#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
PSD	5662	broad.mit.edu	37	10	104174958	104174959	+	Frame_Shift_Ins	INS	-	-	G	rs571611854		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:104174958_104174959insG	ENST00000020673.5	-	4	1311_1312	c.785_786insC	c.(784-786)ccafs	p.P262fs	PSD_ENST00000406432.1_Frame_Shift_Ins_p.P262fs|PSD_ENST00000492902.2_5'Flank	NM_001270966.1|NM_002779.4	NP_001257895.1|NP_002770.3	A5PKW4	PSD1_HUMAN	pleckstrin and Sec7 domain containing	262					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)	p.S48fs*38(1)|p.S263fs*38(1)		breast(4)|endometrium(2)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				Epithelial(162;1.27e-08)|all cancers(201;2.85e-07)		CAGGTGGAGATGGGGGGGCCTG	0.624																																					p.P262fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.786_787insC	10						.																																			104164949	SO:0001589	frameshift_variant	5662	exon4			X99688	CCDS31272.1, CCDS73187.1	10q24	2013-01-10	2004-04-28		ENSG00000059915	ENSG00000059915		"""Pleckstrin homology (PH) domain containing"""	9507	protein-coding gene	gene with protein product		602327	"""pleckstrin and Sec7 domain protein"""			9417912	Standard	NM_002779		Approved	KIAA2011, TYL, PSD1	uc009xxd.2	A5PKW4	OTTHUMG00000018954	ENST00000020673.5:c.786dupC	10.37:g.104174965_104174965dupG	ENSP00000020673:p.Pro262fs	Somatic		Capture	Illumina HiSeq	Phase_I	104164948	NM_002779	B1AKX7|D3DR87|Q15673|Q8IVG0	Frame_Shift_Ins	INS	ENST00000020673.5	37	CCDS31272.1																																																																																				0.624	PSD-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050041.2		
LOXL4	84171	broad.mit.edu	37	10	100017908	100017908	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:100017908C>T	ENST00000260702.3	-	7	1085	c.935G>A	c.(934-936)cGc>cAc	p.R312H	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	312	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|receptor complex (GO:0043235)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)	p.R312H(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(8)|ovary(4)|prostate(1)|skin(2)	26		Colorectal(252;0.234)		Epithelial(162;2.14e-11)|all cancers(201;2.49e-09)		GGAGCGCAGGCGCACCCTCGG	0.697																																					p.R312H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G935A	10						.						27.0	26.0	26.0					10																	100017908		2202	4296	6498	100007898	SO:0001583	missense	84171	exon7			AF338441	CCDS7473.1	10q24	2008-08-01			ENSG00000138131	ENSG00000138131			17171	protein-coding gene	gene with protein product		607318				11292829	Standard	XM_005270216		Approved	FLJ21889, LOXC	uc001kpa.1	Q96JB6	OTTHUMG00000018874	ENST00000260702.3:c.935G>A	10.37:g.100017908C>T	ENSP00000260702:p.Arg312His	Somatic		Capture	Illumina HiSeq	Phase_I	100007898	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	37	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	C	32	5.183637	0.94885	.	.	ENSG00000138131	ENST00000260702	T	0.53857	0.6	4.94	4.94	0.65067	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	D	0.83547	0.5278	H	0.99391	4.545	0.80722	D	1	D	0.89917	1.0	P	0.61003	0.882	D	0.91686	0.5362	10	0.87932	D	0	.	18.1558	0.89690	0.0:1.0:0.0:0.0	.	312	Q96JB6	LOXL4_HUMAN	H	312	ENSP00000260702:R312H	ENSP00000260702:R312H	R	-	2	0	LOXL4	100007898	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.669000	0.83911	2.283000	0.76528	0.549000	0.68633	CGC		0.697	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211	
BTRC	8945	broad.mit.edu	37	10	103292173	103292173	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:103292173G>A	ENST00000370187.3	+	8	1080	c.962G>A	c.(961-963)cGa>cAa	p.R321Q	BTRC_ENST00000393441.4_Missense_Mutation_p.R280Q|BTRC_ENST00000408038.2_Missense_Mutation_p.R285Q	NM_033637.3	NP_378663.1	Q9Y297	FBW1A_HUMAN	beta-transducin repeat containing E3 ubiquitin protein ligase	321					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cellular response to organic cyclic compound (GO:0071407)|G2/M transition of mitotic cell cycle (GO:0000086)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of circadian rhythm (GO:0042753)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein dephosphorylation (GO:0006470)|protein destabilization (GO:0031648)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of circadian rhythm (GO:0042752)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|signal transduction (GO:0007165)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.R321Q(1)		endometrium(4)|kidney(2)|large_intestine(6)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	27		Colorectal(252;0.234)		Epithelial(162;1.05e-08)|all cancers(201;6.59e-07)		AGCGGCCTTCGAGACAACACA	0.413																																					p.R285Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G854A	10						.						114.0	112.0	113.0					10																	103292173		2203	4300	6503	103282163	SO:0001583	missense	8945	exon7			Y14153	CCDS7511.1, CCDS7512.1, CCDS73183.1	10q24.32	2013-01-10	2012-02-23		ENSG00000166167	ENSG00000166167		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	1144	protein-coding gene	gene with protein product		603482	"""beta-transducin repeat containing"""			9660940, 10331953, 18354483	Standard	NM_033637		Approved	bTrCP, betaTrCP, FBXW1A, Fwd1, beta-TrCP1, bTrCP1	uc001kta.4	Q9Y297	OTTHUMG00000018932	ENST00000370187.3:c.962G>A	10.37:g.103292173G>A	ENSP00000359206:p.Arg321Gln	Somatic		Capture	Illumina HiSeq	Phase_I	103282163	NM_003939	B5MD49|Q5W141|Q5W142|Q9Y213	Missense_Mutation	SNP	ENST00000370187.3	37	CCDS7512.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815261	0.90790	.	.	ENSG00000166167	ENST00000370187;ENST00000393441;ENST00000408038	T;T;T	0.62941	-0.01;-0.01;-0.01	5.96	5.96	0.96718	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000008	T	0.78742	0.4331	M	0.67700	2.07	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.928;0.975	T	0.75348	-0.3349	10	0.40728	T	0.16	-5.7218	20.4008	0.98991	0.0:0.0:1.0:0.0	.	295;285;321	B7Z3H4;Q9Y297-2;Q9Y297	.;.;FBW1A_HUMAN	Q	321;280;285	ENSP00000359206:R321Q;ENSP00000377088:R280Q;ENSP00000385339:R285Q	ENSP00000359206:R321Q	R	+	2	0	BTRC	103282163	1.000000	0.71417	1.000000	0.80357	0.312000	0.27988	9.869000	0.99810	2.826000	0.97356	0.655000	0.94253	CGA		0.413	BTRC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049936.1	NM_033637	
LDB1	8861	broad.mit.edu	37	10	103868029	103868029	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:103868029C>T	ENST00000425280.1	-	11	1399	c.1057G>A	c.(1057-1059)Gag>Aag	p.E353K	LDB1_ENST00000361198.5_Missense_Mutation_p.E317K|LDB1_ENST00000490751.1_5'Flank	NM_001113407.1	NP_001106878.1	Q86U70	LDB1_HUMAN	LIM domain binding 1	353	LIM-binding domain (LID). {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|cellular component assembly (GO:0022607)|cerebellar Purkinje cell differentiation (GO:0021702)|epithelial structure maintenance (GO:0010669)|gastrulation with mouth forming second (GO:0001702)|hair follicle development (GO:0001942)|head development (GO:0060322)|histone H3-K4 acetylation (GO:0043973)|multicellular organismal development (GO:0007275)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|positive regulation of cell adhesion (GO:0045785)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell maintenance (GO:0035019)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery (GO:0000972)|Wnt signaling pathway (GO:0016055)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enhancer sequence-specific DNA binding (GO:0001158)|enzyme binding (GO:0019899)|LIM domain binding (GO:0030274)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|transcription corepressor activity (GO:0003714)	p.E317K(1)		breast(1)|central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)	21		Colorectal(252;0.122)		Epithelial(162;1.11e-07)|all cancers(201;1.82e-06)		CTCTCGTCCTCGTCCCCGAAC	0.637																																					p.E353K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1057A	10						.						116.0	85.0	96.0					10																	103868029		2203	4300	6503	103858019	SO:0001583	missense	8861	exon11			AF068652	CCDS7528.1, CCDS44472.1	10q24-q25	2008-08-01			ENSG00000198728	ENSG00000198728			6532	protein-coding gene	gene with protein product	"""carboxy terminal LIM domain protein 2"""	603451				9503020, 9799849	Standard	NM_003893		Approved	NLI, CLIM2	uc009xwz.3	Q86U70	OTTHUMG00000018950	ENST00000425280.1:c.1057G>A	10.37:g.103868029C>T	ENSP00000392466:p.Glu353Lys	Somatic		Capture	Illumina HiSeq	Phase_I	103858019	NM_001113407	B4DUC4|O75479|O96010|Q1EQX1|Q9UGM4	Missense_Mutation	SNP	ENST00000425280.1	37	CCDS44472.1	.	.	.	.	.	.	.	.	.	.	C	36	5.701303	0.96812	.	.	ENSG00000198728	ENST00000361198;ENST00000425280	T;T	0.26373	1.74;1.74	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.55257	0.1909	M	0.82716	2.605	0.80722	D	1	D	0.63046	0.992	P	0.62649	0.905	T	0.59306	-0.7479	10	0.87932	D	0	-0.014	19.6346	0.95724	0.0:1.0:0.0:0.0	.	353	Q86U70	LDB1_HUMAN	K	317;353	ENSP00000354616:E317K;ENSP00000392466:E353K	ENSP00000354616:E317K	E	-	1	0	LDB1	103858019	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.776000	0.85560	2.742000	0.94016	0.455000	0.32223	GAG		0.637	LDB1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113407	
CFAP43	80217	broad.mit.edu	37	10	105990460	105990460	+	Silent	SNP	G	G	A	rs374123628		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:105990460G>A	ENST00000357060.3	-	2	322	c.207C>T	c.(205-207)ggC>ggT	p.G69G	WDR96_ENST00000428666.1_Silent_p.G69G|WDR96_ENST00000369719.1_5'UTR|WDR96_ENST00000278064.2_5'UTR|WDR96_ENST00000369720.1_5'UTR	NM_025145.5	NP_079421.5												p.G69G(2)		NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						TTGCCATGACGCCCACAATTC	0.408																																					p.G69G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C207T	10						.	G		0,4406		0,0,2203	144.0	132.0	136.0		207	1.3	1.0	10		136	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	WDR96	NM_025145.5		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		69/1666	105990460	1,13005	2203	4300	6503	105980450	SO:0001819	synonymous_variant	80217	exon2																														ENST00000357060.3:c.207C>T	10.37:g.105990460G>A		Somatic		Capture	Illumina HiSeq	Phase_I	105980450	NM_025145		Silent	SNP	ENST00000357060.3	37	CCDS31281.1																																																																																				0.408	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ADD3	120	broad.mit.edu	37	10	111893230	111893230	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:111893230G>A	ENST00000356080.4	+	15	2342	c.1975G>A	c.(1975-1977)Gag>Aag	p.E659K	ADD3_ENST00000360162.3_Missense_Mutation_p.E627K|ADD3_ENST00000277900.8_Missense_Mutation_p.E627K	NM_016824.3	NP_058432.1	Q9UEY8	ADDG_HUMAN	adducin 3 (gamma)	659						cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)	p.E659K(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	29		Breast(234;0.052)|Lung NSC(174;0.223)		Epithelial(162;4.15e-05)|all cancers(201;0.000587)|BRCA - Breast invasive adenocarcinoma(275;0.0742)		AGAAAACATCGAGATTACTAT	0.418																																					p.E627K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1879A	10						.						133.0	129.0	130.0					10																	111893230		2203	4300	6503	111883220	SO:0001583	missense	120	exon14			U37122	CCDS7561.1, CCDS7562.1	10q25.2	2005-11-08			ENSG00000148700	ENSG00000148700			245	protein-coding gene	gene with protein product		601568		ADDL		8893809	Standard	XM_005269529		Approved		uc001kyv.3	Q9UEY8	OTTHUMG00000019032	ENST00000356080.4:c.1975G>A	10.37:g.111893230G>A	ENSP00000348381:p.Glu659Lys	Somatic		Capture	Illumina HiSeq	Phase_I	111883220	NM_019903	D3DRA8|O43243|Q5VU09|Q92773|Q9UEY7	Missense_Mutation	SNP	ENST00000356080.4	37	CCDS7561.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.969869	0.74246	.	.	ENSG00000148700	ENST00000360162;ENST00000356080;ENST00000277900	T;T;T	0.52754	0.65;0.65;0.65	5.71	4.81	0.61882	.	0.111389	0.64402	D	0.000005	T	0.64605	0.2613	L	0.58810	1.83	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.67098	-0.5756	10	0.56958	D	0.05	-19.2002	14.878	0.70510	0.0688:0.0:0.9312:0.0	.	659;627	Q9UEY8;Q9UEY8-2	ADDG_HUMAN;.	K	627;659;627	ENSP00000353286:E627K;ENSP00000348381:E659K;ENSP00000277900:E627K	ENSP00000277900:E627K	E	+	1	0	ADD3	111883220	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.572000	0.90756	1.564000	0.49628	0.650000	0.86243	GAG		0.418	ADD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050289.1	NM_019903	
ACSL5	51703	broad.mit.edu	37	10	114182198	114182198	+	Splice_Site	SNP	C	C	T	rs375823791		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:114182198C>T	ENST00000393081.1	+	17	1899	c.1592C>T	c.(1591-1593)cCg>cTg	p.P531L	ACSL5_ENST00000356116.1_Splice_Site_p.P587L|ACSL5_ENST00000354273.4_Splice_Site_p.P531L|ACSL5_ENST00000354655.4_Splice_Site_p.P531L|ACSL5_ENST00000369410.3_Splice_Site_p.P313L|ACSL5_ENST00000433418.1_Splice_Site_p.P531L|RP11-324O2.6_ENST00000424422.1_RNA	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	531					cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)	p.P587L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		CGCTGGCTCCCGGTAGGTATA	0.478																																					p.P587L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1760T	10						.	C	LEU/PRO,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	90.0	91.0	91.0		1760,1592,1592	4.8	1.0	10		91	0,8600		0,0,4300	no	missense-near-splice,missense-near-splice,missense-near-splice	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	98,98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	587/740,531/684,531/684	114182198	1,13005	2203	4300	6503	114172188	SO:0001630	splice_region_variant	51703	exon17			AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.1593+1C>T	10.37:g.114182198C>T		Somatic		Capture	Illumina HiSeq	Phase_I	114172188	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.673831	0.88445	2.27E-4	0.0	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273;ENST00000369410	T;T;T;T;T;T	0.12879	2.64;2.64;2.64;2.64;2.64;2.64	5.71	4.79	0.61399	AMP-dependent synthetase/ligase (1);	0.104341	0.64402	D	0.000003	T	0.51550	0.1681	H	0.96518	3.835	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.989;0.995	D;D;P;P	0.77557	0.988;0.99;0.634;0.862	T	0.69989	-0.4995	10	0.87932	D	0	-8.8735	15.845	0.78879	0.1369:0.8631:0.0:0.0	.	313;531;587;531	B4DX30;A6GV77;Q9ULC5-3;Q9ULC5	.;.;.;ACSL5_HUMAN	L	531;531;587;531;531;313	ENSP00000346680:P531L;ENSP00000376796:P531L;ENSP00000348429:P587L;ENSP00000403647:P531L;ENSP00000346223:P531L;ENSP00000358418:P313L	ENSP00000346223:P531L	P	+	2	0	ACSL5	114172188	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	6.018000	0.70811	1.370000	0.46153	0.555000	0.69702	CCG		0.478	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	Missense_Mutation
GFRA1	2674	broad.mit.edu	37	10	117853275	117853275	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:117853275C>T	ENST00000355422.6	-	8	1503	c.953G>A	c.(952-954)aGt>aAt	p.S318N	GFRA1_ENST00000439649.3_Missense_Mutation_p.S313N|GFRA1_ENST00000544592.1_Missense_Mutation_p.S197N|GFRA1_ENST00000369236.1_Missense_Mutation_p.S313N	NM_005264.4	NP_005255.1	P56159	GFRA1_HUMAN	GDNF family receptor alpha 1	318					axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)|receptor binding (GO:0005102)	p.S313N(1)		endometrium(2)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(174;0.21)		all cancers(201;0.0337)		GTCGTTCCCACTGTTGCTGCA	0.408																																					p.S313N	Ovarian(128;329 1725 45498 46808 50759)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G938A	10						.						92.0	87.0	88.0					10																	117853275		2203	4300	6503	117843265	SO:0001583	missense	2674	exon7			AF038421	CCDS7593.1, CCDS44481.1	10q25-q26	2011-01-25			ENSG00000151892	ENSG00000151892			4243	protein-coding gene	gene with protein product		601496		GDNFRA		9465905, 9545641	Standard	NM_005264		Approved	RETL1, GDNFR, GFR-ALPHA-1, RET1L, TRNR1	uc001lcj.3	P56159	OTTHUMG00000019097	ENST00000355422.6:c.953G>A	10.37:g.117853275C>T	ENSP00000347591:p.Ser318Asn	Somatic		Capture	Illumina HiSeq	Phase_I	117843265	NM_001145453	A8KA21|O15507|O43912	Missense_Mutation	SNP	ENST00000355422.6	37	CCDS44481.1	.	.	.	.	.	.	.	.	.	.	C	32	5.159260	0.94686	.	.	ENSG00000151892	ENST00000439649;ENST00000369236;ENST00000355422;ENST00000544592;ENST00000369234	T;T	0.65732	-0.17;-0.17	5.93	5.93	0.95920	GDNF/GAS1 (2);	0.000000	0.85682	D	0.000000	D	0.83238	0.5211	M	0.87758	2.905	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.997	D	0.84540	0.0638	10	0.66056	D	0.02	-19.8416	20.3334	0.98727	0.0:1.0:0.0:0.0	.	318;313	P56159;P56159-2	GFRA1_HUMAN;.	N	318;313;313;197;313	ENSP00000358239:S313N;ENSP00000442179:S197N	ENSP00000347591:S313N	S	-	2	0	GFRA1	117843265	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.146000	0.77373	2.818000	0.97014	0.591000	0.81541	AGT		0.408	GFRA1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050512.2	NM_145793	
WDR11	55717	broad.mit.edu	37	10	122619679	122619679	+	Silent	SNP	G	G	A	rs374824479		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:122619679G>A	ENST00000263461.6	+	4	657	c.411G>A	c.(409-411)ccG>ccA	p.P137P		NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	291					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.P137P(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CTATCCACCCGCCAAATTACA	0.428																																					p.P137P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G411A	10						.	G		0,4406		0,0,2203	143.0	122.0	129.0		411	-9.4	0.6	10		129	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WDR11	NM_018117.11		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		137/1225	122619679	2,13004	2203	4300	6503	122609669	SO:0001819	synonymous_variant	55717	exon4			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.411G>A	10.37:g.122619679G>A		Somatic		Capture	Illumina HiSeq	Phase_I	122609669	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																				0.428	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
ADARB2	105	broad.mit.edu	37	10	1245981	1245981	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:1245981G>A	ENST00000381312.1	-	8	2114	c.1789C>T	c.(1789-1791)Cgc>Tgc	p.R597C	ADARB2_ENST00000381305.1_De_novo_Start_OutOfFrame|ADARB2_ENST00000381310.3_Missense_Mutation_p.R106C	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	597	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.R597C(1)		breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTCATGACGCGTGCGAGGTGG	0.706																																					p.R597C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1789T	10						.						40.0	36.0	37.0					10																	1245981		2198	4295	6493	1235981	SO:0001583	missense	105	exon8			AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.1789C>T	10.37:g.1245981G>A	ENSP00000370713:p.Arg597Cys	Somatic		Capture	Illumina HiSeq	Phase_I	1235981	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.270580	0.59540	.	.	ENSG00000185736	ENST00000381312;ENST00000381310	D;D	0.95724	-3.79;-3.79	5.77	2.6	0.31112	Adenosine deaminase/editase (3);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	H	0.95114	3.625	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99338	1.0911	10	0.87932	D	0	-40.8606	14.3643	0.66795	0.0:0.0:0.5247:0.4753	.	597;106	Q9NS39;Q5VW42	RED2_HUMAN;.	C	597;106	ENSP00000370713:R597C;ENSP00000370711:R106C	ENSP00000370711:R106C	R	-	1	0	ADARB2	1235981	1.000000	0.71417	0.981000	0.43875	0.540000	0.34992	1.696000	0.37773	1.408000	0.46895	0.655000	0.94253	CGC		0.706	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
WDR11	55717	broad.mit.edu	37	10	122662711	122662711	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:122662711C>T	ENST00000263461.6	+	23	3144	c.2898C>T	c.(2896-2898)tgC>tgT	p.C966C	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Mediates interaction with IRS1. {ECO:0000250}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)	p.C966C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						TGGATATATGCTATGACGTGC	0.448																																					p.C966C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2898T	10						.						84.0	73.0	77.0					10																	122662711		2203	4300	6503	122652701	SO:0001819	synonymous_variant	55717	exon23			AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2898C>T	10.37:g.122662711C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122652701	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																				0.448	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
DMBT1	1755	broad.mit.edu	37	10	124331831	124331831	+	Splice_Site	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:124331831T>C	ENST00000338354.3	+	5	295	c.189T>C	c.(187-189)ggT>ggC	p.G63G	DMBT1_ENST00000344338.3_Splice_Site_p.G63G|DMBT1_ENST00000368955.3_Splice_Site_p.G63G|DMBT1_ENST00000359586.6_Splice_Site_p.G63G|DMBT1_ENST00000368909.3_Splice_Site_p.G63G|DMBT1_ENST00000330163.4_Splice_Site_p.G63G|DMBT1_ENST00000368956.2_Splice_Site_p.G63G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	63					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)	p.G63G(1)		breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				ACCCTGCAGGTTCTCCGATTT	0.527																																					p.G63G	Ovarian(182;93 2026 18125 22222 38972)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T189C	10						.						172.0	172.0	172.0					10																	124331831		1911	4122	6033	124321821	SO:0001630	splice_region_variant	1755	exon5				CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.188-1T>C	10.37:g.124331831T>C		Somatic		Capture	Illumina HiSeq	Phase_I	124321821	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																					0.527	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	Silent
LHPP	64077	broad.mit.edu	37	10	126205813	126205813	+	Missense_Mutation	SNP	C	C	T	rs201380619		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:126205813C>T	ENST00000368842.5	+	6	717	c.689C>T	c.(688-690)gCg>gTg	p.A230V	LHPP_ENST00000368839.1_Intron	NM_022126.3	NP_071409.3	Q9H008	LHPP_HUMAN	phospholysine phosphohistidine inorganic pyrophosphate phosphatase	230					phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|phosphohistidine phosphatase activity (GO:0008969)|protein homodimerization activity (GO:0042803)	p.A230V(1)		large_intestine(2)|lung(2)	4		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.163)|Colorectal(40;0.187)		GGAATGAGAGCGCTGCAGGTG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		15683	0.0		0.001	False		,,,				2504	0.0				p.A230V	GBM(165;1980 2715 15999 18454)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C689T	10						.	C	,VAL/ALA	0,4406		0,0,2203	86.0	78.0	81.0		,689	4.8	1.0	10		81	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	LHPP	NM_001167880.1,NM_022126.3	,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,possibly-damaging	,230/271	126205813	1,13005	2203	4300	6503	126195803	SO:0001583	missense	64077	exon6			AB049629	CCDS7640.1, CCDS53587.1	10q26.2	2010-02-17			ENSG00000107902	ENSG00000107902	3.6.1.1		30042	protein-coding gene	gene with protein product						12801912, 16430861	Standard	NM_022126		Approved	HDHD2B	uc001lhs.2	Q9H008	OTTHUMG00000019214	ENST00000368842.5:c.689C>T	10.37:g.126205813C>T	ENSP00000357835:p.Ala230Val	Somatic		Capture	Illumina HiSeq	Phase_I	126195803	NM_022126	B3KP20|Q2TBE9|Q5VUV9|Q5VUW0	Missense_Mutation	SNP	ENST00000368842.5	37	CCDS7640.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	28.2	4.900500	0.92035	0.0	1.16E-4	ENSG00000107902	ENST00000368842	T	0.28895	1.59	4.83	4.83	0.62350	HAD-like domain (2);	0.068782	0.64402	D	0.000020	T	0.47469	0.1447	L	0.58101	1.795	0.80722	D	1	D	0.67145	0.996	P	0.58820	0.846	T	0.40098	-0.9581	10	0.42905	T	0.14	-27.4571	16.4736	0.84125	0.0:1.0:0.0:0.0	.	230	Q9H008	LHPP_HUMAN	V	230	ENSP00000357835:A230V	ENSP00000357835:A230V	A	+	2	0	LHPP	126195803	0.969000	0.33509	0.982000	0.44146	0.996000	0.88848	2.205000	0.42770	2.404000	0.81709	0.484000	0.47621	GCG		0.552	LHPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050870.1	NM_022126	
EDRF1	26098	broad.mit.edu	37	10	127414345	127414345	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:127414345T>A	ENST00000356792.4	+	6	962	c.730T>A	c.(730-732)Tca>Aca	p.S244T	C10orf137_ENST00000337623.3_Missense_Mutation_p.S244T	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		244					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(20)|ovary(8)|pancreas(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	61		all_lung(145;0.0096)|Lung NSC(174;0.0145)|Colorectal(57;0.0846)|all_neural(114;0.0936)				GGAAGGGGCTTCATGGCCTGC	0.488																																					p.S244T												.	.	0			c.T730A	10						.						92.0	86.0	88.0					10																	127414345		2203	4300	6503	127404335	SO:0001583	missense	26098	exon6																														ENST00000356792.4:c.730T>A	10.37:g.127414345T>A	ENSP00000349244:p.Ser244Thr	None		Capture	Illumina HiSeq	Phase_I	127404335	NM_015608	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	T	14.30	2.493260	0.44352	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	.	.	.	4.85	3.69	0.42338	.	0.118078	0.64402	D	0.000014	T	0.26268	0.0641	N	0.11201	0.11	0.38173	D	0.939391	P;B;P	0.46142	0.873;0.042;0.873	B;B;B	0.40782	0.34;0.057;0.34	T	0.07177	-1.0786	9	0.16896	T	0.51	.	11.1439	0.48419	0.0:0.0:0.2931:0.7069	.	244;244;244	Q3B7T1;Q3B7T1-5;Q3B7T1-3	EDRF1_HUMAN;.;.	T	244	.	ENSP00000336727:S244T	S	+	1	0	C10orf137	127404335	1.000000	0.71417	0.650000	0.29550	0.873000	0.50193	4.239000	0.58694	0.957000	0.37930	0.528000	0.53228	TCA		0.488	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1		
C10orf90	118611	broad.mit.edu	37	10	128193313	128193313	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:128193313G>A	ENST00000284694.7	-	3	576	c.456C>T	c.(454-456)cgC>cgT	p.R152R	C10orf90_ENST00000454341.1_Silent_p.R152R|C10orf90_ENST00000392694.1_Silent_p.R105R|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000544758.1_Silent_p.R249R|C10orf90_ENST00000356858.3_Silent_p.R105R	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	152	Required for interaction with HDAC1. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R152R(2)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		ACACCAGGGCGCGGGCTGGGG	0.697											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R152R												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C456T	10						.						25.0	31.0	29.0					10																	128193313		2174	4265	6439	128183303	SO:0001819	synonymous_variant	118611	exon3			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.456C>T	10.37:g.128193313G>A		Somatic	1563	Capture	Illumina HiSeq	Phase_I	128183303	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																				0.697	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
C10orf90	118611	broad.mit.edu	37	10	128193375	128193375	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:128193375C>A	ENST00000284694.7	-	3	514	c.394G>T	c.(394-396)Ggc>Tgc	p.G132C	C10orf90_ENST00000454341.1_Missense_Mutation_p.G132C|C10orf90_ENST00000392694.1_Missense_Mutation_p.G85C|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000544758.1_Missense_Mutation_p.G229C|C10orf90_ENST00000356858.3_Missense_Mutation_p.G85C	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	132	Required for interaction with HDAC1. {ECO:0000250}.				mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell growth (GO:0030308)|protein stabilization (GO:0050821)|response to ionizing radiation (GO:0010212)|response to UV (GO:0009411)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.G132C(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(19)|liver(1)|lung(29)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	65		all_epithelial(44;4.51e-05)|all_lung(145;0.0068)|Lung NSC(174;0.0105)|Colorectal(57;0.0848)|all_neural(114;0.0936)|Breast(234;0.203)		COAD - Colon adenocarcinoma(40;0.0442)|Colorectal(40;0.0479)		CTGCGGGGGCCCCCACAGGGT	0.662											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G132C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G394T	10						.						30.0	34.0	33.0					10																	128193375		2194	4293	6487	128183365	SO:0001583	missense	118611	exon3			BC034828	CCDS31310.1	10q26.2	2012-05-31			ENSG00000154493	ENSG00000154493			26563	protein-coding gene	gene with protein product	"""fragile-site associated tumor suppressor"""					20843368, 20154723	Standard	NM_001004298		Approved	FLJ32938, bA422P15.2, FATS	uc001ljq.3	Q96M02	OTTHUMG00000019245	ENST00000284694.7:c.394G>T	10.37:g.128193375C>A	ENSP00000284694:p.Gly132Cys	Somatic	1563	Capture	Illumina HiSeq	Phase_I	128183365	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Missense_Mutation	SNP	ENST00000284694.7	37	CCDS31310.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.080716	0.55753	.	.	ENSG00000154493	ENST00000356858;ENST00000284694;ENST00000454341;ENST00000544758;ENST00000432642;ENST00000368674;ENST00000392694	T;T;T;T;T	0.25579	2.11;2.1;2.12;2.11;1.79	4.82	-2.18	0.07037	.	0.977622	0.08403	N	0.951181	T	0.39963	0.1098	L	0.59436	1.845	0.09310	N	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.995	D;D;D;D;P	0.72338	0.964;0.964;0.977;0.939;0.847	T	0.34204	-0.9838	10	0.72032	D	0.01	-1.462	5.2589	0.15561	0.0:0.3546:0.2635:0.3819	.	229;229;85;132;132	F5GZL2;B4DMQ6;Q5T024;Q96M02;Q96M02-2	.;.;.;CJ090_HUMAN;.	C	85;132;132;229;132;85;85	ENSP00000284694:G132C;ENSP00000398786:G132C;ENSP00000444369:G229C;ENSP00000405995:G132C;ENSP00000376459:G85C	ENSP00000284694:G132C	G	-	1	0	C10orf90	128183365	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.026000	0.12392	-0.257000	0.09459	0.561000	0.74099	GGC		0.662	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298	
ZMYND11	10771	broad.mit.edu	37	10	287975	287975	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:287975G>A	ENST00000397962.3	+	10	1274	c.846G>A	c.(844-846)gaG>gaA	p.E282E	ZMYND11_ENST00000403354.1_Silent_p.E202E|ZMYND11_ENST00000545619.1_Silent_p.E162E|ZMYND11_ENST00000509513.2_Silent_p.E281E|ZMYND11_ENST00000381604.4_Silent_p.E242E|ZMYND11_ENST00000381584.1_Silent_p.E265E|ZMYND11_ENST00000381591.1_Silent_p.E282E|ZMYND11_ENST00000602682.1_Silent_p.E197E|ZMYND11_ENST00000397959.3_Silent_p.E197E|ZMYND11_ENST00000381602.4_Silent_p.E242E|ZMYND11_ENST00000558098.2_Silent_p.E282E|ZMYND11_ENST00000381607.4_Silent_p.E188E|ZMYND11_ENST00000535374.1_Silent_p.E77E|ZMYND11_ENST00000309776.4_Silent_p.E242E|ZMYND11_ENST00000402736.1_Silent_p.E251E			Q15326	ZMY11_HUMAN	zinc finger, MYND-type containing 11	282	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.				cell cycle (GO:0007049)|cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription elongation from RNA polymerase II promoter (GO:0034243)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.E242E(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	24		all_cancers(4;1.32e-05)|all_lung(4;3.67e-05)|Lung NSC(4;0.000301)|all_epithelial(10;0.000416)|Colorectal(49;0.14)	OV - Ovarian serous cystadenocarcinoma(33;0.132)	Epithelial(11;0.00289)|all cancers(11;0.0108)|Lung(33;0.0689)|OV - Ovarian serous cystadenocarcinoma(14;0.106)		CTAATCATGAGCTGGTTTGGG	0.358																																					p.E281E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G843A	10						.						129.0	126.0	127.0					10																	287975		2203	4300	6503	277975	SO:0001819	synonymous_variant	10771	exon10			X86098	CCDS7052.1, CCDS7053.1, CCDS7052.2, CCDS55696.1, CCDS55697.1, CCDS7053.2, CCDS73060.1, CCDS73061.1	10p14	2011-01-26	2011-01-26		ENSG00000015171	ENSG00000015171		"""Zinc fingers, MYND-type"""	16966	protein-coding gene	gene with protein product		608668	"""zinc finger, MYND domain containing 11"""			7621829, 10734313	Standard	NM_006624		Approved	BS69	uc010pzx.2	Q15326	OTTHUMG00000017526	ENST00000397962.3:c.846G>A	10.37:g.287975G>A		Somatic		Capture	Illumina HiSeq	Phase_I	277975	NM_212479	B2R6G8|B7Z293|F6UH50|Q2LD45|Q2LD46|Q2LD47|Q2LD48|Q5VUI1|Q8N4B3	Silent	SNP	ENST00000397962.3	37	CCDS7052.2																																																																																				0.358	ZMYND11-206	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046382.4	NM_006624	
FAM208B	54906	broad.mit.edu	37	10	5789986	5789986	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:5789986C>T	ENST00000328090.5	+	15	5227	c.4602C>T	c.(4600-4602)tgC>tgT	p.C1534C		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1534																	CTGCCAAATGCACAGGTGACT	0.423																																					p.C1534C												.	.	0			c.C4602T	10						.						62.0	64.0	63.0					10																	5789986		1915	4152	6067	5829992	SO:0001819	synonymous_variant	54906	exon15			BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.4602C>T	10.37:g.5789986C>T		None		Capture	Illumina HiSeq	Phase_I	5829992	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	37	CCDS41485.1																																																																																				0.423	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
ITIH5	80760	broad.mit.edu	37	10	7679284	7679284	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:7679284C>T	ENST00000256861.6	-	5	637	c.559G>A	c.(559-561)Gtg>Atg	p.V187M	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_De_novo_Start_InFrame|ITIH5_ENST00000397145.2_Missense_Mutation_p.V187M|ITIH5_ENST00000397146.2_Missense_Mutation_p.V187M	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	187					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.V187M(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TTCACGTCCACGCTCAGCCTC	0.642																																					p.V187M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G559A	10						.						62.0	63.0	62.0					10																	7679284		2203	4300	6503	7719290	SO:0001583	missense	80760	exon5					10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.559G>A	10.37:g.7679284C>T	ENSP00000256861:p.Val187Met	Somatic		Capture	Illumina HiSeq	Phase_I	7719290	NM_030569	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Missense_Mutation	SNP	ENST00000256861.6	37		.	.	.	.	.	.	.	.	.	.	C	16.99	3.273166	0.59649	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000397145	T;T;T	0.03413	4.45;3.94;3.94	5.88	5.88	0.94601	.	0.055926	0.64402	D	0.000001	T	0.21022	0.0506	.	.	.	0.49798	D	0.999824	D;D	0.89917	0.999;1.0	D;D	0.72625	0.978;0.967	T	0.00029	-1.2294	9	0.87932	D	0	-33.3352	20.2092	0.98286	0.0:1.0:0.0:0.0	.	187;187	G5E9D8;Q86UX2	.;ITIH5_HUMAN	M	187	ENSP00000256861:V187M;ENSP00000380333:V187M;ENSP00000380332:V187M	ENSP00000256861:V187M	V	-	1	0	ITIH5	7719290	1.000000	0.71417	0.966000	0.40874	0.096000	0.18686	5.781000	0.68964	2.776000	0.95493	0.655000	0.94253	GTG		0.642	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
DCLRE1C	64421	broad.mit.edu	37	10	14976519	14976519	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:14976519C>T	ENST00000378278.2	-	8	575	c.538G>A	c.(538-540)Gag>Aag	p.E180K	DCLRE1C_ENST00000378249.1_Splice_Site_p.E65K|DCLRE1C_ENST00000453695.2_Splice_Site_p.E60K|DCLRE1C_ENST00000396817.2_Splice_Site_p.E60K|DCLRE1C_ENST00000378254.1_Splice_Site_p.E60K|DCLRE1C_ENST00000378246.2_Splice_Site_p.E65K|DCLRE1C_ENST00000357717.2_Splice_Site_p.E65K|DCLRE1C_ENST00000378255.1_Splice_Site_p.E60K|DCLRE1C_ENST00000378289.4_Splice_Site_p.E180K|DCLRE1C_ENST00000378258.1_Splice_Site_p.E60K			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	180					B cell differentiation (GO:0030183)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|response to ionizing radiation (GO:0010212)|telomere maintenance (GO:0000723)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)	p.E180K(1)|p.E65K(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)	17						AAACACTCCTCCTAGACAGGA	0.507								Non-homologous end-joining																													p.E180K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G538A	10						.						143.0	150.0	147.0					10																	14976519		2203	4300	6503	15016525	SO:0001630	splice_region_variant	64421	exon8			BC022254	CCDS7105.1, CCDS31149.1, CCDS31150.1	10p13	2014-09-17	2010-06-24		ENSG00000152457	ENSG00000152457			17642	protein-coding gene	gene with protein product	"""PSO2 homolog (S. cerevisiae)"""	605988	"""severe combined immunodeficiency, type a (Athabascan)"", ""DNA cross-link repair 1C (PSO2 homolog, S. cerevisiae)"""	SCIDA		11336668, 9443881	Standard	XM_005252558		Approved	ARTEMIS, FLJ11360, SNM1C, A-SCID	uc001inn.3	Q96SD1	OTTHUMG00000017716	ENST00000378278.2:c.538-1G>A	10.37:g.14976519C>T		Somatic		Capture	Illumina HiSeq	Phase_I	15016525	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	16.07	3.020102	0.54576	.	.	ENSG00000152457	ENST00000378289;ENST00000453695;ENST00000378246;ENST00000357717;ENST00000378249;ENST00000396817;ENST00000378255;ENST00000378254;ENST00000378278;ENST00000378258;ENST00000418843;ENST00000378241	T;T;T;T;T;T;T;T;T;T;T;T	0.79749	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-1.3;-0.69	5.51	4.6	0.57074	.	0.294402	0.41712	D	0.000836	T	0.77738	0.4175	L	0.41356	1.27	0.58432	D	0.999999	B;P;B	0.39480	0.011;0.675;0.008	B;B;B	0.43658	0.041;0.426;0.069	T	0.78086	-0.2341	10	0.49607	T	0.09	.	14.3014	0.66355	0.0:0.9281:0.0:0.0718	.	180;65;180	Q96SD1-4;Q96SD1-3;Q96SD1	.;.;DCR1C_HUMAN	K	180;60;65;65;65;60;60;60;180;60;34;60	ENSP00000367538:E180K;ENSP00000400529:E60K;ENSP00000367492:E65K;ENSP00000350349:E65K;ENSP00000367496:E65K;ENSP00000380030:E60K;ENSP00000367503:E60K;ENSP00000367502:E60K;ENSP00000367527:E180K;ENSP00000367506:E60K;ENSP00000391428:E34K;ENSP00000367487:E60K	ENSP00000350349:E65K	E	-	1	0	DCLRE1C	15016525	1.000000	0.71417	0.755000	0.31263	0.332000	0.28634	6.075000	0.71261	1.327000	0.45338	0.650000	0.86243	GAG		0.507	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487	Missense_Mutation
ITGA8	8516	broad.mit.edu	37	10	15697375	15697375	+	Missense_Mutation	SNP	C	C	T	rs143077215		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:15697375C>T	ENST00000378076.3	-	11	1332	c.979G>A	c.(979-981)Gta>Ata	p.V327I		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	327					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)	p.V327I(1)		NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						ACATCTGATACGACAACGGTA	0.318													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20704	0.0		0.0	False		,,,				2504	0.0				p.V327I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G979A	10						.						158.0	147.0	151.0					10																	15697375		2203	4300	6503	15737381	SO:0001583	missense	8516	exon11			L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.979G>A	10.37:g.15697375C>T	ENSP00000367316:p.Val327Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15737381	NM_003638	B0YJ31|Q5VX94	Missense_Mutation	SNP	ENST00000378076.3	37	CCDS31155.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	19.49	3.837786	0.71373	.	.	ENSG00000077943	ENST00000378076;ENST00000538044	T	0.72835	-0.69	5.95	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.84320	0.5446	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.85657	0.1286	10	0.49607	T	0.09	.	15.3796	0.74645	0.0:0.9332:0.0:0.0668	.	312;327	F5H818;P53708	.;ITA8_HUMAN	I	327;312	ENSP00000367316:V327I	ENSP00000367316:V327I	V	-	1	0	ITGA8	15737381	1.000000	0.71417	0.841000	0.33234	0.422000	0.31414	5.902000	0.69869	1.534000	0.49203	-0.244000	0.11960	GTA		0.318	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638	
CUBN	8029	broad.mit.edu	37	10	16992052	16992052	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:16992052T>C	ENST00000377833.4	-	34	5093	c.5028A>G	c.(5026-5028)gcA>gcG	p.A1676A		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	1676	CUB 11. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.A1676A(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAAAGTCACGTGCACACGTTG	0.463																																					p.A1676A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A5028G	10						.						82.0	74.0	77.0					10																	16992052		2203	4300	6503	17032058	SO:0001819	synonymous_variant	8029	exon34			AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.5028A>G	10.37:g.16992052T>C		Somatic		Capture	Illumina HiSeq	Phase_I	17032058	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																				0.463	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
TRDMT1	1787	broad.mit.edu	37	10	17195560	17195560	+	Nonsense_Mutation	SNP	G	G	A	rs151176125		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:17195560G>A	ENST00000377799.3	-	10	1068	c.1021C>T	c.(1021-1023)Cga>Tga	p.R341*	TRDMT1_ENST00000358282.7_3'UTR|TRDMT1_ENST00000412821.3_Nonsense_Mutation_p.R317*|TRDMT1_ENST00000457442.2_Nonsense_Mutation_p.R260*|TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000377766.5_3'UTR|TRDMT1_ENST00000488990.1_Nonsense_Mutation_p.R218*|TRDMT1_ENST00000351358.4_Nonsense_Mutation_p.R295*	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	341	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)			breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	GTGAAATATCGCAGTTTAAGT	0.353																																					p.R341X												.	.	0			c.C1021T	10						.						156.0	146.0	149.0					10																	17195560		2203	4300	6503	17235566	SO:0001587	stop_gained	1787	exon10			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.1021C>T	10.37:g.17195560G>A	ENSP00000367030:p.Arg341*	None		Capture	Illumina HiSeq	Phase_I	17235566	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Nonsense_Mutation	SNP	ENST00000377799.3	37	CCDS7114.1	.	.	.	.	.	.	.	.	.	.	G	38	7.057112	0.98032	.	.	ENSG00000107614	ENST00000377799;ENST00000412821;ENST00000351358;ENST00000457442;ENST00000488990	.	.	.	5.62	4.72	0.59763	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3549	10.7606	0.46261	0.0703:0.0:0.7919:0.1379	.	.	.	.	X	341;317;295;260;218	.	ENSP00000324328:R295X	R	-	1	2	TRDMT1	17235566	1.000000	0.71417	0.994000	0.49952	0.941000	0.58515	4.261000	0.58841	1.508000	0.48769	-0.157000	0.13467	CGA		0.353	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412	
