.2	-	12	1880	c.1723C>T	c.(1723-1725)Cga>Tga	p.R575*	DDX58_ENST00000545044.1_Nonsense_Mutation_p.R372*|DDX58_ENST00000379882.1_Nonsense_Mutation_p.R530*|DDX58_ENST00000379868.1_Nonsense_Mutation_p.R372*|DDX58_ENST00000542096.1_Nonsense_Mutation_p.R504*	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	575	Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.R575*(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CCTGCTGCTCGGACATTGCTG	0.413																																					p.R575X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1723T	9						.	G	stop/ARG	0,4406		0,0,2203	152.0	133.0	139.0		1723	2.6	1.0	9		139	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	DDX58	NM_014314.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		575/926	32480268	1,13005	2203	4300	6503	32470268	SO:0001587	stop_gained	23586	exon12			AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.1723C>T	9.37:g.32480268G>A	ENSP00000369213:p.Arg575*	Somatic		Capture	Illumina HiSeq	Phase_I	32470268	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Nonsense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	.	.	.	.	.	.	.	.	.	.	G	41	8.877516	0.98988	0.0	1.16E-4	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	.	.	.	4.67	2.62	0.31277	.	0.481250	0.18583	N	0.136967	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.7526	10.6591	0.45692	0.0:0.0:0.4597:0.5402	.	.	.	.	X	530;575;372;504;372	.	ENSP00000369197:R372X	R	-	1	2	DDX58	32470268	0.129000	0.22400	0.997000	0.53966	0.991000	0.79684	0.903000	0.28475	1.260000	0.44134	-0.182000	0.12963	CGA		0.413	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
KIAA1161	57462	broad.mit.edu	37	9	34371826	34371826	+	Silent	SNP	G	G	A			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr9:34371826G>A	ENST00000297625.7	-	2	1239	c.1014C>T	c.(1012-1014)aaC>aaT	p.N338N		NM_020702.3	NP_065753.2	Q6NSJ0	K1161_HUMAN	KIAA1161	372					carbohydrate metabolic process (GO:0005975)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of protein kinase B signaling (GO:0051897)|skeletal muscle fiber development (GO:0048741)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.N338N(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.126)		TGTCGCTGGCGTTGGGGAATT	0.602																																					p.N372N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1116T	9						.						97.0	101.0	99.0					9																	34371826		2178	4260	6438	34361826	SO:0001819	synonymous_variant	57462	exon2			AB032987		9p11.2	2009-11-06			ENSG00000164976	ENSG00000164976			19918	protein-coding gene	gene with protein product						10574461	Standard	XM_006716808		Approved	NET37	uc003zue.4	Q6NSJ0	OTTHUMG00000019816	ENST00000297625.7:c.1014C>T	9.37:g.34371826G>A		Somatic		Capture	Illumina HiSeq	Phase_I	34361826	NM_020702	Q5T587|Q5T588|Q9ULQ9	Silent	SNP	ENST00000297625.7	37																																																																																					0.602	KIAA1161-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000052158.1	XM_351807	