MLLT10	8028	broad.mit.edu	37	10	22021981	22021981	+	Missense_Mutation	SNP	C	C	T	rs368104484		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:22021981C>T	ENST00000307729.7	+	18	2550	c.2372C>T	c.(2371-2373)cCg>cTg	p.P791L	MLLT10_ENST00000377072.3_Missense_Mutation_p.P807L|MLLT10_ENST00000446906.2_Missense_Mutation_p.P791L|MLLT10_ENST00000377059.3_Missense_Mutation_p.P791L			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	791					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.P807L(1)		NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						AATCCTAGTCCGTCTCATCAA	0.338			T	"""MLL, PICALM, CDK6"""	AL																																p.P791L			Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2372T	10						.	C	LEU/PRO,LEU/PRO	0,4406		0,0,2203	103.0	98.0	100.0		2372,2420	6.0	1.0	10		100	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	MLLT10	NM_001195626.1,NM_004641.3	98,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	791/1069,807/1028	22021981	1,13005	2203	4300	6503	22061987	SO:0001583	missense	8028	exon17			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.2372C>T	10.37:g.22021981C>T	ENSP00000307411:p.Pro791Leu	Somatic		Capture	Illumina HiSeq	Phase_I	22061987	NM_001195626	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.341277	0.81911	0.0	1.16E-4	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059	T;T;T;T	0.15372	2.44;2.45;2.43;2.45	6.01	6.01	0.97437	.	0.422646	0.28940	N	0.013659	T	0.35393	0.0930	L	0.44542	1.39	0.80722	D	1	D;D;P;D	0.76494	0.999;0.998;0.897;0.998	P;P;B;P	0.62560	0.904;0.608;0.148;0.608	T	0.00726	-1.1592	10	0.62326	D	0.03	.	20.5182	0.99214	0.0:1.0:0.0:0.0	.	486;791;791;807	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	L	807;791;791;626;791	ENSP00000366272:P807L;ENSP00000401406:P791L;ENSP00000307411:P791L;ENSP00000366258:P791L	ENSP00000307411:P791L	P	+	2	0	MLLT10	22061987	0.781000	0.28676	0.953000	0.39169	0.997000	0.91878	2.107000	0.41844	2.860000	0.98153	0.655000	0.94253	CCG		0.338	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
KIAA1217	56243	broad.mit.edu	37	10	24762236	24762236	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:24762236C>T	ENST00000376454.3	+	6	956	c.926C>T	c.(925-927)gCg>gTg	p.A309V	KIAA1217_ENST00000396445.1_Missense_Mutation_p.A27V|KIAA1217_ENST00000376451.2_Missense_Mutation_p.A27V|KIAA1217_ENST00000458595.1_Missense_Mutation_p.A309V|KIAA1217_ENST00000430453.2_Missense_Mutation_p.A230V|KIAA1217_ENST00000396446.1_Missense_Mutation_p.A27V|KIAA1217_ENST00000376452.3_Missense_Mutation_p.A309V|KIAA1217_ENST00000307544.6_Missense_Mutation_p.A27V|KIAA1217_ENST00000376462.1_Missense_Mutation_p.A229V	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	309	Pro-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.A309V(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CCACCCCATGCGATTCCAAAT	0.572																																					p.A309V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C926T	10						.						85.0	80.0	81.0					10																	24762236		2203	4300	6503	24802242	SO:0001583	missense	56243	exon6			BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.926C>T	10.37:g.24762236C>T	ENSP00000365637:p.Ala309Val	Somatic		Capture	Illumina HiSeq	Phase_I	24802242	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Missense_Mutation	SNP	ENST00000376454.3	37	CCDS31165.1	.	.	.	.	.	.	.	.	.	.	c	1.968	-0.437295	0.04636	.	.	ENSG00000120549	ENST00000376462;ENST00000376456;ENST00000458595;ENST00000442879;ENST00000376454;ENST00000376452;ENST00000438429;ENST00000430453;ENST00000307544;ENST00000450158;ENST00000396445;ENST00000376451;ENST00000396446	T;T;T;T;T;T;T;T;T;T;T	0.50548	0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74;0.74	5.74	1.7	0.24286	.	0.667599	0.15566	N	0.255717	T	0.28333	0.0700	N	0.22421	0.69	0.20489	N	0.999892	B;B;B;B;B;B;B;B	0.33841	0.153;0.12;0.161;0.296;0.428;0.161;0.244;0.038	B;B;B;B;B;B;B;B	0.25405	0.041;0.015;0.043;0.06;0.06;0.043;0.037;0.016	T	0.06427	-1.0827	10	0.35671	T	0.21	.	9.7571	0.40510	0.0:0.7114:0.0:0.2886	.	309;309;27;27;27;27;309;309	Q5T5P2-7;A6NLF3;Q5T5P2-4;Q5T5P2-8;Q5T5P2-3;Q5T5P2-6;Q5T5P2;Q5T5P2-2	.;.;.;.;.;.;SKT_HUMAN;.	V	229;309;309;27;309;309;159;230;27;27;27;27;27	ENSP00000365645:A229V;ENSP00000365639:A309V;ENSP00000392625:A309V;ENSP00000365637:A309V;ENSP00000365635:A309V;ENSP00000404798:A159V;ENSP00000389680:A230V;ENSP00000302343:A27V;ENSP00000379722:A27V;ENSP00000365634:A27V;ENSP00000379723:A27V	ENSP00000302343:A27V	A	+	2	0	KIAA1217	24802242	0.238000	0.23825	0.116000	0.21606	0.005000	0.04900	1.457000	0.35212	0.057000	0.16193	-1.112000	0.02068	GCG		0.572	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
ARHGAP21	57584	broad.mit.edu	37	10	25010821	25010821	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:25010821G>A	ENST00000396432.2	-	2	494	c.8C>T	c.(7-9)gCc>gTc	p.A3V		NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	2					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)	p.A2V(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						CCGACGCGTGGCCATCATTTC	0.582																																					p.A3V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8T	10						.						59.0	50.0	53.0					10																	25010821		2203	4300	6503	25050827	SO:0001583	missense	57584	exon2			AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.8C>T	10.37:g.25010821G>A	ENSP00000379709:p.Ala3Val	Somatic		Capture	Illumina HiSeq	Phase_I	25050827	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	35	5.503924	0.96371	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000376410;ENST00000446003	T;T;T	0.53640	2.59;0.61;0.63	5.05	5.05	0.67936	.	0.102793	0.38663	N	0.001614	T	0.59293	0.2183	L	0.40543	1.245	0.80722	D	1	D;D;D	0.67145	0.996;0.993;0.993	D;D;D	0.77557	0.99;0.978;0.978	T	0.61337	-0.7083	10	0.87932	D	0	.	13.7761	0.63055	0.0:0.0:1.0:0.0	.	3;2;2	F8W9U9;Q5T5U2;Q5T5U3	.;.;RHG21_HUMAN	V	3;2;3;3	ENSP00000379709:A3V;ENSP00000365592:A3V;ENSP00000405018:A3V	ENSP00000365592:A3V	A	-	2	0	ARHGAP21	25050827	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.888000	0.63164	2.620000	0.88729	0.563000	0.77884	GCC		0.582	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
ENKUR	219670	broad.mit.edu	37	10	25284663	25284663	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:25284663delT	ENST00000331161.4	-	3	578	c.359delA	c.(358-360)aagfs	p.K120fs	ENKUR_ENST00000376363.1_Frame_Shift_Del_p.K120fs	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	120						motile cilium (GO:0031514)		p.K120fs*22(1)		endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						TGGTTTAGGCTTTTTAGCCAC	0.383																																					p.K120fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.359delA	10						.						149.0	145.0	146.0					10																	25284663		2203	4300	6503	25324669	SO:0001589	frameshift_variant	219670	exon3			AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"""chromosome 10 open reading frame 63"""	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.359delA	10.37:g.25284663delT	ENSP00000331044:p.Lys120fs	Somatic		Capture	Illumina HiSeq	Phase_I	25324669	NM_145010	A8K8Y0|D3DRV2	Frame_Shift_Del	DEL	ENST00000331161.4	37	CCDS7146.1																																																																																				0.383	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010	
MYO3A	53904	broad.mit.edu	37	10	26310576	26310576	+	Splice_Site	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:26310576A>T	ENST00000265944.5	+	8	896	c.730A>T	c.(730-732)Agg>Tgg	p.R244W	MYO3A_ENST00000543632.1_Splice_Site_p.R244W|MYO3A_ENST00000376302.1_Missense_Mutation_p.R244W	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	244	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R244W(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAAAATACCAAGGTCAGATGA	0.483																																					p.R244W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A730T	10						.						118.0	103.0	108.0					10																	26310576		2203	4300	6503	26350582	SO:0001630	splice_region_variant	53904	exon8			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.731+1A>T	10.37:g.26310576A>T		Somatic		Capture	Illumina HiSeq	Phase_I	26350582	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.487221	0.84854	.	.	ENSG00000095777	ENST00000265944;ENST00000376302;ENST00000543632	T;T;T	0.67523	-0.27;2.49;-0.27	6.03	6.03	0.97812	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	0.80491	0.4633	M	0.64260	1.97	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;1.0	T	0.82100	-0.0624	10	0.87932	D	0	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	244;244;244;244	F5H0U9;Q0VD65;Q8NEV4;Q4G0X2	.;.;MYO3A_HUMAN;.	W	244	ENSP00000265944:R244W;ENSP00000365479:R244W;ENSP00000445909:R244W	ENSP00000265944:R244W	R	+	1	2	MYO3A	26350582	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	3.988000	0.56951	2.308000	0.77769	0.533000	0.62120	AGG		0.483	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	Missense_Mutation
MYO3A	53904	broad.mit.edu	37	10	26462709	26462709	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:26462709A>C	ENST00000265944.5	+	30	3682	c.3516A>C	c.(3514-3516)gaA>gaC	p.E1172D	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1172					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1172D(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						TCAAACCTGAAGAGGAAACCA	0.368																																					p.E1172D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3516C	10						.						62.0	60.0	61.0					10																	26462709		2203	4300	6503	26502715	SO:0001583	missense	53904	exon30			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3516A>C	10.37:g.26462709A>C	ENSP00000265944:p.Glu1172Asp	Somatic		Capture	Illumina HiSeq	Phase_I	26502715	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.803968	0.31869	.	.	ENSG00000095777	ENST00000265944	T	0.78707	-1.2	5.2	-6.92	0.01644	.	0.620100	0.18234	N	0.147479	T	0.56804	0.2010	L	0.29908	0.895	0.19300	N	0.999973	B	0.11235	0.004	B	0.09377	0.004	T	0.32640	-0.9899	10	0.30078	T	0.28	.	8.4488	0.32858	0.5184:0.1031:0.3785:0.0	.	1172	Q8NEV4	MYO3A_HUMAN	D	1172	ENSP00000265944:E1172D	ENSP00000265944:E1172D	E	+	3	2	MYO3A	26502715	0.142000	0.22610	0.000000	0.03702	0.027000	0.11550	-0.276000	0.08514	-1.505000	0.01807	0.533000	0.62120	GAA		0.368	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
MYO3A	53904	broad.mit.edu	37	10	26500807	26500807	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:26500807A>C	ENST00000265944.5	+	35	4932	c.4766A>C	c.(4765-4767)gAg>gCg	p.E1589A	MYO3A_ENST00000543632.1_Silent_p.G604G	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1589					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.E1589A(1)		NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						AAGGAGGAGGAGAGAGAGCCA	0.647																																					p.E1589A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4766C	10						.						49.0	56.0	53.0					10																	26500807		2203	4300	6503	26540813	SO:0001583	missense	53904	exon35			AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.4766A>C	10.37:g.26500807A>C	ENSP00000265944:p.Glu1589Ala	Somatic		Capture	Illumina HiSeq	Phase_I	26540813	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	A	8.893	0.954432	0.18431	.	.	ENSG00000095777	ENST00000265944	T	0.77489	-1.1	1.29	-1.6	0.08426	.	2.474300	0.01344	N	0.011662	T	0.64886	0.2639	L	0.34521	1.04	0.09310	N	1	B	0.18310	0.027	B	0.09377	0.004	T	0.44802	-0.9304	10	0.52906	T	0.07	.	1.4505	0.02374	0.4499:0.0:0.2333:0.3168	.	1589	Q8NEV4	MYO3A_HUMAN	A	1589	ENSP00000265944:E1589A	ENSP00000265944:E1589A	E	+	2	0	MYO3A	26540813	0.056000	0.20664	0.001000	0.08648	0.011000	0.07611	-0.432000	0.06956	-0.483000	0.06772	0.379000	0.24179	GAG		0.647	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
YME1L1	10730	broad.mit.edu	37	10	27405163	27405163	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:27405163C>T	ENST00000326799.3	-	17	2150	c.2002G>A	c.(2002-2004)Gac>Aac	p.D668N	YME1L1_ENST00000375972.3_Missense_Mutation_p.D578N|YME1L1_ENST00000376016.3_Missense_Mutation_p.D611N	NM_139312.2	NP_647473.1	Q96TA2	YMEL1_HUMAN	YME1-like 1 ATPase	668					cell proliferation (GO:0008283)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|mitochondrion organization (GO:0007005)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.D668N(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	23						GTAATATGGTCGGTTCCAAAT	0.353																																					p.D611N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1831A	10						.						107.0	108.0	108.0					10																	27405163		2203	4300	6503	27445169	SO:0001583	missense	10730	exon16			AJ132637	CCDS7151.1, CCDS7152.1, CCDS58072.1	10p14	2013-06-10	2013-06-10		ENSG00000136758	ENSG00000136758		"""ATPases / AAA-type"""	12843	protein-coding gene	gene with protein product		607472	"""YME1 (S.cerevisiae)-like 1"", ""YME1-like 1 (S. cerevisiae)"""			22262461	Standard	NM_139312		Approved		uc001itj.3	Q96TA2	OTTHUMG00000017853	ENST00000326799.3:c.2002G>A	10.37:g.27405163C>T	ENSP00000318480:p.Asp668Asn	Somatic		Capture	Illumina HiSeq	Phase_I	27445169	NM_014263	B4DNM1|D3DRV8|D3DRV9|Q5T8D9|Q9H1Q0|Q9UMR9	Missense_Mutation	SNP	ENST00000326799.3	37	CCDS7152.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550076	0.65311	.	.	ENSG00000136758	ENST00000376016;ENST00000326799;ENST00000375969;ENST00000375972;ENST00000546122	D;D;D	0.86230	-2.09;-2.09;-2.09	5.43	5.43	0.79202	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.045392	0.85682	D	0.000000	D	0.89670	0.6782	L	0.49256	1.55	0.80722	D	1	D;P;D	0.60160	0.979;0.723;0.987	P;B;P	0.53593	0.671;0.091;0.73	D	0.90420	0.4416	10	0.66056	D	0.02	-16.1002	19.2397	0.93877	0.0:1.0:0.0:0.0	.	578;611;668	B4DNM1;Q96TA2-2;Q96TA2	.;.;YMEL1_HUMAN	N	611;668;668;578;414	ENSP00000365184:D611N;ENSP00000318480:D668N;ENSP00000365139:D578N	ENSP00000318480:D668N	D	-	1	0	YME1L1	27445169	1.000000	0.71417	0.896000	0.35187	0.095000	0.18619	7.792000	0.85828	2.538000	0.85594	0.650000	0.86243	GAC		0.353	YME1L1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047306.1	NM_139312	
BAMBI	25805	broad.mit.edu	37	10	28970366	28970366	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:28970366C>T	ENST00000375533.3	+	2	812	c.256C>T	c.(256-258)Cga>Tga	p.R86*		NM_012342.2	NP_036474.1	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor	86					cell migration (GO:0016477)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell shape (GO:0008360)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|type II transforming growth factor beta receptor binding (GO:0005114)	p.R86G(1)|p.R86*(1)		central_nervous_system(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	17						CAAACAGGCCCGAAACCACTC	0.527																																					p.R86X												.	.	2	Substitution - Missense(1)|Substitution - Nonsense(1)	large_intestine(1)|prostate(1)	c.C256T	10						.						111.0	115.0	114.0					10																	28970366		2203	4300	6503	29010372	SO:0001587	stop_gained	25805	exon2			U23070	CCDS7162.1	10p12.3-p11.2	2013-07-23	2013-07-23		ENSG00000095739	ENSG00000095739			30251	protein-coding gene	gene with protein product		604444	"""BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)"""			8621228, 19758997	Standard	NM_012342		Approved	NMA	uc001iuj.1	Q13145	OTTHUMG00000017874	ENST00000375533.3:c.256C>T	10.37:g.28970366C>T	ENSP00000364683:p.Arg86*	Somatic		Capture	Illumina HiSeq	Phase_I	29010372	NM_012342		Nonsense_Mutation	SNP	ENST00000375533.3	37	CCDS7162.1	.	.	.	.	.	.	.	.	.	.	C	41	8.580479	0.98872	.	.	ENSG00000095739	ENST00000375533;ENST00000542444	.	.	.	5.64	5.64	0.86602	.	0.508969	0.24094	N	0.041601	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-12.0904	19.7002	0.96049	0.0:1.0:0.0:0.0	.	.	.	.	X	86;73	.	ENSP00000364683:R86X	R	+	1	2	BAMBI	29010372	0.147000	0.22687	0.135000	0.22099	0.993000	0.82548	3.218000	0.51192	2.663000	0.90544	0.650000	0.86243	CGA		0.527	BAMBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047374.1	NM_012342	
BAMBI	25805	broad.mit.edu	37	10	28971067	28971067	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:28971067A>C	ENST00000375533.3	+	3	1076	c.520A>C	c.(520-522)Agg>Cgg	p.R174R		NM_012342.2	NP_036474.1	Q13145	BAMBI_HUMAN	BMP and activin membrane-bound inhibitor	174					cell migration (GO:0016477)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell shape (GO:0008360)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|type II transforming growth factor beta receptor binding (GO:0005114)			central_nervous_system(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)	17						GTTGGCCCTGAGGATGCTTCG	0.517																																					p.R174R												.	.	0			c.A520C	10						.						118.0	105.0	109.0					10																	28971067		2203	4300	6503	29011073	SO:0001819	synonymous_variant	25805	exon3			U23070	CCDS7162.1	10p12.3-p11.2	2013-07-23	2013-07-23		ENSG00000095739	ENSG00000095739			30251	protein-coding gene	gene with protein product		604444	"""BMP and activin membrane-bound inhibitor homolog (Xenopus laevis)"""			8621228, 19758997	Standard	NM_012342		Approved	NMA	uc001iuj.1	Q13145	OTTHUMG00000017874	ENST00000375533.3:c.520A>C	10.37:g.28971067A>C		None		Capture	Illumina HiSeq	Phase_I	29011073	NM_012342		Silent	SNP	ENST00000375533.3	37	CCDS7162.1																																																																																				0.517	BAMBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047374.1	NM_012342	
KIAA1462	57608	broad.mit.edu	37	10	30316767	30316767	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:30316767G>A	ENST00000375377.1	-	3	2411	c.2310C>T	c.(2308-2310)tcC>tcT	p.S770S		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	770					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.S770S(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						CCTGGTCCACGGACAAGGAAG	0.612																																					p.S770S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2310T	10						.						54.0	58.0	56.0					10																	30316767		2097	4225	6322	30356773	SO:0001819	synonymous_variant	57608	exon3			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.2310C>T	10.37:g.30316767G>A		Somatic		Capture	Illumina HiSeq	Phase_I	30356773	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																				0.612	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
KIAA1462	57608	broad.mit.edu	37	10	30317974	30317974	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:30317974C>A	ENST00000375377.1	-	3	1204	c.1103G>T	c.(1102-1104)gGc>gTc	p.G368V		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	368	Pro-rich.				cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)		p.G368V(1)		breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						ACTGTGACCGCCACACACATT	0.602																																					p.G368V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1103T	10						.						96.0	98.0	97.0					10																	30317974		2109	4237	6346	30357980	SO:0001583	missense	57608	exon3			AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.1103G>T	10.37:g.30317974C>A	ENSP00000364526:p.Gly368Val	Somatic		Capture	Illumina HiSeq	Phase_I	30357980	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Missense_Mutation	SNP	ENST00000375377.1	37	CCDS41500.1	.	.	.	.	.	.	.	.	.	.	C	9.800	1.180169	0.21787	.	.	ENSG00000165757	ENST00000375377	T	0.11712	2.75	4.91	1.77	0.24775	.	1.214470	0.05609	N	0.577825	T	0.10981	0.0268	L	0.47716	1.5	0.09310	N	1	P	0.38677	0.642	B	0.41036	0.346	T	0.28364	-1.0046	10	0.26408	T	0.33	-1.1288	1.1351	0.01753	0.2324:0.3255:0.2639:0.1782	.	368	Q9P266	K1462_HUMAN	V	368	ENSP00000364526:G368V	ENSP00000364526:G368V	G	-	2	0	KIAA1462	30357980	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.162000	0.10012	0.054000	0.16065	0.491000	0.48974	GGC		0.602	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
MTPAP	55149	broad.mit.edu	37	10	30611378	30611378	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:30611378delA	ENST00000263063.4	-	6	1204	c.1161delT	c.(1159-1161)tttfs	p.F387fs	MTPAP_ENST00000488290.1_5'UTR|MTPAP_ENST00000358107.4_Frame_Shift_Del_p.F517fs	NM_018109.3	NP_060579.3	Q9NVV4	PAPD1_HUMAN	mitochondrial poly(A) polymerase	387					cell death (GO:0008219)|histone mRNA catabolic process (GO:0071044)|mRNA polyadenylation (GO:0006378)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|poly(A) RNA binding (GO:0044822)|polynucleotide adenylyltransferase activity (GO:0004652)|protein homodimerization activity (GO:0042803)|UTP binding (GO:0002134)	p.L388fs*12(1)|p.L518fs*12(1)		breast(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						TTCTCTGGAGAAAAAAGATGA	0.403																																					p.F387fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1161delT	10						.						124.0	121.0	122.0					10																	30611378		2203	4300	6503	30651384	SO:0001589	frameshift_variant	55149	exon6			AL122121	CCDS7165.1	10p12.1	2014-01-30	2009-01-12	2009-01-12	ENSG00000107951	ENSG00000107951			25532	protein-coding gene	gene with protein product	"""TUTase1"""	613669	"""PAP associated domain containing 1"""	PAPD1		12239557, 15769737, 15547249	Standard	NM_018109		Approved	FLJ10486, mtPAP, SPAX4	uc001iva.4	Q9NVV4	OTTHUMG00000017895	ENST00000263063.4:c.1161delT	10.37:g.30611378delA	ENSP00000263063:p.Phe387fs	Somatic		Capture	Illumina HiSeq	Phase_I	30651384	NM_018109	D3DRX0|Q659E3|Q6P7E5|Q9HA74	Frame_Shift_Del	DEL	ENST00000263063.4	37	CCDS7165.1																																																																																				0.403	MTPAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047426.2	NM_018109	
MAP3K8	1326	broad.mit.edu	37	10	30739388	30739388	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:30739388C>T	ENST00000263056.1	+	5	1402	c.706C>T	c.(706-708)Cat>Tat	p.H236Y	MAP3K8_ENST00000542547.1_Missense_Mutation_p.H236Y|MAP3K8_ENST00000375321.1_Missense_Mutation_p.H236Y	NM_001244134.1|NM_005204.3	NP_001231063.1|NP_005195.2	P41279	M3K8_HUMAN	mitogen-activated protein kinase kinase kinase 8	236	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|protein phosphorylation (GO:0006468)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|protein serine/threonine kinase activity (GO:0004674)	p.H236Y(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Prostate(175;0.151)				GGTGACAAAGCATGTTCTCAA	0.403																																					p.H236Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C706T	10						.						96.0	91.0	93.0					10																	30739388		2203	4300	6503	30779394	SO:0001583	missense	1326	exon5			D14497	CCDS7166.1	10p11.2	2011-06-09			ENSG00000107968	ENSG00000107968		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6860	protein-coding gene	gene with protein product		191195		COT, ESTF		2072910, 8479752	Standard	NM_005204		Approved	Tpl-2, EST, c-COT, MEKK8	uc009xlf.2	P41279	OTTHUMG00000017889	ENST00000263056.1:c.706C>T	10.37:g.30739388C>T	ENSP00000263056:p.His236Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	30779394	NM_005204	A8K2Q5|D3DRX1|Q14275|Q5T855|Q9HC81	Missense_Mutation	SNP	ENST00000263056.1	37	CCDS7166.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.224116	0.79576	.	.	ENSG00000107968	ENST00000375328;ENST00000263056;ENST00000542547;ENST00000415139;ENST00000375321	T;T;T;T	0.49720	1.08;1.08;0.77;1.08	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047154	0.85682	D	0.000000	T	0.43942	0.1270	L	0.37697	1.125	0.54753	D	0.999982	P	0.36712	0.566	B	0.36534	0.227	T	0.47611	-0.9104	10	0.72032	D	0.01	.	19.3825	0.94543	0.0:1.0:0.0:0.0	.	236	P41279	M3K8_HUMAN	Y	236	ENSP00000263056:H236Y;ENSP00000443610:H236Y;ENSP00000409653:H236Y;ENSP00000364470:H236Y	ENSP00000263056:H236Y	H	+	1	0	MAP3K8	30779394	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.275000	0.78548	2.658000	0.90341	0.650000	0.86243	CAT		0.403	MAP3K8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047416.2	NM_005204	
CREM	1390	broad.mit.edu	37	10	35437369	35437369	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:35437369G>A	ENST00000395895.2	+	3	280	c.118G>A	c.(118-120)Gct>Act	p.A40T	CREM_ENST00000337656.4_Missense_Mutation_p.A40T|CREM_ENST00000489321.1_Missense_Mutation_p.A24T|CREM_ENST00000348787.2_Missense_Mutation_p.A24T|CREM_ENST00000374721.3_Missense_Mutation_p.A24T|CREM_ENST00000374728.3_Missense_Mutation_p.A24T|CREM_ENST00000374726.3_Missense_Mutation_p.A24T|CREM_ENST00000374734.3_Missense_Mutation_p.A40T|CREM_ENST00000474362.1_Intron|CREM_ENST00000345491.3_Missense_Mutation_p.A40T|CREM_ENST00000489388.1_Intron|CREM_ENST00000460270.1_Intron|CREM_ENST00000479070.1_Missense_Mutation_p.A40T|CREM_ENST00000333809.8_Missense_Mutation_p.A40T|CREM_ENST00000469949.2_Missense_Mutation_p.A24T|CREM_ENST00000429130.3_Missense_Mutation_p.A24T|CREM_ENST00000439705.1_Missense_Mutation_p.A40T|CREM_ENST00000354759.3_Missense_Mutation_p.A40T			Q03060	CREM_HUMAN	cAMP responsive element modulator	40					cell differentiation (GO:0030154)|glycosphingolipid metabolic process (GO:0006687)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	cAMP response element binding protein binding (GO:0008140)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A40T(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14						GAGCAAGTCTGCTCATGTGCA	0.413																																					p.A40T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G118A	10						.						103.0	97.0	99.0					10																	35437369		2203	4300	6503	35477375	SO:0001583	missense	1390	exon3				CCDS7180.1, CCDS7181.1, CCDS7182.1, CCDS7183.1, CCDS7184.1, CCDS7185.1, CCDS7186.1, CCDS7187.1, CCDS7188.1, CCDS31181.1, CCDS53519.1, CCDS53520.1, CCDS53517.1, CCDS53518.1, CCDS53521.1, CCDS58074.1, CCDS58075.1, CCDS58076.1	10p12.1-p11.1	2013-01-10			ENSG00000095794	ENSG00000095794		"""basic leucine zipper proteins"""	2352	protein-coding gene	gene with protein product		123812				1461747, 7916662	Standard	NM_182717		Approved	hCREM-2	uc001iyb.3	Q03060	OTTHUMG00000017953	ENST00000395895.2:c.118G>A	10.37:g.35437369G>A	ENSP00000379232:p.Ala40Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35477375	NM_181571	A8K014|A8K3J7|A8K6A1|A8MPQ2|B4DXC1|C9J785|C9JZ10|E9PAR4|E9PHM1|O75519|Q14501|Q14503|Q14504|Q14505|Q14506|Q15731|Q16114|Q16116|Q5T9H7|Q5W1A6|Q5W1A7|Q5W1A8|Q5W1A9|Q5W1B0|Q5W1B2|Q7Z2Q6|Q8IVD4|Q96AG7|Q9NZ98|Q9NZ99|Q9NZB9	Missense_Mutation	SNP	ENST00000395895.2	37		.	.	.	.	.	.	.	.	.	.	G	15.83	2.947785	0.53186	.	.	ENSG00000095794	ENST00000374726;ENST00000354759;ENST00000489321;ENST00000427847;ENST00000345491;ENST00000395895;ENST00000374728;ENST00000487132;ENST00000333809;ENST00000439705;ENST00000374734;ENST00000337656;ENST00000479070;ENST00000462058;ENST00000429130;ENST00000489627;ENST00000493508;ENST00000490263;ENST00000374721;ENST00000348787;ENST00000374722	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.78924	-1.22;0.35;-1.22;-1.2;0.75;0.89;0.77;0.37;0.5;0.48;0.34;0.34;0.74;0.93;0.51;0.77	4.81	3.87	0.44632	.	0.247350	0.28712	N	0.014385	T	0.79834	0.4514	L	0.44542	1.39	0.30544	N	0.766144	P;P;P;P;P;D	0.63046	0.773;0.862;0.773;0.913;0.945;0.992	P;B;P;P;P;P	0.58013	0.493;0.424;0.493;0.769;0.718;0.831	T	0.78211	-0.2292	10	0.59425	D	0.04	.	12.5337	0.56131	0.0:0.1668:0.8332:0.0	.	40;40;24;40;40;24	A8MPQ2;E9PHM1;Q5W1A7;Q03060-16;Q5W1B0;Q96AG7	.;.;.;.;.;.	T	24;40;24;40;40;40;24;24;40;40;40;40;40;24;24;24;24;24;24;24;24	ENSP00000363858:A24T;ENSP00000346804:A40T;ENSP00000419924:A24T;ENSP00000403938:A40T;ENSP00000265372:A40T;ENSP00000379232:A40T;ENSP00000363860:A24T;ENSP00000418798:A24T;ENSP00000333055:A40T;ENSP00000409220:A40T;ENSP00000363866:A40T;ENSP00000337138:A40T;ENSP00000420511:A40T;ENSP00000393538:A24T;ENSP00000363853:A24T;ENSP00000345384:A24T	ENSP00000333055:A40T	A	+	1	0	CREM	35477375	1.000000	0.71417	0.953000	0.39169	0.093000	0.18481	3.969000	0.56816	2.495000	0.84180	0.655000	0.94253	GCT		0.413	CREM-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001881	
RET	5979	broad.mit.edu	37	10	43607555	43607555	+	Missense_Mutation	SNP	G	G	A	rs201553718		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:43607555G>A	ENST00000355710.3	+	8	1763	c.1531G>A	c.(1531-1533)Gag>Aag	p.E511K	RET_ENST00000340058.5_Missense_Mutation_p.E511K	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	511					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.E511K(1)	CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGATGTGGCCGAGGAGGCGGG	0.667		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	1	0.000199681	0.0	0.0	5008	,	,		19147	0.0		0.001	False		,,,				2504	0.0				p.E511K	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1531A	10						.	G	LYS/GLU,LYS/GLU	0,4402		0,0,2201	53.0	49.0	50.0		1531,1531	4.8	0.8	10		50	3,8589		0,3,4293	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	0,3,6494	AA,AG,GG		0.0349,0.0,0.0231	benign,benign	511/1073,511/1115	43607555	3,12991	2201	4296	6497	42927561	SO:0001583	missense	5979	exon8	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.1531G>A	10.37:g.43607555G>A	ENSP00000347942:p.Glu511Lys	Somatic		Capture	Illumina HiSeq	Phase_I	42927561	NM_020975	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	12.42	1.932111	0.34096	0.0	3.49E-4	ENSG00000165731	ENST00000355710;ENST00000498820;ENST00000340058	T;D;T	0.98345	-1.21;-4.88;-1.33	5.73	4.77	0.60923	.	0.310345	0.39834	N	0.001250	D	0.93301	0.7865	L	0.31065	0.9	0.40659	D	0.982117	B;B;B	0.31227	0.01;0.181;0.314	B;B;B	0.19148	0.002;0.011;0.024	D	0.88963	0.3395	10	0.26408	T	0.33	.	4.3684	0.11235	0.1837:0.2099:0.6064:0.0	.	257;511;511	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	K	511;28;511	ENSP00000347942:E511K;ENSP00000419080:E28K;ENSP00000344798:E511K	ENSP00000344798:E511K	E	+	1	0	RET	42927561	0.996000	0.38824	0.793000	0.32043	0.239000	0.25481	2.826000	0.48104	2.712000	0.92718	0.557000	0.71058	GAG		0.667	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
MARCH8	220972	broad.mit.edu	37	10	45954685	45954685	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:45954685G>A	ENST00000319836.3	-	6	1203	c.454C>T	c.(454-456)Cgc>Tgc	p.R152C	MARCH8_ENST00000453424.2_Missense_Mutation_p.R434C|MARCH8_ENST00000395769.2_Missense_Mutation_p.R152C|MARCH8_ENST00000476962.1_5'UTR|MARCH8_ENST00000395771.3_Missense_Mutation_p.R152C	NM_145021.4	NP_659458.2	Q5T0T0	MARH8_HUMAN	membrane-associated ring finger (C3HC4) 8, E3 ubiquitin protein ligase	152					immune system process (GO:0002376)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R152C(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(4)	12						ATCTTCCTGCGCTCGCTGGAC	0.527																																					p.R152C	NSCLC(102;658 1594 2173 16344 34808)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C454T	10						.						192.0	149.0	164.0					10																	45954685		2203	4300	6503	45274691	SO:0001583	missense	220972	exon6			AL833316	CCDS7213.1, CCDS60519.1	10q11.22	2013-01-09	2012-02-23	2005-01-27	ENSG00000165406	ENSG00000165406		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	23356	protein-coding gene	gene with protein product		613335	"""c-mir, cellular modulator of immune recognition"", ""membrane-associated ring finger (C3HC4) 8"""	MIR		12582153, 14722266	Standard	XM_005271804		Approved	c-MIR, MARCH-VIII, RNF178	uc001jch.2	Q5T0T0	OTTHUMG00000019345	ENST00000319836.3:c.454C>T	10.37:g.45954685G>A	ENSP00000317087:p.Arg152Cys	Somatic		Capture	Illumina HiSeq	Phase_I	45274691	NM_001002266	B2R8E7|H0Y7C6|Q5T0S8|Q8TC72	Missense_Mutation	SNP	ENST00000319836.3	37	CCDS7213.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.33|16.33	3.091839|3.091839	0.55968|0.55968	.|.	.|.	ENSG00000165406|ENSG00000165406	ENST00000453424|ENST00000395771;ENST00000319836;ENST00000395769	.|T;T;T	.|0.14144	.|2.53;2.53;2.53	5.9|5.9	2.95|2.95	0.34219|0.34219	.|.	.|0.094753	.|0.64402	.|N	.|0.000002	T|T	0.30510|0.30510	0.0767|0.0767	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.78314	.|0.991;0.973	T|T	0.01496|0.01496	-1.1340|-1.1340	5|10	.|0.46703	.|T	.|0.11	-23.2897|-23.2897	7.5183|7.5183	0.27614|0.27614	0.0755:0.0:0.5101:0.4144|0.0755:0.0:0.5101:0.4144	.|.	.|152;316	.|Q5T0T0;Q5JQ16	.|MARH8_HUMAN;.	V|C	316|152	.|ENSP00000379118:R152C;ENSP00000317087:R152C;ENSP00000379116:R152C	.|ENSP00000317087:R152C	A|R	-|-	2|1	0|0	MARCH8|MARCH8	45274691|45274691	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.472000|0.472000	0.32918|0.32918	2.168000|2.168000	0.42424|0.42424	0.836000|0.836000	0.34901|0.34901	-0.182000|-0.182000	0.12963|0.12963	GCG|CGC		0.527	MARCH8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051217.1	NM_145021	
RBP3	5949	broad.mit.edu	37	10	48382200	48382200	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:48382200G>A	ENST00000224600.4	-	4	3562	c.3449C>T	c.(3448-3450)aCc>aTc	p.T1150I		NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	1150	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)	p.T1150I(1)		central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CTCCTCCGCGGTGCCGGCCGT	0.602																																					p.T1150I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3449T	10						.						42.0	45.0	44.0					10																	48382200		2203	4300	6503	48002206	SO:0001583	missense	5949	exon4			M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.3449C>T	10.37:g.48382200G>A	ENSP00000224600:p.Thr1150Ile	Somatic		Capture	Illumina HiSeq	Phase_I	48002206	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Missense_Mutation	SNP	ENST00000224600.4	37	CCDS7218.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902749	0.52227	.	.	ENSG00000107618	ENST00000224600	T	0.62639	0.01	5.66	5.66	0.87406	Interphotoreceptor retinol-binding (2);	0.101705	0.64402	D	0.000002	T	0.33498	0.0865	N	0.00332	-1.63	0.35760	D	0.820092	B	0.23185	0.081	B	0.25506	0.061	T	0.51919	-0.8644	10	0.87932	D	0	-9.6963	18.7936	0.91985	0.0:0.0:1.0:0.0	.	1150	P10745	RET3_HUMAN	I	1150	ENSP00000224600:T1150I	ENSP00000224600:T1150I	T	-	2	0	RBP3	48002206	1.000000	0.71417	0.023000	0.16930	0.303000	0.27691	9.321000	0.96353	2.688000	0.91661	0.650000	0.86243	ACC		0.602	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
VSTM4	196740	broad.mit.edu	37	10	50315720	50315720	+	Missense_Mutation	SNP	C	C	T	rs145294709	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:50315720C>T	ENST00000332853.4	-	2	399	c.376G>A	c.(376-378)Gtc>Atc	p.V126I	VSTM4_ENST00000298454.3_Missense_Mutation_p.V126I	NM_001031746.3	NP_001026916.2	Q8IW00	VSTM4_HUMAN	V-set and transmembrane domain containing 4	126	Ig-like.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.V126I(2)		breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(14)|skin(2)	31						ACTCTGCAGACGTAATGCCCT	0.627													c|||	2	0.000399361	0.0015	0.0	5008	,	,		18680	0.0		0.0	False		,,,				2504	0.0				p.V126I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G376A	10						.	T	ILE/VAL,ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	119.0	112.0	114.0		376,376	3.8	0.6	10	dbSNP_134	114	0,8600		0,0,4300	yes	missense,missense	VSTM4	NM_001031746.3,NM_144984.2	29,29	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	benign,benign	126/321,126/192	50315720	7,12999	2203	4300	6503	49985726	SO:0001583	missense	196740	exon2			BC041414	CCDS7228.1, CCDS31198.1	10q11.23	2013-01-11	2011-07-01	2011-07-01	ENSG00000165633	ENSG00000165633		"""Immunoglobulin superfamily / V-set domain containing"""	26470	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 72"""	C10orf72			Standard	XR_246075		Approved	FLJ31737	uc001jhf.2	Q8IW00	OTTHUMG00000018184	ENST00000332853.4:c.376G>A	10.37:g.50315720C>T	ENSP00000331062:p.Val126Ile	Somatic		Capture	Illumina HiSeq	Phase_I	49985726	NM_144984	B4DNI6|Q96MX7	Missense_Mutation	SNP	ENST00000332853.4	37	CCDS31198.1	.	.	.	.	.	.	.	.	.	.	c	7.621	0.676907	0.14841	0.001589	0.0	ENSG00000165633	ENST00000332853;ENST00000298454	T;T	0.64991	-0.13;-0.13	5.75	3.75	0.43078	.	0.722466	0.13838	N	0.359264	T	0.33673	0.0871	N	0.04203	-0.255	0.23003	N	0.99845	B;B	0.12630	0.006;0.004	B;B	0.08055	0.002;0.003	T	0.18178	-1.0345	10	0.19590	T	0.45	-12.5068	4.8102	0.13340	0.0:0.3502:0.0:0.6498	.	126;126	Q8IW00-2;Q8IW00	.;VSTM4_HUMAN	I	126	ENSP00000331062:V126I;ENSP00000298454:V126I	ENSP00000298454:V126I	V	-	1	0	VSTM4	49985726	0.995000	0.38212	0.599000	0.28851	0.622000	0.37654	2.662000	0.46766	0.675000	0.31264	-0.119000	0.15052	GTC		0.627	VSTM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047966.2	NM_144984	
CHAT	1103	broad.mit.edu	37	10	50857591	50857591	+	Missense_Mutation	SNP	G	G	A	rs371719364		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:50857591G>A	ENST00000337653.2	+	10	1573	c.1420G>A	c.(1420-1422)Gtc>Atc	p.V474I	CHAT_ENST00000339797.1_Missense_Mutation_p.V356I|CHAT_ENST00000395559.2_Missense_Mutation_p.V356I|CHAT_ENST00000395562.2_Missense_Mutation_p.V392I|CHAT_ENST00000351556.3_Missense_Mutation_p.V356I|CHAT_ENST00000455728.2_Missense_Mutation_p.V356I	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	474					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.V474I(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	AGCAGACTCCGTCAGCGAGCT	0.617																																					p.V356I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1066A	10						.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	1,4405		0,1,2202	38.0	45.0	42.0		1066,1174,1066,1420,1066,1066,1066	4.1	0.8	10		42	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	29,29,29,29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign,benign,benign,benign	356/631,392/667,356/631,474/749,356/631,356/631,356/631	50857591	1,13005	2203	4300	6503	50527597	SO:0001583	missense	1103	exon10			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1420G>A	10.37:g.50857591G>A	ENSP00000337103:p.Val474Ile	Somatic		Capture	Illumina HiSeq	Phase_I	50527597	NM_001142929	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	G	10.66	1.413789	0.25465	2.27E-4	0.0	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.04	4.14	0.48551	.	0.250206	0.39759	N	0.001263	D	0.83585	0.5286	L	0.42529	1.33	0.42711	D	0.993647	B;B	0.06786	0.0;0.001	B;B	0.06405	0.0;0.002	T	0.77316	-0.2633	10	0.19147	T	0.46	-26.2046	13.4395	0.61104	0.0764:0.0:0.9236:0.0	.	356;474	F8W8I2;P28329	.;CLAT_HUMAN	I	356;356;356;474;392;356	ENSP00000343486:V356I;ENSP00000345878:V356I;ENSP00000378926:V356I;ENSP00000337103:V474I;ENSP00000378929:V392I;ENSP00000390521:V356I	ENSP00000337103:V474I	V	+	1	0	CHAT	50527597	1.000000	0.71417	0.759000	0.31340	0.455000	0.32408	6.373000	0.73128	1.113000	0.41760	0.462000	0.41574	GTC		0.617	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
CHAT	1103	broad.mit.edu	37	10	50863176	50863176	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:50863176C>T	ENST00000337653.2	+	12	1823	c.1670C>T	c.(1669-1671)gCg>gTg	p.A557V	CHAT_ENST00000339797.1_Missense_Mutation_p.A439V|CHAT_ENST00000395559.2_Missense_Mutation_p.A439V|CHAT_ENST00000395562.2_Missense_Mutation_p.A475V|CHAT_ENST00000351556.3_Missense_Mutation_p.A439V|CHAT_ENST00000455728.2_Missense_Mutation_p.A439V	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	557					adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)	p.A557V(1)		central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	TACGAGAGCGCGTCCATCCGC	0.547																																					p.A439V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1316T	10						.						56.0	56.0	56.0					10																	50863176		2203	4300	6503	50533182	SO:0001583	missense	1103	exon12			AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.1670C>T	10.37:g.50863176C>T	ENSP00000337103:p.Ala557Val	Somatic		Capture	Illumina HiSeq	Phase_I	50533182	NM_001142929	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	.	.	.	.	.	.	.	.	.	.	C	32	5.110207	0.94292	.	.	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.94138	-3.36;-3.36;-3.36;-3.36;-3.36;-3.36	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	D	0.97105	0.9054	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.97631	1.0142	10	0.87932	D	0	-22.8974	19.0718	0.93140	0.0:1.0:0.0:0.0	.	439;557	F8W8I2;P28329	.;CLAT_HUMAN	V	439;439;439;557;475;439	ENSP00000343486:A439V;ENSP00000345878:A439V;ENSP00000378926:A439V;ENSP00000337103:A557V;ENSP00000378929:A475V;ENSP00000390521:A439V	ENSP00000337103:A557V	A	+	2	0	CHAT	50533182	1.000000	0.71417	0.112000	0.21494	0.742000	0.42306	7.818000	0.86416	2.514000	0.84764	0.591000	0.81541	GCG		0.547	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
DKK1	22943	broad.mit.edu	37	10	54074315	54074315	+	Missense_Mutation	SNP	G	G	A	rs145640971		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:54074315G>A	ENST00000373970.3	+	1	260	c.121G>A	c.(121-123)Gct>Act	p.A41T	PRKG1-AS1_ENST00000420193.1_RNA	NM_012242.2	NP_036374.1	O94907	DKK1_HUMAN	dickkopf WNT signaling pathway inhibitor 1	41					cell morphogenesis involved in differentiation (GO:0000904)|embryonic limb morphogenesis (GO:0030326)|endoderm formation (GO:0001706)|extracellular negative regulation of signal transduction (GO:1900116)|face morphogenesis (GO:0060325)|forebrain development (GO:0030900)|hair follicle development (GO:0001942)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901296)|negative regulation of cardiac muscle cell differentiation (GO:2000726)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway (GO:0090082)|regulation of endodermal cell fate specification (GO:0042663)|regulation of receptor internalization (GO:0002090)|response to retinoic acid (GO:0032526)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|signal transducer activity (GO:0004871)	p.A41T(1)		kidney(2)|large_intestine(4)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	16						CAATTCCAACGCTATCAAGAA	0.667											OREG0020191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A41T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	10						.	G	THR/ALA	0,4404		0,0,2202	40.0	46.0	44.0		121	3.7	1.0	10	dbSNP_134	44	3,8587	3.0+/-9.4	0,3,4292	no	missense	DKK1	NM_012242.2	58	0,3,6494	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	41/267	54074315	3,12991	2202	4295	6497	53744321	SO:0001583	missense	22943	exon1				CCDS7246.1	10q11.2	2013-05-15	2013-05-15		ENSG00000107984	ENSG00000107984			2891	protein-coding gene	gene with protein product		605189	"""dickkopf (Xenopus laevis) homolog 1"", ""dickkopf 1 homolog (Xenopus laevis)"""				Standard	NM_012242		Approved	SK, DKK-1	uc001jjr.3	O94907	OTTHUMG00000018247	ENST00000373970.3:c.121G>A	10.37:g.54074315G>A	ENSP00000363081:p.Ala41Thr	Somatic	997	Capture	Illumina HiSeq	Phase_I	53744321	NM_012242	B2RC19	Missense_Mutation	SNP	ENST00000373970.3	37	CCDS7246.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.472725	0.84640	0.0	3.49E-4	ENSG00000107984	ENST00000373970	T	0.52526	0.66	4.65	3.72	0.42706	.	0.276731	0.33834	N	0.004514	T	0.33614	0.0869	L	0.34521	1.04	0.44409	D	0.997326	P	0.52842	0.956	B	0.38712	0.28	T	0.12915	-1.0529	10	0.46703	T	0.11	-4.898	11.5802	0.50887	0.0:0.0:0.821:0.179	.	41	O94907	DKK1_HUMAN	T	41	ENSP00000363081:A41T	ENSP00000363081:A41T	A	+	1	0	DKK1	53744321	1.000000	0.71417	0.997000	0.53966	0.940000	0.58332	6.011000	0.70760	1.045000	0.40225	0.655000	0.94253	GCT		0.667	DKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048100.1		
CCDC6	8030	broad.mit.edu	37	10	61552833	61552833	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:61552833A>T	ENST00000263102.6	-	9	1498	c.1267T>A	c.(1267-1269)Ttc>Atc	p.F423I		NM_005436.4	NP_005427.2	Q16204	CCDC6_HUMAN	coiled-coil domain containing 6	423						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	structural constituent of cytoskeleton (GO:0005200)	p.F423I(1)	CCDC6/RET(4)	breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(3)|stomach(1)	18				Kidney(211;0.0597)		GGCCGTTTGAATTTGTCAGGA	0.597			T	RET	NSCLC																																p.F423I			Dom	yes		10	10q21	8030	coiled-coil domain containing 6		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1267A	10						.						156.0	148.0	150.0					10																	61552833		2203	4300	6503	61222839	SO:0001583	missense	8030	exon9			S72869	CCDS7257.1	10q21.2	2006-11-09	2004-01-20		ENSG00000108091	ENSG00000108091			18782	protein-coding gene	gene with protein product	"""DNA segment, single copy, probe pH4 (transforming sequence, thyroid-1"""	601985	"""DNA segment on chromosome 10 (unique) 170"""	TST1, D10S170		8058316, 6745938	Standard	NM_005436		Approved	PTC, TPC, H4	uc001jks.4	Q16204	OTTHUMG00000018284	ENST00000263102.6:c.1267T>A	10.37:g.61552833A>T	ENSP00000263102:p.Phe423Ile	Somatic		Capture	Illumina HiSeq	Phase_I	61222839	NM_005436	Q15250|Q6GSG7	Missense_Mutation	SNP	ENST00000263102.6	37	CCDS7257.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.567569	0.86439	.	.	ENSG00000108091	ENST00000263102	T	0.54675	0.56	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.67906	0.2943	L	0.56769	1.78	0.80722	D	1	D	0.54601	0.967	D	0.63597	0.916	T	0.70000	-0.4992	10	0.62326	D	0.03	-14.9365	16.0859	0.81049	1.0:0.0:0.0:0.0	.	423	Q16204	CCDC6_HUMAN	I	423	ENSP00000263102:F423I	ENSP00000263102:F423I	F	-	1	0	CCDC6	61222839	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.910000	0.92685	2.248000	0.74166	0.460000	0.39030	TTC		0.597	CCDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048176.2	NM_005436	
MYPN	84665	broad.mit.edu	37	10	69881209	69881209	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:69881209G>T	ENST00000358913.5	+	2	502	c.14G>T	c.(13-15)aGc>aTc	p.S5I	MYPN_ENST00000373675.3_Missense_Mutation_p.S5I|MYPN_ENST00000354393.2_Intron|MYPN_ENST00000540630.1_Missense_Mutation_p.S5I	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	5	Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.S5I(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						CAAGACGACAGCATAGAAGCT	0.413																																					p.S5I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14T	10						.						65.0	64.0	64.0					10																	69881209		2203	4300	6503	69551215	SO:0001583	missense	84665	exon2			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.14G>T	10.37:g.69881209G>T	ENSP00000351790:p.Ser5Ile	Somatic		Capture	Illumina HiSeq	Phase_I	69551215	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030390	0.35797	.	.	ENSG00000138347	ENST00000358913;ENST00000540630;ENST00000373675	T;T;T	0.65364	0.25;0.23;-0.15	6.03	2.74	0.32292	.	0.179231	0.64402	D	0.000013	T	0.49474	0.1559	L	0.47716	1.5	0.35582	D	0.806378	B;P	0.42409	0.402;0.779	B;B	0.39258	0.295;0.231	T	0.55866	-0.8073	9	.	.	.	.	7.2554	0.26173	0.2009:0.2408:0.5583:0.0	.	5;5	Q86TC9-3;Q86TC9	.;MYPN_HUMAN	I	5	ENSP00000351790:S5I;ENSP00000441668:S5I;ENSP00000362779:S5I	.	S	+	2	0	MYPN	69551215	1.000000	0.71417	0.922000	0.36590	0.936000	0.57629	2.097000	0.41748	0.872000	0.35775	0.655000	0.94253	AGC		0.413	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
RUFY2	55680	broad.mit.edu	37	10	70136608	70136608	+	Splice_Site	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:70136608A>G	ENST00000602465.1	-	13	1426		c.e13+1		RUFY2_ENST00000265865.3_Splice_Site|RUFY2_ENST00000388768.2_Splice_Site|RUFY2_ENST00000472394.2_5'Flank			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2							nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.?(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)	20						TGAAATACTCACAGCTGTTTC	0.333																																					.												.	.	1	Unknown(1)	large_intestine(1)	.	10						.						176.0	157.0	163.0					10																	70136608		1822	4087	5909	69806614	SO:0001630	splice_region_variant	55680	.			AF461266	CCDS41534.1, CCDS44414.1, CCDS60544.1	10q22.2	2007-01-29			ENSG00000204130	ENSG00000204130		"""Zinc fingers, FYVE domain containing"""	19761	protein-coding gene	gene with protein product		610328				11877430	Standard	NM_001042417		Approved	RABIP4R, FLJ10063, KIAA1537, ZFYVE13	uc001job.3	Q8WXA3	OTTHUMG00000018353	ENST00000602465.1:c.1325+1T>C	10.37:g.70136608A>G		Somatic		Capture	Illumina HiSeq	Phase_I	69806614	.	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Splice_Site	SNP	ENST00000602465.1	37		.	.	.	.	.	.	.	.	.	.	A	20.3	3.969166	0.74131	.	.	ENSG00000204130	ENST00000388768;ENST00000265865	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.5923	0.76543	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RUFY2	69806614	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.890000	0.87313	2.323000	0.78572	0.528000	0.53228	.		0.333	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987	Intron
HKDC1	80201	broad.mit.edu	37	10	70987019	70987019	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:70987019G>T	ENST00000354624.5	+	2	253	c.120G>T	c.(118-120)atG>atT	p.M40I	RP11-227H15.4_ENST00000450995.1_RNA|HKDC1_ENST00000395086.2_Missense_Mutation_p.M40I	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	40	Hexokinase type-1 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)	p.M40I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						TGGACATCATGAGGCGGTTCC	0.612																																					p.M40I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G120T	10						.						129.0	113.0	118.0					10																	70987019		2203	4300	6503	70657025	SO:0001583	missense	80201	exon2				CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.120G>T	10.37:g.70987019G>T	ENSP00000346643:p.Met40Ile	Somatic		Capture	Illumina HiSeq	Phase_I	70657025	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.922897	0.33908	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98937	-5.25;-5.25	4.91	4.91	0.64330	Hexokinase, N-terminal (1);	0.090204	0.85682	D	0.000000	D	0.97343	0.9131	L	0.61036	1.89	0.38127	D	0.938032	P	0.34837	0.472	B	0.35931	0.214	D	0.98183	1.0458	10	0.48119	T	0.1	-36.339	13.9692	0.64228	0.0758:0.0:0.9242:0.0	.	40	Q2TB90	HKDC1_HUMAN	I	40	ENSP00000346643:M40I;ENSP00000378521:M40I	ENSP00000346643:M40I	M	+	3	0	HKDC1	70657025	0.941000	0.31946	1.000000	0.80357	0.476000	0.33039	1.582000	0.36568	2.707000	0.92482	0.655000	0.94253	ATG		0.612	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
SGPL1	8879	broad.mit.edu	37	10	72629616	72629616	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:72629616C>T	ENST00000373202.3	+	9	972	c.772C>T	c.(772-774)Cgg>Tgg	p.R258W		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	258					androgen metabolic process (GO:0008209)|apoptotic signaling pathway (GO:0097190)|ceramide metabolic process (GO:0006672)|estrogen metabolic process (GO:0008210)|face morphogenesis (GO:0060325)|fatty acid metabolic process (GO:0006631)|fibroblast migration (GO:0010761)|hemopoiesis (GO:0030097)|kidney development (GO:0001822)|Leydig cell differentiation (GO:0033327)|luteinization (GO:0001553)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic development (GO:0009791)|regulation of multicellular organism growth (GO:0040014)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid catabolic process (GO:0030149)|sphingolipid metabolic process (GO:0006665)|vasculogenesis (GO:0001570)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)|sphinganine-1-phosphate aldolase activity (GO:0008117)	p.R258W(2)		large_intestine(4)	4						GAAGATTGTGCGGGTCCCATT	0.537																																					p.R258W	Colon(151;1054 2458 6676 40971)											.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C772T	10						.						145.0	139.0	141.0					10																	72629616		2203	4300	6503	72299622	SO:0001583	missense	8879	exon9			AI128825	CCDS31216.1	10q21	2008-08-01			ENSG00000166224	ENSG00000166224			10817	protein-coding gene	gene with protein product		603729				9464245, 17090686	Standard	NM_003901		Approved	SPL	uc001jrm.3	O95470	OTTHUMG00000018421	ENST00000373202.3:c.772C>T	10.37:g.72629616C>T	ENSP00000362298:p.Arg258Trp	Somatic		Capture	Illumina HiSeq	Phase_I	72299622	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Missense_Mutation	SNP	ENST00000373202.3	37	CCDS31216.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.389511	0.82902	.	.	ENSG00000166224	ENST00000373202	T	0.37752	1.18	5.65	4.73	0.59995	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.100546	0.64402	D	0.000002	T	0.38241	0.1033	L	0.45470	1.425	0.44447	D	0.997377	P	0.39903	0.694	B	0.42361	0.385	T	0.15065	-1.0450	10	0.40728	T	0.16	-17.473	15.8072	0.78524	0.1371:0.8629:0.0:0.0	.	258	O95470	SGPL1_HUMAN	W	258	ENSP00000362298:R258W	ENSP00000362298:R258W	R	+	1	2	SGPL1	72299622	1.000000	0.71417	0.296000	0.24974	0.919000	0.55068	5.711000	0.68400	1.341000	0.45600	0.591000	0.81541	CGG		0.537	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901	
UNC5B	219699	broad.mit.edu	37	10	73051363	73051363	+	Missense_Mutation	SNP	C	C	T	rs543519250		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:73051363C>T	ENST00000335350.6	+	10	1885	c.1469C>T	c.(1468-1470)aCg>aTg	p.T490M	UNC5B_ENST00000373192.4_Missense_Mutation_p.T479M	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	490					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)		p.T490M(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						TCCAGCACCACGGGCTCTGGG	0.622													c|||	1	0.000199681	0.0	0.0	5008	,	,		17504	0.001		0.0	False		,,,				2504	0.0				p.T490M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1469T	10						.						56.0	57.0	57.0					10																	73051363		2203	4300	6503	72721369	SO:0001583	missense	219699	exon10			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1469C>T	10.37:g.73051363C>T	ENSP00000334329:p.Thr490Met	Somatic		Capture	Illumina HiSeq	Phase_I	72721369	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	c	4.137	0.023704	0.08006	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48522	0.86;0.81	4.47	0.948	0.19561	.	0.606055	0.17896	N	0.158344	T	0.32496	0.0831	L	0.37630	1.12	0.21105	N	0.999787	B;B	0.23937	0.094;0.057	B;B	0.15052	0.012;0.009	T	0.17048	-1.0382	10	0.38643	T	0.18	-14.2103	8.0398	0.30515	0.0:0.5829:0.0:0.4171	.	479;490	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	M	490;479	ENSP00000334329:T490M;ENSP00000362288:T479M	ENSP00000334329:T490M	T	+	2	0	UNC5B	72721369	.	.	0.482000	0.27366	0.142000	0.21351	.	.	0.419000	0.25927	-0.141000	0.14075	ACG		0.622	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
UNC5B	219699	broad.mit.edu	37	10	73059019	73059019	+	Silent	SNP	C	C	T	rs368414601		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:73059019C>T	ENST00000335350.6	+	17	3239	c.2823C>T	c.(2821-2823)acC>acT	p.T941T	UNC5B_ENST00000373192.4_Silent_p.T930T	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	941	Death.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)		p.T941T(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						CTGTGGCCACCGACGGGGACT	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		17199	0.0		0.001	False		,,,				2504	0.0				p.T941T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2823T	10						.	C		0,4406		0,0,2203	107.0	106.0	106.0		2823	-11.2	0.0	10		106	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UNC5B	NM_170744.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		941/946	73059019	1,13005	2203	4300	6503	72729025	SO:0001819	synonymous_variant	219699	exon17			AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.2823C>T	10.37:g.73059019C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72729025	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																				0.662	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
NDST2	8509	broad.mit.edu	37	10	75567575	75567575	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:75567575delA	ENST00000309979.6	-	3	1128	c.572delT	c.(571-573)ttafs	p.L191fs	NDST2_ENST00000398701.2_5'Flank|NDST2_ENST00000299641.4_Frame_Shift_Del_p.L68fs|RP11-574K11.31_ENST00000603027.1_Frame_Shift_Del_p.L191fs			P52849	NDST2_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 2	191	Heparan sulfate N-deacetylase 2.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|hydrolase activity (GO:0016787)	p.L191fs*12(1)		cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30	Prostate(51;0.0112)					GTTTGAGTGTAAAAAAAGGGG	0.587																																					p.L191fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.572delT	10						.						50.0	51.0	51.0					10																	75567575		2203	4300	6503	75237581	SO:0001589	frameshift_variant	8509	exon3			U36601	CCDS7335.1	10q22	2007-03-14			ENSG00000166507	ENSG00000166507		"""Sulfotransferases, membrane-bound"""	7681	protein-coding gene	gene with protein product		603268				9601056	Standard	NM_003635		Approved	NST2, HSST2	uc001jvk.2	P52849	OTTHUMG00000018489	ENST00000309979.6:c.572delT	10.37:g.75567575delA	ENSP00000310657:p.Leu191fs	Somatic		Capture	Illumina HiSeq	Phase_I	75237581	NM_003635	Q2TB32|Q59H89	Frame_Shift_Del	DEL	ENST00000309979.6	37	CCDS7335.1																																																																																				0.587	NDST2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048710.1	NM_003635	
CAMK2G	818	broad.mit.edu	37	10	75574949	75574949	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:75574949C>T	ENST00000351293.3	-	18	1369	c.1312G>A	c.(1312-1314)Gtg>Atg	p.V438M	CAMK2G_ENST00000423381.1_Missense_Mutation_p.V531M|CAMK2G_ENST00000372765.1_Missense_Mutation_p.V459M|CAMK2G_ENST00000394762.2_Missense_Mutation_p.V476M|CAMK2G_ENST00000322635.3_Missense_Mutation_p.V470M|CAMK2G_ENST00000322680.3_Missense_Mutation_p.V499M|CAMK2G_ENST00000305762.7_Missense_Mutation_p.V472M|CAMK2G_ENST00000472912.1_5'UTR|RP11-574K11.5_ENST00000434147.1_RNA	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	501					calcium ion transport (GO:0006816)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|dephosphorylation (GO:0016311)|G1/S transition of mitotic cell cycle (GO:0000082)|insulin secretion (GO:0030073)|interferon-gamma-mediated signaling pathway (GO:0060333)|nervous system development (GO:0007399)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of calcium ion transport (GO:0051924)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of skeletal muscle adaptation (GO:0014733)|synaptic transmission (GO:0007268)	calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-dependent protein serine/threonine phosphatase activity (GO:0004723)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)	p.V438M(1)		kidney(2)|large_intestine(2)|lung(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	15	Prostate(51;0.0112)				Bosutinib(DB06616)	TCCCCAATCACGTGGACGTGT	0.617																																					p.V470M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1408A	10						.						154.0	125.0	135.0					10																	75574949		2203	4300	6503	75244955	SO:0001583	missense	818	exon20			U81554	CCDS7336.1, CCDS7337.1, CCDS7338.1, CCDS73153.1	10q22	2008-10-30	2008-10-30		ENSG00000148660	ENSG00000148660			1463	protein-coding gene	gene with protein product		602123	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma"""	CAMKG		8287681	Standard	NM_001204492		Approved		uc001jvm.2	Q13555	OTTHUMG00000018492	ENST00000351293.3:c.1312G>A	10.37:g.75574949C>T	ENSP00000277853:p.Val438Met	Somatic		Capture	Illumina HiSeq	Phase_I	75244955	NM_172169	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	37	CCDS7336.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.52|17.52	3.409621|3.409621	0.62399|0.62399	.|.	.|.	ENSG00000148660|ENSG00000148660	ENST00000441192|ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765	.|T;T;T;T;T;T;T;T	.|0.41758	.|0.99;0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.51|5.51	5.51|5.51	0.81932|0.81932	.|Calcium/calmodulin-dependent protein kinase II, association-domain (1);	.|0.082083	.|0.50627	.|D	.|0.000113	T|T	0.35624|0.35624	0.0938|0.0938	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	D|D	1|1	.|B;B;P;P;B;B;B	.|0.46457	.|0.148;0.334;0.625;0.878;0.299;0.14;0.068	.|B;B;P;P;B;B;B	.|0.52627	.|0.08;0.064;0.532;0.704;0.106;0.016;0.064	T|T	0.40701|0.40701	-0.9549|-0.9549	5|10	.|0.31617	.|T	.|0.26	.|.	19.4394|19.4394	0.94811|0.94811	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|472;531;438;461;501;470;499	.|Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8	.|.;.;.;.;KCC2G_HUMAN;.;.	H|M	277|438;470;531;501;499;476;396;472;459	.|ENSP00000277853:V438M;ENSP00000315599:V470M;ENSP00000410298:V531M;ENSP00000319060:V499M;ENSP00000378243:V476M;ENSP00000393784:V396M;ENSP00000307082:V472M;ENSP00000361851:V459M	.|ENSP00000307082:V472M	R|V	-|-	2|1	0|0	CAMK2G|CAMK2G	75244955|75244955	1.000000|1.000000	0.71417|0.71417	0.513000|0.513000	0.27749|0.27749	0.999000|0.999000	0.98932|0.98932	3.832000|3.832000	0.55783|0.55783	2.581000|2.581000	0.87130|0.87130	0.655000|0.655000	0.94253|0.94253	CGT|GTG		0.617	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169	
C10orf55	414236	broad.mit.edu	37	10	75676249	75676249	+	Intron	SNP	G	G	A	rs200165551		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:75676249G>A	ENST00000409178.1	-	2	268				C10orf55_ENST00000412307.2_Intron|PLAU_ENST00000372762.4_Missense_Mutation_p.V372I|PLAU_ENST00000446342.1_Missense_Mutation_p.V391I|PLAU_ENST00000372764.3_Missense_Mutation_p.V408I	NM_001001791.2	NP_001001791.2	Q5SWW7	CJ055_HUMAN	chromosome 10 open reading frame 55									p.V408I(1)		endometrium(1)	1	Prostate(51;0.0112)					CAAGCCAGGCGTCTACACGAG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		18257	0.0		0.001	False		,,,				2504	0.0				p.V408I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1222A	10						.						62.0	50.0	54.0					10																	75676249		2203	4300	6503	75346255	SO:0001627	intron_variant	5328	exon11				CCDS53541.1	10q22.2	2012-05-24			ENSG00000222047	ENSG00000222047			31008	protein-coding gene	gene with protein product							Standard	NM_001001791		Approved	bA417O11.3	uc001jvz.2	Q5SWW7	OTTHUMG00000018496	ENST00000409178.1:c.72+27C>T	10.37:g.75676249G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75346255	NM_002658	Q3KRG4|Q8NAK4	Missense_Mutation	SNP	ENST00000409178.1	37	CCDS53541.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.6	4.545836	0.86022	.	.	ENSG00000122861	ENST00000446342;ENST00000372764;ENST00000372762;ENST00000372761	D;D;D	0.90732	-2.72;-2.72;-2.72	5.62	5.62	0.85841	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.85682	D	0.000000	D	0.95236	0.8455	M	0.76838	2.35	0.80722	D	1	D;D;D;D	0.89917	0.995;0.996;1.0;0.982	D;D;D;D	0.97110	0.952;0.972;1.0;0.95	D	0.95111	0.8238	10	0.56958	D	0.05	.	17.1577	0.86795	0.0:0.0:1.0:0.0	.	391;372;408;408	E7ET40;E7ESM2;B2R7F2;P00749	.;.;.;UROK_HUMAN	I	391;408;372;372	ENSP00000388474:V391I;ENSP00000361850:V408I;ENSP00000361848:V372I	ENSP00000361847:V372I	V	+	1	0	PLAU	75346255	1.000000	0.71417	0.982000	0.44146	0.779000	0.44077	8.325000	0.90007	2.650000	0.89964	0.555000	0.69702	GTC		0.602	C10orf55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048746.1	NM_001001791	
MMRN2	79812	broad.mit.edu	37	10	88703592	88703592	+	Missense_Mutation	SNP	C	C	T	rs138085924		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:88703592C>T	ENST00000372027.5	-	6	1270	c.949G>A	c.(949-951)Gcc>Acc	p.A317T	MMRN2_ENST00000488950.1_5'Flank	NM_024756.2	NP_079032.2	Q9H8L6	MMRN2_HUMAN	multimerin 2	317					angiogenesis (GO:0001525)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.A317T(1)		breast(1)|kidney(1)|large_intestine(6)|lung(7)|prostate(2)|skin(1)|stomach(1)	19						AAGTGCTGGGCGTGCAGGCGG	0.597																																					p.A317T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G949A	10						.	C	THR/ALA	0,4406		0,0,2203	67.0	66.0	67.0		949	2.0	0.4	10	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	no	missense	MMRN2	NM_024756.2	58	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	317/950	88703592	2,13004	2203	4300	6503	88693572	SO:0001583	missense	79812	exon6			AK023527	CCDS7379.1	10q23.31	2004-03-10	2004-03-02	2004-03-02	ENSG00000173269	ENSG00000173269		"""EMI domain containing"""	19888	protein-coding gene	gene with protein product		608925	"""elastin microfibril interfacer 3"""	EMILIN3		11559704	Standard	NM_024756		Approved	EndoGlyx-1, FLJ13465	uc001kea.3	Q9H8L6	OTTHUMG00000018663	ENST00000372027.5:c.949G>A	10.37:g.88703592C>T	ENSP00000361097:p.Ala317Thr	Somatic		Capture	Illumina HiSeq	Phase_I	88693572	NM_024756	Q504V7|Q6P2N2	Missense_Mutation	SNP	ENST00000372027.5	37	CCDS7379.1	.	.	.	.	.	.	.	.	.	.	C	10.30	1.312529	0.23908	0.0	2.33E-4	ENSG00000173269	ENST00000372027	T	0.15487	2.42	4.88	2.02	0.26589	.	0.845980	0.10365	N	0.683511	T	0.22244	0.0536	M	0.67953	2.075	0.09310	N	1	D;P	0.67145	0.996;0.916	P;B	0.50490	0.642;0.343	T	0.16630	-1.0396	10	0.16896	T	0.51	-7.344	4.8724	0.13639	0.0:0.4477:0.1475:0.4048	.	256;317	B4E3H8;Q9H8L6	.;MMRN2_HUMAN	T	317	ENSP00000361097:A317T	ENSP00000361097:A317T	A	-	1	0	MMRN2	88693572	0.001000	0.12720	0.381000	0.26106	0.088000	0.18126	0.087000	0.14958	0.135000	0.18707	-0.379000	0.06801	GCC		0.597	MMRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049179.2	NM_024756	
GLUD1	2746	broad.mit.edu	37	10	88818959	88818959	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:88818959G>A	ENST00000277865.4	-	10	1446	c.1350C>T	c.(1348-1350)agC>agT	p.S450S	GLUD1_ENST00000537649.1_Silent_p.S283S|GLUD1_ENST00000544149.1_Silent_p.S317S|GLUD1_ENST00000465164.1_5'Flank	NM_005271.3	NP_005262.1	P00367	DHE3_HUMAN	glutamate dehydrogenase 1	450					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.S450S(1)		endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(11)|prostate(1)	22					Hexachlorophene(DB00756)	AACGGCCATAGCTGACATGAT	0.388																																					p.S450S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1350T	10						.						189.0	184.0	186.0					10																	88818959		2203	4297	6500	88808939	SO:0001819	synonymous_variant	2746	exon10			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.1350C>T	10.37:g.88818959G>A		Somatic		Capture	Illumina HiSeq	Phase_I	88808939	NM_005271	B3KV55|B4DGN5|Q5TBU3	Silent	SNP	ENST00000277865.4	37	CCDS7382.1																																																																																				0.388	GLUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049188.1	NM_005271	
ATAD1	84896	broad.mit.edu	37	10	89574213	89574213	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:89574213delT	ENST00000308448.7	-	2	522	c.144delA	c.(142-144)aaafs	p.K48fs	ATAD1_ENST00000328142.3_Frame_Shift_Del_p.K48fs|ATAD1_ENST00000495903.1_5'UTR|ATAD1_ENST00000541004.1_Frame_Shift_Del_p.K48fs	NM_032810.2	NP_116199.2	Q8NBU5	ATAD1_HUMAN	ATPase family, AAA domain containing 1	48					ATP catabolic process (GO:0006200)|learning (GO:0007612)|memory (GO:0007613)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|positive regulation of receptor internalization (GO:0002092)	cell junction (GO:0030054)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.V49fs*1(1)		kidney(1)|large_intestine(4)|lung(4)|ovary(1)	10		all_cancers(4;6.78e-12)|Prostate(4;3.56e-12)|all_epithelial(4;5.58e-09)|Melanoma(5;0.0273)|Breast(4;0.0424)|all_hematologic(4;0.0846)|Colorectal(252;0.207)|Glioma(4;0.217)|all_neural(4;0.224)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00131)|GBM - Glioblastoma multiforme(1;1.1e-32)|Lung(2;1.4e-05)|LUSC - Lung squamous cell carcinoma(2;2.69e-05)|Colorectal(12;7.09e-05)|COAD - Colon adenocarcinoma(12;0.000261)|STAD - Stomach adenocarcinoma(243;0.235)		GAGCTTCTACTTTTTGCTTTC	0.338																																					p.K48fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.144delA	10						.						154.0	137.0	143.0					10																	89574213		2202	4300	6502	89564193	SO:0001589	frameshift_variant	84896	exon2			AL834370	CCDS7386.1	10q23.31	2010-04-21		2007-02-08	ENSG00000138138	ENSG00000138138		"""ATPases / AAA-type"""	25903	protein-coding gene	gene with protein product		614452				12477932	Standard	NM_032810		Approved	FLJ14600	uc001kez.1	Q8NBU5	OTTHUMG00000018685	ENST00000308448.7:c.144delA	10.37:g.89574213delT	ENSP00000339017:p.Lys48fs	Somatic		Capture	Illumina HiSeq	Phase_I	89564193	NM_032810	D3DR26|Q6DKG1|Q6P4B9|Q8N3G1|Q8WYR9|Q969Y3	Frame_Shift_Del	DEL	ENST00000308448.7	37	CCDS7386.1																																																																																				0.338	ATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049235.1	NM_032810	
ACTA2	59	broad.mit.edu	37	10	90703596	90703596	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:90703596C>A	ENST00000458208.1	-	4	801	c.327G>T	c.(325-327)gaG>gaT	p.E109D	STAMBPL1_ENST00000371927.3_Intron|ACTA2_ENST00000224784.6_Missense_Mutation_p.E109D|ACTA2_ENST00000480297.1_5'UTR	NM_001141945.1	NP_001135417.1	P62736	ACTA_HUMAN	actin, alpha 2, smooth muscle, aorta	109					glomerular mesangial cell development (GO:0072144)|muscle contraction (GO:0006936)|regulation of blood pressure (GO:0008217)|response to virus (GO:0009615)|vascular smooth muscle contraction (GO:0014829)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|smooth muscle contractile fiber (GO:0030485)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)	p.E109D(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(1)|urinary_tract(2)	17		Colorectal(252;0.0161)		Colorectal(12;0.000123)|COAD - Colon adenocarcinoma(12;0.00018)		TCAGGGGTGCCTCCGTGAGCA	0.532																																					p.E109D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G327T	10						.						126.0	113.0	118.0					10																	90703596		2203	4300	6503	90693576	SO:0001583	missense	59	exon4			X13839	CCDS7392.1	10q23.31	2014-09-17			ENSG00000107796	ENSG00000107796			130	protein-coding gene	gene with protein product		102620				2398629	Standard	NM_001141945		Approved	ACTSA	uc001kfp.3	P62736	OTTHUMG00000018700	ENST00000458208.1:c.327G>T	10.37:g.90703596C>A	ENSP00000402373:p.Glu109Asp	Somatic		Capture	Illumina HiSeq	Phase_I	90693576	NM_001141945	B2R8A4|P03996|P04108|Q6FI19	Missense_Mutation	SNP	ENST00000458208.1	37	CCDS7392.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.928786	0.52759	.	.	ENSG00000107796	ENST00000224784;ENST00000458208;ENST00000544901;ENST00000415557;ENST00000458159	D;D;D;D	0.96940	-4.18;-4.18;-4.18;-4.18	5.86	4.02	0.46733	Actin/actin-like conserved site (1);	0.055319	0.64402	D	0.000001	D	0.97626	0.9222	M	0.81341	2.54	0.43632	D	0.99602	D;B	0.62365	0.991;0.236	D;P	0.79108	0.992;0.698	D	0.97340	0.9956	10	0.87932	D	0	.	9.8427	0.41008	0.0:0.7764:0.0:0.2236	.	109;109	B7Z6I1;P62736	.;ACTA_HUMAN	D	109;109;64;109;109	ENSP00000224784:E109D;ENSP00000402373:E109D;ENSP00000396730:E109D;ENSP00000398239:E109D	ENSP00000224784:E109D	E	-	3	2	ACTA2	90693576	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	2.164000	0.42387	0.826000	0.34661	0.655000	0.94253	GAG		0.532	ACTA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049264.1	NM_001613	
IFIT1	3434	broad.mit.edu	37	10	91162429	91162429	+	Missense_Mutation	SNP	C	C	T	rs376965843		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:91162429C>T	ENST00000371804.3	+	2	564	c.397C>T	c.(397-399)Cgc>Tgc	p.R133C	IFIT1_ENST00000546318.1_Missense_Mutation_p.R102C|LIPA_ENST00000371837.1_Intron	NM_001270927.1|NM_001548.4	NP_001257856.1|NP_001539.3	P09914	IFIT1_HUMAN	interferon-induced protein with tetratricopeptide repeats 1	133					cellular response to exogenous dsRNA (GO:0071360)|cellular response to type I interferon (GO:0071357)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|intracellular transport of viral protein in host cell (GO:0019060)|negative regulation of defense response to virus by host (GO:0050689)|negative regulation of helicase activity (GO:0051097)|negative regulation of protein binding (GO:0032091)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	RNA binding (GO:0003723)	p.R133C(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(2)|prostate(2)|upper_aerodigestive_tract(1)	15						AAATCCCTTCCGCTATAGAAT	0.473																																					p.R133C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C397T	10						.	C	CYS/ARG	0,4406		0,0,2203	55.0	56.0	56.0		397	-2.0	0.0	10		56	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFIT1	NM_001548.3	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	133/479	91162429	1,13005	2203	4300	6503	91152409	SO:0001583	missense	3434	exon2			M24594	CCDS31243.1, CCDS59220.1	10q23.31	2014-05-22			ENSG00000185745	ENSG00000185745		"""Tetratricopeptide (TTC) repeat domain containing"""	5407	protein-coding gene	gene with protein product		147690		G10P1, IFI56, IFNAI1		1377167, 3360121	Standard	NM_001548		Approved	GARG-16	uc001kgi.4	P09914	OTTHUMG00000018712	ENST00000371804.3:c.397C>T	10.37:g.91162429C>T	ENSP00000360869:p.Arg133Cys	Somatic		Capture	Illumina HiSeq	Phase_I	91152409	NM_001548	B3KS50|D3DR31|Q5T7J1|Q96QM5	Missense_Mutation	SNP	ENST00000371804.3	37	CCDS31243.1	.	.	.	.	.	.	.	.	.	.	C	5.418	0.262328	0.10239	0.0	1.16E-4	ENSG00000185745	ENST00000371804;ENST00000546318	T;T	0.15017	2.46;2.46	5.35	-1.95	0.07548	Tetratricopeptide-like helical (1);	0.867295	0.10335	N	0.686981	T	0.11452	0.0279	L	0.37561	1.115	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.28522	-1.0041	10	0.46703	T	0.11	.	5.3492	0.16026	0.1473:0.4591:0.0:0.3936	.	133;133	Q5T7J1;P09914	.;IFIT1_HUMAN	C	133;102	ENSP00000360869:R133C;ENSP00000441968:R102C	ENSP00000360869:R133C	R	+	1	0	IFIT1	91152409	0.000000	0.05858	0.001000	0.08648	0.130000	0.20726	-0.132000	0.10467	-0.632000	0.05553	0.563000	0.77884	CGC		0.473	IFIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049302.1	NM_001548	
KIF20B	9585	broad.mit.edu	37	10	91478553	91478553	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:91478553T>C	ENST00000371728.3	+	12	1423	c.1358T>C	c.(1357-1359)aTt>aCt	p.I453T	KIF20B_ENST00000394289.2_Missense_Mutation_p.I453T|KIF20B_ENST00000416354.1_Missense_Mutation_p.I453T|KIF20B_ENST00000260753.4_Missense_Mutation_p.I453T	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	453	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)	p.I453T(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						ATTTGTATGATTGTCAATATC	0.313																																					p.I453T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1358C	10						.						53.0	57.0	56.0					10																	91478553		2203	4297	6500	91468533	SO:0001583	missense	9585	exon12			L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.1358T>C	10.37:g.91478553T>C	ENSP00000360793:p.Ile453Thr	Somatic		Capture	Illumina HiSeq	Phase_I	91468533	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		.	.	.	.	.	.	.	.	.	.	T	23.3	4.398682	0.83120	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36	5.51	5.51	0.81932	Kinesin, motor domain (3);	0.000000	0.52532	D	0.000073	D	0.90981	0.7164	M	0.88775	2.98	0.80722	D	1	D;D	0.67145	0.996;0.994	D;D	0.72625	0.978;0.958	D	0.92694	0.6169	10	0.87932	D	0	-16.5048	15.9043	0.79412	0.0:0.0:0.0:1.0	.	453;453	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	T	453	ENSP00000260753:I453T;ENSP00000411545:I453T;ENSP00000377830:I453T;ENSP00000360793:I453T	ENSP00000260753:I453T	I	+	2	0	KIF20B	91468533	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.560000	0.82277	2.219000	0.72066	0.533000	0.62120	ATT		0.313	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
IDE	3416	broad.mit.edu	37	10	94214246	94214246	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:94214246A>G	ENST00000265986.6	-	25	3071	c.3015T>C	c.(3013-3015)ttT>ttC	p.F1005F	IDE_ENST00000496903.1_5'UTR|IDE_ENST00000371581.5_Silent_p.F450F	NM_004969.3	NP_004960.2	P14735	IDE_HUMAN	insulin-degrading enzyme	1005					beta-amyloid metabolic process (GO:0050435)|bradykinin catabolic process (GO:0010815)|determination of adult lifespan (GO:0008340)|hormone catabolic process (GO:0042447)|insulin catabolic process (GO:1901143)|insulin metabolic process (GO:1901142)|insulin receptor signaling pathway (GO:0008286)|negative regulation of proteolysis (GO:0045861)|positive regulation of protein oligomerization (GO:0032461)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein homotetramerization (GO:0051289)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|ubiquitin homeostasis (GO:0010992)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|beta-amyloid binding (GO:0001540)|beta-endorphin binding (GO:0031626)|glycoprotein binding (GO:0001948)|insulin binding (GO:0043559)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.F1005F(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|urinary_tract(2)	33					"""""""Insulin(DB00071)|Bacitracin(DB00626)|Insulin Regular(DB00030)"""	TCACAAGGGGAAACAGTGGCA	0.423																																					p.F1005F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3015C	10						.						164.0	162.0	163.0					10																	94214246		2203	4300	6503	94204226	SO:0001819	synonymous_variant	3416	exon25			M21188	CCDS7421.1, CCDS53554.1	10q23-q25	2007-03-27			ENSG00000119912	ENSG00000119912			5381	protein-coding gene	gene with protein product	"""insulysin"""	146680				2293021	Standard	NM_004969		Approved		uc001kia.3	P14735	OTTHUMG00000018759	ENST00000265986.6:c.3015T>C	10.37:g.94214246A>G		Somatic		Capture	Illumina HiSeq	Phase_I	94204226	NM_004969	B2R721|B7ZAU2|D3DR35|Q5T5N2	Silent	SNP	ENST00000265986.6	37	CCDS7421.1																																																																																				0.423	IDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049393.1	NM_004969	
TBC1D12	23232	broad.mit.edu	37	10	96269849	96269849	+	Splice_Site	SNP	T	T	C	rs183691357		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:96269849T>C	ENST00000225235.4	+	8	1712	c.1602T>C	c.(1600-1602)ggT>ggC	p.G534G	TBC1D12_ENST00000485048.1_3'UTR	NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	534	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.						Rab GTPase activator activity (GO:0005097)	p.G534G(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(2)	20		Colorectal(252;0.0429)				TAAATGCAGGTGTATCTGTTG	0.368													T|||	1	0.000199681	0.0008	0.0	5008	,	,		15828	0.0		0.0	False		,,,				2504	0.0				p.G534G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1602C	10						.						165.0	154.0	158.0					10																	96269849		1850	4105	5955	96259839	SO:0001630	splice_region_variant	23232	exon8			AB011180	CCDS41553.1	10q23.33	2013-09-20			ENSG00000108239	ENSG00000108239			29082	protein-coding gene	gene with protein product						9628581	Standard	NM_015188		Approved	KIAA0608	uc001kjr.2	O60347	OTTHUMG00000018794	ENST00000225235.4:c.1601-1T>C	10.37:g.96269849T>C		Somatic		Capture	Illumina HiSeq	Phase_I	96259839	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Silent	SNP	ENST00000225235.4	37	CCDS41553.1																																																																																				0.368	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2		Silent
CYP2C9	1559	broad.mit.edu	37	10	96708915	96708915	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:96708915C>A	ENST00000260682.6	+	5	705	c.693C>A	c.(691-693)aaC>aaA	p.N231K		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	231					arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)	p.N231K(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	GAACTCACAACAAATTACTTA	0.274																																					p.N231K	Ovarian(54;1266 1406 16072 35076)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C693A	10						.						48.0	53.0	51.0					10																	96708915		2202	4299	6501	96698905	SO:0001583	missense	1559	exon5			M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.693C>A	10.37:g.96708915C>A	ENSP00000260682:p.Asn231Lys	Somatic		Capture	Illumina HiSeq	Phase_I	96698905	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	.	.	.	.	.	.	.	.	.	.	.	1.468	-0.560542	0.03939	.	.	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.67345	-0.26	3.29	-6.59	0.01830	.	0.487586	0.18873	U	0.128790	T	0.29158	0.0725	N	0.05124	-0.11	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.09377	0.004;0.004	T	0.41538	-0.9503	10	0.06494	T	0.89	.	5.5144	0.16898	0.2218:0.1499:0.5372:0.0912	.	231;231	Q5VX92;P11712	.;CP2C9_HUMAN	K	231	ENSP00000260682:N231K	ENSP00000260682:N231K	N	+	3	2	CYP2C9	96698905	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-4.973000	0.00164	-1.519000	0.01775	0.491000	0.48974	AAC		0.274	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
ALDH18A1	5832	broad.mit.edu	37	10	97397115	97397115	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:97397115G>A	ENST00000371224.2	-	4	519	c.382C>T	c.(382-384)Cgc>Tgc	p.R128C	ALDH18A1_ENST00000483788.1_5'UTR|ALDH18A1_ENST00000371221.3_Missense_Mutation_p.R128C	NM_002860.3	NP_002851.2	P54886	P5CS_HUMAN	aldehyde dehydrogenase 18 family, member A1	128	Glutamate 5-kinase.				cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|glutamate metabolic process (GO:0006536)|L-proline biosynthetic process (GO:0055129)|ornithine biosynthetic process (GO:0006592)|proline biosynthetic process (GO:0006561)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glutamate 5-kinase activity (GO:0004349)|glutamate-5-semialdehyde dehydrogenase activity (GO:0004350)|poly(A) RNA binding (GO:0044822)	p.R128C(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(9)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Colorectal(252;0.0402)		Epithelial(162;9.1e-07)|all cancers(201;2.55e-05)		ATCTCATGGCGCAAGCGTTGT	0.547																																					p.R128C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C382T	10						.						129.0	109.0	116.0					10																	97397115		2203	4300	6503	97387105	SO:0001583	missense	5832	exon4			X94453	CCDS7443.1, CCDS31257.1	10q24.3-q24.6	2004-08-12	2004-08-12	2004-08-12	ENSG00000059573	ENSG00000059573		"""Aldehyde dehydrogenases"""	9722	protein-coding gene	gene with protein product		138250	"""pyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)"""	GSAS, PYCS		8921385	Standard	XM_006717933		Approved	P5CS	uc001kkz.3	P54886	OTTHUMG00000018815	ENST00000371224.2:c.382C>T	10.37:g.97397115G>A	ENSP00000360268:p.Arg128Cys	Somatic		Capture	Illumina HiSeq	Phase_I	97387105	NM_001017423	B2R5Q4|B7Z350|B7Z5X8|B7ZLP1|D3DR44|O95952|Q3KQU2|Q5T566|Q5T567|Q9UM72	Missense_Mutation	SNP	ENST00000371224.2	37	CCDS7443.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537260	0.85812	.	.	ENSG00000059573	ENST00000371224;ENST00000371221	T;T	0.73258	-0.73;-0.73	5.6	5.6	0.85130	Aspartate/glutamate/uridylate kinase (3);	0.000000	0.85682	D	0.000000	D	0.85252	0.5654	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.962	D	0.87084	0.2168	10	0.87932	D	0	-13.5957	17.102	0.86652	0.0:0.0:1.0:0.0	.	128;128	P54886;P54886-2	P5CS_HUMAN;.	C	128	ENSP00000360268:R128C;ENSP00000360265:R128C	ENSP00000360265:R128C	R	-	1	0	ALDH18A1	97387105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.630000	0.61297	2.642000	0.89623	0.555000	0.69702	CGC		0.547	ALDH18A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049552.1	NM_002860	