TLN1	7094	broad.mit.edu	37	9	35704339	35704339	+	Missense_Mutation	SNP	C	C	T	rs144809355	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr9:35704339C>T	ENST00000314888.9	-	45	6390	c.6037G>A	c.(6037-6039)Gct>Act	p.A2013T	TLN1_ENST00000464379.1_5'UTR|TLN1_ENST00000540444.1_Missense_Mutation_p.A1907T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	2013					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.A2013T(1)		NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CGGTGGTCAGCGAAAGTTTCA	0.587													C|||	5	0.000998403	0.0	0.0058	5008	,	,		22135	0.0		0.001	False		,,,				2504	0.0				p.A2013T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6037A	9						.	C	THR/ALA	0,4406		0,0,2203	158.0	146.0	150.0		6037	5.0	1.0	9	dbSNP_134	150	8,8592	7.1+/-27.0	0,8,4292	yes	missense	TLN1	NM_006289.3	58	0,8,6495	TT,TC,CC		0.093,0.0,0.0615	probably-damaging	2013/2542	35704339	8,12998	2203	4300	6503	35694339	SO:0001583	missense	7094	exon45			AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.6037G>A	9.37:g.35704339C>T	ENSP00000316029:p.Ala2013Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35694339	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	31	5.068987	0.93950	0.0	9.3E-4	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.14144	2.53;2.53	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.19446	0.0467	L	0.60012	1.86	0.80722	D	1	D	0.63046	0.992	P	0.44359	0.447	T	0.02975	-1.1087	10	0.30078	T	0.28	-7.5663	18.2971	0.90150	0.0:1.0:0.0:0.0	.	2013	Q9Y490	TLN1_HUMAN	T	2013;1907	ENSP00000316029:A2013T;ENSP00000442981:A1907T	ENSP00000316029:A2013T	A	-	1	0	TLN1	35694339	1.000000	0.71417	0.961000	0.40146	0.974000	0.67602	7.814000	0.86154	2.319000	0.78375	0.561000	0.74099	GCT		0.587	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
CNTRL	11064	broad.mit.edu	37	9	123852666	123852666	+	Missense_Mutation	SNP	G	G	A	rs140149582	byFrequency	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chr9:123852666G>A	ENST00000373855.1	+	4	591	c.331G>A	c.(331-333)Ggt>Agt	p.G111S	CNTRL_ENST00000373865.2_Missense_Mutation_p.G111S|CNTRL_ENST00000238341.5_Missense_Mutation_p.G111S			Q7Z7A1	CNTRL_HUMAN	centriolin	111					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)		p.G111S(1)		haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						TTCTAAAGACGGTGGCAAGAA	0.323																																					p.G111S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G331A	9						.	G	SER/GLY	0,4406		0,0,2203	78.0	83.0	81.0		331	1.7	1.0	9	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTRL	NM_007018.4	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	111/2326	123852666	1,13005	2203	4300	6503	122892487	SO:0001583	missense	11064	exon2			AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.331G>A	9.37:g.123852666G>A	ENSP00000362962:p.Gly111Ser	Somatic		Capture	Illumina HiSeq	Phase_I	122892487	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.803001	0.50315	0.0	1.16E-4	ENSG00000119397	ENST00000373865;ENST00000373855;ENST00000238341;ENST00000454238	T;T	0.26810	1.71;1.71	4.69	1.71	0.24356	.	.	.	.	.	T	0.12263	0.0298	N	0.11284	0.12	0.36928	D	0.89175	D	0.57571	0.98	B	0.42138	0.377	T	0.17868	-1.0355	9	0.30854	T	0.27	.	7.9618	0.30076	0.1574:0.1338:0.7087:0.0	.	111	Q7Z7A1	CNTRL_HUMAN	S	111	ENSP00000362962:G111S;ENSP00000238341:G111S	ENSP00000238341:G111S	G	+	1	0	CNTRL	122892487	1.000000	0.71417	0.996000	0.52242	0.730000	0.41778	3.252000	0.51461	0.491000	0.27793	-0.224000	0.12420	GGT		0.323	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