BLNK	29760	broad.mit.edu	37	10	97969596	97969596	+	Silent	SNP	G	G	A	rs147455437	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:97969596G>A	ENST00000224337.5	-	9	885	c.744C>T	c.(742-744)gcC>gcT	p.A248A	BLNK_ENST00000371176.2_Silent_p.A225A|BLNK_ENST00000427367.2_Silent_p.A248A|BLNK_ENST00000413476.2_Silent_p.A248A	NM_013314.3	NP_037446.1	Q8WV28	BLNK_HUMAN	B-cell linker	248	Pro-rich.				B cell differentiation (GO:0030183)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.A248A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(2)|stomach(1)	14		Colorectal(252;0.083)		Epithelial(162;7.89e-08)|all cancers(201;2.27e-06)		GTACTTACCCGGCCCGTGGCA	0.552													G|||	5	0.000998403	0.0	0.0	5008	,	,		18754	0.0		0.0	False		,,,				2504	0.0051				p.A248A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C744T	10						.	G	,	0,4406		0,0,2203	148.0	144.0	145.0		675,744	-11.2	0.0	10	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	BLNK	NM_001114094.1,NM_013314.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	225/434,248/457	97969596	2,13004	2203	4300	6503	97959586	SO:0001819	synonymous_variant	29760	exon9			AF068180	CCDS7446.1, CCDS44464.1, CCDS58091.1, CCDS73171.1	10q23.2-q23.33	2014-09-17			ENSG00000095585	ENSG00000095585		"""SH2 domain containing"""	14211	protein-coding gene	gene with protein product	"""B-cell adapter containing a SH2 domain protein"", ""B-cell activation"", ""Src homology [SH2] domain-containing leukocyte protein of 65 kD"", ""B cell adaptor containing SH2 domain"""	604515				9697839, 10583958	Standard	NM_013314		Approved	SLP65, Ly57, SLP-65, BLNK-s, BASH, bca	uc001kls.4	Q8WV28	OTTHUMG00000018827	ENST00000224337.5:c.744C>T	10.37:g.97969596G>A		Somatic		Capture	Illumina HiSeq	Phase_I	97959586	NM_013314	O75498|O75499|Q2MD49	Silent	SNP	ENST00000224337.5	37	CCDS7446.1																																																																																				0.552	BLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049593.1	NM_013314	
MMS19	64210	broad.mit.edu	37	10	99220685	99220685	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:99220685C>A	ENST00000438925.2	-	24	2726	c.2391G>T	c.(2389-2391)caG>caT	p.Q797H	MMS19_ENST00000355839.6_Missense_Mutation_p.Q754H|MMS19_ENST00000370782.2_Missense_Mutation_p.Q797H|MMS19_ENST00000327238.10_Missense_Mutation_p.Q699H|MMS19_ENST00000327277.7_3'UTR	NM_022362.4	NP_071757.4	Q96T76	MMS19_HUMAN	MMS19 nucleotide excision repair homolog (S. cerevisiae)	797					cellular response to DNA damage stimulus (GO:0006974)|chromosome segregation (GO:0007059)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|iron-sulfur cluster assembly (GO:0016226)|nucleotide-excision repair (GO:0006289)|phosphorelay signal transduction system (GO:0000160)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|membrane (GO:0016020)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)	estrogen receptor binding (GO:0030331)|protein binding, bridging (GO:0030674)|receptor signaling complex scaffold activity (GO:0030159)|transcription coactivator activity (GO:0003713)	p.Q797H(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|stomach(1)	16		Colorectal(252;0.0846)		Epithelial(162;3.33e-10)|all cancers(201;2.74e-08)		GAGTGAAGGCCTGACTACGAC	0.502								Direct reversal of damage																													p.Q797H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2391T	10						.						37.0	36.0	36.0					10																	99220685		2202	4296	6498	99210675	SO:0001583	missense	64210	exon24			AF007151	CCDS7464.1, CCDS73177.1	10q24-q25	2007-08-15	2007-08-15	2007-08-15	ENSG00000155229	ENSG00000155229			13824	protein-coding gene	gene with protein product	"""MET18 homolog (S. cerevisiae)"""	614777		MMS19L		11071939	Standard	NM_022362		Approved	MET18, hMMS19	uc001kns.4	Q96T76	OTTHUMG00000018857	ENST00000438925.2:c.2391G>T	10.37:g.99220685C>A	ENSP00000412698:p.Gln797His	Somatic		Capture	Illumina HiSeq	Phase_I	99210675	NM_022362	B0QZ75|B3KPE5|B4DQX2|B4E2I3|D3DR55|F8W9Y2|Q17RZ8|Q5T455|Q66K82|Q7L4W8|Q969Z1|Q96DF1|Q96MR1|Q96RK5|Q96SK1|Q9BUE2|Q9BYS9	Missense_Mutation	SNP	ENST00000438925.2	37	CCDS7464.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.44|19.44	3.827874|3.827874	0.71143|0.71143	.|.	.|.	ENSG00000155229|ENSG00000155229	ENST00000438925;ENST00000370782;ENST00000327238;ENST00000422291;ENST00000355839|ENST00000434538	T;T;T;T|.	0.32988|.	1.43;1.43;1.43;1.43|.	5.66|5.66	4.76|4.76	0.60689|0.60689	Armadillo-type fold (1);|.	0.233048|.	0.45361|.	D|.	0.000371|.	T|T	0.71082|0.71082	0.3298|0.3298	M|M	0.65975|0.65975	2.015|2.015	0.80722|0.80722	D|D	1|1	D;D;D;P;D|.	0.76494|.	0.997;0.998;0.999;0.456;0.997|.	P;D;D;B;P|.	0.71870|.	0.907;0.946;0.975;0.219;0.907|.	T|T	0.70695|0.70695	-0.4801|-0.4801	10|5	0.33940|.	T|.	0.23|.	.|.	14.1752|14.1752	0.65537|0.65537	0.0:0.9272:0.0:0.0728|0.0:0.9272:0.0:0.0728	.|.	818;699;754;797;754|.	B4DQX2;Q96T76-5;F8W9Y2;Q96T76;B4E2I3|.	.;.;.;MMS19_HUMAN;.|.	H|M	797;797;699;776;754|372	ENSP00000412698:Q797H;ENSP00000359818:Q797H;ENSP00000320059:Q699H;ENSP00000348097:Q754H|.	ENSP00000320059:Q699H|.	Q|R	-|-	3|2	2|0	MMS19|MMS19	99210675|99210675	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.881000|0.881000	0.50899|0.50899	2.148000|2.148000	0.42235|0.42235	1.399000|1.399000	0.46721|0.46721	-0.350000|-0.350000	0.07774|0.07774	CAG|AGG		0.502	MMS19-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049706.2		
TAF5	6877	broad.mit.edu	37	10	105139368	105139368	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:105139368delT	ENST00000369839.3	+	4	1140	c.1117delT	c.(1117-1119)tttfs	p.F374fs	TAF5_ENST00000351396.4_Frame_Shift_Del_p.F374fs	NM_006951.3	NP_008882.2	Q15542	TAF5_HUMAN	TAF5 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 100kDa	374					chromatin modification (GO:0016568)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	protein dimerization activity (GO:0046983)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.F374fs*4(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)	15		Colorectal(252;0.0747)|Breast(234;0.128)		Epithelial(162;1.83e-09)|all cancers(201;1.4e-08)|BRCA - Breast invasive adenocarcinoma(275;0.198)		CTTGTAGGTATTTTTTGGTTT	0.289																																					p.F373fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1117delT	10						.						39.0	39.0	39.0					10																	105139368		2201	4297	6498	105129358	SO:0001589	frameshift_variant	6877	exon4			X95525	CCDS7547.1	10q24-q25.2	2013-01-10	2002-08-29	2001-12-07	ENSG00000148835	ENSG00000148835		"""WD repeat domain containing"""	11539	protein-coding gene	gene with protein product		601787	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, D, 100kD"""	TAF2D		8884287, 8942982	Standard	NM_006951		Approved	TAFII100	uc001kwv.3	Q15542	OTTHUMG00000018985	ENST00000369839.3:c.1117delT	10.37:g.105139368delT	ENSP00000358854:p.Phe374fs	Somatic		Capture	Illumina HiSeq	Phase_I	105129358	NM_006951	A8K5B4|B2RMR0|B7ZKJ6|Q53EM4|Q5SYD5|Q86UZ7|Q9Y4K5	Frame_Shift_Del	DEL	ENST00000369839.3	37	CCDS7547.1																																																																																				0.289	TAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050144.1		
MKI67	4288	broad.mit.edu	37	10	129913839	129913839	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr10:129913839T>C	ENST00000368654.3	-	7	1208	c.833A>G	c.(832-834)gAt>gGt	p.D278G	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	278					cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)	p.D278G(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				CTGTAAACCATCAGCACTTTC	0.443																																					p.D278G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A833G	10						.						91.0	95.0	93.0					10																	129913839		2203	4300	6503	129803829	SO:0001583	missense	4288	exon7			X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.833A>G	10.37:g.129913839T>C	ENSP00000357643:p.Asp278Gly	Somatic		Capture	Illumina HiSeq	Phase_I	129803829	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	0.083	-1.179715	0.01633	.	.	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.23552	1.9	2.98	-1.88	0.07713	.	0.733493	0.11682	N	0.539753	T	0.12050	0.0293	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21109	-1.0255	10	0.87932	D	0	.	8.379	0.32459	0.0:0.4152:0.0:0.5848	.	278	P46013	KI67_HUMAN	G	278	ENSP00000357643:D278G	ENSP00000357643:D278G	D	-	2	0	MKI67	129803829	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.336000	0.02660	-0.801000	0.04427	-1.139000	0.01908	GAT		0.443	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
OR8I2	120586	broad.mit.edu	37	11	55861307	55861308	+	Frame_Shift_Ins	INS	-	-	T	rs201548817|rs112181516|rs144690814	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:55861307_55861308insT	ENST00000302124.2	+	1	555_556	c.524_525insT	c.(523-528)cattttfs	p.HF175fs		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H175fs*10(1)|p.C178fs*2(1)		NS(1)|breast(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(24)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	53	Esophageal squamous(21;0.00693)					AGCATCAATCATTTTTTTTGTG	0.441																																					p.H175fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	ovary(1)|large_intestine(1)	c.524_525insT	11						.			0,4264		0,0,2132						3.2	1.0		dbSNP_132	145	1,8253		0,1,4126	no	frameshift	OR8I2	NM_001003750.1		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				55617884	SO:0001589	frameshift_variant	120586	exon1			AB065656	CCDS31517.1	11q11	2012-08-09			ENSG00000172154	ENSG00000172154		"""GPCR / Class A : Olfactory receptors"""	15310	protein-coding gene	gene with protein product							Standard	NM_001003750		Approved		uc010rix.2	Q8N0Y5	OTTHUMG00000166831	ENST00000302124.2:c.532dupT	11.37:g.55861315_55861315dupT	ENSP00000303864:p.His175fs	Somatic		Capture	Illumina HiSeq	Phase_I	55617883	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Frame_Shift_Ins	INS	ENST00000302124.2	37	CCDS31517.1																																																																																				0.441	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750	
MUC6	4588	broad.mit.edu	37	11	1019473	1019473	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:1019473C>T	ENST00000421673.2	-	30	3882	c.3832G>A	c.(3832-3834)Gtc>Atc	p.V1278I		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1278	Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.V1278I(1)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGTGGGGTGACGGCCGTGGTT	0.642																																					p.V1278I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3832A	11						.						138.0	159.0	152.0					11																	1019473		2139	4235	6374	1009473	SO:0001583	missense	4588	exon30			U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.3832G>A	11.37:g.1019473C>T	ENSP00000406861:p.Val1278Ile	Somatic		Capture	Illumina HiSeq	Phase_I	1009473	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	1.297	-0.605861	0.03717	.	.	ENSG00000184956	ENST00000421673	T	0.19532	2.14	2.64	-5.27	0.02763	.	.	.	.	.	T	0.06600	0.0169	N	0.01874	-0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44605	-0.9317	9	0.13470	T	0.59	.	11.4029	0.49880	0.0:0.2128:0.0:0.7872	.	1278	Q6W4X9	MUC6_HUMAN	I	1278	ENSP00000406861:V1278I	ENSP00000406861:V1278I	V	-	1	0	MUC6	1009473	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-2.777000	0.00775	-1.685000	0.01441	-0.680000	0.03767	GTC		0.642	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ANGPTL5	253935	broad.mit.edu	37	11	101762169	101762169	+	Missense_Mutation	SNP	G	G	C	rs139900371	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:101762169G>C	ENST00000334289.3	-	9	1603	c.1008C>G	c.(1006-1008)aaC>aaG	p.N336K		NM_178127.4	NP_835228.2	Q86XS5	ANGL5_HUMAN	angiopoietin-like 5	336	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.					extracellular region (GO:0005576)		p.N336K(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(2)|skin(3)	29		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.043)		BRCA - Breast invasive adenocarcinoma(274;0.0328)		GACCACACTCGTTAAACCACC	0.478																																					p.N336K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1008G	11						.						184.0	176.0	178.0					11																	101762169		2203	4299	6502	101267379	SO:0001583	missense	253935	exon9			BC049170	CCDS8312.1	11q22.2	2013-02-06				ENSG00000187151		"""Fibrinogen C domain containing"""	19705	protein-coding gene	gene with protein product		607666				12624729	Standard	NM_178127		Approved		uc001pgl.3	Q86XS5		ENST00000334289.3:c.1008C>G	11.37:g.101762169G>C	ENSP00000335255:p.Asn336Lys	Somatic		Capture	Illumina HiSeq	Phase_I	101267379	NM_178127	A8K658|Q86VR9	Missense_Mutation	SNP	ENST00000334289.3	37	CCDS8312.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.122374	0.56613	.	.	ENSG00000187151	ENST00000334289	D	0.81739	-1.53	5.26	3.01	0.34805	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);Fibrinogen, conserved site (1);	0.273891	0.45867	D	0.000335	T	0.77968	0.4210	L	0.44542	1.39	0.43588	D	0.99593	P	0.38395	0.629	P	0.45310	0.476	T	0.77996	-0.2377	10	0.51188	T	0.08	.	11.6912	0.51516	0.2165:0.0:0.7835:0.0	.	336	Q86XS5	ANGL5_HUMAN	K	336	ENSP00000335255:N336K	ENSP00000335255:N336K	N	-	3	2	ANGPTL5	101267379	0.923000	0.31300	0.365000	0.25901	0.827000	0.46813	1.162000	0.31786	1.209000	0.43321	0.655000	0.94253	AAC		0.478	ANGPTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394138.1	NM_178127	
MRVI1	10335	broad.mit.edu	37	11	10651174	10651174	+	Missense_Mutation	SNP	G	G	A	rs375197703		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:10651174G>A	ENST00000436272.1	-	4	536	c.458C>T	c.(457-459)gCg>gTg	p.A153V	MRVI1_ENST00000532037.1_5'Flank|MRVI1_ENST00000531107.1_Missense_Mutation_p.A153V|MRVI1_ENST00000552103.1_Missense_Mutation_p.A71V|MRVI1_ENST00000545852.1_5'UTR|MRVI1_ENST00000421747.1_Missense_Mutation_p.A153V|MRVI1_ENST00000541483.1_Missense_Mutation_p.A162V|MRVI1_ENST00000547195.1_Missense_Mutation_p.A71V|MRVI1_ENST00000423302.2_Missense_Mutation_p.A162V|MRVI1_ENST00000534266.2_5'UTR|MRVI1_ENST00000424001.1_5'UTR|MRVI1_ENST00000558540.1_5'UTR|MRVI1_ENST00000527509.2_Missense_Mutation_p.A71V			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	153	Interaction with PRKG1. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|relaxation of vascular smooth muscle (GO:0060087)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)		p.A153V(1)		central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)	22				all cancers(16;2.68e-07)|Epithelial(150;3.04e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0723)		TTCCAGCAGCGCCAGGTTTTT	0.592																																					p.A71V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C212T	11						.	G	VAL/ALA,VAL/ALA,,VAL/ALA,,VAL/ALA	0,4130		0,0,2065	78.0	84.0	82.0		458,212,,485,,485	4.6	1.0	11		82	1,8381		0,1,4190	no	missense,missense,utr-5,missense,utr-5,missense	MRVI1	NM_001098579.2,NM_001100163.2,NM_001100167.2,NM_001206880.1,NM_001206881.1,NM_130385.3	64,64,,64,,64	0,1,6255	AA,AG,GG		0.0119,0.0,0.0080	possibly-damaging,possibly-damaging,,possibly-damaging,,possibly-damaging	153/905,71/822,,162/707,,162/913	10651174	1,12511	2065	4191	6256	10607750	SO:0001583	missense	10335	exon5			AF081249	CCDS44538.1, CCDS44539.1, CCDS44540.1, CCDS44538.2, CCDS55745.1, CCDS55746.1	11p15.4	2014-09-11			ENSG00000072952	ENSG00000072952			7237	protein-coding gene	gene with protein product	"""inositol 1,4,5-triphosphate-associated cGMP kinase substrate"", ""IP3R-associated cGMP kinase substrate"""	604673				10321731	Standard	NM_001098579		Approved	JAW1L, IRAG	uc010rcb.1	Q9Y6F6	OTTHUMG00000165773	ENST00000436272.1:c.458C>T	11.37:g.10651174G>A	ENSP00000412229:p.Ala153Val	Somatic		Capture	Illumina HiSeq	Phase_I	10607750	NM_001100163	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Missense_Mutation	SNP	ENST00000436272.1	37		.	.	.	.	.	.	.	.	.	.	G	21.4	4.150458	0.78001	0.0	1.19E-4	ENSG00000072952	ENST00000421747;ENST00000308763;ENST00000436272;ENST00000547195;ENST00000552103;ENST00000423302;ENST00000541483;ENST00000531107;ENST00000527509	T;T;T;T;T;T;T;T	0.15834	3.01;3.01;2.45;2.45;2.83;2.39;3.01;2.45	5.62	4.64	0.57946	.	0.062221	0.64402	D	0.000007	T	0.19525	0.0469	L	0.51422	1.61	0.80722	D	1	D;P;P;D	0.56035	0.974;0.955;0.955;0.974	P;B;B;P	0.45310	0.476;0.284;0.284;0.476	T	0.00496	-1.1705	10	0.54805	T	0.06	-13.4555	11.2074	0.48778	0.0:0.0:0.597:0.403	.	162;153;153;153	F5H6A1;Q9Y6F6;E9PQY6;Q9Y6F6-4	.;MRVI1_HUMAN;.;.	V	153;154;153;71;71;162;162;153;71	ENSP00000414598:A153V;ENSP00000412229:A153V;ENSP00000448278:A71V;ENSP00000446764:A71V;ENSP00000412130:A162V;ENSP00000437784:A162V;ENSP00000432436:A153V;ENSP00000432067:A71V	ENSP00000307885:A154V	A	-	2	0	MRVI1	10607750	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.390000	0.73204	2.644000	0.89710	0.561000	0.74099	GCG		0.592	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579	
EIF4G2	1982	broad.mit.edu	37	11	10821282	10821282	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:10821282C>T	ENST00000526148.1	-	19	2651	c.2141G>A	c.(2140-2142)cGc>cAc	p.R714H	EIF4G2_ENST00000339995.5_Missense_Mutation_p.R714H|EIF4G2_ENST00000396525.2_Missense_Mutation_p.R676H|SNORD97_ENST00000459187.1_RNA|EIF4G2_ENST00000525681.1_Missense_Mutation_p.R714H|RP11-685M7.5_ENST00000532365.1_RNA	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2									p.R714H(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		CTCCAACATGCGGTCCTTATT	0.418																																					p.R714H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2141A	11						.						103.0	99.0	100.0					11																	10821282		2201	4294	6495	10777858	SO:0001583	missense	1982	exon19			U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2141G>A	11.37:g.10821282C>T	ENSP00000433664:p.Arg714His	Somatic		Capture	Illumina HiSeq	Phase_I	10777858	NM_001418		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.270710	0.80469	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000379653	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	5.71	5.71	0.89125	Armadillo-type fold (1);	0.107006	0.64402	D	0.000005	T	0.58293	0.2112	M	0.62266	1.93	0.47308	D	0.999387	D;D	0.89917	0.999;1.0	P;P	0.55508	0.665;0.777	T	0.57700	-0.7766	9	0.52906	T	0.07	-4.1326	19.8493	0.96733	0.0:1.0:0.0:0.0	.	714;787	P78344;B4DZF2	IF4G2_HUMAN;.	H	714;714;714;676;787;96	ENSP00000433664:R714H;ENSP00000433371:R714H;ENSP00000340281:R714H;ENSP00000379778:R676H	ENSP00000340281:R714H	R	-	2	0	EIF4G2	10777858	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.022000	0.70839	2.701000	0.92244	0.563000	0.77884	CGC		0.418	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
BIRC2	329	broad.mit.edu	37	11	102221659	102221659	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:102221659C>T	ENST00000227758.2	+	3	2379	c.980C>T	c.(979-981)gCc>gTc	p.A327V	BIRC2_ENST00000532672.1_Missense_Mutation_p.A306V|BIRC2_ENST00000527910.1_3'UTR|BIRC2_ENST00000530675.1_Missense_Mutation_p.A278V	NM_001166.4|NM_001256163.1	NP_001157.1|NP_001243092.1	Q13490	BIRC2_HUMAN	baculoviral IAP repeat containing 2	327					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein K48-linked ubiquitination (GO:1902524)|positive regulation of protein K63-linked ubiquitination (GO:1902523)|positive regulation of protein monoubiquitination (GO:1902527)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cell cycle (GO:0051726)|regulation of cell differentiation (GO:0045595)|regulation of cell proliferation (GO:0042127)|regulation of cysteine-type endopeptidase activity (GO:2000116)|regulation of inflammatory response (GO:0050727)|regulation of innate immune response (GO:0045088)|regulation of necroptotic process (GO:0060544)|regulation of nucleotide-binding oligomerization domain containing signaling pathway (GO:0070424)|regulation of RIG-I signaling pathway (GO:0039535)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription, DNA-templated (GO:0006355)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|protein N-terminus binding (GO:0047485)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A327V(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|liver(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(8;0.00044)|all_epithelial(12;0.00348)|Lung NSC(15;0.227)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0093)	Lung(13;0.109)|Epithelial(9;0.11)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0144)		GTAGAACATGCCAAGTGGTTT	0.378																																					p.A327V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C980T	11						.						301.0	283.0	289.0					11																	102221659		2203	4299	6502	101726869	SO:0001583	missense	329	exon3			L49431	CCDS8316.1, CCDS58169.1	11q22	2011-01-25	2011-01-25		ENSG00000110330	ENSG00000110330		"""Baculoviral IAP repeat containing"", ""RING-type (C3HC4) zinc fingers"""	590	protein-coding gene	gene with protein product	"""NFR2-TRAF signalling complex protein"", ""apoptosis inhibitor 1"""	601712	"""baculoviral IAP repeat-containing 2"""	API1		8552191, 8548810	Standard	NM_001166		Approved	cIAP1, hiap-2, MIHB, RNF48, c-IAP1	uc010ruq.3	Q13490	OTTHUMG00000167325	ENST00000227758.2:c.980C>T	11.37:g.102221659C>T	ENSP00000227758:p.Ala327Val	Somatic		Capture	Illumina HiSeq	Phase_I	101726869	NM_001166	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092617	0.94149	.	.	ENSG00000110330	ENST00000530675;ENST00000227758;ENST00000541741;ENST00000532672	T;T;T	0.72725	-0.68;-0.68;-0.68	5.86	5.86	0.93980	Baculoviral inhibition of apoptosis protein repeat (5);	0.000000	0.85682	D	0.000000	D	0.87257	0.6132	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88331	0.2968	10	0.87932	D	0	-26.5225	20.2019	0.98263	0.0:1.0:0.0:0.0	.	327	Q13490	BIRC2_HUMAN	V	278;327;327;306	ENSP00000431723:A278V;ENSP00000227758:A327V;ENSP00000434979:A306V	ENSP00000227758:A327V	A	+	2	0	BIRC2	101726869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.776000	0.95493	0.655000	0.94253	GCC		0.378	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166	
TTC12	54970	broad.mit.edu	37	11	113200680	113200680	+	Silent	SNP	G	G	T	rs147993824		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:113200680G>T	ENST00000529221.1	+	7	588	c.483G>T	c.(481-483)gtG>gtT	p.V161V	TTC12_ENST00000393020.1_Silent_p.V161V|TTC12_ENST00000483239.2_Silent_p.V161V|TTC12_ENST00000314756.3_Silent_p.V161V	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	161								p.V161V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		AGGCACTGGTGGATTGTGAGT	0.438																																					p.V161V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G483T	11						.						228.0	216.0	220.0					11																	113200680		2201	4296	6497	112705890	SO:0001819	synonymous_variant	54970	exon7			AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.483G>T	11.37:g.113200680G>T		Somatic		Capture	Illumina HiSeq	Phase_I	112705890	NM_017868	Q8N5H9|Q9NWY3	Silent	SNP	ENST00000529221.1	37	CCDS8360.2																																																																																				0.438	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
ANKK1	255239	broad.mit.edu	37	11	113266109	113266109	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:113266109A>G	ENST00000303941.3	+	4	755	c.661A>G	c.(661-663)Act>Gct	p.T221A		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	221	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.T221A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(14)|ovary(1)|stomach(1)	29		all_cancers(61;1.53e-11)|all_epithelial(67;3e-06)|Melanoma(852;4.04e-05)|all_hematologic(158;0.000315)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0461)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)|Prostate(24;0.194)		BRCA - Breast invasive adenocarcinoma(274;4.82e-06)|Epithelial(105;5.41e-05)|all cancers(92;0.000442)|OV - Ovarian serous cystadenocarcinoma(223;0.238)		GGAGCTACTCACTCAGAAGAA	0.567																																					p.T221A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A661G	11						.						61.0	64.0	63.0					11																	113266109		1951	4135	6086	112771319	SO:0001583	missense	255239	exon4			AJ541797	CCDS44734.1	11q23.2	2013-01-10			ENSG00000170209	ENSG00000170209		"""Ankyrin repeat domain containing"""	21027	protein-coding gene	gene with protein product		608774				15146457	Standard	NM_178510		Approved	X-kinase	uc001pny.3	Q8NFD2	OTTHUMG00000167715	ENST00000303941.3:c.661A>G	11.37:g.113266109A>G	ENSP00000306678:p.Thr221Ala	Somatic		Capture	Illumina HiSeq	Phase_I	112771319	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141180	0.56936	.	.	ENSG00000170209	ENST00000303941	T	0.38887	1.11	4.38	4.38	0.52667	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.249770	0.26907	U	0.021893	T	0.30696	0.0773	L	0.28192	0.835	0.40050	D	0.975764	P	0.38504	0.634	B	0.42163	0.378	T	0.08106	-1.0738	10	0.26408	T	0.33	-18.8361	7.7601	0.28946	0.9059:0.0:0.0941:0.0	.	221	Q8NFD2	ANKK1_HUMAN	A	221	ENSP00000306678:T221A	ENSP00000306678:T221A	T	+	1	0	ANKK1	112771319	0.996000	0.38824	1.000000	0.80357	0.846000	0.48090	3.125000	0.50469	1.823000	0.53134	0.374000	0.22700	ACT		0.567	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510	
NXPE4	54827	broad.mit.edu	37	11	114450890	114450890	+	Missense_Mutation	SNP	G	G	A	rs201579260		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:114450890G>A	ENST00000375478.3	-	5	1243	c.1063C>T	c.(1063-1065)Cgc>Tgc	p.R355C	NXPE4_ENST00000424261.2_Missense_Mutation_p.R71C	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	355						extracellular vesicular exosome (GO:0070062)		p.R355C(1)									ATCCACTGGCGGATCGTGGAA	0.423																																					p.R71C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C211T	11						.						198.0	189.0	191.0					11																	114450890		1862	4113	5975	113956100	SO:0001583	missense	54827	exon5			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.1063C>T	11.37:g.114450890G>A	ENSP00000364627:p.Arg355Cys	Somatic		Capture	Illumina HiSeq	Phase_I	113956100	NM_017678	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083386	0.55861	.	.	ENSG00000137634	ENST00000424261;ENST00000375478	T;T	0.57107	0.42;1.66	5.11	3.21	0.36854	.	0.205226	0.34002	N	0.004343	T	0.75110	0.3805	M	0.92507	3.315	0.49130	D	0.999755	D	0.89917	1.0	D	0.76575	0.988	T	0.76642	-0.2884	10	0.62326	D	0.03	.	9.0842	0.36570	0.083:0.148:0.7689:0.0	.	355	Q6UWF7	FA55D_HUMAN	C	71;355	ENSP00000401503:R71C;ENSP00000364627:R355C	ENSP00000364627:R355C	R	-	1	0	FAM55D	113956100	0.676000	0.27567	0.834000	0.33040	0.626000	0.37791	0.858000	0.27845	0.642000	0.30620	-0.176000	0.13171	CGC		0.423	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
NXPE4	54827	broad.mit.edu	37	11	114453599	114453599	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:114453599G>T	ENST00000375478.3	-	3	421	c.241C>A	c.(241-243)Cag>Aag	p.Q81K	NXPE4_ENST00000424261.2_5'UTR	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	81						extracellular vesicular exosome (GO:0070062)		p.Q81K(1)									GGGATCTGCTGATCTAGTTTC	0.478																																					p.Q81K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C241A	11						.						318.0	310.0	312.0					11																	114453599		2097	4217	6314	113958809	SO:0001583	missense	54827	exon3			AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.241C>A	11.37:g.114453599G>T	ENSP00000364627:p.Gln81Lys	Somatic		Capture	Illumina HiSeq	Phase_I	113958809	NM_001077639	Q6QDB4|Q9NXP5	Missense_Mutation	SNP	ENST00000375478.3	37	CCDS41718.1	.	.	.	.	.	.	.	.	.	.	G	4.149	0.026007	0.08054	.	.	ENSG00000137634	ENST00000375478	T	0.10668	2.85	4.86	3.93	0.45458	.	0.271754	0.26650	N	0.023202	T	0.09024	0.0223	L	0.48642	1.525	0.22728	N	0.998803	B	0.14805	0.011	B	0.20384	0.029	T	0.40251	-0.9573	10	0.05525	T	0.97	.	10.7842	0.46395	0.0:0.0:0.6584:0.3416	.	81	Q6UWF7	FA55D_HUMAN	K	81	ENSP00000364627:Q81K	ENSP00000364627:Q81K	Q	-	1	0	FAM55D	113958809	0.152000	0.22762	0.899000	0.35326	0.273000	0.26683	0.251000	0.18257	1.127000	0.42034	0.585000	0.79938	CAG		0.478	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
SIK3	23387	broad.mit.edu	37	11	116746118	116746118	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:116746118A>G	ENST00000292055.4	-	10	1150	c.1115T>C	c.(1114-1116)cTg>cCg	p.L372P	SIK3_ENST00000375300.1_Missense_Mutation_p.L430P|SIK3_ENST00000375288.1_5'UTR|SIK3_ENST00000542607.1_Missense_Mutation_p.L324P|SIK3_ENST00000446921.2_Missense_Mutation_p.L382P|SIK3_ENST00000434315.2_Missense_Mutation_p.L271P	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	372					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.L430P(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	57						TGGGTTGATCAGCTGCACCTG	0.488																																					p.L372P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1115C	11						.						131.0	106.0	114.0					11																	116746118		2201	4296	6497	116251328	SO:0001583	missense	23387	exon10			AB023216	CCDS8379.1, CCDS60974.1, CCDS8379.2	11q23.3	2010-02-17			ENSG00000160584	ENSG00000160584			29165	protein-coding gene	gene with protein product		614776				10231032, 8889548	Standard	NM_025164		Approved	FLJ12240, L19, KIAA0999, QSK	uc001ppy.3	Q9Y2K2	OTTHUMG00000066628	ENST00000292055.4:c.1115T>C	11.37:g.116746118A>G	ENSP00000292055:p.Leu372Pro	Somatic		Capture	Illumina HiSeq	Phase_I	116251328	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.861952	0.71949	.	.	ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000542607;ENST00000434315	T;T;T;T	0.73469	-0.69;-0.72;-0.75;-0.31	5.59	4.44	0.53790	Protein kinase-like domain (1);	0.000000	0.34460	U	0.003943	D	0.84492	0.5484	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.994;0.994	D	0.84694	0.0724	10	0.56958	D	0.05	.	11.9945	0.53194	0.8702:0.0:0.0:0.1298	.	324;271;372	A1A5A8;A1A5A9;Q9Y2K2	.;.;SIK3_HUMAN	P	430;372;324;271	ENSP00000364449:L430P;ENSP00000292055:L372P;ENSP00000438108:L324P;ENSP00000415873:L271P	ENSP00000292055:L372P	L	-	2	0	SIK3	116251328	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	6.529000	0.73812	0.915000	0.36847	0.528000	0.53228	CTG		0.488	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164	
DSCAML1	57453	broad.mit.edu	37	11	117307884	117307884	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:117307884G>T	ENST00000321322.6	-	26	4855	c.4854C>A	c.(4852-4854)ggC>ggA	p.G1618G	DSCAML1_ENST00000527706.1_Silent_p.G1348G	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1558					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.G1618G(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		CATTGCCGCAGCCCGCACTGT	0.637																																					p.G1618G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4854A	11						.						91.0	84.0	87.0					11																	117307884		2201	4296	6497	116813094	SO:0001819	synonymous_variant	57453	exon26				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.4854C>A	11.37:g.117307884G>T		Somatic		Capture	Illumina HiSeq	Phase_I	116813094	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																				0.637	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
PHLDB1	23187	broad.mit.edu	37	11	118498200	118498200	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:118498200C>T	ENST00000361417.2	+	7	1072	c.661C>T	c.(661-663)Cca>Tca	p.P221S	PHLDB1_ENST00000356063.5_Missense_Mutation_p.P221S	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	221								p.P221S(1)		breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		CGCAACCTCTCCACTGTCACC	0.597																																					p.P221S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C661T	11						.						77.0	76.0	77.0					11																	118498200		2200	4295	6495	118003410	SO:0001583	missense	23187	exon6				CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.661C>T	11.37:g.118498200C>T	ENSP00000354498:p.Pro221Ser	Somatic		Capture	Illumina HiSeq	Phase_I	118003410	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.379647	0.61845	.	.	ENSG00000019144	ENST00000361417;ENST00000543207;ENST00000545313;ENST00000356063	T;T	0.31769	1.49;1.48	5.66	4.74	0.60224	.	0.181996	0.49916	D	0.000123	T	0.34600	0.0903	L	0.53249	1.67	0.80722	D	1	B;P;P;P	0.46064	0.069;0.48;0.872;0.798	B;B;P;B	0.48454	0.082;0.299;0.578;0.374	T	0.15178	-1.0446	10	0.05959	T	0.93	-10.1363	15.6087	0.76696	0.1389:0.8611:0.0:0.0	.	220;221;221;221	B4DIX4;Q86UU1-3;Q86UU1-2;Q86UU1	.;.;.;PHLB1_HUMAN	S	221;220;221;221	ENSP00000354498:P221S;ENSP00000348359:P221S	ENSP00000348359:P221S	P	+	1	0	PHLDB1	118003410	0.973000	0.33851	0.850000	0.33497	0.962000	0.63368	3.671000	0.54576	1.360000	0.45960	0.563000	0.77884	CCA		0.597	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
DDX6	1656	broad.mit.edu	37	11	118656864	118656864	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:118656864C>A	ENST00000526070.2	-	2	457	c.97G>T	c.(97-99)Gga>Tga	p.G33*	DDX6_ENST00000264018.4_Nonsense_Mutation_p.G33*|DDX6_ENST00000534980.1_Nonsense_Mutation_p.G33*	NM_001257191.1	NP_001244120.1	P26196	DDX6_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 6	33					cytoplasmic mRNA processing body assembly (GO:0033962)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)	p.G22*(1)		NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)	13	all_hematologic(175;0.0839)	Renal(330;0.0183)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)|Hepatocellular(160;0.0893)|Breast(348;0.0979)|all_hematologic(192;0.103)		OV - Ovarian serous cystadenocarcinoma(223;3.39e-06)|BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Colorectal(284;0.0377)		GTGCCCCCTCCTCCAGGGCCA	0.517			T	IGH@	B-NHL																																p.G33X			Dom	yes		11	11q23.3	1656	DEAD (Asp-Glu-Ala-Asp) box polypeptide 6		L	.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G97T	11						.						107.0	106.0	106.0					11																	118656864		1941	4141	6082	118162074	SO:0001587	stop_gained	1656	exon2			D17532	CCDS44751.1	11q23.3	2012-02-23	2012-02-23		ENSG00000110367	ENSG00000110367		"""DEAD-boxes"""	2747	protein-coding gene	gene with protein product		600326	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6 (RNA helicase, 54kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 6"""	HLR2		1579499, 11839790	Standard	NM_004397		Approved	RCK	uc001pub.2	P26196	OTTHUMG00000166411	ENST00000526070.2:c.97G>T	11.37:g.118656864C>A	ENSP00000433704:p.Gly33*	Somatic		Capture	Illumina HiSeq	Phase_I	118162074	NM_004397	Q5D048	Nonsense_Mutation	SNP	ENST00000526070.2	37	CCDS44751.1	.	.	.	.	.	.	.	.	.	.	C	38	6.883059	0.97908	.	.	ENSG00000110367	ENST00000264018;ENST00000545741;ENST00000534980;ENST00000526070	.	.	.	5.26	5.26	0.73747	.	0.050524	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.6556	0.91452	0.0:1.0:0.0:0.0	.	.	.	.	X	33	.	ENSP00000264018:G33X	G	-	1	0	DDX6	118162074	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.617000	0.67716	2.727000	0.93392	0.655000	0.94253	GGA		0.517	DDX6-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000389647.2	NM_004397	
VPS11	55823	broad.mit.edu	37	11	118949009	118949009	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:118949009C>T	ENST00000300793.6	+	12	1927	c.1885C>T	c.(1885-1887)Cga>Tga	p.R629*	VPS11_ENST00000527798.1_3'UTR	NM_021729.4	NP_068375.3	Q9H270	VPS11_HUMAN	vacuolar protein sorting 11 homolog (S. cerevisiae)	630					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	endocytic vesicle (GO:0030139)|endosome (GO:0005768)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)	p.R629*(1)		autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(2)	29	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.88e-05)		CCTTGAGCTGCGACTGCAGAA	0.567																																					p.C629C												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1887T	11						.						121.0	121.0	121.0					11																	118949009		2004	4175	6179	118454219	SO:0001587	stop_gained	55823	exon11			AB027508	CCDS73404.1	11q23	2008-02-05	2006-12-19			ENSG00000160695		"""RING-type (C3HC4) zinc fingers"""	14583	protein-coding gene	gene with protein product		608549	"""vacuolar protein sorting 11 (yeast homolog)"""				Standard	NM_021729		Approved	RNF108, PEP5	uc010ryx.2	Q9H270		ENST00000300793.6:c.1885C>T	11.37:g.118949009C>T	ENSP00000475301:p.Arg629*	Somatic		Capture	Illumina HiSeq	Phase_I	118454219	NM_021729	Q8WY89|Q96EP8|Q9H6D9|Q9HCS6	Nonsense_Mutation	SNP	ENST00000300793.6	37																																																																																					0.567	VPS11-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_021729	
HINFP	25988	broad.mit.edu	37	11	119003663	119003663	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:119003663G>A	ENST00000350777.2	+	8	1028	c.965G>A	c.(964-966)aGt>aAt	p.S322N	HINFP_ENST00000527410.1_Missense_Mutation_p.S322N	NM_001243259.1|NM_015517.4|NM_198971.2	NP_001230188.1|NP_056332.2|NP_945322.1	Q9BQA5	HINFP_HUMAN	histone H4 transcription factor	322					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|establishment of protein localization (GO:0045184)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|myoblast differentiation (GO:0045445)|negative regulation of gene expression (GO:0010629)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)	p.S322N(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23						TGCACCTTCAGTGCCCGATCC	0.532																																					p.S322N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G965A	11						.						112.0	106.0	108.0					11																	119003663		2200	4295	6495	118508873	SO:0001583	missense	25988	exon9			AL080201	CCDS8414.1, CCDS58188.1	11q23.3	2013-01-08	2009-01-22	2009-01-22	ENSG00000172273	ENSG00000172273		"""Zinc fingers, C2H2-type"""	17850	protein-coding gene	gene with protein product	"""histone nuclear factor P"""	607099	"""MBD2-interacting zinc finger 1"", ""MBD2-interacting zinc finger"""	MIZF		11553631	Standard	NM_015517		Approved	DKFZP434F162, HiNF-P, ZNF743	uc001pvq.3	Q9BQA5	OTTHUMG00000166168	ENST00000350777.2:c.965G>A	11.37:g.119003663G>A	ENSP00000318085:p.Ser322Asn	Somatic		Capture	Illumina HiSeq	Phase_I	118508873	NM_015517	B3KPH6|B4DWB4|E9PQF4|Q96E65|Q9Y4M7	Missense_Mutation	SNP	ENST00000350777.2	37	CCDS8414.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977106	0.34848	.	.	ENSG00000172273	ENST00000350777;ENST00000527410	T;T	0.01767	4.65;4.65	5.62	1.25	0.21368	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.379769	0.31542	N	0.007476	T	0.04182	0.0116	M	0.74546	2.27	0.22811	N	0.998701	P	0.43094	0.799	B	0.38378	0.272	T	0.28650	-1.0037	10	0.72032	D	0.01	-1.3833	20.934	0.99941	0.0:0.5442:0.4558:0.0	.	322	Q9BQA5	HINFP_HUMAN	N	322	ENSP00000318085:S322N;ENSP00000436815:S322N	ENSP00000318085:S322N	S	+	2	0	HINFP	118508873	0.528000	0.26314	0.174000	0.22961	0.751000	0.42716	1.051000	0.30417	0.029000	0.15352	-0.795000	0.03280	AGT		0.532	HINFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388201.2	NM_015517	
PVRL1	5818	broad.mit.edu	37	11	119535589	119535589	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:119535589G>A	ENST00000264025.3	-	6	1952	c.1422C>T	c.(1420-1422)gcC>gcT	p.A474A	PVRL1_ENST00000341398.2_Intron	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	474					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)	p.A474A(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		GACGGGCCTCGGCCTCATCCA	0.657																																					p.A474A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1422T	11						.						53.0	47.0	49.0					11																	119535589		2199	4295	6494	119040799	SO:0001819	synonymous_variant	5818	exon6			X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000264025.3:c.1422C>T	11.37:g.119535589G>A		Somatic		Capture	Illumina HiSeq	Phase_I	119040799	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Silent	SNP	ENST00000264025.3	37	CCDS8426.1																																																																																				0.657	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1		
GRIK4	2900	broad.mit.edu	37	11	120745871	120745871	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:120745871C>T	ENST00000527524.2	+	11	1370	c.1083C>T	c.(1081-1083)ggC>ggT	p.G361G	RP11-640N11.2_ENST00000505153.2_RNA|GRIK4_ENST00000438375.2_Silent_p.G361G	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	361					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)	p.G361G(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		GTCTTACCGGCCACATTGAAT	0.488																																					p.G361G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1083T	11						.						124.0	108.0	113.0					11																	120745871		2203	4299	6502	120251081	SO:0001819	synonymous_variant	2900	exon9			S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1083C>T	11.37:g.120745871C>T		Somatic		Capture	Illumina HiSeq	Phase_I	120251081	NM_014619	A8K9L1	Silent	SNP	ENST00000527524.2	37	CCDS8433.1																																																																																				0.488	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
MICAL2	9645	broad.mit.edu	37	11	12234942	12234942	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:12234942C>A	ENST00000256194.4	+	7	1120	c.832C>A	c.(832-834)Ctt>Att	p.L278I	MICAL2_ENST00000537344.1_Missense_Mutation_p.L278I|MICAL2_ENST00000342902.5_Missense_Mutation_p.L278I|MICAL2_ENST00000379612.3_Missense_Mutation_p.L278I|MICAL2_ENST00000527546.1_Missense_Mutation_p.L278I	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	278	Monooxygenase domain. {ECO:0000250}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.L278I(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		TTTTCAGGACCTTAAAGAAGA	0.463																																					p.L278I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C832A	11						.						119.0	135.0	130.0					11																	12234942		2201	4294	6495	12191518	SO:0001583	missense	9645	exon7			AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.832C>A	11.37:g.12234942C>A	ENSP00000256194:p.Leu278Ile	Somatic		Capture	Illumina HiSeq	Phase_I	12191518	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.160606	0.78226	.	.	ENSG00000133816	ENST00000537344;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.09350	2.99;2.99;2.99;2.99;2.99	4.98	4.06	0.47325	.	0.075345	0.51477	D	0.000097	T	0.41373	0.1156	M	0.91717	3.235	0.58432	D	0.999999	D;D;P;D;P	0.63880	0.993;0.98;0.717;0.989;0.588	D;D;P;D;P	0.78314	0.973;0.991;0.597;0.941;0.597	T	0.56329	-0.7997	10	0.87932	D	0	.	15.1507	0.72696	0.0:0.8579:0.142:0.0	.	278;278;278;278;278	G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;MICA2_HUMAN	I	278	ENSP00000441689:L278I;ENSP00000256194:L278I;ENSP00000433965:L278I;ENSP00000344894:L278I;ENSP00000368932:L278I	ENSP00000256194:L278I	L	+	1	0	MICAL2	12191518	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.930000	0.70104	1.305000	0.44909	0.563000	0.77884	CTT		0.463	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
MICAL2	9645	broad.mit.edu	37	11	12247855	12247855	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:12247855G>A	ENST00000256194.4	+	14	2114	c.1826G>A	c.(1825-1827)aGc>aAc	p.S609N	MICAL2_ENST00000537344.1_Missense_Mutation_p.S609N|MICAL2_ENST00000342902.5_Missense_Mutation_p.S609N|MICAL2_ENST00000379612.3_Missense_Mutation_p.S609N|MICAL2_ENST00000527546.1_Missense_Mutation_p.S609N	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	609	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)	p.S609N(1)		breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		GACAAGCTCAGCATGGTCATG	0.577																																					p.S609N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1826A	11						.						126.0	108.0	114.0					11																	12247855		2201	4294	6495	12204431	SO:0001583	missense	9645	exon14			AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.1826G>A	11.37:g.12247855G>A	ENSP00000256194:p.Ser609Asn	Somatic		Capture	Illumina HiSeq	Phase_I	12204431	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.381540	0.61845	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.28	4.37	0.52481	Calponin homology domain (5);	0.102841	0.64402	D	0.000005	D	0.82323	0.5012	H	0.94264	3.515	0.38988	D	0.959093	P;P;B;P;B;P	0.47253	0.721;0.643;0.331;0.663;0.196;0.892	P;P;B;P;B;P	0.61275	0.545;0.495;0.319;0.588;0.319;0.886	D	0.85764	0.1351	10	0.39692	T	0.17	.	13.3938	0.60838	0.0765:0.0:0.9235:0.0	.	142;609;609;609;609;609	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	N	609;142;609;609;609;609	ENSP00000441689:S609N;ENSP00000256194:S609N;ENSP00000433965:S609N;ENSP00000344894:S609N;ENSP00000368932:S609N	ENSP00000256194:S609N	S	+	2	0	MICAL2	12204431	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.245000	0.58734	1.224000	0.43551	0.563000	0.77884	AGC		0.577	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
TECTA	7007	broad.mit.edu	37	11	121016639	121016639	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:121016639C>A	ENST00000392793.1	+	12	4190	c.3919C>A	c.(3919-3921)Cag>Aag	p.Q1307K	TECTA_ENST00000264037.2_Missense_Mutation_p.Q1307K|TECTA_ENST00000478058.1_3'UTR			O75443	TECTA_HUMAN	tectorin alpha	1307	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.Q1307K(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GATCCCCAACCAGAACGCTGC	0.572																																					p.Q1307K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3919A	11						.						110.0	99.0	103.0					11																	121016639		2203	4299	6502	120521849	SO:0001583	missense	7007	exon11			AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.3919C>A	11.37:g.121016639C>A	ENSP00000376543:p.Gln1307Lys	Somatic		Capture	Illumina HiSeq	Phase_I	120521849	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	.	.	.	.	.	.	.	.	.	.	C	3.027	-0.200472	0.06219	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.75938	-0.98;-0.98	5.76	5.76	0.90799	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.136430	0.52532	D	0.000080	T	0.49779	0.1577	N	0.05259	-0.085	0.32492	N	0.540083	B	0.06786	0.001	B	0.06405	0.002	T	0.47573	-0.9107	10	0.02654	T	1	.	13.4213	0.60998	0.2744:0.7256:0.0:0.0	.	1307	O75443	TECTA_HUMAN	K	1307	ENSP00000376543:Q1307K;ENSP00000264037:Q1307K	ENSP00000264037:Q1307K	Q	+	1	0	TECTA	120521849	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	3.060000	0.49955	2.721000	0.93114	0.591000	0.81541	CAG		0.572	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
OR10G9	219870	broad.mit.edu	37	11	123893867	123893867	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:123893867G>A	ENST00000375024.1	+	1	148	c.148G>A	c.(148-150)Gat>Aat	p.D50N		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	50						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.D50N(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GATCAGGGTGGATTCTCACCT	0.552																																					p.D50N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G148A	11						.						66.0	63.0	64.0					11																	123893867		2200	4277	6477	123399077	SO:0001583	missense	219870	exon1			AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.148G>A	11.37:g.123893867G>A	ENSP00000364164:p.Asp50Asn	Somatic		Capture	Illumina HiSeq	Phase_I	123399077	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.803678	0.31869	.	.	ENSG00000236981	ENST00000375024	T	0.02837	4.14	3.33	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.420814	0.20192	N	0.097286	T	0.04318	0.0119	L	0.58810	1.83	0.09310	N	1	B	0.18461	0.028	B	0.24394	0.053	T	0.20773	-1.0265	10	0.51188	T	0.08	.	8.835	0.35107	0.1081:0.0:0.8919:0.0	.	50	Q8NGN4	O10G9_HUMAN	N	50	ENSP00000364164:D50N	ENSP00000364164:D50N	D	+	1	0	OR10G9	123399077	0.000000	0.05858	0.571000	0.28486	0.985000	0.73830	0.107000	0.15375	1.854000	0.53819	0.655000	0.94253	GAT		0.552	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
VWA5A	4013	broad.mit.edu	37	11	124012399	124012399	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:124012399C>T	ENST00000456829.2	+	16	2225	c.1974C>T	c.(1972-1974)gaC>gaT	p.D658D	VWA5A_ENST00000392748.1_Silent_p.D658D|VWA5A_ENST00000360334.4_Missense_Mutation_p.T420M	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	658								p.D658D(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						TCCAGATGGACGATTACAGTC	0.443																																					p.D658D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1974T	11						.						198.0	170.0	179.0					11																	124012399		2201	4299	6500	123517609	SO:0001819	synonymous_variant	4013	exon15			AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.1974C>T	11.37:g.124012399C>T		Somatic		Capture	Illumina HiSeq	Phase_I	123517609	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Silent	SNP	ENST00000456829.2	37	CCDS8444.1	.	.	.	.	.	.	.	.	.	.	C	3.006	-0.204913	0.06180	.	.	ENSG00000110002	ENST00000360334	T	0.25749	1.78	2.71	-2.05	0.07321	.	.	.	.	.	T	0.20618	0.0496	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32107	-0.9919	6	0.54805	T	0.06	2.859	3.9317	0.09288	0.0:0.1418:0.445:0.4132	.	.	.	.	M	420	ENSP00000353485:T420M	ENSP00000353485:T420M	T	+	2	0	VWA5A	123517609	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.645000	0.05409	-0.304000	0.08843	-0.657000	0.03884	ACG		0.443	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
PRDM10	56980	broad.mit.edu	37	11	129787027	129787027	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:129787027C>T	ENST00000360871.3	-	15	2551	c.2320G>A	c.(2320-2322)Gat>Aat	p.D774N	PRDM10_ENST00000528746.1_Missense_Mutation_p.D748N|PRDM10_ENST00000304538.6_Missense_Mutation_p.D688N|PRDM10_ENST00000526082.1_Missense_Mutation_p.D692N|PRDM10_ENST00000358825.5_Missense_Mutation_p.D778N|PRDM10_ENST00000423662.2_Missense_Mutation_p.D692N	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	778					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.D774N(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		TTTACCTTATCGCAATACTGA	0.378																																					p.D778N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2332A	11						.						174.0	157.0	163.0					11																	129787027		2201	4297	6498	129292237	SO:0001583	missense	56980	exon16			AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.2320G>A	11.37:g.129787027C>T	ENSP00000354118:p.Asp774Asn	Somatic		Capture	Illumina HiSeq	Phase_I	129292237	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	37	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780475	0.49891	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082;ENST00000533431	T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;2.8;1.6;2.8;1.6	5.52	4.61	0.57282	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	T	0.37517	0.1006	N	0.19112	0.55	0.54753	D	0.999983	D;D;D;D;D;D	0.69078	0.996;0.995;0.996;0.995;0.997;0.995	P;P;P;P;P;P	0.60117	0.869;0.794;0.869;0.794;0.689;0.794	T	0.35847	-0.9772	10	0.66056	D	0.02	-26.986	15.8563	0.78979	0.1366:0.8634:0.0:0.0	.	688;774;778;692;688;692	B7ZL72;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;PRD10_HUMAN;.;.;.	N	778;688;774;692;748;692;491	ENSP00000351686:D778N;ENSP00000302669:D688N;ENSP00000354118:D774N;ENSP00000398431:D692N;ENSP00000431262:D748N;ENSP00000432237:D692N;ENSP00000435940:D491N	ENSP00000302669:D688N	D	-	1	0	PRDM10	129292237	1.000000	0.71417	0.997000	0.53966	0.139000	0.21198	7.268000	0.78473	1.331000	0.45412	-0.152000	0.13540	GAT		0.378	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
IGSF9B	22997	broad.mit.edu	37	11	133791167	133791167	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:133791167G>A	ENST00000321016.8	-	18	2683	c.2453C>T	c.(2452-2454)tCg>tTg	p.S818L	IGSF9B_ENST00000533871.2_Missense_Mutation_p.S818L			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	818					homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.S274L(1)		breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CTTGTACAGCGACAGCTCCTT	0.652																																					p.S818L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2453T	11						.						53.0	54.0	53.0					11																	133791167		2146	4249	6395	133296377	SO:0001583	missense	22997	exon18			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.2453C>T	11.37:g.133791167G>A	ENSP00000317980:p.Ser818Leu	Somatic		Capture	Illumina HiSeq	Phase_I	133296377	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	23.5	4.429175	0.83776	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.68903	-0.03;-0.36	4.47	4.47	0.54385	.	0.000000	0.42682	D	0.000678	T	0.71995	0.3406	L	0.49350	1.555	0.54753	D	0.999984	D	0.69078	0.997	P	0.53649	0.731	T	0.76828	-0.2815	10	0.87932	D	0	.	16.9242	0.86172	0.0:0.0:1.0:0.0	.	818	Q9UPX0	TUTLB_HUMAN	L	818;660	ENSP00000317980:S818L;ENSP00000436552:S660L	ENSP00000317980:S818L	S	-	2	0	IGSF9B	133296377	1.000000	0.71417	0.953000	0.39169	0.980000	0.70556	7.386000	0.79775	2.320000	0.78422	0.561000	0.74099	TCG		0.652	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
IGSF9B	22997	broad.mit.edu	37	11	133816128	133816128	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:133816128G>A	ENST00000321016.8	-	2	320	c.90C>T	c.(88-90)ccC>ccT	p.P30P	IGSF9B_ENST00000533871.2_Silent_p.P30P			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	30	Ig-like 1.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.P30P(1)		breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		TCACAAACTCGGGCTCCTCTC	0.632																																					p.P30P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C90T	11						.																																			133321338	SO:0001819	synonymous_variant	22997	exon2			AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.90C>T	11.37:g.133816128G>A		Somatic		Capture	Illumina HiSeq	Phase_I	133321338	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																					0.632	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
NCAPD3	23310	broad.mit.edu	37	11	134073971	134073971	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:134073971G>T	ENST00000534548.2	-	10	1249	c.1185C>A	c.(1183-1185)gcC>gcA	p.A395A		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	395					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)	p.A395A(1)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TGTAAAGCCAGGCAATGAACA	0.428																																					p.A395A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1185A	11						.						98.0	92.0	94.0					11																	134073971		2201	4297	6498	133579181	SO:0001819	synonymous_variant	23310	exon10			AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1185C>A	11.37:g.134073971G>T		Somatic		Capture	Illumina HiSeq	Phase_I	133579181	NM_015261	A6NFS2|Q4KMQ9	Silent	SNP	ENST00000534548.2	37	CCDS31723.1																																																																																				0.428	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
KRTAP5-3	387266	broad.mit.edu	37	11	1629253	1629253	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:1629253G>A	ENST00000399685.1	-	1	440	c.363C>T	c.(361-363)tgC>tgT	p.C121C		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	121	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.C121C(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		CACAAGAACCGCAGCCCCCCT	0.647																																					p.C121C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C363T	11						.						73.0	94.0	87.0					11																	1629253		2199	4299	6498	1585829	SO:0001819	synonymous_variant	387266	exon1			AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.363C>T	11.37:g.1629253G>A		Somatic		Capture	Illumina HiSeq	Phase_I	1585829	NM_001012708	Q6PL44|Q701N3	Silent	SNP	ENST00000399685.1	37	CCDS41591.1																																																																																				0.647	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1		
LSP1	4046	broad.mit.edu	37	11	1902786	1902786	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:1902786delC	ENST00000311604.3	+	3	491	c.316delC	c.(316-318)cccfs	p.P107fs	LSP1_ENST00000485341.1_3'UTR|LSP1_ENST00000406638.2_Frame_Shift_Del_p.P45fs|LSP1_ENST00000381775.1_Frame_Shift_Del_p.P235fs|LSP1_ENST00000405957.2_Frame_Shift_Del_p.P45fs	NM_002339.2	NP_002330.1	P33241	LSP1_HUMAN	lymphocyte-specific protein 1	107					cellular component movement (GO:0006928)|cellular defense response (GO:0006968)|chemotaxis (GO:0006935)	actin cytoskeleton (GO:0015629)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|signal transducer activity (GO:0004871)	p.Q46fs*31(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	16		all_epithelial(84;0.000138)|Breast(177;0.000962)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|Lung(200;0.0729)|LUSC - Lung squamous cell carcinoma(625;0.0856)		CAGCGGAGAGCCCCCCCAGTG	0.701																																					p.P44fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.130delC	11						.						13.0	14.0	13.0					11																	1902786		2116	4162	6278	1859362	SO:0001589	frameshift_variant	4046	exon3			M33552	CCDS31334.1, CCDS31335.1, CCDS58110.1	11p15.5	2008-02-05			ENSG00000130592	ENSG00000130592			6707	protein-coding gene	gene with protein product		153432				2174784	Standard	NM_001242932		Approved	WP34	uc001luj.3	P33241	OTTHUMG00000012252	ENST00000311604.3:c.316delC	11.37:g.1902786delC	ENSP00000308383:p.Pro107fs	Somatic		Capture	Illumina HiSeq	Phase_I	1859362	NM_001013253	B3KPP1|B3KRR6|E9PBV6|E9PFP3|Q16096|Q53H48|Q6FHM3|Q9BUY8	Frame_Shift_Del	DEL	ENST00000311604.3	37	CCDS31334.1																																																																																				0.701	LSP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034045.3	NM_002339	
CARS	833	broad.mit.edu	37	11	3028166	3028166	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:3028166C>T	ENST00000397111.5	-	18	2088	c.1843G>A	c.(1843-1845)Gat>Aat	p.D615N	CARS_ENST00000397114.3_Missense_Mutation_p.D605N|CARS_ENST00000470221.2_5'UTR|CARS_ENST00000401769.3_Missense_Mutation_p.D628N|CARS_ENST00000278224.9_Missense_Mutation_p.D615N|CARS_ENST00000380525.4_Missense_Mutation_p.D698N			P49589	SYCC_HUMAN	cysteinyl-tRNA synthetase	615					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)	p.D615N(1)	CARS/ALK(5)	central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)	31		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00317)|LUSC - Lung squamous cell carcinoma(625;0.218)	L-Cysteine(DB00151)	CGCAGGGCATCGCTGAGCTGC	0.587			T	ALK	ALCL																																p.D698N	Ovarian(61;932 1157 5961 20446 52152)		Dom	yes		11	11p15.5	833	cysteinyl-tRNA synthetase		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2092A	11						.						152.0	145.0	148.0					11																	3028166		2202	4298	6500	2984742	SO:0001583	missense	833	exon19			AF288207	CCDS7742.1, CCDS41600.1, CCDS41602.1	11p15.5	2011-07-01			ENSG00000110619	ENSG00000110619	6.1.1.16	"""Aminoacyl tRNA synthetases / Class I"""	1493	protein-coding gene	gene with protein product	"""cysteine tRNA ligase 1, cytoplasmic"""	123859				8468064	Standard	NM_139273		Approved	CARS1	uc001lxf.3	P49589	OTTHUMG00000010927	ENST00000397111.5:c.1843G>A	11.37:g.3028166C>T	ENSP00000380300:p.Asp615Asn	Somatic		Capture	Illumina HiSeq	Phase_I	2984742	NM_001014437	Q53XI8|Q5HYE4|Q9HD24|Q9HD25	Missense_Mutation	SNP	ENST00000397111.5	37	CCDS7742.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470038	0.63625	.	.	ENSG00000110619	ENST00000380525;ENST00000397111;ENST00000278224;ENST00000397114;ENST00000401769	D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79	4.68	4.68	0.58851	Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.053155	0.64402	D	0.000001	D	0.92883	0.7736	M	0.93978	3.48	0.80722	D	1	D;D;D;D;D;D	0.76494	0.998;0.993;0.987;0.999;0.994;0.995	D;P;P;D;D;P	0.69654	0.94;0.584;0.83;0.95;0.965;0.893	D	0.94670	0.7856	10	0.87932	D	0	-17.7687	15.9423	0.79768	0.0:1.0:0.0:0.0	.	628;698;615;615;698;605	B4DKY1;B4DPV7;P49589;P49589-2;Q5HYE4;A8MVQ3	.;.;SYCC_HUMAN;.;.;.	N	698;615;615;605;628	ENSP00000369897:D698N;ENSP00000380300:D615N;ENSP00000278224:D615N;ENSP00000380303:D605N;ENSP00000384069:D628N	ENSP00000278224:D615N	D	-	1	0	CARS	2984742	1.000000	0.71417	0.818000	0.32626	0.039000	0.13416	6.621000	0.74228	2.431000	0.82371	0.462000	0.41574	GAT		0.587	CARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000030117.4	NM_001751	
MRGPRE	116534	broad.mit.edu	37	11	3249827	3249827	+	Missense_Mutation	SNP	G	G	A	rs200110994		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:3249827G>A	ENST00000389832.5	-	2	509	c.203C>T	c.(202-204)gCg>gTg	p.A68V	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.A67V			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	68						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A67V(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(6)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	19		Medulloblastoma(188;0.00106)|all_epithelial(84;0.00111)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00529)|LUSC - Lung squamous cell carcinoma(625;0.19)		GATGAGATCCGCGCAGGCCAC	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18125	0.0		0.0	False		,,,				2504	0.0				p.A67V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C200T	11						.						78.0	96.0	90.0					11																	3249827		2128	4243	6371	3206403	SO:0001583	missense	116534	exon2			AY255572	CCDS41603.1, CCDS41603.2	11p15.5	2012-08-21	2004-03-25		ENSG00000184350	ENSG00000184350		"""GPCR / Class A : Orphans"""	30694	protein-coding gene	gene with protein product		607232	"""G protein-coupled receptor 167"""	GPR167		11551509	Standard	NM_001039165		Approved	mrgE	uc001lxq.5	Q86SM8	OTTHUMG00000011708	ENST00000389832.5:c.203C>T	11.37:g.3249827G>A	ENSP00000374482:p.Ala68Val	Somatic		Capture	Illumina HiSeq	Phase_I	3206403	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	0	0.0	g	17.09	3.301164	0.60195	.	.	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	3.5	3.5	0.40072	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43416	U	0.000579	T	0.70378	0.3217	M	0.87180	2.865	0.22342	N	0.999184	D	0.89917	1.0	D	0.97110	1.0	T	0.63695	-0.6579	9	0.87932	D	0	-10.5861	12.5295	0.56106	0.0:0.0:1.0:0.0	.	67	Q86SM8	MRGRE_HUMAN	V	68;67	.	ENSP00000374482:A67V	A	-	2	0	MRGPRE	3206403	0.083000	0.21467	0.025000	0.17156	0.662000	0.39071	2.285000	0.43487	1.769000	0.52152	0.484000	0.47621	GCG		0.642	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536	
NUP98	4928	broad.mit.edu	37	11	3740678	3740678	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:3740678T>A	ENST00000324932.7	-	18	2783	c.2363A>T	c.(2362-2364)gAt>gTt	p.D788V	NUP98_ENST00000359171.4_Missense_Mutation_p.D788V|NUP98_ENST00000397007.4_Missense_Mutation_p.D805V|NUP98_ENST00000355260.3_Missense_Mutation_p.D788V|NUP98_ENST00000397004.4_Missense_Mutation_p.D788V	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	805	Peptidase S59. {ECO:0000255|PROSITE- ProRule:PRU00765}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.D788V(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		TTTTTGGTTATCATCTAAGTA	0.318			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.D805V			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2414T	11						.						130.0	130.0	130.0					11																	3740678		2201	4295	6496	3697254	SO:0001583	missense	4928	exon18			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.2363A>T	11.37:g.3740678T>A	ENSP00000316032:p.Asp788Val	Somatic		Capture	Illumina HiSeq	Phase_I	3697254	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Missense_Mutation	SNP	ENST00000324932.7	37	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.512596	0.85389	.	.	ENSG00000110713	ENST00000324932;ENST00000359171;ENST00000355260;ENST00000397004;ENST00000397007	.	.	.	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77725	0.4173	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	0.994;0.983;1.0;0.996	D;P;D;D	0.87578	0.94;0.768;0.998;0.971	T	0.79364	-0.1834	9	0.52906	T	0.07	.	13.111	0.59273	0.0:0.0:0.0:1.0	.	805;788;788;788	P52948-3;P52948-4;P52948-2;P52948-5	.;.;.;.	V	788;788;788;788;805	.	ENSP00000316032:D788V	D	-	2	0	NUP98	3697254	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.475000	0.81041	2.029000	0.59856	0.460000	0.39030	GAT		0.318	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
NUP98	4928	broad.mit.edu	37	11	3746392	3746392	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:3746392A>C	ENST00000324932.7	-	15	2208	c.1788T>G	c.(1786-1788)ccT>ccG	p.P596P	NUP98_ENST00000359171.4_Silent_p.P596P|NUP98_ENST00000397007.4_Silent_p.P613P|NUP98_ENST00000355260.3_Silent_p.P596P|NUP98_ENST00000397004.4_Silent_p.P596P	NM_016320.4|NM_139132.3	NP_057404.2|NP_624358.2	P52948	NUP98_HUMAN	nucleoporin 98kDa	613					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|DNA replication (GO:0006260)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore organization (GO:0006999)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nuclear pore outer ring (GO:0031080)|nucleoplasm (GO:0005654)	peptide binding (GO:0042277)|structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)	p.P596P(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0403)|LUSC - Lung squamous cell carcinoma(625;0.116)|Lung(200;0.199)		CACGATTAACAGGAGAAAAGA	0.333			T	"""HOXA9, NSD1, WHSC1L1, DDX10, TOP1, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1, HOXC11"""	AML																																p.P613P			Dom	yes		11	11p15	4928	nucleoporin 98kDa		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1839G	11						.						90.0	91.0	91.0					11																	3746392		2200	4297	6497	3702968	SO:0001819	synonymous_variant	4928	exon15			AF071076, AF231130, BC012906, BG773331	CCDS7746.1, CCDS31347.1, CCDS41605.1, CCDS41606.1	11p15	2008-02-26	2002-08-29		ENSG00000110713	ENSG00000110713			8068	protein-coding gene	gene with protein product		601021	"""nucleoporin 98kD"""			9166830	Standard	NM_139131		Approved	NUP96	uc001lyh.3	P52948	OTTHUMG00000011846	ENST00000324932.7:c.1788T>G	11.37:g.3746392A>C		Somatic		Capture	Illumina HiSeq	Phase_I	3702968	NM_005387	Q8IUT2|Q8WYB0|Q96E54|Q9H3Q4|Q9NT02|Q9UF57|Q9UHX0|Q9Y6J4|Q9Y6J5	Silent	SNP	ENST00000324932.7	37	CCDS7746.1	.	.	.	.	.	.	.	.	.	.	A	8.053	0.766473	0.15983	.	.	ENSG00000110713	ENST00000527104	.	.	.	5.59	4.46	0.54185	.	.	.	.	.	T	0.57257	0.2041	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50783	-0.8787	4	.	.	.	.	6.797	0.23731	0.7447:0.0:0.1389:0.1164	.	.	.	.	G	216	.	.	C	-	1	0	NUP98	3702968	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	1.098000	0.31000	0.400000	0.25396	-1.811000	0.00612	TGT		0.333	NUP98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032766.3	NM_016320	
STIM1	6786	broad.mit.edu	37	11	4104728	4104728	+	Splice_Site	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:4104728T>C	ENST00000300737.4	+	10	2043	c.1474T>C	c.(1474-1476)Tcc>Ccc	p.S492P	STIM1_ENST00000527651.1_Splice_Site_p.S492P|STIM1_ENST00000533977.1_Splice_Site_p.S319P	NM_003156.3	NP_003147.2	Q13586	STIM1_HUMAN	stromal interaction molecule 1	492					activation of store-operated calcium channel activity (GO:0032237)|blood coagulation (GO:0007596)|detection of calcium ion (GO:0005513)|regulation of calcium ion transport (GO:0051924)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|growth cone (GO:0030426)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of plasma membrane (GO:0005887)|microtubule (GO:0005874)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|microtubule plus-end binding (GO:0051010)|store-operated calcium channel activity (GO:0015279)	p.S492P(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|liver(1)|lung(14)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30		Breast(177;0.00159)|Medulloblastoma(188;0.00258)|all_neural(188;0.0233)		BRCA - Breast invasive adenocarcinoma(625;0.114)|LUSC - Lung squamous cell carcinoma(625;0.141)		GTCCATGCAGTGTAGGTGACC	0.527																																					p.S492P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1474C	11						.						51.0	31.0	38.0					11																	4104728		2201	4298	6499	4061304	SO:0001630	splice_region_variant	6786	exon10			BC021300, U52426	CCDS7749.1, CCDS60706.1, CCDS73247.1	11p15.5	2014-09-17			ENSG00000167323	ENSG00000167323		"""Sterile alpha motif (SAM) domain containing"""	11386	protein-coding gene	gene with protein product		605921				8921403, 11463338, 11983428	Standard	NM_003156		Approved	GOK, D11S4896E	uc021qco.1	Q13586	OTTHUMG00000133360	ENST00000300737.4:c.1474+1T>C	11.37:g.4104728T>C		Somatic		Capture	Illumina HiSeq	Phase_I	4061304	NM_003156	E9PQJ4|Q8N382	Missense_Mutation	SNP	ENST00000300737.4	37	CCDS7749.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.800435	0.50315	.	.	ENSG00000167323	ENST00000300737;ENST00000527651;ENST00000533977	T;T;T	0.53640	0.61;0.61;0.61	5.69	5.69	0.88448	.	0.052564	0.85682	D	0.000000	T	0.45115	0.1326	L	0.55481	1.735	0.51233	D	0.999918	P;B	0.50943	0.94;0.006	B;B	0.41666	0.363;0.007	T	0.41980	-0.9478	10	0.33940	T	0.23	-13.2956	15.122	0.72450	0.0:0.0:0.0:1.0	.	492;492	E9PQJ4;Q13586	.;STIM1_HUMAN	P	492;492;319	ENSP00000300737:S492P;ENSP00000436208:S492P;ENSP00000434767:S319P	ENSP00000300737:S492P	S	+	1	0	STIM1	4061304	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.345000	0.79337	2.178000	0.69098	0.455000	0.32223	TCC		0.527	STIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257196.1	NM_003156	Missense_Mutation
TRIM68	55128	broad.mit.edu	37	11	4621818	4621818	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:4621818C>A	ENST00000300747.5	-	7	1435	c.1146G>T	c.(1144-1146)aaG>aaT	p.K382N		NM_018073.6	NP_060543.5	Q6AZZ1	TRI68_HUMAN	tripartite motif containing 68	382	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein autoubiquitination (GO:0051865)|regulation of androgen receptor signaling pathway (GO:0060765)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|histone acetyltransferase binding (GO:0035035)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K382N(1)		breast(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	15		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;9.49e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		AGACCACCTCCTTCCGGTCTA	0.557																																					p.K382N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1146T	11						.						63.0	60.0	61.0					11																	4621818		2201	4298	6499	4578394	SO:0001583	missense	55128	exon7			AF360739	CCDS31356.1	11p15.4	2013-01-09	2011-01-25	2004-11-17		ENSG00000167333		"""RING-type (C3HC4) zinc fingers"", ""Tripartite motif containing / Tripartite motif containing"""	21161	protein-coding gene	gene with protein product		613184	"""ring finger protein 137"", ""tripartite motif-containing 68"""	RNF137		11597395	Standard	NM_018073		Approved	SS-56, FLJ10369	uc001lzf.2	Q6AZZ1		ENST00000300747.5:c.1146G>T	11.37:g.4621818C>A	ENSP00000300747:p.Lys382Asn	Somatic		Capture	Illumina HiSeq	Phase_I	4578394	NM_018073	A6NI19|A8K551|B3KPM5|B4DVK4|Q8WZ70|Q96LE5|Q96PF7|Q9H9C2|Q9NW18	Missense_Mutation	SNP	ENST00000300747.5	37	CCDS31356.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629646	0.67015	.	.	ENSG00000167333	ENST00000300747;ENST00000544055	T	0.66280	-0.2	5.52	1.47	0.22746	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.53938	D	0.000041	T	0.71863	0.3390	M	0.69358	2.11	0.37808	D	0.927952	D	0.89917	1.0	D	0.97110	1.0	T	0.70644	-0.4815	10	0.39692	T	0.17	.	8.4064	0.32616	0.0:0.5907:0.0:0.4093	.	382	Q6AZZ1	TRI68_HUMAN	N	382;103	ENSP00000300747:K382N	ENSP00000300747:K382N	K	-	3	2	TRIM68	4578394	0.936000	0.31750	1.000000	0.80357	0.953000	0.61014	0.160000	0.16462	0.377000	0.24735	0.561000	0.74099	AAG		0.557	TRIM68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385948.1	NM_018073	
OR51A7	119687	broad.mit.edu	37	11	4929079	4929079	+	Silent	SNP	C	C	A	rs556415088		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:4929079C>A	ENST00000359350.4	+	1	480	c.480C>A	c.(478-480)ccC>ccA	p.P160P	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001004749.1	NP_001004749.1	Q8NH64	O51A7_HUMAN	olfactory receptor, family 51, subfamily A, member 7	160						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P160P(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(13)|ovary(1)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		TTCCATTTCCCTTCACCTTAA	0.388																																					p.P160P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C480A	11						.						102.0	99.0	100.0					11																	4929079		2201	4298	6499	4885655	SO:0001819	synonymous_variant	119687	exon1			AB065525	CCDS31364.1	11p15.4	2012-08-09			ENSG00000176895	ENSG00000176895		"""GPCR / Class A : Olfactory receptors"""	15188	protein-coding gene	gene with protein product							Standard	NM_001004749		Approved		uc010qyq.2	Q8NH64	OTTHUMG00000066502	ENST00000359350.4:c.480C>A	11.37:g.4929079C>A		Somatic		Capture	Illumina HiSeq	Phase_I	4885655	NM_001004749	Q6IFH8	Silent	SNP	ENST00000359350.4	37	CCDS31364.1																																																																																				0.388	OR51A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142175.1	NM_001004749	
OR52A1	23538	broad.mit.edu	37	11	5173120	5173120	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:5173120T>C	ENST00000380367.1	-	2	897	c.480A>G	c.(478-480)ccA>ccG	p.P160P	OR52A1_ENST00000328942.1_Silent_p.P160P			Q9UKL2	O52A1_HUMAN	olfactory receptor, family 52, subfamily A, member 1	160					sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|transmembrane signaling receptor activity (GO:0004888)	p.P160P(1)		breast(2)|endometrium(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	19		Medulloblastoma(188;0.00106)|Breast(177;0.0155)|all_neural(188;0.0189)		Epithelial(150;2.9e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTACTAGGCATGGGGCTACAA	0.458																																					p.P160P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A480G	11						.						124.0	121.0	122.0					11																	5173120		2201	4298	6499	5129696	SO:0001819	synonymous_variant	23538	exon1			AF154673	CCDS31374.1	11p15.4	2012-08-09			ENSG00000182070	ENSG00000182070		"""GPCR / Class A : Olfactory receptors"""	8318	protein-coding gene	gene with protein product						10512676	Standard	NM_012375		Approved	HPFH1OR	uc010qyy.2	Q9UKL2	OTTHUMG00000066603	ENST00000380367.1:c.480A>G	11.37:g.5173120T>C		Somatic		Capture	Illumina HiSeq	Phase_I	5129696	NM_012375	Q6IF31	Silent	SNP	ENST00000380367.1	37	CCDS31374.1																																																																																				0.458	OR52A1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142810.2	NM_012375	
OR51V1	283111	broad.mit.edu	37	11	5221754	5221754	+	Nonsense_Mutation	SNP	C	C	T	rs61738413	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:5221754C>T	ENST00000321255.1	-	1	176	c.177G>A	c.(175-177)tgG>tgA	p.W59*		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	59					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.W59*(1)		endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGGCTCAGTCCATATCACAT	0.532																																					p.W59X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G177A	11						.						126.0	108.0	114.0					11																	5221754		2201	4298	6499	5178330	SO:0001587	stop_gained	283111	exon1			BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.177G>A	11.37:g.5221754C>T	ENSP00000321729:p.Trp59*	Somatic		Capture	Illumina HiSeq	Phase_I	5178330	NM_001004760		Nonsense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812898	0.50527	.	.	ENSG00000176742	ENST00000321255	.	.	.	5.48	1.42	0.22433	.	0.758004	0.10878	N	0.624178	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	4.334	0.11078	0.0:0.3815:0.3076:0.3108	.	.	.	.	X	59	.	ENSP00000321729:W59X	W	-	3	0	OR51V1	5178330	0.000000	0.05858	0.873000	0.34254	0.421000	0.31385	-1.299000	0.02754	0.109000	0.17891	0.650000	0.86243	TGG		0.532	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760	
HBG1	3047	broad.mit.edu	37	11	5270637	5270637	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:5270637C>T	ENST00000330597.3	-	2	363	c.276G>A	c.(274-276)ctG>ctA	p.L92L		NM_000559.2	NP_000550.2	P69891	HBG1_HUMAN	hemoglobin, gamma A	92					blood coagulation (GO:0007596)	cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.L92L(1)		large_intestine(1)|lung(3)|skin(1)	5		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCACAGTGCAGTTCACTCA	0.517																																					p.L92L	Ovarian(117;2080 2193 33416 49679)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G276A	11						.						35.0	33.0	34.0					11																	5270637		2035	3993	6028	5227213	SO:0001819	synonymous_variant	3047	exon2			M91036	CCDS7754.1	11p15.5	2014-05-19			ENSG00000213934	ENSG00000213934			4831	protein-coding gene	gene with protein product		142200				2649166	Standard	NM_000559		Approved	HBG-T2	uc001mah.1	P69891	OTTHUMG00000066681	ENST00000330597.3:c.276G>A	11.37:g.5270637C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5227213	NM_000559	P02096|P62027|Q549G1|Q8TDA1|Q96FH7	Silent	SNP	ENST00000330597.3	37	CCDS7754.1																																																																																				0.517	HBG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142982.1	NM_000559	
HBG2	3048	broad.mit.edu	37	11	5275561	5275561	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:5275561C>T	ENST00000380259.2	-	7	1516	c.276G>A	c.(274-276)ctG>ctA	p.L92L	HBG2_ENST00000380252.1_Silent_p.L82L|HBG2_ENST00000336906.4_Silent_p.L92L			P69892	HBG2_HUMAN	hemoglobin, gamma G	92					blood coagulation (GO:0007596)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.L92L(1)		endometrium(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	13		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.76e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGTCACAGTGCAGTTCACTCA	0.502																																					p.L92L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G276A	11						.						187.0	146.0	160.0					11																	5275561		2201	4295	6496	5232137	SO:0001819	synonymous_variant	3048	exon2			BC029387	CCDS7755.1	11p15.5	2014-05-19			ENSG00000196565	ENSG00000196565			4832	protein-coding gene	gene with protein product		142250				2649166	Standard	NM_000184		Approved	HBG-T1		P69892	OTTHUMG00000066673	ENST00000380259.2:c.276G>A	11.37:g.5275561C>T		Somatic		Capture	Illumina HiSeq	Phase_I	5232137	NM_000184	A8MZE0|P02096|P62027|Q14491|Q68NH9|Q96FH6|Q96FH7	Silent	SNP	ENST00000380259.2	37	CCDS7755.1																																																																																				0.502	HBG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142967.2	NM_000184	
UBQLNL	143630	broad.mit.edu	37	11	5536745	5536745	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:5536745T>C	ENST00000380184.1	-	1	1190	c.927A>G	c.(925-927)tcA>tcG	p.S309S	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	309								p.S309S(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		GAGGTGGGGGTGAAGACTGGA	0.478																																					p.S309S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A927G	11						.						168.0	150.0	156.0					11																	5536745		2201	4297	6498	5493321	SO:0001819	synonymous_variant	143630	exon1			AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.927A>G	11.37:g.5536745T>C		Somatic		Capture	Illumina HiSeq	Phase_I	5493321	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	37	CCDS31385.1																																																																																				0.478	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
OR52W1	120787	broad.mit.edu	37	11	6220850	6220850	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:6220850C>T	ENST00000311352.2	+	1	475	c.397C>T	c.(397-399)Cgt>Tgt	p.R133C	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	133						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R133C(2)		endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCAATAGGGCGTCCACTGCA	0.547																																					p.R133C												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C397T	11						.						150.0	103.0	119.0					11																	6220850		2201	4296	6497	6177426	SO:0001583	missense	120787	exon1			AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"""GPCR / Class A : Olfactory receptors"""	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.397C>T	11.37:g.6220850C>T	ENSP00000309673:p.Arg133Cys	None		Capture	Illumina HiSeq	Phase_I	6177426	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	C	9.159	1.018275	0.19355	.	.	ENSG00000175485	ENST00000311352	T	0.00554	6.64	5.95	0.147	0.14838	GPCR, rhodopsin-like superfamily (1);	0.848919	0.09840	N	0.749018	T	0.00580	0.0019	L	0.46947	1.48	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38436	-0.9661	10	0.46703	T	0.11	.	8.2524	0.31735	0.3367:0.5189:0.0819:0.0626	.	133	Q6IF63	O52W1_HUMAN	C	133	ENSP00000309673:R133C	ENSP00000309673:R133C	R	+	1	0	OR52W1	6177426	0.000000	0.05858	0.911000	0.35937	0.809000	0.45718	-1.122000	0.03267	0.113000	0.18004	-0.940000	0.02684	CGT		0.547	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178	
APBB1	322	broad.mit.edu	37	11	6415745	6415745	+	IGR	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:6415745C>T	ENST00000609360.1	-	0	2642				SMPD1_ENST00000356761.2_Missense_Mutation_p.R546C|APBB1_ENST00000526240.1_5'Flank|SMPD1_ENST00000342245.4_Missense_Mutation_p.R602C|SMPD1_ENST00000527275.1_Missense_Mutation_p.R601C|SMPD1_ENST00000299397.3_Missense_Mutation_p.R558C	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)						apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.R558C(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		GCTCTCTGCCCGTGCTGACAG	0.637																																					p.R601C	GBM(147;1810 2556 5672 39622)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1801T	11						.						66.0	68.0	68.0					11																	6415745		2201	4296	6497	6372321	SO:0001628	intergenic_variant	6609	exon6			L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213			11.37:g.6415745C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6372321	NM_001007593	A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37		.	.	.	.	.	.	.	.	.	.	C	17.65	3.443000	0.63067	.	.	ENSG00000166311	ENST00000299397;ENST00000356761;ENST00000342245;ENST00000527275	D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41	5.41	4.49	0.54785	.	0.090805	0.42294	D	0.000735	D	0.93986	0.8074	M	0.86178	2.8	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69824	0.959;0.966;0.951	D	0.94005	0.7279	10	0.62326	D	0.03	-14.1481	11.1727	0.48582	0.3347:0.6653:0.0:0.0	.	601;558;600	E9PKS3;G3XAB5;P17405	.;.;ASM_HUMAN	C	558;546;602;601	ENSP00000299397:R558C;ENSP00000349203:R546C;ENSP00000340409:R602C;ENSP00000435350:R601C	ENSP00000299397:R558C	R	+	1	0	SMPD1	6372321	1.000000	0.71417	0.843000	0.33291	0.710000	0.40934	2.859000	0.48364	1.257000	0.44085	0.462000	0.41574	CGT		0.637	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164	
DNHD1	144132	broad.mit.edu	37	11	6592175	6592175	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:6592175G>A	ENST00000527990.2	+	40	13433	c.13433G>A	c.(13432-13434)cGg>cAg	p.R4478Q	DNHD1_ENST00000254579.6_Missense_Mutation_p.R4478Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4478					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)	p.R4478Q(1)		NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		CCAAATGCACGGCGGCCTCTG	0.612																																					p.R4478Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G13433A	11						.						44.0	51.0	48.0					11																	6592175		2045	4174	6219	6548751	SO:0001583	missense	144132	exon42			AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.13433G>A	11.37:g.6592175G>A	ENSP00000436180:p.Arg4478Gln	Somatic		Capture	Illumina HiSeq	Phase_I	6548751	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	11.11	1.542933	0.27563	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.08720	3.06;3.06	4.48	-4.67	0.03319	Dynein heavy chain (1);	1.410220	0.04375	N	0.359794	T	0.05273	0.0140	L	0.41236	1.265	0.09310	N	1	B;B;B	0.17465	0.022;0.022;0.022	B;B;B	0.13407	0.004;0.004;0.009	T	0.40590	-0.9555	10	0.13108	T	0.6	-0.4014	0.1984	0.00142	0.2954:0.2692:0.1814:0.2541	.	3566;531;4478	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	Q	4478;4478;746	ENSP00000254579:R4478Q;ENSP00000436180:R4478Q	ENSP00000254579:R4478Q	R	+	2	0	DNHD1	6548751	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	-1.945000	0.01537	-0.659000	0.05359	0.563000	0.77884	CGG		0.612	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