PCDH11X	27328	broad.mit.edu	37	X	91091027	91091027	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chrX:91091027A>T	ENST00000373094.1	+	1	1369	c.524A>T	c.(523-525)aAc>aTc	p.N175I	PCDH11X_ENST00000373088.1_Missense_Mutation_p.N175I|PCDH11X_ENST00000361724.1_Missense_Mutation_p.N175I|PCDH11X_ENST00000298274.8_Missense_Mutation_p.N175I|PCDH11X_ENST00000395337.2_Missense_Mutation_p.N175I|PCDH11X_ENST00000373097.1_Missense_Mutation_p.N175I|PCDH11X_ENST00000406881.1_Missense_Mutation_p.N175I|PCDH11X_ENST00000504220.2_Missense_Mutation_p.N175I|PCDH11X_ENST00000361655.2_Missense_Mutation_p.N175I	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	175	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N175I(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						GGAGTTCAAAACTACGAACTA	0.303																																					p.N175I	NSCLC(38;925 1092 2571 38200 45895)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A524T	X						.						36.0	37.0	36.0					X																	91091027		2199	4296	6495	90977683	SO:0001583	missense	27328	exon1			AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.524A>T	X.37:g.91091027A>T	ENSP00000362186:p.Asn175Ile	Somatic		Capture	Illumina HiSeq	Phase_I	90977683	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Missense_Mutation	SNP	ENST00000373094.1	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	15.90	2.969566	0.53614	.	.	ENSG00000102290	ENST00000395337;ENST00000373094;ENST00000373097;ENST00000361724;ENST00000373088;ENST00000504220;ENST00000361655;ENST00000406881;ENST00000356934;ENST00000298274	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	4.44	3.26	0.37387	Cadherin (4);Cadherin-like (1);	0.303114	0.34484	N	0.003929	T	0.53094	0.1775	L	0.41236	1.265	0.33022	D	0.529021	D;B;D;D;D;D;D;D	0.64830	0.98;0.109;0.993;0.993;0.993;0.994;0.98;0.98	P;B;P;P;P;D;P;P	0.63597	0.782;0.064;0.863;0.863;0.863;0.916;0.708;0.708	T	0.63466	-0.6631	10	0.72032	D	0.01	.	8.3614	0.32361	0.9043:0.0:0.0957:0.0	.	175;175;175;175;175;175;175;175	Q9BZA7-6;Q9BZA7-5;Q9BZA7-4;Q9BZA7-8;Q9BZA7-3;Q9BZA7;Q9BZA7-7;Q9BZA7-2	.;.;.;.;.;PC11X_HUMAN;.;.	I	175	ENSP00000378746:N175I;ENSP00000362186:N175I;ENSP00000362189:N175I;ENSP00000355040:N175I;ENSP00000362180:N175I;ENSP00000423762:N175I;ENSP00000355105:N175I;ENSP00000384758:N175I;ENSP00000298274:N175I	ENSP00000298274:N175I	N	+	2	0	PCDH11X	90977683	1.000000	0.71417	0.974000	0.42286	0.807000	0.45602	8.349000	0.90067	0.648000	0.30732	0.412000	0.27726	AAC		0.303	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
F8	2157	broad.mit.edu	37	X	154157327	154157327	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3952-01A-01W-0995-10	TCGA-AA-3952-10A-01W-0995-10	g.chrX:154157327G>C	ENST00000360256.4	-	14	4938	c.4738C>G	c.(4738-4740)Cta>Gta	p.L1580V		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1580	B.				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)	p.L1580V(2)		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)	GGATCCAATAGCTTGGAGGGA	0.438																																					p.L1580V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4738G	X						.						157.0	154.0	155.0					X																	154157327		2203	4300	6503	153810521	SO:0001583	missense	2157	exon14			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.4738C>G	X.37:g.154157327G>C	ENSP00000353393:p.Leu1580Val	Somatic		Capture	Illumina HiSeq	Phase_I	153810521	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	g	0.585	-0.835542	0.02713	.	.	ENSG00000185010	ENST00000360256	D	0.99113	-5.44	4.8	-3.05	0.05396	.	0.616021	0.14078	N	0.342927	D	0.95714	0.8606	M	0.73598	2.24	0.09310	N	1	P	0.43094	0.799	B	0.33339	0.162	D	0.91546	0.5253	10	0.13108	T	0.6	-0.4004	1.1059	0.01693	0.3587:0.2606:0.2468:0.1338	.	1580	P00451	FA8_HUMAN	V	1580	ENSP00000353393:L1580V	ENSP00000353393:L1580V	L	-	1	2	F8	153810521	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.026000	0.12392	-0.403000	0.07622	-1.100000	0.02121	CTA		0.438	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