DCHS1	8642	broad.mit.edu	37	11	6648416	6648416	+	Missense_Mutation	SNP	C	C	T	rs377529145		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:6648416C>T	ENST00000299441.3	-	14	6265	c.5854G>A	c.(5854-5856)Gat>Aat	p.D1952N		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1952	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D1952N(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATTGACATCGCGCACCGTG	0.617																																					p.D1952N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5854A	11						.	C	ASN/ASP	0,4402		0,0,2201	91.0	77.0	82.0		5854	5.2	0.9	11		82	1,8591	1.2+/-3.3	0,1,4295	no	missense	DCHS1	NM_003737.2	23	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1952/3299	6648416	1,12993	2201	4296	6497	6604992	SO:0001583	missense	8642	exon14			AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.5854G>A	11.37:g.6648416C>T	ENSP00000299441:p.Asp1952Asn	Somatic		Capture	Illumina HiSeq	Phase_I	6604992	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.691334	0.68271	0.0	1.16E-4	ENSG00000166341	ENST00000299441	T	0.75050	-0.9	5.18	5.18	0.71444	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.48767	D	0.000180	D	0.88869	0.6554	M	0.90082	3.085	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.90445	0.4434	10	0.62326	D	0.03	.	17.8548	0.88759	0.0:1.0:0.0:0.0	.	1952	Q96JQ0	PCD16_HUMAN	N	1952	ENSP00000299441:D1952N	ENSP00000299441:D1952N	D	-	1	0	DCHS1	6604992	1.000000	0.71417	0.909000	0.35828	0.254000	0.26022	7.651000	0.83577	2.700000	0.92200	0.462000	0.41574	GAT		0.617	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
STK33	65975	broad.mit.edu	37	11	8496312	8496312	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:8496312G>T	ENST00000447869.1	-	1	1059	c.141C>A	c.(139-141)agC>agA	p.S47R	STK33_ENST00000358872.3_Intron|STK33_ENST00000534493.1_Missense_Mutation_p.S6R|STK33_ENST00000396673.1_Missense_Mutation_p.S47R|STK33_ENST00000315204.1_Missense_Mutation_p.S47R|STK33_ENST00000396672.1_Missense_Mutation_p.S47R			Q9BYT3	STK33_HUMAN	serine/threonine kinase 33	47					protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.S47R(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|skin(3)	23				Epithelial(150;2.13e-06)|BRCA - Breast invasive adenocarcinoma(625;0.239)		CACTACCAATGCTTGATGTCT	0.368																																					p.S47R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C141A	11						.						122.0	124.0	123.0					11																	8496312		2201	4296	6497	8452888	SO:0001583	missense	65975	exon3			AJ303380	CCDS7789.1, CCDS73253.1, CCDS73254.1	11p15.3	2010-03-10			ENSG00000130413	ENSG00000130413			14568	protein-coding gene	gene with protein product		607670				11738831	Standard	NM_030906		Approved		uc001mgj.1	Q9BYT3	OTTHUMG00000140275	ENST00000447869.1:c.141C>A	11.37:g.8496312G>T	ENSP00000416750:p.Ser47Arg	Somatic		Capture	Illumina HiSeq	Phase_I	8452888	NM_030906	Q658S6|Q8NEF5	Missense_Mutation	SNP	ENST00000447869.1	37	CCDS7789.1	.	.	.	.	.	.	.	.	.	.	G	14.57	2.574248	0.45902	.	.	ENSG00000130413	ENST00000447869;ENST00000315204;ENST00000396672;ENST00000396673;ENST00000534493;ENST00000418597;ENST00000422559;ENST00000457885;ENST00000431279	T;T;T;T;T;T;T;T;T	0.71461	-0.49;-0.49;-0.49;-0.5;-0.57;-0.35;0.28;1.24;0.15	4.59	-1.76	0.08006	.	0.446585	0.22402	N	0.060525	T	0.57504	0.2058	L	0.53249	1.67	0.09310	N	0.999999	B	0.17038	0.02	B	0.17433	0.018	T	0.51028	-0.8757	10	0.87932	D	0	.	4.114	0.10072	0.452:0.0:0.3893:0.1587	.	47	Q9BYT3	STK33_HUMAN	R	47;47;47;47;6;6;6;47;47	ENSP00000416750:S47R;ENSP00000320754:S47R;ENSP00000379905:S47R;ENSP00000379906:S47R;ENSP00000436418:S6R;ENSP00000391362:S6R;ENSP00000411510:S6R;ENSP00000403599:S47R;ENSP00000397569:S47R	ENSP00000320754:S47R	S	-	3	2	STK33	8452888	0.021000	0.18746	0.008000	0.14137	0.103000	0.19146	-0.092000	0.11129	-0.436000	0.07254	-0.214000	0.12660	AGC		0.368	STK33-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276819.2	NM_030906	
ST5	6764	broad.mit.edu	37	11	8719178	8719178	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:8719178G>A	ENST00000534127.1	-	20	3331	c.2946C>T	c.(2944-2946)gaC>gaT	p.D982D	ST5_ENST00000526099.1_Silent_p.D495D|ST5_ENST00000313726.6_Silent_p.D982D|ST5_ENST00000526757.1_Silent_p.D562D|ST5_ENST00000534278.1_Silent_p.D173D|ST5_ENST00000530991.1_Silent_p.D454D|RP11-152H18.3_ENST00000529883.1_RNA|ST5_ENST00000530438.1_Silent_p.D562D|ST5_ENST00000357665.1_Silent_p.D982D|RPL27A_ENST00000531102.1_Intron	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	982					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.D982D(1)		NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		TGTCTTCGTCGTCCATCTGCA	0.493																																					p.D982D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2946T	11						.						116.0	89.0	98.0					11																	8719178		2201	4296	6497	8675754	SO:0001819	synonymous_variant	6764	exon20			U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2946C>T	11.37:g.8719178G>A		Somatic		Capture	Illumina HiSeq	Phase_I	8675754	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Silent	SNP	ENST00000534127.1	37	CCDS7791.1																																																																																				0.493	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
INSC	387755	broad.mit.edu	37	11	15212263	15212263	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:15212263T>A	ENST00000379554.3	+	6	783	c.737T>A	c.(736-738)aTt>aAt	p.I246N	INSC_ENST00000447214.2_3'UTR|INSC_ENST00000525218.1_Missense_Mutation_p.I199N|INSC_ENST00000530161.1_Missense_Mutation_p.I199N|INSC_ENST00000379556.3_Missense_Mutation_p.I199N|INSC_ENST00000528567.1_Missense_Mutation_p.I199N|INSC_ENST00000424273.1_Missense_Mutation_p.I199N	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	246					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)		p.I246N(1)		NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GTGAGAAAAATTGATGCCTCA	0.517																																					p.I199N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T596A	11						.						142.0	149.0	147.0					11																	15212263		1972	4144	6116	15168839	SO:0001583	missense	387755	exon6			AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.737T>A	11.37:g.15212263T>A	ENSP00000368872:p.Ile246Asn	Somatic		Capture	Illumina HiSeq	Phase_I	15168839	NM_001042536	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.982033	0.74474	.	.	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000416761;ENST00000528567;ENST00000530161;ENST00000525218	T;T;T;T;T;T	0.52526	0.66;0.66;0.69;0.66;0.66;0.69	6.16	6.16	0.99307	Armadillo-like helical (1);Armadillo-type fold (1);	0.051719	0.85682	D	0.000000	T	0.56337	0.1978	L	0.46157	1.445	0.50171	D	0.999859	D;P;D;D	0.65815	0.995;0.848;0.967;0.967	P;B;P;P	0.55577	0.779;0.387;0.62;0.62	T	0.59177	-0.7503	10	0.87932	D	0	-19.9263	14.3293	0.66545	0.0:0.0:0.0:1.0	.	234;199;199;246	Q1MX18-5;Q1MX18-4;A0PJX5;Q1MX18	.;.;.;INSC_HUMAN	N	246;199;199;234;199;199;199	ENSP00000368872:I246N;ENSP00000368874:I199N;ENSP00000389161:I199N;ENSP00000435022:I199N;ENSP00000436194:I199N;ENSP00000436113:I199N	ENSP00000368872:I246N	I	+	2	0	INSC	15168839	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	5.134000	0.64770	2.367000	0.80283	0.528000	0.53228	ATT		0.517	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
PLEKHA7	144100	broad.mit.edu	37	11	16848056	16848056	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:16848056G>A	ENST00000355661.3	-	10	964	c.954C>T	c.(952-954)ccC>ccT	p.P318P	PLEKHA7_ENST00000531066.1_Silent_p.P318P|PLEKHA7_ENST00000448080.2_Silent_p.P318P|PLEKHA7_ENST00000532079.1_Intron			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	318					epithelial cell-cell adhesion (GO:0090136)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|zonula adherens (GO:0005915)	delta-catenin binding (GO:0070097)	p.P318P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(13)|ovary(1)|prostate(2)|skin(7)|urinary_tract(1)	37						TCGTATGTCCGGGTCCCACCC	0.592																																					p.P318P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C954T	11						.						89.0	84.0	86.0					11																	16848056		2200	4294	6494	16804632	SO:0001819	synonymous_variant	144100	exon10			BC033239	CCDS31434.1	11p15	2013-01-10			ENSG00000166689	ENSG00000166689		"""Pleckstrin homology (PH) domain containing"""	27049	protein-coding gene	gene with protein product		612686				12477932	Standard	NM_175058		Approved	DKFZp686M22243	uc001mmo.3	Q6IQ23	OTTHUMG00000165954	ENST00000355661.3:c.954C>T	11.37:g.16848056G>A		Somatic		Capture	Illumina HiSeq	Phase_I	16804632	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	37	CCDS31434.1																																																																																				0.592	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058	
NAV2	89797	broad.mit.edu	37	11	20005717	20005717	+	Missense_Mutation	SNP	C	C	T	rs201439491		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:20005717C>T	ENST00000396087.3	+	12	2860	c.2761C>T	c.(2761-2763)Cgg>Tgg	p.R921W	NAV2_ENST00000349880.4_Missense_Mutation_p.R898W|NAV2_ENST00000540292.1_Missense_Mutation_p.R852W|NAV2_ENST00000527559.2_Missense_Mutation_p.R850W|NAV2_ENST00000396085.1_Missense_Mutation_p.R898W|NAV2-AS3_ENST00000534036.1_RNA|NAV2_ENST00000360655.4_Missense_Mutation_p.R834W	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	921					glossopharyngeal nerve development (GO:0021563)|locomotory behavior (GO:0007626)|optic nerve development (GO:0021554)|regulation of systemic arterial blood pressure by baroreceptor feedback (GO:0003025)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|vagus nerve development (GO:0021564)	interstitial matrix (GO:0005614)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|heparin binding (GO:0008201)	p.R921W(1)		NS(1)|breast(2)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(26)|lung(38)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	116						TCGCCTGAACCGGCTCCCTGA	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		20621	0.0		0.001	False		,,,				2504	0.0				p.R834W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2500T	11						.						138.0	130.0	132.0					11																	20005717		2203	4300	6503	19962293	SO:0001583	missense	89797	exon11			AB037840	CCDS7850.1, CCDS7851.2, CCDS44552.1, CCDS53612.1, CCDS58126.1	11p15.1	2008-07-18			ENSG00000166833	ENSG00000166833	3.6.1.1		15997	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 2"", ""retinoic acid inducible gene in neuroblastoma 1"", ""helicase, APC down-regulated 1"""	607026				12079279, 12062803	Standard	NM_145117		Approved	FLJ10633, FLJ11030, HELAD1, KIAA1419, POMFIL2, RAINB1, FLJ23707	uc010rdm.2	Q8IVL1	OTTHUMG00000151837	ENST00000396087.3:c.2761C>T	11.37:g.20005717C>T	ENSP00000379396:p.Arg921Trp	Somatic		Capture	Illumina HiSeq	Phase_I	19962293	NM_001111018	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	25.1	4.608245	0.87258	.	.	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292	T;T;T;T;T;T	0.46819	0.91;0.94;0.95;0.95;0.86;0.86	5.65	5.65	0.86999	.	0.000000	0.56097	D	0.000029	T	0.59155	0.2173	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.979	T	0.53380	-0.8447	9	.	.	.	.	14.3888	0.66963	0.1484:0.8516:0.0:0.0	.	898;834	Q8IVL1-3;Q8IVL1-4	.;.	W	834;898;898;921;850;852	ENSP00000353871:R834W;ENSP00000379394:R898W;ENSP00000309577:R898W;ENSP00000379396:R921W;ENSP00000435395:R850W;ENSP00000443489:R852W	.	R	+	1	2	NAV2	19962293	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.860000	0.55995	2.824000	0.97209	0.655000	0.94253	CGG		0.542	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
NELL1	4745	broad.mit.edu	37	11	20950023	20950023	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:20950023G>A	ENST00000357134.5	+	9	1147	c.995G>A	c.(994-996)cGa>cAa	p.R332Q	NELL1_ENST00000532434.1_Missense_Mutation_p.R332Q|NELL1_ENST00000298925.5_Missense_Mutation_p.R360Q|NELL1_ENST00000325319.5_Missense_Mutation_p.R275Q	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	332	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)	p.R332Q(1)		NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AAGGTCTGCCGACGTAAGTAC	0.488																																					p.R332Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G995A	11						.						140.0	111.0	121.0					11																	20950023		2203	4300	6503	20906599	SO:0001583	missense	4745	exon9			AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.995G>A	11.37:g.20950023G>A	ENSP00000349654:p.Arg332Gln	Somatic		Capture	Illumina HiSeq	Phase_I	20906599	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.719105	0.68844	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.68	5.68	0.88126	von Willebrand factor, type C (1);	0.059595	0.64402	D	0.000016	T	0.55768	0.1941	L	0.38531	1.155	0.42002	D	0.990897	P;D;B;D	0.69078	0.695;0.997;0.125;0.992	B;P;B;P	0.50825	0.231;0.651;0.018;0.558	T	0.50684	-0.8799	10	0.10111	T	0.7	-10.7311	10.8246	0.46625	0.1147:0.0:0.8853:0.0	.	275;360;332;332	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	Q	360;332;275;332	ENSP00000298925:R360Q;ENSP00000349654:R332Q;ENSP00000317837:R275Q;ENSP00000437170:R332Q	ENSP00000298925:R360Q	R	+	2	0	NELL1	20906599	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.639000	0.61361	2.679000	0.91253	0.561000	0.74099	CGA		0.488	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
MUC15	143662	broad.mit.edu	37	11	26587102	26587102	+	Missense_Mutation	SNP	G	G	T	rs563199813		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:26587102G>T	ENST00000455601.2	-	2	422	c.304C>A	c.(304-306)Ccc>Acc	p.P102T	ANO3_ENST00000531568.1_Intron|MUC15_ENST00000529533.1_Missense_Mutation_p.P129T|MUC15_ENST00000436318.2_Missense_Mutation_p.P129T|ANO3_ENST00000256737.3_Intron|MUC15_ENST00000281268.8_Missense_Mutation_p.P129T|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000525139.1_Intron|MUC15_ENST00000527569.1_Missense_Mutation_p.P129T	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	102					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P102T(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						GTAGATGTGGGTTTTAGACTG	0.458													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18918	0.0		0.0	False		,,,				2504	0.0				p.P129T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C385A	11						.						177.0	159.0	165.0					11																	26587102		2203	4300	6503	26543678	SO:0001583	missense	143662	exon3			AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"""Mucins"""	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.304C>A	11.37:g.26587102G>T	ENSP00000397339:p.Pro102Thr	Somatic		Capture	Illumina HiSeq	Phase_I	26543678	NM_001135092	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	G	13.32	2.201122	0.38905	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.29397	1.7;1.66;1.57;1.66;1.57	4.85	0.476	0.16779	.	0.741143	0.12518	N	0.461931	T	0.20941	0.0504	L	0.43923	1.385	0.09310	N	1	P;B;B	0.42203	0.773;0.301;0.301	B;B;B	0.38428	0.273;0.082;0.082	T	0.13019	-1.0525	10	0.51188	T	0.08	-0.9614	3.5616	0.07884	0.1906:0.0:0.4638:0.3456	.	129;102;129	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	T	102;129;129;129;129	ENSP00000397339:P102T;ENSP00000416753:P129T;ENSP00000281268:P129T;ENSP00000431983:P129T;ENSP00000431945:P129T	ENSP00000281268:P129T	P	-	1	0	MUC15	26543678	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	0.057000	0.14279	0.299000	0.22661	0.650000	0.86243	CCC		0.458	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650	
KIF18A	81930	broad.mit.edu	37	11	28058000	28058000	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:28058000T>C	ENST00000263181.6	-	14	2450	c.2160A>G	c.(2158-2160)gtA>gtG	p.V720V		NM_031217.3	NP_112494.3	Q8NI77	KI18A_HUMAN	kinesin family member 18A	720					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|protein transport (GO:0015031)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore microtubule (GO:0005828)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|ruffle (GO:0001726)	actin binding (GO:0003779)|ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|plus-end-directed microtubule motor activity (GO:0008574)|tubulin-dependent ATPase activity (GO:0070463)|ubiquitin binding (GO:0043130)	p.V720V(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(1)|urinary_tract(2)	36						TCATTAAGGTTACTGTAGACG	0.358																																					p.V720V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2160G	11						.						129.0	130.0	129.0					11																	28058000		2202	4298	6500	28014576	SO:0001819	synonymous_variant	81930	exon14			AL136819	CCDS7867.1	11p14.1	2014-06-12			ENSG00000121621	ENSG00000121621		"""Kinesins"""	29441	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 99"""	611271				11230166	Standard	NM_031217		Approved	DKFZP434G2226, PPP1R99	uc001msc.2	Q8NI77	OTTHUMG00000166195	ENST00000263181.6:c.2160A>G	11.37:g.28058000T>C		Somatic		Capture	Illumina HiSeq	Phase_I	28014576	NM_031217	Q4VPE3|Q86VS5|Q9H0F3	Silent	SNP	ENST00000263181.6	37	CCDS7867.1																																																																																				0.358	KIF18A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388328.3	NM_031217	
KCNA4	3739	broad.mit.edu	37	11	30032627	30032627	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:30032627G>T	ENST00000328224.6	-	2	2832	c.1599C>A	c.(1597-1599)atC>atA	p.I533I	KCNA4_ENST00000526518.1_5'Flank	NM_002233.3	NP_002224.1	P22459	KCNA4_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 4	533					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	potassium ion binding (GO:0030955)|voltage-gated potassium channel activity (GO:0005249)	p.I533I(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(39)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	78					Dalfampridine(DB06637)	CCCCTACAGTGATGGGCTTCA	0.502																																					p.I533I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1599A	11						.						58.0	61.0	60.0					11																	30032627		2188	4296	6484	29989203	SO:0001819	synonymous_variant	3739	exon2			M55514	CCDS41629.1	11p14	2012-07-05	2002-07-10			ENSG00000182255		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6222	protein-coding gene	gene with protein product		176266	"""potassium voltage-gated channel, shaker-related subfamily, member 4-like"""	KCNA4L		2263489, 16382104	Standard	NM_002233		Approved	Kv1.4, HK1, HPCN2	uc001msk.3	P22459		ENST00000328224.6:c.1599C>A	11.37:g.30032627G>T		Somatic		Capture	Illumina HiSeq	Phase_I	29989203	NM_002233		Silent	SNP	ENST00000328224.6	37	CCDS41629.1																																																																																				0.502	KCNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388074.2	NM_002233	
ELF5	2001	broad.mit.edu	37	11	34527247	34527247	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:34527247C>T	ENST00000312319.2	-	2	309	c.80G>A	c.(79-81)tGc>tAc	p.C27Y	ELF5_ENST00000429939.2_Missense_Mutation_p.C17Y|ELF5_ENST00000528709.1_5'UTR|ELF5_ENST00000257832.2_Missense_Mutation_p.C17Y|ELF5_ENST00000532417.1_Missense_Mutation_p.C17Y	NM_001243081.1|NM_198381.1	NP_001230010.1|NP_938195.1	Q9UKW6	ELF5_HUMAN	E74-like factor 5 (ets domain transcription factor)	27					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|ectoderm development (GO:0007398)|mammary gland epithelial cell differentiation (GO:0060644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.C27Y(1)		large_intestine(4)|skin(1)	5		Acute lymphoblastic leukemia(5;0.0087)|all_hematologic(20;0.0384)				CAGGGGATCGCAGAAGGATGC	0.537																																					p.C17Y	Melanoma(61;202 1660 4348 21594)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G50A	11						.						191.0	142.0	158.0					11																	34527247		2202	4298	6500	34483823	SO:0001583	missense	2001	exon2			AF049703	CCDS7892.1, CCDS7893.1, CCDS58129.1, CCDS73273.1	11p13-p12	2008-05-14			ENSG00000135374	ENSG00000135374			3320	protein-coding gene	gene with protein product		605169				9840936	Standard	NM_001422		Approved		uc001mvp.2	Q9UKW6	OTTHUMG00000166451	ENST00000312319.2:c.80G>A	11.37:g.34527247C>T	ENSP00000311010:p.Cys27Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	34483823	NM_001422	A6XAE6|A8K452|O95175|Q8N2K9|Q96QY3|Q9UKW5	Missense_Mutation	SNP	ENST00000312319.2	37	CCDS7892.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.166829	0.38217	.	.	ENSG00000135374	ENST00000257832;ENST00000312319;ENST00000429939;ENST00000532417	T;T;T;T	0.34072	2.51;2.49;1.85;1.38	5.38	4.46	0.54185	Sterile alpha motif/pointed domain (1);	3.120010	0.01230	U	0.008336	T	0.45994	0.1370	N	0.19112	0.55	0.36858	D	0.888233	P;D;D	0.64830	0.742;0.994;0.989	B;D;P	0.77004	0.069;0.989;0.648	T	0.56817	-0.7916	10	0.02654	T	1	.	13.2031	0.59780	0.0:0.84:0.16:0.0	.	17;17;27	A6XAE6;Q9UKW6-3;Q9UKW6	.;.;ELF5_HUMAN	Y	17;27;17;17	ENSP00000257832:C17Y;ENSP00000311010:C27Y;ENSP00000407589:C17Y;ENSP00000436386:C17Y	ENSP00000257832:C17Y	C	-	2	0	ELF5	34483823	0.991000	0.36638	0.997000	0.53966	0.162000	0.22319	2.774000	0.47694	1.249000	0.43950	0.555000	0.69702	TGC		0.537	ELF5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389845.1	NM_198381	
MAPK8IP1	9479	broad.mit.edu	37	11	45924465	45924465	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:45924465C>T	ENST00000241014.2	+	5	1317	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	MAPK8IP1_ENST00000395629.2_Silent_p.L373L	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	383	Interaction with MAP3K7.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)	p.L383L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CAAGTACACGCTGGTGGTAGA	0.642																																					p.L383L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1147T	11						.						38.0	31.0	33.0					11																	45924465		2203	4297	6500	45881041	SO:0001819	synonymous_variant	9479	exon5				CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1147C>T	11.37:g.45924465C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45881041	NM_005456	D3DQP4|O43407	Silent	SNP	ENST00000241014.2	37	CCDS7916.1																																																																																				0.642	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
PHF21A	51317	broad.mit.edu	37	11	45955694	45955694	+	Missense_Mutation	SNP	C	C	T	rs370627435		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:45955694C>T	ENST00000418153.2	-	18	2067	c.1868G>A	c.(1867-1869)cGc>cAc	p.R623H	PHF21A_ENST00000323180.6_Missense_Mutation_p.R577H|PHF21A_ENST00000257821.4_Missense_Mutation_p.R624H			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	623	Required for transcriptional repression.				blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R577H(1)		central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(10)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	29						GTGGATGAGGCGAATCAGCTG	0.577																																					p.R623H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1868A	11						.	C	HIS/ARG,HIS/ARG	2,4402	4.2+/-10.8	0,2,2200	99.0	101.0	100.0		1868,1730	5.8	1.0	11		100	0,8598		0,0,4299	no	missense,missense	PHF21A	NM_001101802.1,NM_016621.3	29,29	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	623/681,577/635	45955694	2,13000	2202	4299	6501	45912270	SO:0001583	missense	51317	exon18			AL359593	CCDS31474.1, CCDS44578.1	11p11.2	2013-01-28			ENSG00000135365	ENSG00000135365		"""Zinc fingers, PHD-type"""	24156	protein-coding gene	gene with protein product		608325				11214970, 12032298	Standard	NM_001101802		Approved	BHC80, KIAA1696, BM-006	uc001ncc.4	Q96BD5	OTTHUMG00000167038	ENST00000418153.2:c.1868G>A	11.37:g.45955694C>T	ENSP00000398824:p.Arg623His	Somatic		Capture	Illumina HiSeq	Phase_I	45912270	NM_001101802	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Missense_Mutation	SNP	ENST00000418153.2	37	CCDS44578.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.26|15.26	2.781240|2.781240	0.49891|0.49891	4.54E-4|4.54E-4	0.0|0.0	ENSG00000135365|ENSG00000135365	ENST00000525676|ENST00000257821;ENST00000323180;ENST00000418153;ENST00000532028	.|T;T;T	.|0.59502	.|0.26;0.26;0.26	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68476|0.68476	0.3005|0.3005	L|L	0.46157|0.46157	1.445|1.445	0.80722|0.80722	D|D	1|1	.|D;P	.|0.59357	.|0.985;0.897	.|P;B	.|0.57425	.|0.82;0.196	T|T	0.68754|0.68754	-0.5325|-0.5325	5|10	.|0.62326	.|D	.|0.03	-5.6981|-5.6981	19.9976|19.9976	0.97389|0.97389	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|623;577	.|Q96BD5;Q96BD5-2	.|PF21A_HUMAN;.	T|H	80|624;577;623;98	.|ENSP00000257821:R624H;ENSP00000323152:R577H;ENSP00000398824:R623H	.|ENSP00000257821:R624H	A|R	-|-	1|2	0|0	PHF21A|PHF21A	45912270|45912270	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.060000|6.060000	0.71141|0.71141	2.737000|2.737000	0.93849|0.93849	0.563000|0.563000	0.77884|0.77884	GCC|CGC		0.577	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621	
CKAP5	9793	broad.mit.edu	37	11	46783671	46783671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:46783671G>A	ENST00000529230.1	-	32	4146	c.4100C>T	c.(4099-4101)gCc>gTc	p.A1367V	SNORD67_ENST00000390833.1_RNA|CKAP5_ENST00000415402.1_Missense_Mutation_p.A1367V|CKAP5_ENST00000354558.3_Missense_Mutation_p.A1367V|CKAP5_ENST00000312055.5_Missense_Mutation_p.A1367V			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1367					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TTCCTTTAAGGCTTTTCCTGG	0.478																																					p.A1367V	Ovarian(4;85 273 2202 4844 13323)											.	.	0			c.C4100T	11						.						113.0	95.0	101.0					11																	46783671		2201	4299	6500	46740247	SO:0001583	missense	9793	exon32				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.4100C>T	11.37:g.46783671G>A	ENSP00000432768:p.Ala1367Val	None		Capture	Illumina HiSeq	Phase_I	46740247	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.688404	0.88639	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558;ENST00000526876	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	6.03	6.03	0.97812	Armadillo-like helical (1);Armadillo-type fold (1);CLASP N-terminal domain (1);	0.098152	0.64402	D	0.000001	T	0.68026	0.2956	M	0.78344	2.41	0.58432	D	0.999999	P;P;P	0.50819	0.782;0.925;0.939	B;B;P	0.48368	0.327;0.439;0.575	T	0.64457	-0.6403	10	0.25106	T	0.35	-17.0977	20.5568	0.99304	0.0:0.0:1.0:0.0	.	1367;1367;1367	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	V	1367;1367;1367;1367;90	ENSP00000432768:A1367V;ENSP00000395302:A1367V;ENSP00000310227:A1367V;ENSP00000346566:A1367V	ENSP00000310227:A1367V	A	-	2	0	CKAP5	46740247	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.922000	0.87538	2.861000	0.98227	0.655000	0.94253	GCC		0.478	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
CKAP5	9793	broad.mit.edu	37	11	46818455	46818455	+	Silent	SNP	G	G	A	rs147577269	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:46818455G>A	ENST00000529230.1	-	12	1420	c.1374C>T	c.(1372-1374)gcC>gcT	p.A458A	CKAP5_ENST00000415402.1_Silent_p.A458A|CKAP5_ENST00000354558.3_Silent_p.A458A|CKAP5_ENST00000532321.1_5'Flank|CKAP5_ENST00000312055.5_Silent_p.A458A			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	458					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)		p.A458A(1)		breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						CTTCAAATGCGGCATCTCTGA	0.398													G|||	3	0.000599042	0.0023	0.0	5008	,	,		20885	0.0		0.0	False		,,,				2504	0.0				p.A458A	Ovarian(4;85 273 2202 4844 13323)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1374T	11						.	G	,	9,4393	15.5+/-35.6	0,9,2192	144.0	125.0	131.0		1374,1374	3.1	1.0	11	dbSNP_134	131	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	CKAP5	NM_001008938.3,NM_014756.3	,	0,9,6491	AA,AG,GG		0.0,0.2045,0.0692	,	458/2033,458/1973	46818455	9,12991	2201	4299	6500	46775031	SO:0001819	synonymous_variant	9793	exon12				CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.1374C>T	11.37:g.46818455G>A		Somatic		Capture	Illumina HiSeq	Phase_I	46775031	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Silent	SNP	ENST00000529230.1	37	CCDS31477.1																																																																																				0.398	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
LRP4	4038	broad.mit.edu	37	11	46921049	46921049	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:46921049G>A	ENST00000378623.1	-	5	678	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	146					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)	p.R146C(1)		breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAGCACTTGCGCATGTCTGGG	0.602																																					p.R146C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C436T	11						.						106.0	88.0	94.0					11																	46921049		2201	4299	6500	46877625	SO:0001583	missense	4038	exon5			AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.436C>T	11.37:g.46921049G>A	ENSP00000367888:p.Arg146Cys	Somatic		Capture	Illumina HiSeq	Phase_I	46877625	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	G	19.94	3.920750	0.73213	.	.	ENSG00000134569	ENST00000378623;ENST00000534404	D;D	0.95518	-3.73;-2.88	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.939	D	0.97415	1.0005	10	0.51188	T	0.08	.	12.5928	0.56453	0.0:0.0:0.722:0.278	.	191;146	C9JRN7;O75096	.;LRP4_HUMAN	C	146;97	ENSP00000367888:R146C;ENSP00000434763:R97C	ENSP00000367888:R146C	R	-	1	0	LRP4	46877625	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	5.919000	0.70005	2.621000	0.88768	0.561000	0.74099	CGC		0.602	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
ARFGAP2	84364	broad.mit.edu	37	11	47195030	47195030	+	Missense_Mutation	SNP	G	G	A	rs372871965		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:47195030G>A	ENST00000524782.1	-	7	794	c.566C>T	c.(565-567)cCg>cTg	p.P189L	ARFGAP2_ENST00000419701.2_Missense_Mutation_p.P82L|ARFGAP2_ENST00000319543.6_Intron|ARFGAP2_ENST00000395449.3_5'UTR|ARFGAP2_ENST00000426335.2_Intron	NM_001242832.1|NM_032389.4	NP_001229761.1|NP_115765.2	Q8N6H7	ARFG2_HUMAN	ADP-ribosylation factor GTPase activating protein 2	189	Required for interaction with coatomer.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.P189L(1)		breast(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						GCCATGCTCCGGCTCTGTGGA	0.582																																					p.P189L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C566T	11						.	G	LEU/PRO,LEU/PRO	1,4389		0,1,2194	59.0	50.0	53.0		566,482	3.9	0.4	11		53	1,8571		0,1,4285	no	missense,missense	ARFGAP2	NM_032389.4,NM_001242832.1	98,98	0,2,6479	AA,AG,GG		0.0117,0.0228,0.0154	benign,benign	189/522,161/494	47195030	2,12960	2195	4286	6481	47151606	SO:0001583	missense	84364	exon7			AK027482	CCDS7926.1, CCDS73283.1	11p11.2-p11.12	2012-10-05	2008-01-09	2008-01-09	ENSG00000149182	ENSG00000149182		"""ADP-ribosylation factor GTPase activating proteins"""	13504	protein-coding gene	gene with protein product		606908	"""zinc finger protein 289, ID1 regulated"""	ZNF289		11278321, 14690497	Standard	NM_032389		Approved	IRZ, Zfp289, FLJ14576	uc001ndt.3	Q8N6H7	OTTHUMG00000166773	ENST00000524782.1:c.566C>T	11.37:g.47195030G>A	ENSP00000434442:p.Pro189Leu	Somatic		Capture	Illumina HiSeq	Phase_I	47151606	NM_032389	B4DX29|B7Z9M7|D3DQQ9|Q3LIF2|Q8N3I1|Q96SX7	Missense_Mutation	SNP	ENST00000524782.1	37	CCDS7926.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.007783	0.35415	2.28E-4	1.17E-4	ENSG00000149182	ENST00000524782;ENST00000419701;ENST00000525398;ENST00000525314;ENST00000528444	T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89	5.93	3.87	0.44632	.	0.233294	0.43747	D	0.000539	T	0.32346	0.0826	L	0.53249	1.67	0.80722	D	1	B;B;B	0.31859	0.343;0.132;0.107	B;B;B	0.21360	0.034;0.026;0.017	T	0.06881	-1.0802	10	0.30078	T	0.28	-2.4634	8.9125	0.35561	0.0835:0.0:0.7724:0.1442	.	203;82;189	B7Z6H9;B4DX29;Q8N6H7	.;.;ARFG2_HUMAN	L	189;82;203;189;214	ENSP00000434442:P189L;ENSP00000389264:P82L;ENSP00000431939:P203L;ENSP00000434809:P189L;ENSP00000431684:P214L	ENSP00000389264:P82L	P	-	2	0	ARFGAP2	47151606	0.957000	0.32711	0.434000	0.26772	0.423000	0.31445	2.772000	0.47678	0.693000	0.31634	0.655000	0.94253	CCG		0.582	ARFGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391425.1	NM_032389	
NUP160	23279	broad.mit.edu	37	11	47837187	47837187	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:47837187T>C	ENST00000378460.2	-	13	1576	c.1530A>G	c.(1528-1530)gtA>gtG	p.V510V	NUP160_ENST00000530326.1_Silent_p.V396V|NUP160_ENST00000531016.1_5'UTR|NUP160_ENST00000528501.1_Silent_p.V74V|NUP160_ENST00000528071.1_Silent_p.V396V	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	510					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 export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)	p.V510V(1)		NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						CATACTCTGTTACACTTCCTT	0.368																																					p.V510V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1530G	11						.						89.0	92.0	91.0					11																	47837187		2201	4298	6499	47793763	SO:0001819	synonymous_variant	23279	exon13			D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"""nucleoporin 160kD"""			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.1530A>G	11.37:g.47837187T>C		Somatic		Capture	Illumina HiSeq	Phase_I	47793763	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Silent	SNP	ENST00000378460.2	37	CCDS31484.1																																																																																				0.368	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
OR5D14	219436	broad.mit.edu	37	11	55563621	55563621	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:55563621C>A	ENST00000335605.1	+	1	590	c.590C>A	c.(589-591)cCc>cAc	p.P197H		NM_001004735.1	NP_001004735.1	Q8NGL3	OR5DE_HUMAN	olfactory receptor, family 5, subfamily D, member 14	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P197H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(30)|ovary(2)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	48		all_epithelial(135;0.196)				ATACTCATCCCCCACCTGCTG	0.418																																					p.P197H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C590A	11						.						208.0	201.0	203.0					11																	55563621		2200	4296	6496	55320197	SO:0001583	missense	219436	exon1			AB065779	CCDS31508.1	11q11	2012-08-09			ENSG00000186113	ENSG00000186113		"""GPCR / Class A : Olfactory receptors"""	15281	protein-coding gene	gene with protein product							Standard	NM_001004735		Approved		uc010rim.2	Q8NGL3	OTTHUMG00000166809	ENST00000335605.1:c.590C>A	11.37:g.55563621C>A	ENSP00000334456:p.Pro197His	Somatic		Capture	Illumina HiSeq	Phase_I	55320197	NM_001004735	Q6IF69|Q6IFD4|Q96RB5	Missense_Mutation	SNP	ENST00000335605.1	37	CCDS31508.1	.	.	.	.	.	.	.	.	.	.	c	0.928	-0.713787	0.03206	.	.	ENSG00000186113	ENST00000335605	T	0.00069	8.77	4.87	2.86	0.33363	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	D	0.000397	T	0.00073	0.0002	N	0.04148	-0.265	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.22730	-1.0208	10	0.52906	T	0.07	-25.416	4.851	0.13537	0.1715:0.6487:0.0:0.1797	.	197	Q8NGL3	OR5DE_HUMAN	H	197	ENSP00000334456:P197H	ENSP00000334456:P197H	P	+	2	0	OR5D14	55320197	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.167000	0.09940	1.051000	0.40369	-0.152000	0.13540	CCC		0.418	OR5D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391513.1	NM_001004735	
OR5W2	390148	broad.mit.edu	37	11	55681391	55681391	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:55681391A>G	ENST00000344514.1	-	1	667	c.668T>C	c.(667-669)cTa>cCa	p.L223P		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L223P(1)		breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CAAGACTGATAGGATGATATA	0.413																																					p.L223P	Melanoma(48;171 1190 15239 43886 49348)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T668C	11						.						63.0	69.0	67.0					11																	55681391		2201	4296	6497	55437967	SO:0001583	missense	390148	exon1			BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.668T>C	11.37:g.55681391A>G	ENSP00000342448:p.Leu223Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55437967	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	A	7.245	0.602025	0.13939	.	.	ENSG00000187612	ENST00000344514	T	0.39406	1.08	5.0	1.45	0.22620	GPCR, rhodopsin-like superfamily (1);	0.561433	0.13349	N	0.394577	T	0.45196	0.1330	M	0.73430	2.235	0.09310	N	0.999999	B	0.19445	0.036	B	0.33454	0.164	T	0.49826	-0.8898	10	0.62326	D	0.03	.	7.2829	0.26322	0.7266:0.0:0.2734:0.0	.	223	Q8NH69	OR5W2_HUMAN	P	223	ENSP00000342448:L223P	ENSP00000342448:L223P	L	-	2	0	OR5W2	55437967	0.000000	0.05858	0.000000	0.03702	0.348000	0.29142	-0.813000	0.04491	0.262000	0.21774	0.443000	0.29094	CTA		0.413	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
OR5AK2	390181	broad.mit.edu	37	11	56756444	56756444	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:56756444C>T	ENST00000326855.2	+	1	98	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A19V(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						GGATTTGGTGCCCAGCATGAG	0.403																																					p.A19V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C56T	11						.						148.0	142.0	144.0					11																	56756444		2201	4296	6497	56513020	SO:0001583	missense	390181	exon1			AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.56C>T	11.37:g.56756444C>T	ENSP00000322784:p.Ala19Val	Somatic		Capture	Illumina HiSeq	Phase_I	56513020	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	.	.	.	.	.	.	.	.	.	.	C	3.199	-0.164155	0.06502	.	.	ENSG00000181273	ENST00000326855	T	0.00438	7.42	3.66	-7.32	0.01436	.	1.000240	0.08070	N	0.999644	T	0.00178	0.0005	N	0.13098	0.295	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.44682	-0.9312	10	0.56958	D	0.05	-3.9225	0.8527	0.01175	0.269:0.1731:0.3283:0.2296	.	19	Q8NH90	O5AK2_HUMAN	V	19	ENSP00000322784:A19V	ENSP00000322784:A19V	A	+	2	0	OR5AK2	56513020	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-2.777000	0.00775	-2.406000	0.00574	0.194000	0.17425	GCC		0.403	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
OR6Q1	219952	broad.mit.edu	37	11	57798999	57798999	+	Missense_Mutation	SNP	C	C	T	rs138474678		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:57798999C>T	ENST00000302622.3	+	1	598	c.575C>T	c.(574-576)tCg>tTg	p.S192L	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S192L(1)		biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTAGCCTTGTCGTGCTCAGAT	0.493																																					p.S192L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C575T	11						.	C	LEU/SER	0,4402		0,0,2201	254.0	224.0	234.0		575	5.0	1.0	11	dbSNP_134	234	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR6Q1	NM_001005186.2	145	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	192/318	57798999	1,12993	2201	4296	6497	57555575	SO:0001583	missense	219952	exon1			AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.575C>T	11.37:g.57798999C>T	ENSP00000307734:p.Ser192Leu	Somatic		Capture	Illumina HiSeq	Phase_I	57555575	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Missense_Mutation	SNP	ENST00000302622.3	37	CCDS31541.1	.	.	.	.	.	.	.	.	.	.	C	19.19	3.780361	0.70222	0.0	1.16E-4	ENSG00000172381	ENST00000302622	T	0.00291	8.27	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.211899	0.23879	N	0.043680	T	0.00845	0.0028	M	0.89095	3.005	0.23150	N	0.998217	D	0.71674	0.998	D	0.66084	0.941	T	0.36016	-0.9765	10	0.87932	D	0	.	17.154	0.86785	0.0:1.0:0.0:0.0	.	192	Q8NGQ2	OR6Q1_HUMAN	L	192	ENSP00000307734:S192L	ENSP00000307734:S192L	S	+	2	0	OR6Q1	57555575	0.002000	0.14202	0.971000	0.41717	0.891000	0.51852	1.393000	0.34497	2.336000	0.79503	0.638000	0.83543	TCG		0.493	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
OR1S2	219958	broad.mit.edu	37	11	57971603	57971603	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:57971603T>G	ENST00000302592.6	-	1	50	c.51A>C	c.(49-51)gaA>gaC	p.E17D		NM_001004459.1	NP_001004459.1	Q8NGQ3	OR1S2_HUMAN	olfactory receptor, family 1, subfamily S, member 2	17						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E17D(1)		endometrium(11)|kidney(1)|large_intestine(4)|lung(23)|ovary(2)|skin(2)|stomach(2)|urinary_tract(1)	46		Breast(21;0.0589)				TGGTTTGGTTTTCTTGATGCA	0.413																																					p.E17D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A51C	11						.						137.0	136.0	136.0					11																	57971603		2201	4296	6497	57728179	SO:0001583	missense	219958	exon1			BK004297	CCDS31545.1	11q12.1	2012-08-09			ENSG00000197887	ENSG00000197887		"""GPCR / Class A : Olfactory receptors"""	15141	protein-coding gene	gene with protein product							Standard	NM_001004459		Approved		uc010rkb.2	Q8NGQ3	OTTHUMG00000167541	ENST00000302592.6:c.51A>C	11.37:g.57971603T>G	ENSP00000305469:p.Glu17Asp	Somatic		Capture	Illumina HiSeq	Phase_I	57728179	NM_001004459	Q6IFG5|Q96R85	Missense_Mutation	SNP	ENST00000302592.6	37	CCDS31545.1	.	.	.	.	.	.	.	.	.	.	T	1.687	-0.505007	0.04261	.	.	ENSG00000197887	ENST00000302592	T	0.00466	7.23	4.25	1.92	0.25849	.	1.003600	0.08031	N	0.993489	T	0.00356	0.0011	L	0.39147	1.195	0.21841	N	0.999519	B	0.24368	0.102	B	0.19148	0.024	T	0.40572	-0.9556	10	0.32370	T	0.25	.	5.7476	0.18128	0.0:0.2195:0.0:0.7805	.	17	Q8NGQ3	OR1S2_HUMAN	D	17	ENSP00000305469:E17D	ENSP00000305469:E17D	E	-	3	2	OR1S2	57728179	0.958000	0.32768	0.913000	0.36048	0.034000	0.12701	1.589000	0.36644	0.293000	0.22520	-0.263000	0.10527	GAA		0.413	OR1S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394703.2	NM_001004459	
STX3	6809	broad.mit.edu	37	11	59556356	59556356	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:59556356T>C	ENST00000337979.4	+	4	772	c.225T>C	c.(223-225)gaT>gaC	p.D75D	STX3_ENST00000437946.2_5'UTR|STX3_ENST00000529177.1_Silent_p.D75D|STX3_ENST00000535361.1_Silent_p.D75D|STX3_ENST00000300150.7_Silent_p.D44D	NM_001178040.1|NM_004177.4	NP_001171511.1|NP_004168.1	Q13277	STX3_HUMAN	syntaxin 3	75					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|long-term synaptic potentiation (GO:0060291)|membrane fusion (GO:0061025)|neuron projection development (GO:0031175)|neurotransmitter transport (GO:0006836)	apical plasma membrane (GO:0016324)|azurophil granule (GO:0042582)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|SNARE complex (GO:0031201)|specific granule (GO:0042581)|vacuole (GO:0005773)	arachidonic acid binding (GO:0050544)	p.D75D(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|skin(1)	13						AAACCAAGGATGACCTAGAGC	0.473																																					p.D75D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T225C	11						.						90.0	78.0	82.0					11																	59556356		2201	4295	6496	59312932	SO:0001819	synonymous_variant	6809	exon4			AJ002076	CCDS7975.1, CCDS53637.1	11q12.1	2008-02-05	2006-04-25	2006-04-25	ENSG00000166900	ENSG00000166900			11438	protein-coding gene	gene with protein product		600876	"""syntaxin 3A"""	STX3A		16598260, 16339081	Standard	NM_004177		Approved		uc001nog.3	Q13277	OTTHUMG00000167353	ENST00000337979.4:c.225T>C	11.37:g.59556356T>C		Somatic		Capture	Illumina HiSeq	Phase_I	59312932	NM_001178040	B4DME0|O43750|O43751|Q15360	Silent	SNP	ENST00000337979.4	37	CCDS7975.1																																																																																				0.473	STX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394264.1	NM_004177	
ZP1	22917	broad.mit.edu	37	11	60641222	60641222	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:60641222G>T	ENST00000278853.5	+	9	1546	c.1546G>T	c.(1546-1548)Ggc>Tgc	p.G516C		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	516	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)		p.G516C(1)		breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						CCTGGACTCAGGCTCCCAGAG	0.602																																					p.G516C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1546T	11						.						85.0	88.0	87.0					11																	60641222		2203	4299	6502	60397798	SO:0001583	missense	22917	exon9			BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1546G>T	11.37:g.60641222G>T	ENSP00000278853:p.Gly516Cys	Somatic		Capture	Illumina HiSeq	Phase_I	60397798	NM_207341		Missense_Mutation	SNP	ENST00000278853.5	37	CCDS31572.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143159	0.37825	.	.	ENSG00000149506	ENST00000278853;ENST00000544498	T	0.24723	1.84	5.29	2.16	0.27623	Zona pellucida sperm-binding protein (3);	1.444650	0.03698	N	0.248101	T	0.35451	0.0932	L	0.29908	0.895	0.09310	N	1	D	0.58268	0.982	D	0.65140	0.932	T	0.10314	-1.0635	10	0.52906	T	0.07	-7.3558	3.6884	0.08336	0.4291:0.0:0.4035:0.1674	.	516	P60852	ZP1_HUMAN	C	516;223	ENSP00000278853:G516C	ENSP00000278853:G516C	G	+	1	0	ZP1	60397798	0.000000	0.05858	0.014000	0.15608	0.601000	0.36947	-0.121000	0.10643	0.128000	0.18479	0.313000	0.20887	GGC		0.602	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
TMEM109	79073	broad.mit.edu	37	11	60689458	60689458	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:60689458C>T	ENST00000227525.3	+	4	956	c.553C>T	c.(553-555)Cgg>Tgg	p.R185W	TMEM132A_ENST00000453848.2_5'Flank|TMEM109_ENST00000536171.1_Missense_Mutation_p.R185W|TMEM132A_ENST00000005286.4_5'Flank|RP11-881M11.4_ENST00000543907.1_RNA	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	185					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)		p.R185W(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						CCCTTCCACCCGGGCCCTGCT	0.672																																					p.R185W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C553T	11						.						69.0	69.0	69.0					11																	60689458		2203	4299	6502	60446034	SO:0001583	missense	79073	exon4				CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.553C>T	11.37:g.60689458C>T	ENSP00000227525:p.Arg185Trp	Somatic		Capture	Illumina HiSeq	Phase_I	60446034	NM_024092		Missense_Mutation	SNP	ENST00000227525.3	37	CCDS7996.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.730095	0.69074	.	.	ENSG00000110108	ENST00000227525;ENST00000446886;ENST00000540407;ENST00000536171	.	.	.	4.9	3.99	0.46301	.	0.000000	0.48767	D	0.000163	T	0.57286	0.2043	M	0.61703	1.905	0.37845	D	0.929193	B	0.25521	0.128	B	0.18871	0.023	T	0.61662	-0.7017	9	0.66056	D	0.02	-28.2172	11.1326	0.48356	0.0:0.9125:0.0:0.0875	.	185	Q9BVC6	TM109_HUMAN	W	185;185;107;185	.	ENSP00000227525:R185W	R	+	1	2	TMEM109	60446034	0.994000	0.37717	1.000000	0.80357	0.807000	0.45602	3.231000	0.51294	1.065000	0.40693	-0.136000	0.14681	CGG		0.672	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092	
DAGLA	747	broad.mit.edu	37	11	61504707	61504707	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:61504707G>A	ENST00000257215.5	+	14	1541	c.1425G>A	c.(1423-1425)gcG>gcA	p.A475A		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	475					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.A475A(1)		breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		CCCTGGGCGCGGGCACTGCTG	0.652																																					p.A475A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1425A	11						.						140.0	147.0	145.0					11																	61504707		2202	4299	6501	61261283	SO:0001819	synonymous_variant	747	exon14			AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.1425G>A	11.37:g.61504707G>A		Somatic		Capture	Illumina HiSeq	Phase_I	61261283	NM_006133	A7E233|Q6WQJ0	Silent	SNP	ENST00000257215.5	37	CCDS31578.1																																																																																				0.652	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
MYRF	745	broad.mit.edu	37	11	61547322	61547322	+	Silent	SNP	C	C	T	rs142542699	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:61547322C>T	ENST00000278836.5	+	17	2352	c.2256C>T	c.(2254-2256)tcC>tcT	p.S752S	TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000327797.1_Silent_p.S398S|MYRF_ENST00000389602.4_Silent_p.S143S|MYRF_ENST00000265460.5_Silent_p.S743S	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	752					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S743S(1)									AGTCATCGTCCGTGGTTCCGG	0.612													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20745	0.0		0.0	False		,,,				2504	0.0				p.S743S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2229T	11						.	C	,	16,4388	22.3+/-47.3	2,12,2188	81.0	75.0	77.0		2256,2229	-10.5	0.0	11	dbSNP_134	77	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	C11orf9	NM_001127392.1,NM_013279.2	,	2,12,6487	TT,TC,CC		0.0,0.3633,0.1231	,	752/1152,743/1112	61547322	16,12986	2202	4299	6501	61303898	SO:0001819	synonymous_variant	745	exon17				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2256C>T	11.37:g.61547322C>T		Somatic		Capture	Illumina HiSeq	Phase_I	61303898	NM_013279	O43582|Q9P1Q6	Silent	SNP	ENST00000278836.5	37	CCDS44622.1																																																																																				0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
TMEM258	746	broad.mit.edu	37	11	61558075	61558075	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:61558075C>A	ENST00000537328.1	-	2	55		c.e2-1		TMEM258_ENST00000535042.1_5'UTR|TMEM258_ENST00000543510.1_Splice_Site|FEN1_ENST00000305885.2_5'Flank|FADS2_ENST00000574708.1_5'Flank|MIR611_ENST00000384869.1_RNA	NM_014206.3	NP_055021.1	P61165	TM258_HUMAN	transmembrane protein 258							integral component of membrane (GO:0016021)		p.?(1)									CCTCGAGCTCCTAGAGGAGGG	0.537																																					.												.	.	1	Unknown(1)	large_intestine(1)	.	11						.						83.0	67.0	72.0					11																	61558075		2201	4299	6500	61314651	SO:0001630	splice_region_variant	746	.				CCDS8009.1	11q12.2	2012-12-03	2012-12-03	2012-12-03	ENSG00000134825	ENSG00000134825			1164	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 10"""	C11orf10		12427278	Standard	NM_014206		Approved		uc001nsf.3	P61165	OTTHUMG00000168172	ENST00000537328.1:c.4-1G>T	11.37:g.61558075C>A		Somatic		Capture	Illumina HiSeq	Phase_I	61314651	.	A8K6L8|Q9D953|Q9Y2Q7	Splice_Site	SNP	ENST00000537328.1	37	CCDS8009.1	.	.	.	.	.	.	.	.	.	.	C	16.51	3.144493	0.57044	.	.	ENSG00000134825	ENST00000537328	.	.	.	5.46	4.55	0.56014	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0798	0.64914	0.0:0.9268:0.0:0.0732	.	.	.	.	.	-1	.	.	.	-	.	.	C11orf10	61314651	1.000000	0.71417	0.997000	0.53966	0.832000	0.47134	7.361000	0.79497	1.449000	0.47699	0.655000	0.94253	.		0.537	TMEM258-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398577.1	NM_014206	Intron
AHNAK	79026	broad.mit.edu	37	11	62286069	62286069	+	Missense_Mutation	SNP	C	C	T	rs144898392		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:62286069C>T	ENST00000378024.4	-	5	16094	c.15820G>A	c.(15820-15822)Gaa>Aaa	p.E5274K	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_5'Flank|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5274					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.E5274K(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TCGGGCCCTTCGAGCTTAACA	0.537																																					p.E5274K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G15820A	11						.	C	LYS/GLU,	0,4404		0,0,2202	67.0	68.0	68.0		15820,	2.7	0.5	11	dbSNP_134	68	1,8597	1.2+/-3.3	0,1,4298	no	missense,intron	AHNAK	NM_001620.1,NM_024060.2	56,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,	5274/5891,	62286069	1,13001	2202	4299	6501	62042645	SO:0001583	missense	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.15820G>A	11.37:g.62286069C>T	ENSP00000367263:p.Glu5274Lys	Somatic		Capture	Illumina HiSeq	Phase_I	62042645	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.673121	0.47781	0.0	1.16E-4	ENSG00000124942	ENST00000378024	T	0.01126	5.3	4.82	2.74	0.32292	.	0.159038	0.29159	U	0.012973	T	0.01558	0.0050	L	0.35593	1.075	0.25234	N	0.989802	D	0.59357	0.985	P	0.54431	0.752	T	0.45789	-0.9237	10	0.10111	T	0.7	-13.1118	6.014	0.19592	0.0:0.5273:0.3153:0.1574	.	5274	Q09666	AHNK_HUMAN	K	5274	ENSP00000367263:E5274K	ENSP00000367263:E5274K	E	-	1	0	AHNAK	62042645	0.000000	0.05858	0.477000	0.27303	0.899000	0.52679	0.082000	0.14847	0.972000	0.38314	0.638000	0.83543	GAA		0.537	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
AHNAK	79026	broad.mit.edu	37	11	62292856	62292856	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:62292856C>A	ENST00000378024.4	-	5	9307	c.9033G>T	c.(9031-9033)gtG>gtT	p.V3011V	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3011					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.V3011V(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGAACGCCCACATCCGGGA	0.532																																					p.V3011V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G9033T	11						.						145.0	154.0	151.0					11																	62292856		2202	4299	6501	62049432	SO:0001819	synonymous_variant	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.9033G>T	11.37:g.62292856C>A		Somatic		Capture	Illumina HiSeq	Phase_I	62049432	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	37	CCDS31584.1																																																																																				0.532	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
AHNAK	79026	broad.mit.edu	37	11	62299097	62299097	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:62299097C>T	ENST00000378024.4	-	5	3066	c.2792G>A	c.(2791-2793)gGc>gAc	p.G931D	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	931					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)	p.G931D(1)		NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				GAACTTGGGGCCCTTCAGCTT	0.478																																					p.G931D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2792A	11						.						133.0	144.0	140.0					11																	62299097		2202	4299	6501	62055673	SO:0001583	missense	79026	exon5			M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.2792G>A	11.37:g.62299097C>T	ENSP00000367263:p.Gly931Asp	Somatic		Capture	Illumina HiSeq	Phase_I	62055673	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	c	9.557	1.117394	0.20877	.	.	ENSG00000124942	ENST00000378024	T	0.03330	3.97	4.78	3.87	0.44632	.	0.176939	0.35870	N	0.002940	T	0.16685	0.0401	M	0.86268	2.805	0.39502	D	0.968217	D	0.71674	0.998	D	0.80764	0.994	T	0.31081	-0.9956	10	0.12103	T	0.63	-13.374	13.1554	0.59514	0.0:0.9205:0.0:0.0795	.	931	Q09666	AHNK_HUMAN	D	931	ENSP00000367263:G931D	ENSP00000367263:G931D	G	-	2	0	AHNAK	62055673	0.087000	0.21565	0.999000	0.59377	0.852000	0.48524	1.375000	0.34295	1.138000	0.42230	-0.463000	0.05309	GGC		0.478	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
TAF6L	10629	broad.mit.edu	37	11	62554021	62554021	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:62554021C>A	ENST00000294168.3	+	11	1323	c.1122C>A	c.(1120-1122)gcC>gcA	p.A374A	TMEM179B_ENST00000333449.4_5'Flank|TMEM223_ENST00000527073.1_Intron|TMEM179B_ENST00000533861.1_5'Flank|RP11-727F15.12_ENST00000601484.1_RNA	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	374					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)	p.A374A(1)		endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						AGATGAAGGCCCAGGCAGCAG	0.582											OREG0021030	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A374A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1122A	11						.						18.0	19.0	18.0					11																	62554021		2200	4297	6497	62310597	SO:0001819	synonymous_variant	10629	exon11			BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"""TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.1122C>A	11.37:g.62554021C>A		Somatic	1062	Capture	Illumina HiSeq	Phase_I	62310597	NM_006473	B2RAT0|Q96HA6	Silent	SNP	ENST00000294168.3	37	CCDS8035.1																																																																																				0.582	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473	
MACROD1	28992	broad.mit.edu	37	11	63884950	63884950	+	Intron	SNP	C	C	T	rs369112014		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:63884950C>T	ENST00000255681.6	-	3	584				FLRT1_ENST00000246841.3_Missense_Mutation_p.T404M|RP11-21A7A.3_ENST00000543817.1_RNA	NM_014067.3	NP_054786.2	Q9BQ69	MACD1_HUMAN	MACRO domain containing 1						cellular response to DNA damage stimulus (GO:0006974)|protein de-ADP-ribosylation (GO:0051725)|purine nucleoside metabolic process (GO:0042278)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	deacetylase activity (GO:0019213)|hydrolase activity, acting on glycosyl bonds (GO:0016798)	p.T404M(1)		breast(1)|large_intestine(3)|lung(6)|skin(1)	11						TCTGCCACCACGCCCCAGGGT	0.647																																					p.T404M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1211T	11						.						47.0	46.0	46.0					11																	63884950		2200	4297	6497	63641526	SO:0001627	intron_variant	23769	exon2			AF202922	CCDS8056.1	11q13.1	2007-07-24	2007-06-11		ENSG00000133315	ENSG00000133315			29598	protein-coding gene	gene with protein product		610400				15691879	Standard	NM_014067		Approved	LRP16	uc001nyh.3	Q9BQ69	OTTHUMG00000167843	ENST00000255681.6:c.517+33760G>A	11.37:g.63884950C>T		Somatic		Capture	Illumina HiSeq	Phase_I	63641526	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319804	0.60634	.	.	ENSG00000126500	ENST00000246841	T	0.55052	0.54	5.4	5.4	0.78164	.	0.071304	0.56097	D	0.000037	T	0.53254	0.1785	N	0.22421	0.69	0.38485	D	0.947814	D	0.57571	0.98	P	0.53360	0.724	T	0.59553	-0.7433	10	0.54805	T	0.06	-14.029	17.9416	0.89027	0.0:1.0:0.0:0.0	.	376	Q9NZU1	FLRT1_HUMAN	M	404	ENSP00000246841:T404M	ENSP00000246841:T404M	T	+	2	0	FLRT1	63641526	1.000000	0.71417	0.979000	0.43373	0.939000	0.58152	5.886000	0.69743	2.512000	0.84698	0.650000	0.86243	ACG		0.647	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067	
RASGRP2	10235	broad.mit.edu	37	11	64509569	64509569	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:64509569A>G	ENST00000354024.3	-	3	341	c.89T>C	c.(88-90)gTg>gCg	p.V30A	RASGRP2_ENST00000394429.1_Intron|RASGRP2_ENST00000377486.3_Missense_Mutation_p.V30A|RASGRP2_ENST00000377497.3_Missense_Mutation_p.V30A|RASGRP2_ENST00000377489.1_Missense_Mutation_p.V30A|RASGRP2_ENST00000394430.1_Missense_Mutation_p.V30A|RASGRP2_ENST00000394432.3_Missense_Mutation_p.V30A|RASGRP2_ENST00000377487.1_Missense_Mutation_p.V30A|RASGRP2_ENST00000377494.1_Missense_Mutation_p.V30A|RASGRP2_ENST00000394428.1_Intron	NM_153819.1	NP_722541.1	Q7LDG7	GRP2_HUMAN	RAS guanyl releasing protein 2 (calcium and DAG-regulated)	30	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				blood coagulation (GO:0007596)|cellular response to calcium ion (GO:0071277)|platelet activation (GO:0030168)|positive regulation of Rap GTPase activity (GO:0032854)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|diacylglycerol binding (GO:0019992)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)	p.V92A(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGGGTCCCGCACCTTCCCGGA	0.622																																					p.V30A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T89C	11						.						33.0	31.0	32.0					11																	64509569		2198	4297	6495	64266145	SO:0001583	missense	10235	exon3			U78170	CCDS31598.1	11q13	2014-09-17			ENSG00000068831	ENSG00000068831		"""EF-hand domain containing"""	9879	protein-coding gene	gene with protein product		605577				9789079	Standard	NM_001098670		Approved	CALDAG-GEFI	uc009ypv.3	Q7LDG7	OTTHUMG00000045420	ENST00000354024.3:c.89T>C	11.37:g.64509569A>G	ENSP00000338864:p.Val30Ala	Somatic		Capture	Illumina HiSeq	Phase_I	64266145	NM_001098670	A6NDC7|O00538|Q9UL65	Missense_Mutation	SNP	ENST00000354024.3	37	CCDS31598.1	.	.	.	.	.	.	.	.	.	.	A	16.88	3.244026	0.58995	.	.	ENSG00000068831	ENST00000377494;ENST00000394432;ENST00000377497;ENST00000354024;ENST00000431822;ENST00000377486;ENST00000377487;ENST00000377489;ENST00000394430;ENST00000439594;ENST00000377485;ENST00000430645	T;T;T;T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	4.67	4.67	0.58626	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.373661	0.24502	N	0.037974	T	0.27454	0.0674	L	0.38175	1.15	0.43279	D	0.995241	B	0.33318	0.408	B	0.36885	0.235	T	0.07214	-1.0784	10	0.42905	T	0.14	-1.1613	12.6951	0.56999	1.0:0.0:0.0:0.0	.	30	Q7LDG7	GRP2_HUMAN	A	30	ENSP00000366714:V30A;ENSP00000377953:V30A;ENSP00000366717:V30A;ENSP00000338864:V30A;ENSP00000399114:V30A;ENSP00000366706:V30A;ENSP00000366707:V30A;ENSP00000366709:V30A;ENSP00000377951:V30A;ENSP00000366705:V30A;ENSP00000401314:V30A	ENSP00000338864:V30A	V	-	2	0	RASGRP2	64266145	0.990000	0.36364	1.000000	0.80357	0.795000	0.44927	3.106000	0.50322	2.049000	0.60858	0.260000	0.18958	GTG		0.622	RASGRP2-002	NOVEL	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142062.1	NM_153819	
PYGM	5837	broad.mit.edu	37	11	64525297	64525297	+	Missense_Mutation	SNP	C	C	T	rs375724338		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:64525297C>T	ENST00000164139.3	-	5	1012	c.614G>A	c.(613-615)gGc>gAc	p.G205D	PYGM_ENST00000377432.3_Missense_Mutation_p.G117D	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	205			G -> S (in GSD5; dbSNP:rs119103251). {ECO:0000269|PubMed:10382911, ECO:0000269|PubMed:10382912, ECO:0000269|PubMed:11706962, ECO:0000269|PubMed:7603523, ECO:0000269|PubMed:8316268}.		carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)	p.G205D(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTCCACATGGCCGTAGAAGTG	0.637																																					p.G117D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G350A	11						.	C	ASP/GLY,ASP/GLY	0,4402		0,0,2201	74.0	66.0	69.0		350,614	5.7	1.0	11		69	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	PYGM	NM_001164716.1,NM_005609.2	94,94	0,1,6497	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	117/755,205/843	64525297	1,12995	2201	4297	6498	64281873	SO:0001583	missense	5837	exon3				CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.614G>A	11.37:g.64525297C>T	ENSP00000164139:p.Gly205Asp	Somatic		Capture	Illumina HiSeq	Phase_I	64281873	NM_001164716	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	37	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	C	34	5.391137	0.95988	0.0	1.16E-4	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.99382	-4.29;-5.8	5.7	5.7	0.88788	.	0.000000	0.64402	D	0.000010	D	0.99399	0.9788	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99097	1.0842	10	0.87932	D	0	-30.206	17.3277	0.87253	0.0:1.0:0.0:0.0	.	117;205	A6NDY6;P11217	.;PYGM_HUMAN	D	117;205;186	ENSP00000366650:G117D;ENSP00000164139:G205D	ENSP00000164139:G205D	G	-	2	0	PYGM	64281873	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.818000	0.86416	2.700000	0.92200	0.563000	0.77884	GGC		0.637	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
SF1	7536	broad.mit.edu	37	11	64543993	64543993	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:64543993C>T	ENST00000377390.3	-	2	474	c.137G>A	c.(136-138)cGa>cAa	p.R46Q	SF1_ENST00000227503.9_Missense_Mutation_p.R46Q|SF1_ENST00000377387.1_Missense_Mutation_p.R171Q|SF1_ENST00000433274.2_Missense_Mutation_p.R20Q|SF1_ENST00000377394.3_Missense_Mutation_p.R46Q|SF1_ENST00000422298.2_5'UTR|SF1_ENST00000334944.5_Missense_Mutation_p.R46Q|AP001462.6_ENST00000594089.1_lincRNA	NM_004630.3	NP_004621.2	Q15637	SF01_HUMAN	splicing factor 1	46					Leydig cell differentiation (GO:0033327)|male sex determination (GO:0030238)|mRNA 3'-splice site recognition (GO:0000389)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of steroid biosynthetic process (GO:0050810)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|ribosome (GO:0005840)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.R46Q(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|skin(2)	31						TTCTTGTTCTCGAGTAAGTCC	0.413																																					p.R46Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G137A	11						.						148.0	137.0	141.0					11																	64543993		2201	4297	6498	64300569	SO:0001583	missense	7536	exon2			D26120	CCDS8080.1, CCDS8081.1, CCDS31599.1, CCDS44642.1, CCDS44642.2, CCDS53660.1, CCDS53661.1	11q13	2014-09-17	2001-12-19	2002-01-11	ENSG00000168066	ENSG00000168066		"""Zinc fingers, CCHC domain containing"""	12950	protein-coding gene	gene with protein product		601516	"""zinc finger protein 162"""	ZNF162		7912130, 9573336	Standard	NM_201997		Approved	ZFM1, ZCCHC25	uc001oaz.2	Q15637	OTTHUMG00000066833	ENST00000377390.3:c.137G>A	11.37:g.64543993C>T	ENSP00000366607:p.Arg46Gln	Somatic		Capture	Illumina HiSeq	Phase_I	64300569	NM_201998	B7Z1Q1|C9JJE2|Q14818|Q14819|Q15913|Q8IY00|Q92744|Q92745|Q969H7|Q9BW01|Q9UEI0	Missense_Mutation	SNP	ENST00000377390.3	37	CCDS31599.1	.	.	.	.	.	.	.	.	.	.	C	14.51	2.558196	0.45590	.	.	ENSG00000168066	ENST00000377387;ENST00000377390;ENST00000227503;ENST00000377394;ENST00000334944;ENST00000433274;ENST00000432725;ENST00000416674	T;T;T;T;T;T	0.40225	1.05;1.05;1.06;1.04;1.05;1.04	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	N	0.04959	-0.14	0.80722	D	1	D;P;B;B;B;B	0.89917	1.0;0.554;0.363;0.248;0.363;0.363	D;B;B;B;B;B	0.83275	0.996;0.093;0.068;0.031;0.068;0.068	T	0.40440	-0.9563	10	0.18276	T	0.48	.	16.0208	0.80486	0.0:1.0:0.0:0.0	.	46;46;46;46;46;171	Q14820;Q15637-6;Q15637-4;Q15637;Q15637-2;Q15637-5	.;.;.;SF01_HUMAN;.;.	Q	171;46;46;46;46;20;20;46	ENSP00000366604:R171Q;ENSP00000366607:R46Q;ENSP00000227503:R46Q;ENSP00000366611:R46Q;ENSP00000334414:R46Q;ENSP00000396793:R20Q	ENSP00000227503:R46Q	R	-	2	0	SF1	64300569	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.771000	0.68881	2.366000	0.80165	0.563000	0.77884	CGA		0.413	SF1-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000143242.1	NM_004630	
NAALADL1	10004	broad.mit.edu	37	11	64812885	64812885	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:64812885G>A	ENST00000358658.3	-	18	2108	c.2081C>T	c.(2080-2082)cCg>cTg	p.P694L	NAALADL1_ENST00000340252.4_Missense_Mutation_p.P745L|NAALADL1_ENST00000355721.3_Missense_Mutation_p.P653L|NAALADL1_ENST00000526799.1_Missense_Mutation_p.P41L|NAALADL1_ENST00000355369.2_3'UTR|NAALADL1_ENST00000356632.3_Missense_Mutation_p.P659L|NAALADL1_ENST00000339885.2_3'UTR	NM_005468.2	NP_005459.2	Q9UQQ1	NALDL_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 1	694						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)	p.P694L(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	29						GGATAGGCCCGGGAATGTGAC	0.592																																					p.P694L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2081T	11						.						30.0	30.0	30.0					11																	64812885		2201	4297	6498	64569461	SO:0001583	missense	10004	exon18			AF010141	CCDS31604.1	11q12	2011-08-16			ENSG00000168060	ENSG00000168060			23536	protein-coding gene	gene with protein product	"""ileal peptidase I100"""	602640				10085079	Standard	NM_005468		Approved		uc001ocn.3	Q9UQQ1	OTTHUMG00000165595	ENST00000358658.3:c.2081C>T	11.37:g.64812885G>A	ENSP00000351484:p.Pro694Leu	Somatic		Capture	Illumina HiSeq	Phase_I	64569461	NM_005468	C9J8A1|C9J964|C9JL35|C9JSN0|O43176	Missense_Mutation	SNP	ENST00000358658.3	37	CCDS31604.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.412755	0.62511	.	.	ENSG00000168060	ENST00000358658;ENST00000526799;ENST00000453486;ENST00000340252;ENST00000355721;ENST00000356632;ENST00000526516;ENST00000532802;ENST00000530995	T;T;T;T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43;-0.43	4.57	4.57	0.56435	Transferrin receptor-like, dimerisation domain (3);	0.057021	0.64402	D	0.000001	D	0.84352	0.5453	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87824	0.2640	10	0.87932	D	0	-23.9095	14.8939	0.70630	0.0:0.0:1.0:0.0	.	694	Q9UQQ1	NALDL_HUMAN	L	694;41;693;745;653;659;41;41;41	ENSP00000351484:P694L;ENSP00000431977:P41L;ENSP00000344244:P745L;ENSP00000347955:P653L;ENSP00000349045:P659L;ENSP00000433538:P41L;ENSP00000435267:P41L;ENSP00000431322:P41L	ENSP00000344244:P745L	P	-	2	0	NAALADL1	64569461	1.000000	0.71417	0.762000	0.31397	0.243000	0.25628	7.042000	0.76565	2.387000	0.81309	0.561000	0.74099	CCG		0.592	NAALADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385162.1	NM_005468	
SLC25A45	283130	broad.mit.edu	37	11	65143967	65143967	+	Missense_Mutation	SNP	G	G	A	rs375819010		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:65143967G>A	ENST00000527174.1	-	6	833	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W	SLC25A45_ENST00000526432.1_Missense_Mutation_p.R198W|SLC25A45_ENST00000360662.3_Missense_Mutation_p.R236W|SLC25A45_ENST00000294187.6_Missense_Mutation_p.R218W|SLC25A45_ENST00000377152.2_Missense_Mutation_p.R156W|SLC25A45_ENST00000398802.1_Missense_Mutation_p.R260W|SLC25A45_ENST00000417511.2_Missense_Mutation_p.R218W|RP11-867O8.5_ENST00000533886.1_RNA|SLC25A45_ENST00000534028.1_Missense_Mutation_p.R236W			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	260					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.R260W(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						GTGACCCCCCGGAAGAAGACT	0.607																																					p.R218W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C652T	11						.	G	TRP/ARG,TRP/ARG	0,4246		0,0,2123	100.0	110.0	107.0		652,778	3.8	1.0	11		107	1,8455		0,1,4227	no	missense,missense	SLC25A45	NM_001077241.1,NM_182556.2	101,101	0,1,6350	AA,AG,GG		0.0118,0.0,0.0079	probably-damaging,probably-damaging	218/247,260/289	65143967	1,12701	2123	4228	6351	64900543	SO:0001583	missense	283130	exon6			BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.778C>T	11.37:g.65143967G>A	ENSP00000435489:p.Arg260Trp	Somatic		Capture	Illumina HiSeq	Phase_I	64900543	NM_001077241	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809011	0.70797	0.0	1.18E-4	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	D;D;D;D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6	4.76	3.82	0.43975	Mitochondrial carrier domain (2);	.	.	.	.	D	0.93360	0.7883	H	0.97564	4.03	0.33283	D	0.56247	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.74674	0.942;0.973;0.984	D	0.95125	0.8250	9	0.87932	D	0	3.1696	10.0423	0.42166	0.0:0.0:0.619:0.381	.	198;236;260	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	W	260;236;260;236;156;218;218;198	ENSP00000435489:R260W;ENSP00000431769:R236W;ENSP00000381782:R260W;ENSP00000353879:R236W;ENSP00000366357:R156W;ENSP00000294187:R218W;ENSP00000407530:R218W;ENSP00000435547:R198W	ENSP00000294187:R218W	R	-	1	2	SLC25A45	64900543	0.301000	0.24444	0.997000	0.53966	0.952000	0.60782	0.633000	0.24598	1.317000	0.45149	0.561000	0.74099	CGG		0.607	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556	
KAT5	10524	broad.mit.edu	37	11	65482186	65482186	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:65482186G>A	ENST00000377046.3	+	8	1084	c.812G>A	c.(811-813)cGt>cAt	p.R271H	KAT5_ENST00000341318.4_Missense_Mutation_p.R304H|KAT5_ENST00000352980.4_Missense_Mutation_p.R219H|KAT5_ENST00000530446.1_Missense_Mutation_p.R252H|KAT5_ENST00000534650.1_Missense_Mutation_p.R60H	NM_006388.3	NP_006379.2	Q92993	KAT5_HUMAN	K(lysine) acetyltransferase 5	271	MYST-type HAT.				androgen receptor signaling pathway (GO:0030521)|cellular response to estradiol stimulus (GO:0071392)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|double-strand break repair (GO:0006302)|histone acetylation (GO:0016573)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of growth (GO:0040008)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|histone acetyltransferase activity (GO:0004402)|metal ion binding (GO:0046872)|repressing transcription factor binding (GO:0070491)|transcription coactivator activity (GO:0003713)	p.R304H(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)	21						AAGTACGGCCGTAGTCTCAAG	0.592																																					p.R304H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G911A	11						.						255.0	225.0	235.0					11																	65482186		2201	4297	6498	65238762	SO:0001583	missense	10524	exon7			U74667	CCDS8109.1, CCDS8110.1, CCDS31610.1, CCDS55771.1	11q13	2013-01-10	2008-07-04	2008-07-04	ENSG00000172977	ENSG00000172977		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"""	5275	protein-coding gene	gene with protein product	"""Tat interacting protein, 60kDa"", ""K-acetyltransferase 5"""	601409	"""HIV-1 Tat interactive protein, 60kDa"""	HTATIP		8607265	Standard	NM_006388		Approved	TIP60, PLIP, cPLA2, HTATIP1, ESA1, ZC2HC5	uc001ofk.3	Q92993	OTTHUMG00000166617	ENST00000377046.3:c.812G>A	11.37:g.65482186G>A	ENSP00000366245:p.Arg271His	Somatic		Capture	Illumina HiSeq	Phase_I	65238762	NM_182710	B4E3C7|C9JL99|O95624|Q13430|Q17RW5|Q561W3|Q6GSE8|Q9BWK7	Missense_Mutation	SNP	ENST00000377046.3	37	CCDS31610.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.941532	0.53079	.	.	ENSG00000172977	ENST00000377046;ENST00000352980;ENST00000341318;ENST00000530446;ENST00000531880;ENST00000534650	T;T;T;T;T	0.46819	0.9;0.91;0.9;0.9;0.86	4.97	3.98	0.46160	Acyl-CoA N-acyltransferase (1);	0.072360	0.56097	D	0.000028	T	0.38241	0.1033	L	0.42686	1.345	0.38519	D	0.948671	B;B;B;B	0.21147	0.009;0.052;0.001;0.007	B;B;B;B	0.13407	0.004;0.009;0.005;0.002	T	0.43032	-0.9416	10	0.66056	D	0.02	-11.1993	10.1097	0.42555	0.1058:0.0:0.8942:0.0	.	252;304;219;271	B4E3C7;Q92993-3;Q92993-2;Q92993	.;.;.;KAT5_HUMAN	H	271;219;304;252;265;60	ENSP00000366245:R271H;ENSP00000344955:R219H;ENSP00000340330:R304H;ENSP00000434765:R252H;ENSP00000436012:R265H	ENSP00000340330:R304H	R	+	2	0	KAT5	65238762	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	7.006000	0.76329	2.567000	0.86603	0.561000	0.74099	CGT		0.592	KAT5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390866.2	NM_006388	
SLC29A2	3177	broad.mit.edu	37	11	66133689	66133689	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:66133689G>A	ENST00000357440.2	-	9	1109	c.881C>T	c.(880-882)gCg>gTg	p.A294V	SLC29A2_ENST00000544554.1_Missense_Mutation_p.A294V|SLC29A2_ENST00000546034.1_Missense_Mutation_p.A294V|SLC29A2_ENST00000311161.7_Silent_p.S249S	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	294					cell proliferation (GO:0008283)|nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)	p.A294V(1)		breast(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10					Didanosine(DB00900)|Gemcitabine(DB00441)|Mercaptopurine(DB01033)|Zalcitabine(DB00943)|Zidovudine(DB00495)	AAGGCACAGCGCTGTCAGCCA	0.632																																					p.A294V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C881T	11						.						63.0	64.0	64.0					11																	66133689		2200	4295	6495	65890265	SO:0001583	missense	3177	exon9			X86681	CCDS8137.1, CCDS73326.1	11q13	2013-07-17	2013-07-17		ENSG00000174669	ENSG00000174669		"""Solute carriers"""	11004	protein-coding gene	gene with protein product		602110	"""solute carrier family 29 (nucleoside transporters), member 2"""	ENT2, HNP36		9192854, 9478986	Standard	NM_001532		Approved	DER12	uc001oht.3	Q14542	OTTHUMG00000169056	ENST00000357440.2:c.881C>T	11.37:g.66133689G>A	ENSP00000350024:p.Ala294Val	Somatic		Capture	Illumina HiSeq	Phase_I	65890265	NM_001532	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Missense_Mutation	SNP	ENST00000357440.2	37	CCDS8137.1	.	.	.	.	.	.	.	.	.	.	G	35	5.462948	0.96257	.	.	ENSG00000174669	ENST00000357440;ENST00000544554;ENST00000546034	T;T;T	0.80909	-1.43;-1.43;-1.43	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.88833	0.6544	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85926	0.1449	10	0.23891	T	0.37	-21.5322	17.2644	0.87081	0.0:0.0:1.0:0.0	.	294	Q14542	S29A2_HUMAN	V	294	ENSP00000350024:A294V;ENSP00000439456:A294V;ENSP00000440329:A294V	ENSP00000350024:A294V	A	-	2	0	SLC29A2	65890265	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.433000	0.97501	2.682000	0.91365	0.644000	0.83932	GCG		0.632	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532	
CTSF	8722	broad.mit.edu	37	11	66333182	66333182	+	Silent	SNP	G	G	A	rs147269500		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:66333182G>A	ENST00000310325.5	-	8	1114	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	ACTN3_ENST00000513398.1_RNA|CTSF_ENST00000533168.1_5'Flank|ACTN3_ENST00000502692.1_RNA	NM_003793.3	NP_003784.2	Q9UBX1	CATF_HUMAN	cathepsin F	335					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|vesicle (GO:0031982)	cysteine-type endopeptidase activity (GO:0004197)	p.G335G(1)		endometrium(1)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	19						AGGGCAAGCCGCCCATGCAGG	0.562																																					p.G335G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1005T	11						.	G		1,4399	2.1+/-5.4	0,1,2199	105.0	110.0	108.0		1005	-10.2	0.1	11	dbSNP_134	108	0,8590		0,0,4295	no	coding-synonymous	CTSF	NM_003793.3		0,1,6494	AA,AG,GG		0.0,0.0227,0.0077		335/485	66333182	1,12989	2200	4295	6495	66089758	SO:0001819	synonymous_variant	8722	exon8			AF071749	CCDS8144.1	11q13.2	2012-02-29			ENSG00000174080	ENSG00000174080		"""Cathepsins"""	2531	protein-coding gene	gene with protein product		603539				9822672, 10318784	Standard	NM_003793		Approved	CATSF, CLN13	uc001oip.3	Q9UBX1	OTTHUMG00000167090	ENST00000310325.5:c.1005C>T	11.37:g.66333182G>A		Somatic		Capture	Illumina HiSeq	Phase_I	66089758	NM_003793	B2R964|O95240|Q9NSU4|Q9UKQ5	Silent	SNP	ENST00000310325.5	37	CCDS8144.1	.	.	.	.	.	.	.	.	.	.	G	0.153	-1.089472	0.01873	2.27E-4	0.0	ENSG00000174080	ENST00000524994	.	.	.	5.11	-10.2	0.00374	.	.	.	.	.	T	0.49660	0.1570	.	.	.	0.38930	D	0.957914	.	.	.	.	.	.	T	0.61292	-0.7092	4	.	.	.	.	11.3622	0.49651	0.1205:0.0:0.6393:0.2403	.	.	.	.	W	183	.	.	R	-	1	2	CTSF	66089758	0.000000	0.05858	0.073000	0.20177	0.044000	0.14063	-2.821000	0.00749	-1.953000	0.01026	-0.345000	0.07892	CGG		0.562	CTSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393047.1	NM_003793	
GPR152	390212	broad.mit.edu	37	11	67219165	67219165	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:67219165G>A	ENST00000312457.2	-	1	1035	c.1031C>T	c.(1030-1032)cCg>cTg	p.P344L	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	344						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P344L(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			CTCTGCCATCGGCTCTGGCAG	0.637																																					p.P344L	Pancreas(102;800 1581 2723 7382 33622)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1031T	11						.						45.0	42.0	43.0					11																	67219165		2200	4295	6495	66975741	SO:0001583	missense	390212	exon1			AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"""GPCR / Class A : Orphans"""	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.1031C>T	11.37:g.67219165G>A	ENSP00000310255:p.Pro344Leu	Somatic		Capture	Illumina HiSeq	Phase_I	66975741	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.615843	0.46631	.	.	ENSG00000175514	ENST00000312457	T	0.17213	2.29	4.02	1.06	0.20224	.	0.597232	0.12963	N	0.424822	T	0.25344	0.0616	L	0.29908	0.895	0.09310	N	0.999999	D	0.89917	1.0	D	0.85130	0.997	T	0.10177	-1.0641	10	0.62326	D	0.03	.	7.1952	0.25849	0.3137:0.0:0.6863:0.0	.	344	Q8TDT2	GP152_HUMAN	L	344	ENSP00000310255:P344L	ENSP00000310255:P344L	P	-	2	0	GPR152	66975741	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.425000	0.07017	0.113000	0.18004	0.491000	0.48974	CCG		0.637	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1		
LRP5	4041	broad.mit.edu	37	11	68153972	68153972	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:68153972C>A	ENST00000294304.7	+	6	1310	c.1204C>A	c.(1204-1206)Ctg>Atg	p.L402M		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	402	Beta-propeller 2.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.L402M(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CAGGGCGTACCTGGACGGGTC	0.642																																					p.L402M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1204A	11						.						100.0	81.0	87.0					11																	68153972		2200	4294	6494	67910548	SO:0001583	missense	4041	exon6			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.1204C>A	11.37:g.68153972C>A	ENSP00000294304:p.Leu402Met	Somatic		Capture	Illumina HiSeq	Phase_I	67910548	NM_002335	Q96TD6|Q9UES7|Q9UP66	De_novo_Start_OutOfFrame	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.011373	0.54468	.	.	ENSG00000162337	ENST00000294304	D	0.97279	-4.32	3.81	3.81	0.43845	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.37809	U	0.001935	D	0.96901	0.8988	L	0.37800	1.135	0.43029	D	0.994591	D	0.53151	0.958	D	0.63283	0.913	D	0.97122	0.9812	10	0.48119	T	0.1	.	16.3309	0.83014	0.0:1.0:0.0:0.0	.	402	O75197	LRP5_HUMAN	M	402	ENSP00000294304:L402M	ENSP00000294304:L402M	L	+	1	2	LRP5	67910548	0.520000	0.26250	0.410000	0.26471	0.809000	0.45718	1.105000	0.31086	2.177000	0.69029	0.449000	0.29647	CTG		0.642	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
PPP6R3	55291	broad.mit.edu	37	11	68331809	68331809	+	Missense_Mutation	SNP	G	G	T	rs376551000		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:68331809G>T	ENST00000393800.2	+	9	1138	c.884G>T	c.(883-885)aGc>aTc	p.S295I	PPP6R3_ENST00000265636.5_Missense_Mutation_p.S295I|PPP6R3_ENST00000265637.4_Missense_Mutation_p.S295I|PPP6R3_ENST00000393799.2_Missense_Mutation_p.S295I|PPP6R3_ENST00000524904.1_Missense_Mutation_p.S295I|PPP6R3_ENST00000393801.3_Missense_Mutation_p.S295I|PPP6R3_ENST00000524845.1_Missense_Mutation_p.S295I|PPP6R3_ENST00000529710.1_Missense_Mutation_p.S295I|PPP6R3_ENST00000527403.2_Missense_Mutation_p.S295I|PPP6R3_ENST00000534534.1_Intron	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	295					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)	p.S295I(2)		breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						CCAGGCATGAGCCATTCAGCT	0.418																																					p.S295I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G884T	11						.						104.0	105.0	105.0					11																	68331809		2200	4294	6494	68088385	SO:0001583	missense	55291	exon10			AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.884G>T	11.37:g.68331809G>T	ENSP00000377389:p.Ser295Ile	Somatic		Capture	Illumina HiSeq	Phase_I	68088385	NM_001164164	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123511	0.56613	.	.	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29;-0.29;-0.12;-0.12;-0.29;1.9	5.08	4.17	0.49024	.	0.303447	0.43110	D	0.000619	T	0.57489	0.2057	N	0.22421	0.69	0.36336	D	0.859142	P;B;B;B;B;B;B	0.40619	0.724;0.022;0.074;0.116;0.013;0.225;0.022	P;B;B;B;B;B;B	0.50049	0.629;0.056;0.123;0.182;0.094;0.116;0.03	T	0.60742	-0.7203	10	0.29301	T	0.29	.	5.7361	0.18067	0.2267:0.1454:0.6279:0.0	.	2;295;295;295;295;295;295	B4DYU6;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;PP6R3_HUMAN;.;.	I	295;295;295;295;295;295;295;295;295;26	ENSP00000377388:S295I;ENSP00000377389:S295I;ENSP00000431415:S295I;ENSP00000265637:S295I;ENSP00000433058:S295I;ENSP00000377390:S295I;ENSP00000265636:S295I;ENSP00000437329:S295I;ENSP00000433565:S295I;ENSP00000436209:S26I	ENSP00000265636:S295I	S	+	2	0	PPP6R3	68088385	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.983000	0.40648	1.373000	0.46208	0.462000	0.41574	AGC		0.418	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
SHANK2	22941	broad.mit.edu	37	11	70332663	70332663	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:70332663T>G	ENST00000423696.2	-	15	2634	c.2598A>C	c.(2596-2598)aaA>aaC	p.K866N	SHANK2_ENST00000409161.1_Missense_Mutation_p.K649N|SHANK2_ENST00000449833.2_Missense_Mutation_p.K650N|SHANK2_ENST00000338508.4_Missense_Mutation_p.K1246N			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	866					adult behavior (GO:0030534)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|vocalization behavior (GO:0071625)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|ionotropic glutamate receptor binding (GO:0035255)	p.K650N(1)|p.K1246N(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(30)|ovary(3)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	62			LUSC - Lung squamous cell carcinoma(11;4.72e-09)|STAD - Stomach adenocarcinoma(18;0.071)			TGTAAAGAGGTTTGTTGAGGT	0.642																																					p.K657N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1971C	11						.						80.0	89.0	86.0					11																	70332663		2200	4294	6494	70010311	SO:0001583	missense	22941	exon10			AF141901		11q13.2	2013-01-10			ENSG00000162105	ENSG00000162105		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14295	protein-coding gene	gene with protein product		603290	"""cortactin binding protein 1"""	CORTBP1		10506216	Standard	XM_005277930		Approved	CTTNBP1, ProSAP1, SHANK, SPANK-3	uc001oqc.3	Q9UPX8	OTTHUMG00000154615	ENST00000423696.2:c.2598A>C	11.37:g.70332663T>G	ENSP00000394536:p.Lys866Asn	Somatic		Capture	Illumina HiSeq	Phase_I	70010311	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	T	14.33	2.504713	0.44558	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93;1.93	4.88	-2.54	0.06307	.	0.092279	0.64402	D	0.000001	T	0.42494	0.1205	M	0.70595	2.14	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.992	D;D;D	0.87578	0.919;0.998;0.913	T	0.24476	-1.0159	10	0.26408	T	0.33	.	12.6289	0.56646	0.0:0.5964:0.0:0.4036	.	866;1245;650	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	N	650;649;524;1246;866;884;869	ENSP00000399423:K650N;ENSP00000386491:K649N;ENSP00000402944:K524N;ENSP00000345193:K1246N;ENSP00000394536:K866N;ENSP00000294018:K869N	ENSP00000294018:K869N	K	-	3	2	SHANK2	70010311	0.780000	0.28664	0.986000	0.45419	0.994000	0.84299	-0.156000	0.10100	-0.609000	0.05724	0.459000	0.35465	AAA		0.642	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309	
KRTAP5-10	387273	broad.mit.edu	37	11	71276906	71276906	+	Silent	SNP	G	G	A	rs34154361		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:71276906G>A	ENST00000398531.1	+	1	298	c.273G>A	c.(271-273)aaG>aaA	p.K91K	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	91	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTCCAAGGGGGGCTGTG	0.682																																					p.K91K												.	.	0			c.G273A	11						.																																			70954554	SO:0001819	synonymous_variant	387273	exon1			AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.273G>A	11.37:g.71276906G>A		None		Capture	Illumina HiSeq	Phase_I	70954554	NM_001012710	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																				0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
FOLR3	2352	broad.mit.edu	37	11	71850651	71850651	+	Frame_Shift_Del	DEL	G	G	-	rs372988226	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:71850651delG	ENST00000445078.2	+	5	705	c.634delG	c.(634-636)gggfs	p.G212fs	FOLR3_ENST00000442948.2_Frame_Shift_Del_p.G171fs|FOLR3_ENST00000456237.1_Frame_Shift_Del_p.G214fs			P41439	FOLR3_HUMAN	folate receptor 3 (gamma)	170					folic acid transport (GO:0015884)	extracellular region (GO:0005576)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)	folic acid binding (GO:0005542)	p.A215fs*61(1)		large_intestine(3)|lung(8)|prostate(2)	13					Folic Acid(DB00158)	GTGTCCGGCCGGGGCCCTCTG	0.602																																					p.R171fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.512delG	11						.						44.0	50.0	48.0					11																	71850651		2193	4291	6484	71528299	SO:0001589	frameshift_variant	2352	exon5			U08471	CCDS73344.1	11q13.4	2012-11-14			ENSG00000110203	ENSG00000110203			3795	protein-coding gene	gene with protein product		602469				8110752	Standard	NM_000804		Approved	FR-G	uc001orx.1	P41439	OTTHUMG00000167870	ENST00000445078.2:c.634delG	11.37:g.71850651delG	ENSP00000390338:p.Gly212fs	Somatic		Capture	Illumina HiSeq	Phase_I	71528299	NM_000804	J3KQ90|Q05C14	Frame_Shift_Del	DEL	ENST00000445078.2	37																																																																																					0.602	FOLR3-001	NOVEL	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000396739.1	NM_000804	
INPPL1	3636	broad.mit.edu	37	11	71942173	71942173	+	Silent	SNP	C	C	T	rs201505175	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:71942173C>T	ENST00000298229.2	+	12	1641	c.1437C>T	c.(1435-1437)cgC>cgT	p.R479R	INPPL1_ENST00000541756.1_Silent_p.R237R|INPPL1_ENST00000538751.1_Silent_p.R237R	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	479					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|endochondral ossification (GO:0001958)|endocytosis (GO:0006897)|glucose metabolic process (GO:0006006)|immune system process (GO:0002376)|inositol phosphate metabolic process (GO:0043647)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|post-embryonic development (GO:0009791)|response to insulin (GO:0032868)|ruffle assembly (GO:0097178)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|SH2 domain binding (GO:0042169)	p.R479R(1)		breast(2)|endometrium(9)|kidney(1)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						TGGGCGACCGCGAGTGGCTGG	0.607													C|||	2	0.000399361	0.0	0.0029	5008	,	,		5878	0.0		0.0	False		,,,				2504	0.0				p.R479R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1437T	11						.						151.0	158.0	155.0					11																	71942173		2200	4293	6493	71619821	SO:0001819	synonymous_variant	3636	exon12			Y14385	CCDS8213.1	11q23	2013-02-14			ENSG00000165458	ENSG00000165458		"""Sterile alpha motif (SAM) domain containing"", ""SH2 domain containing"""	6080	protein-coding gene	gene with protein product	"""51C protein"""	600829				8530088	Standard	NM_001567		Approved	SHIP2	uc001osf.3	O15357	OTTHUMG00000167879	ENST00000298229.2:c.1437C>T	11.37:g.71942173C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71619821	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1																																																																																				0.607	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567	
C2CD3	26005	broad.mit.edu	37	11	73768557	73768557	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:73768557G>A	ENST00000334126.7	-	25	5210	c.4984C>T	c.(4984-4986)Ccc>Tcc	p.P1662S	C2CD3_ENST00000313663.7_Missense_Mutation_p.P1662S			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1662	C2 2.				brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					CAACAACTGGGTATCGATACT	0.448																																					p.P1662S												.	.	0			c.C4984T	11						.						113.0	112.0	113.0					11																	73768557		2200	4293	6493	73446205	SO:0001583	missense	26005	exon25			BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.4984C>T	11.37:g.73768557G>A	ENSP00000334379:p.Pro1662Ser	None		Capture	Illumina HiSeq	Phase_I	73446205	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		.	.	.	.	.	.	.	.	.	.	G	24.6	4.553813	0.86231	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.77229	-1.08;-1.08;-1.08	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	D	0.82710	0.5096	M	0.66939	2.045	0.51233	D	0.999914	P	0.35575	0.51	P	0.45538	0.484	D	0.84206	0.0453	10	0.66056	D	0.02	-15.8622	18.3221	0.90242	0.0:0.0:1.0:0.0	.	1662	Q4AC94-1	.	S	1662;1662;1643;470	ENSP00000334379:P1662S;ENSP00000323339:P1662S;ENSP00000388750:P470S	ENSP00000323339:P1662S	P	-	1	0	C2CD3	73446205	1.000000	0.71417	0.997000	0.53966	0.927000	0.56198	8.053000	0.89449	2.505000	0.84491	0.650000	0.86243	CCC		0.448	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
C11orf30	56946	broad.mit.edu	37	11	76227240	76227240	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:76227240C>T	ENST00000529032.1	+	10	1568	c.1568C>T	c.(1567-1569)gCt>gTt	p.A523V	C11orf30_ENST00000524767.1_Missense_Mutation_p.A538V|C11orf30_ENST00000525038.1_Missense_Mutation_p.A538V|C11orf30_ENST00000343878.3_Missense_Mutation_p.A523V|C11orf30_ENST00000525919.1_Missense_Mutation_p.A524V|C11orf30_ENST00000533248.1_Missense_Mutation_p.A537V|C11orf30_ENST00000334736.3_Missense_Mutation_p.A523V|C11orf30_ENST00000524490.1_Missense_Mutation_p.A439V			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	523	Thr-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.A523V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						GGTCGGATGGCTGCAACCCCT	0.473																																					p.A523V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1568T	11						.						118.0	114.0	116.0					11																	76227240		2200	4292	6492	75904888	SO:0001583	missense	56946	exon11			AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.1568C>T	11.37:g.76227240C>T	ENSP00000432327:p.Ala523Val	Somatic		Capture	Illumina HiSeq	Phase_I	75904888	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	37	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870943	0.72065	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000533972;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032;ENST00000531998	.	.	.	5.38	5.38	0.77491	.	0.229760	0.45867	D	0.000324	T	0.36635	0.0974	N	0.24115	0.695	0.51233	D	0.999918	B;B;B;B;P;B	0.43750	0.041;0.041;0.041;0.03;0.816;0.03	B;B;B;B;B;B	0.31442	0.01;0.01;0.01;0.022;0.13;0.022	T	0.24799	-1.0150	9	0.30854	T	0.27	-10.19	19.1179	0.93350	0.0:1.0:0.0:0.0	.	537;538;538;524;439;523	B7ZKT8;B7ZKU2;B7ZKU0;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;EMSY_HUMAN	V	439;523;523;92;538;537;524;538;523;65	.	ENSP00000334130:A523V	A	+	2	0	C11orf30	75904888	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.243000	0.78219	2.508000	0.84585	0.557000	0.71058	GCT		0.473	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
PAK1	5058	broad.mit.edu	37	11	77047282	77047282	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:77047282C>A	ENST00000356341.3	-	13	1793	c.1262G>T	c.(1261-1263)cGg>cTg	p.R421L	PAK1_ENST00000278568.4_Missense_Mutation_p.R421L|PAK1_ENST00000525542.1_5'UTR|PAK1_ENST00000530617.1_Missense_Mutation_p.R421L|PAK1_ENST00000528203.1_Missense_Mutation_p.R323L	NM_002576.4	NP_002567.3	Q13153	PAK1_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 1	421	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cellular response to insulin stimulus (GO:0032869)|dendrite development (GO:0016358)|exocytosis (GO:0006887)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor clustering (GO:0043113)|response to hypoxia (GO:0001666)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|wound healing (GO:0042060)	axon (GO:0030424)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|growth cone (GO:0030426)|intercalated disc (GO:0014704)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|Z disc (GO:0030018)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R421L(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(13)|skin(2)|stomach(1)	29	all_cancers(14;1.75e-18)					CATGGTGCTCCGTTTGCTCTG	0.483																																					p.R421L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1262T	11						.						151.0	147.0	148.0					11																	77047282		2200	4292	6492	76724930	SO:0001583	missense	5058	exon13			U51120	CCDS8250.1, CCDS44687.1	11q13-q14	2008-06-17	2008-06-17						8590	protein-coding gene	gene with protein product	"""STE20 homolog, yeast"""	602590	"""p21/Cdc42/Rac1-activated kinase 1 (yeast Ste20-related)"", ""p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast)"""			8805275, 9533029	Standard	NM_002576		Approved		uc001oyg.4	Q13153		ENST00000356341.3:c.1262G>T	11.37:g.77047282C>A	ENSP00000348696:p.Arg421Leu	Somatic		Capture	Illumina HiSeq	Phase_I	76724930	NM_002576	O75561|Q13567|Q32M53|Q32M54|Q86W79	Missense_Mutation	SNP	ENST00000356341.3	37	CCDS8250.1	.	.	.	.	.	.	.	.	.	.	C	33	5.241068	0.95272	.	.	ENSG00000149269	ENST00000356341;ENST00000530617;ENST00000278568;ENST00000528203	T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0	6.04	6.04	0.98038	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	0.74291	0.3697	L	0.37800	1.135	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;1.0;1.0	D;D;D;D	0.97110	0.939;1.0;1.0;1.0	T	0.74802	-0.3541	10	0.87932	D	0	.	20.5948	0.99439	0.0:1.0:0.0:0.0	.	323;421;421;421	E9PM17;B3KNX7;Q13153;Q13153-2	.;.;PAK1_HUMAN;.	L	421;421;421;323	ENSP00000348696:R421L;ENSP00000433423:R421L;ENSP00000278568:R421L;ENSP00000433211:R323L	ENSP00000278568:R421L	R	-	2	0	PAK1	76724930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.873000	0.98535	0.563000	0.77884	CGG		0.483	PAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382083.2	NM_002576	
TENM4	26011	broad.mit.edu	37	11	78399123	78399123	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:78399123C>A	ENST00000278550.7	-	29	5698	c.5236G>T	c.(5236-5238)Ggc>Tgc	p.G1746C		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1746					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)	p.G1746C(1)									TAGAAGGCGCCTGAGGCAGAC	0.552																																					p.G1746C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5236T	11						.						160.0	165.0	163.0					11																	78399123		2049	4153	6202	78076771	SO:0001583	missense	26011	exon29			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.5236G>T	11.37:g.78399123C>A	ENSP00000278550:p.Gly1746Cys	Somatic		Capture	Illumina HiSeq	Phase_I	78076771	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.362491	0.82353	.	.	ENSG00000149256	ENST00000278550;ENST00000530738	D;T	0.90444	-2.67;0.77	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.92221	0.7533	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91194	0.4986	9	.	.	.	.	18.4218	0.90594	0.0:1.0:0.0:0.0	.	1746	Q6N022	TEN4_HUMAN	C	1746;210	ENSP00000278550:G1746C;ENSP00000431711:G210C	.	G	-	1	0	ODZ4	78076771	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	5.827000	0.69300	2.572000	0.86782	0.655000	0.94253	GGC		0.552	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
TENM4	26011	broad.mit.edu	37	11	78497943	78497943	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:78497943C>T	ENST00000278550.7	-	16	2827	c.2365G>A	c.(2365-2367)Gct>Act	p.A789T		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	789	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)	p.A789T(1)									CCCGCCATACCGATGGTGCAG	0.667																																					p.A789T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2365A	11						.						14.0	16.0	16.0					11																	78497943		2003	4151	6154	78175591	SO:0001630	splice_region_variant	26011	exon16			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.2365+1G>A	11.37:g.78497943C>T		Somatic		Capture	Illumina HiSeq	Phase_I	78175591	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.758635	0.89843	.	.	ENSG00000149256	ENST00000278550	T	0.03272	3.99	5.2	5.2	0.72013	.	0.000000	0.46145	U	0.000320	T	0.08223	0.0205	N	0.12182	0.205	0.53688	D	0.999972	D	0.76494	0.999	D	0.72625	0.978	T	0.57051	-0.7877	9	.	.	.	.	18.9373	0.92590	0.0:1.0:0.0:0.0	.	789	Q6N022	TEN4_HUMAN	T	789	ENSP00000278550:A789T	.	A	-	1	0	ODZ4	78175591	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.609000	0.82925	2.722000	0.93159	0.655000	0.94253	GCT		0.667	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		Missense_Mutation
TENM4	26011	broad.mit.edu	37	11	78525352	78525352	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:78525352delG	ENST00000278550.7	-	13	2232	c.1770delC	c.(1768-1770)cccfs	p.P590fs		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	590	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)	p.D591fs*18(1)									TGCCACAGTCGGGGCCCAGGA	0.562																																					p.P590fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1770delC	11						.						60.0	79.0	73.0					11																	78525352		692	1591	2283	78203000	SO:0001589	frameshift_variant	26011	exon13			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.1770delC	11.37:g.78525352delG	ENSP00000278550:p.Pro590fs	Somatic		Capture	Illumina HiSeq	Phase_I	78203000	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Frame_Shift_Del	DEL	ENST00000278550.7	37	CCDS44688.1																																																																																				0.562	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
TMEM126B	55863	broad.mit.edu	37	11	85346749	85346749	+	Silent	SNP	C	C	T	rs201010232		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:85346749C>T	ENST00000358867.6	+	4	459	c.436C>T	c.(436-438)Ctg>Ttg	p.L146L	TMEM126B_ENST00000534341.1_Silent_p.L146L|TMEM126B_ENST00000393375.1_Silent_p.L116L	NM_018480.4	NP_060950.3	Q8IUX1	T126B_HUMAN	transmembrane protein 126B	146						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.L116L(1)		kidney(1)|large_intestine(2)|lung(3)|prostate(1)	7		Acute lymphoblastic leukemia(157;4.88e-06)|all_hematologic(158;0.00572)				CAGAAGCTCACTGATTGGCAT	0.348																																					p.L126L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C376T	11						.						136.0	138.0	137.0					11																	85346749		2203	4299	6502	85024397	SO:0001819	synonymous_variant	55863	exon5				CCDS8267.1, CCDS8267.2, CCDS53686.1	11q14.1	2013-05-24				ENSG00000171204		"""Mitochondrial respiratory chain complex assembly factors"""	30883	protein-coding gene	gene with protein product		615533				22982022	Standard	NM_018480		Approved	HT007	uc001pap.4	Q8IUX1		ENST00000358867.6:c.436C>T	11.37:g.85346749C>T		Somatic		Capture	Illumina HiSeq	Phase_I	85024397	NM_001193537	A8K535|A8MSS0|Q32Q09|Q8WVU3|Q96EP3|Q9NZ29	Silent	SNP	ENST00000358867.6	37	CCDS8267.2																																																																																				0.348	TMEM126B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392164.1	NM_018480	
EED	8726	broad.mit.edu	37	11	85988174	85988174	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:85988174G>A	ENST00000263360.6	+	10	1805	c.1119G>A	c.(1117-1119)tgG>tgA	p.W373*	EED_ENST00000351625.6_Nonsense_Mutation_p.W398*|EED_ENST00000527888.1_Nonsense_Mutation_p.W38*|EED_ENST00000327320.4_Nonsense_Mutation_p.W373*|EED_ENST00000528180.1_Nonsense_Mutation_p.W293*	NM_003797.3	NP_003788.2	O75530	EED_HUMAN	embryonic ectoderm development	373	Interaction with EZH2. {ECO:0000250}.|Required for interaction with the matrix protein MA of HIV-1.				negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K27 methylation (GO:0061087)|regulation of gene expression by genetic imprinting (GO:0006349)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|identical protein binding (GO:0042802)	p.W373*(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	21		Acute lymphoblastic leukemia(157;7.24e-07)|all_hematologic(158;0.00092)				TGGATTTCTGGCAAAAGGTAT	0.333																																					p.W373X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1119A	11						.						141.0	146.0	144.0					11																	85988174		2202	4299	6501	85665822	SO:0001587	stop_gained	8726	exon10			AF078933	CCDS8273.1, CCDS8274.1	11q14.2-q22.3	2013-01-10			ENSG00000074266	ENSG00000074266		"""WD repeat domain containing"""	3188	protein-coding gene	gene with protein product	"""WD protein associating with integrin cytoplasmic tails 1"""	605984				9765275, 9806832	Standard	NM_003797		Approved	WAIT-1, HEED	uc001pbp.3	O75530	OTTHUMG00000167209	ENST00000263360.6:c.1119G>A	11.37:g.85988174G>A	ENSP00000263360:p.Trp373*	Somatic		Capture	Illumina HiSeq	Phase_I	85665822	NM_152991	A8K7V5|O00149|Q6NTH2|Q7LDA5|Q7LDG8|Q86VV2|Q9UNY7	Nonsense_Mutation	SNP	ENST00000263360.6	37	CCDS8273.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	53|53	21.029228|21.029228	0.99936|0.99936	.|.	.|.	ENSG00000074266|ENSG00000074266	ENST00000534595|ENST00000263360;ENST00000528180;ENST00000351625;ENST00000327320;ENST00000534564;ENST00000524673;ENST00000527888	.|.	.|.	.|.	5.74|5.74	4.82|4.82	0.62117|0.62117	.|.	.|0.057419	.|0.85682	.|D	.|0.000000	T|.	0.65249|.	0.2673|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71104|.	-0.4689|.	3|.	.|.	.|.	.|.	-6.7155|-6.7155	14.6176|14.6176	0.68560|0.68560	0.07:0.0:0.93:0.0|0.07:0.0:0.93:0.0	.|.	.|.	.|.	.|.	D|X	88|373;293;398;373;122;38;38	.|.	.|.	G|W	+|+	2|3	0|0	EED|EED	85665822|85665822	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.357000|9.357000	0.97099|0.97099	1.429000|1.429000	0.47314|0.47314	0.655000|0.655000	0.94253|0.94253	GGC|TGG		0.333	EED-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393733.1	NM_003797	
FAT3	120114	broad.mit.edu	37	11	92616301	92616301	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:92616301delC	ENST00000298047.6	+	23	12696	c.12679delC	c.(12679-12681)cccfs	p.P4228fs	FAT3_ENST00000409404.2_Frame_Shift_Del_p.P4228fs|FAT3_ENST00000533797.1_Frame_Shift_Del_p.P563fs|FAT3_ENST00000525166.1_Frame_Shift_Del_p.P4078fs			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4228					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P803fs*36(1)		NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GGAGGTGGGGCCCCCGCAGGT	0.677										TCGA Ovarian(4;0.039)																											p.P4227fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.12679delC	11						.						56.0	70.0	66.0					11																	92616301		1952	4129	6081	92255949	SO:0001589	frameshift_variant	120114	exon23			AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12679delC	11.37:g.92616301delC	ENSP00000298047:p.Pro4228fs	Somatic		Capture	Illumina HiSeq	Phase_I	92255949	NM_001008781	B5MDB0|Q96AU6	Frame_Shift_Del	DEL	ENST00000298047.6	37																																																																																					0.677	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
PANX1	24145	broad.mit.edu	37	11	93862614	93862614	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:93862614delC	ENST00000227638.3	+	1	521	c.136delC	c.(136-138)cccfs	p.P46fs	PANX1_ENST00000436171.2_Frame_Shift_Del_p.P46fs	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	46					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)	p.L47fs*18(1)		endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	GGTGGGGCTGCCCCTGCTGCT	0.652																																					p.P46fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.136delC	11						.						59.0	55.0	57.0					11																	93862614		2201	4298	6499	93502262	SO:0001589	frameshift_variant	24145	exon1			AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.136delC	11.37:g.93862614delC	ENSP00000227638:p.Pro46fs	Somatic		Capture	Illumina HiSeq	Phase_I	93502262	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Frame_Shift_Del	DEL	ENST00000227638.3	37	CCDS8296.1																																																																																				0.652	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
KDM4D	55693	broad.mit.edu	37	11	94704620	94704620	+	5'Flank	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:94704620G>A	ENST00000335080.5	+	0	0				CWC15_ENST00000279839.6_Missense_Mutation_p.R55C|CWC15_ENST00000545018.1_5'UTR|KDM4D_ENST00000536741.1_5'Flank	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D						chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	blood microparticle (GO:0072562)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(16)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TCACGGTTACGAACCTCTTCA	0.458																																					p.R55C												.	.	0			c.C163T	11						.						54.0	50.0	51.0					11																	94704620		1847	4100	5947	94344268	SO:0001631	upstream_gene_variant	51503	exon3			AK001113	CCDS8302.1	11q21	2012-03-28	2009-04-06	2009-04-06	ENSG00000186280	ENSG00000186280		"""Chromatin-modifying enzymes / K-demethylases"""	25498	protein-coding gene	gene with protein product		609766	"""jumonji domain containing 2D"""	JMJD2D		15138608	Standard	NM_018039		Approved	FLJ10251	uc001pfe.3	Q6B0I6	OTTHUMG00000167838		11.37:g.94704620G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	94344268	NM_016403	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Missense_Mutation	SNP	ENST00000335080.5	37	CCDS8302.1																																																																																				0.458	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039	
ARHGAP42	143872	broad.mit.edu	37	11	100836464	100836464	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:100836464delA	ENST00000298815.8	+	17	1510	c.1507delA	c.(1507-1509)aaafs	p.K503fs	ARHGAP42_ENST00000524892.2_Frame_Shift_Del_p.K469fs	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	503	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)	p.N76fs*8(1)		endometrium(3)|skin(2)	5						ATTGCCGGAGAAAAACAGAGA	0.343																																					p.K503fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1507delA	11						.						174.0	156.0	162.0					11																	100836464		692	1591	2283	100341674	SO:0001589	frameshift_variant	143872	exon17					11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.1507delA	11.37:g.100836464delA	ENSP00000298815:p.Lys503fs	Somatic		Capture	Illumina HiSeq	Phase_I	100341674	NM_152432	Q96M56	Frame_Shift_Del	DEL	ENST00000298815.8	37																																																																																					0.343	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
DLAT	1737	broad.mit.edu	37	11	111896977	111896977	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:111896977delA	ENST00000280346.6	+	2	994	c.335delA	c.(334-336)gaafs	p.E112fs	DLAT_ENST00000393051.1_Frame_Shift_Del_p.E112fs|DLAT_ENST00000537636.1_Frame_Shift_Del_p.E10fs	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	112	Lipoyl-binding 1. {ECO:0000255|PROSITE- ProRule:PRU01066}.			E -> K (in Ref. 4; CAA68787). {ECO:0000305}.	cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)	p.E115fs*10(1)|p.E115fs*7(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)		GCCCGTTGGGAAAAAAAAGAG	0.333																																					p.E112fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.335delA	11						.						45.0	46.0	45.0					11																	111896977		2201	4297	6498	111402187	SO:0001589	frameshift_variant	1737	exon2			Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"""E2 component of pyruvate dehydrogenase complex"""	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.335delA	11.37:g.111896977delA	ENSP00000280346:p.Glu112fs	Somatic		Capture	Illumina HiSeq	Phase_I	111402187	NM_001931	Q16783|Q53EP3	Frame_Shift_Del	DEL	ENST00000280346.6	37	CCDS8354.1																																																																																				0.333	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931	
DSCAML1	57453	broad.mit.edu	37	11	117299188	117299188	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:117299188delG	ENST00000321322.6	-	33	6199	c.6198delC	c.(6196-6198)cccfs	p.P2066fs	DSCAML1_ENST00000527706.1_Frame_Shift_Del_p.P1796fs	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	2006					axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.S2067fs*24(1)		breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GCTCGGTGCTGGGGGCCGGAG	0.736																																					p.P2066fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6198delC	11						.						8.0	9.0	9.0					11																	117299188		1803	3897	5700	116804398	SO:0001589	frameshift_variant	57453	exon33				CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.6198delC	11.37:g.117299188delG	ENSP00000315465:p.Pro2066fs	Somatic		Capture	Illumina HiSeq	Phase_I	116804398	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Frame_Shift_Del	DEL	ENST00000321322.6	37	CCDS8384.1																																																																																				0.736	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
GLB1L2	89944	broad.mit.edu	37	11	134241679	134241679	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr11:134241679C>T	ENST00000535456.2	+	15	1650	c.1462C>T	c.(1462-1464)Cgt>Tgt	p.R488C	GLB1L2_ENST00000339772.7_Missense_Mutation_p.R488C|GLB1L2_ENST00000389881.3_Missense_Mutation_p.R488C|GLB1L2_ENST00000529077.1_3'UTR	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	488					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)	p.R488C(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		GGTGGAGAATCGTGGGCGAGT	0.547																																					p.R488C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1462T	11						.						132.0	117.0	122.0					11																	134241679		2201	4297	6498	133746889	SO:0001583	missense	89944	exon15				CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1462C>T	11.37:g.134241679C>T	ENSP00000444628:p.Arg488Cys	Somatic		Capture	Illumina HiSeq	Phase_I	133746889	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.07|14.07	2.426120|2.426120	0.43020|0.43020	.|.	.|.	ENSG00000149328|ENSG00000149328	ENST00000339772;ENST00000535456;ENST00000389881|ENST00000525089	D;D;D|.	0.92348|.	-3.02;-3.02;-3.02|.	5.6|5.6	-3.21|-3.21	0.05140|0.05140	Galactose-binding domain-like (1);|.	0.341815|.	0.36167|.	N|.	0.002755|.	T|T	0.30665|0.30665	0.0772|0.0772	N|N	0.04768|0.04768	-0.165|-0.165	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.06786|.	0.001|.	B|.	0.04013|.	0.001|.	T|T	0.07751|0.07751	-1.0756|-1.0756	10|5	0.40728|.	T|.	0.16|.	-1.3914|-1.3914	13.4011|13.4011	0.60883|0.60883	0.0:0.3632:0.0:0.6368|0.0:0.3632:0.0:0.6368	.|.	488|.	Q8IW92|.	GLBL2_HUMAN|.	C|L	488|426	ENSP00000344659:R488C;ENSP00000444628:R488C;ENSP00000374531:R488C|.	ENSP00000344659:R488C|.	R|S	+|+	1|2	0|0	GLB1L2|GLB1L2	133746889|133746889	0.714000|0.714000	0.27936|0.27936	0.424000|0.424000	0.26647|0.26647	0.975000|0.975000	0.68041|0.68041	0.016000|0.016000	0.13377|0.13377	-0.553000|-0.553000	0.06158|0.06158	-0.152000|-0.152000	0.13540|0.13540	CGT|TCG		0.547	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342	
PARPBP	55010	broad.mit.edu	37	12	102576371	102576371	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:102576371G>A	ENST00000358383.5	+	9	1274	c.1229G>A	c.(1228-1230)cGc>cAc	p.R410H	PARPBP_ENST00000541394.1_Missense_Mutation_p.R487H|PARPBP_ENST00000392911.2_Missense_Mutation_p.R329H|PARPBP_ENST00000378128.3_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.R329H|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000543784.1_Intron			Q9NWS1	PARI_HUMAN	PARP1 binding protein	410					DNA repair (GO:0006281)|negative regulation of double-strand break repair via homologous recombination (GO:2000042)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R329H(1)		endometrium(1)|lung(8)|urinary_tract(2)	11						CTAAGAGAACGCATCTGTGTG	0.313																																					p.R410H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1229A	12						.						59.0	59.0	59.0					12																	102576371		2203	4300	6503	101100501	SO:0001583	missense	55010	exon9			AK000648	CCDS9090.1, CCDS9090.2	12q23.2	2013-03-14	2012-01-24	2012-01-24		ENSG00000185480			26074	protein-coding gene	gene with protein product	"""PARP-1 binding protein"""	613687	"""chromosome 12 open reading frame 48"""	C12orf48		20931645	Standard	NM_017915		Approved	FLJ20641, PARI	uc001tjf.3	Q9NWS1		ENST00000358383.5:c.1229G>A	12.37:g.102576371G>A	ENSP00000351153:p.Arg410His	Somatic		Capture	Illumina HiSeq	Phase_I	101100501	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179761	0.57800	.	.	ENSG00000185480	ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911;ENST00000417507	T;T;T;T;T	0.64085	0.89;0.89;0.89;0.89;-0.08	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.78805	0.4341	M	0.76328	2.33	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.998	T	0.80549	-0.1333	10	0.87932	D	0	-1.1863	15.3071	0.74001	0.0:0.0:1.0:0.0	.	487;289;410	B4DZ31;Q9NWS1-7;Q9NWS1	.;.;PR1BP_HUMAN	H	329;487;410;329;256	ENSP00000332915:R329H;ENSP00000440850:R487H;ENSP00000351153:R410H;ENSP00000376643:R329H;ENSP00000411313:R256H	ENSP00000332915:R329H	R	+	2	0	C12orf48	101100501	1.000000	0.71417	0.996000	0.52242	0.113000	0.19764	5.031000	0.64134	2.762000	0.94881	0.591000	0.81541	CGC		0.313	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915	
ASCL1	429	broad.mit.edu	37	12	103352411	103352411	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:103352411G>A	ENST00000266744.3	+	1	948	c.389G>A	c.(388-390)cGc>cAc	p.R130H		NM_004316.3	NP_004307.2	P50553	ASCL1_HUMAN	achaete-scute family bHLH transcription factor 1	130	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				adrenal chromaffin cell differentiation (GO:0061104)|carotid body glomus cell differentiation (GO:0061103)|cell maturation (GO:0048469)|cellular response to magnetism (GO:0071259)|central nervous system neuron development (GO:0021954)|cerebral cortex development (GO:0021987)|cerebral cortex GABAergic interneuron differentiation (GO:0021892)|commitment of neuronal cell to specific neuron type in forebrain (GO:0021902)|lung epithelial cell differentiation (GO:0060487)|lung neuroendocrine cell differentiation (GO:0061100)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of apoptotic process (GO:0043066)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription, DNA-templated (GO:0045892)|neuroblast fate determination (GO:0007400)|neuroblast proliferation (GO:0007405)|neurogenesis (GO:0022008)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|noradrenergic neuron development (GO:0003358)|noradrenergic neuron fate commitment (GO:0003359)|Notch signaling pathway (GO:0007219)|olfactory pit development (GO:0060166)|oligodendrocyte development (GO:0014003)|positive regulation of cell cycle (GO:0045787)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of epithelial cell differentiation (GO:0030856)|regulation of gene expression (GO:0010468)|regulation of mitotic cell cycle (GO:0007346)|regulation of timing of subpallium neuron differentiation (GO:0060165)|response to epidermal growth factor (GO:0070849)|response to folic acid (GO:0051593)|response to lithium ion (GO:0010226)|response to retinoic acid (GO:0032526)|spinal cord association neuron differentiation (GO:0021527)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|stomach neuroendocrine cell differentiation (GO:0061102)|subpallium neuron fate commitment (GO:0060163)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|transcription, DNA-templated (GO:0006351)|ventral spinal cord interneuron fate commitment (GO:0060579)|vestibular nucleus development (GO:0021750)	neuronal cell body (GO:0043025)|nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)	p.R130H(1)		NS(3)|large_intestine(1)|lung(1)	5						GAGCGCAACCGCGTCAAGTTG	0.667																																					p.R130H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G389A	12						.						29.0	24.0	26.0					12																	103352411		2203	4300	6503	101876541	SO:0001583	missense	429	exon1			L08424	CCDS31886.1	12q22-q23	2013-10-17	2013-10-17			ENSG00000139352		"""Basic helix-loop-helix proteins"""	738	protein-coding gene	gene with protein product		100790	"""achaete-scute complex (Drosophila) homolog-like 1"", ""achaete-scute complex-like 1 (Drosophila)"", ""achaete-scute complex homolog 1 (Drosophila)"""			8390674	Standard	NM_004316		Approved	ASH1, HASH1, bHLHa46	uc001tjr.4	P50553		ENST00000266744.3:c.389G>A	12.37:g.103352411G>A	ENSP00000266744:p.Arg130His	Somatic		Capture	Illumina HiSeq	Phase_I	101876541	NM_004316	A8K3C4|Q9BQ30	Missense_Mutation	SNP	ENST00000266744.3	37	CCDS31886.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818105	0.90790	.	.	ENSG00000139352	ENST00000266744	D	0.99722	-6.53	4.17	4.17	0.49024	Helix-loop-helix DNA-binding (5);	0.000000	0.64402	U	0.000002	D	0.99854	0.9932	H	0.98918	4.37	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96264	0.9193	10	0.87932	D	0	-15.9224	15.6095	0.76704	0.0:0.0:1.0:0.0	.	130	P50553	ASCL1_HUMAN	H	130	ENSP00000266744:R130H	ENSP00000266744:R130H	R	+	2	0	ASCL1	101876541	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.400000	0.97290	2.028000	0.59812	0.462000	0.41574	CGC		0.667	ASCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406707.1		
STAB2	55576	broad.mit.edu	37	12	104014254	104014254	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:104014254G>T	ENST00000388887.2	+	4	544	c.340G>T	c.(340-342)Ggt>Tgt	p.G114C		NM_017564.9	NP_060034.9			stabilin 2									p.G114C(1)		NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						AGAGTGCCCAGGTGGAGCGGG	0.488																																					p.G114C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G340T	12						.						89.0	76.0	80.0					12																	104014254		2202	4296	6498	102538384	SO:0001583	missense	55576	exon4			AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.340G>T	12.37:g.104014254G>T	ENSP00000373539:p.Gly114Cys	Somatic		Capture	Illumina HiSeq	Phase_I	102538384	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600875	0.66332	.	.	ENSG00000136011	ENST00000388887	D	0.87809	-2.3	4.98	4.98	0.66077	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.205963	0.41294	D	0.000903	D	0.94571	0.8251	M	0.93594	3.435	0.47441	D	0.999427	D	0.89917	1.0	D	0.68943	0.961	D	0.95186	0.8304	10	0.54805	T	0.06	.	14.1125	0.65132	0.0:0.0:1.0:0.0	.	114	Q8WWQ8	STAB2_HUMAN	C	114	ENSP00000373539:G114C	ENSP00000373539:G114C	G	+	1	0	STAB2	102538384	1.000000	0.71417	0.993000	0.49108	0.741000	0.42261	4.980000	0.63812	2.464000	0.83262	0.549000	0.68633	GGT		0.488	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
HSP90B1	7184	broad.mit.edu	37	12	104326699	104326699	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:104326699G>A	ENST00000299767.5	+	4	572	c.390G>A	c.(388-390)gaG>gaA	p.E130E	MIR3652_ENST00000579335.1_RNA|RP11-642P15.1_ENST00000548897.1_RNA	NM_003299.2	NP_003290.1	P14625	ENPL_HUMAN	heat shock protein 90kDa beta (Grp94), member 1	130					actin rod assembly (GO:0031247)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cellular response to ATP (GO:0071318)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|protein folding (GO:0006457)|protein transport (GO:0015031)|regulation of phosphoprotein phosphatase activity (GO:0043666)|response to hypoxia (GO:0001666)|sequestering of calcium ion (GO:0051208)|toll-like receptor signaling pathway (GO:0002224)	cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|low-density lipoprotein particle receptor binding (GO:0050750)|protein phosphatase binding (GO:0019903)|RNA binding (GO:0003723)|virion binding (GO:0046790)	p.E130E(1)		central_nervous_system(1)|kidney(5)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(4)	29					Rifabutin(DB00615)	CTGGAAATGAGGAACTAACAG	0.343																																					p.E130E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G390A	12						.						113.0	112.0	112.0					12																	104326699		2203	4300	6503	102850829	SO:0001819	synonymous_variant	7184	exon4			AY040226	CCDS9094.1	12q24.2-q24.3	2011-09-02	2006-02-24	2006-02-24		ENSG00000166598		"""Heat shock proteins / HSPC"""	12028	protein-coding gene	gene with protein product		191175	"""tumor rejection antigen (gp96) 1"""	TRA1		16269234	Standard	NM_003299		Approved	GP96, GRP94	uc001tkb.2	P14625	OTTHUMG00000170118	ENST00000299767.5:c.390G>A	12.37:g.104326699G>A		Somatic		Capture	Illumina HiSeq	Phase_I	102850829	NM_003299	Q96A97	Silent	SNP	ENST00000299767.5	37	CCDS9094.1																																																																																				0.343	HSP90B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407349.1	NM_003299	
NUAK1	9891	broad.mit.edu	37	12	106461102	106461102	+	Silent	SNP	C	C	T	rs141601761		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:106461102C>T	ENST00000261402.2	-	7	2843	c.1464G>A	c.(1462-1464)tcG>tcA	p.S488S		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	488					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.S488S(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						CCAACAGCTCCGAAGACTCAC	0.597																																					p.S488S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1464A	12						.	C		1,4405	2.1+/-5.4	0,1,2202	64.0	68.0	66.0		1464	-10.7	0.3	12	dbSNP_134	66	0,8600		0,0,4300	no	coding-synonymous	NUAK1	NM_014840.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		488/662	106461102	1,13005	2203	4300	6503	104985232	SO:0001819	synonymous_variant	9891	exon7			AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1464G>A	12.37:g.106461102C>T		Somatic		Capture	Illumina HiSeq	Phase_I	104985232	NM_014840	A7MD39|Q96KA8	Silent	SNP	ENST00000261402.2	37	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	C	3.783	-0.045332	0.07452	2.27E-4	0.0	ENSG00000074590	ENST00000359413	.	.	.	5.34	-10.7	0.00240	.	.	.	.	.	T	0.47746	0.1462	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61969	-0.6953	5	0.87932	D	0	.	1.8713	0.03209	0.1596:0.1772:0.3251:0.3381	.	.	.	.	Q	201	.	ENSP00000352382:R201Q	R	-	2	0	NUAK1	104985232	0.000000	0.05858	0.317000	0.25265	0.662000	0.39071	-3.778000	0.00368	-1.892000	0.01108	0.462000	0.41574	CGG		0.597	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
CMKLR1	1240	broad.mit.edu	37	12	108685839	108685839	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:108685839C>T	ENST00000312143.7	-	3	1264	c.901G>A	c.(901-903)Gcc>Acc	p.A301T	CMKLR1_ENST00000550402.1_Missense_Mutation_p.A301T|CMKLR1_ENST00000552995.1_Missense_Mutation_p.A299T|CMKLR1_ENST00000397688.2_Missense_Mutation_p.A299T|CMKLR1_ENST00000412676.1_Missense_Mutation_p.A301T	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	301					chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of macrophage chemotaxis (GO:0010759)|regulation of calcium-mediated signaling (GO:0050848)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			endometrium(5)|large_intestine(3)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	37						AGGGCAGTGGCCAGGGGCAAA	0.557																																					p.A301T												.	.	0			c.G901A	12						.						62.0	67.0	65.0					12																	108685839		2060	4203	6263	107209969	SO:0001583	missense	1240	exon4			U79526	CCDS41829.1, CCDS44965.1	12q23.3	2013-07-29			ENSG00000174600	ENSG00000174600		"""GPCR / Class A : Resolvin receptors"""	2121	protein-coding gene	gene with protein product	"""resolvin E1 receptor"", ""chemerin receptor"""	602351					Standard	NM_004072		Approved	RVER1	uc009zuw.3	Q99788	OTTHUMG00000169576	ENST00000312143.7:c.901G>A	12.37:g.108685839C>T	ENSP00000311733:p.Ala301Thr	None		Capture	Illumina HiSeq	Phase_I	107209969	NM_001142343	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Missense_Mutation	SNP	ENST00000312143.7	37	CCDS44965.1	.	.	.	.	.	.	.	.	.	.	c	12.02	1.812037	0.32053	.	.	ENSG00000174600	ENST00000312143;ENST00000412676;ENST00000397688;ENST00000552995;ENST00000550402	T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54	5.45	5.45	0.79879	GPCR, rhodopsin-like superfamily (1);	0.312292	0.33217	N	0.005143	T	0.52789	0.1756	N	0.13003	0.285	0.37429	D	0.913962	B	0.31893	0.345	B	0.38056	0.264	T	0.53968	-0.8363	10	0.06757	T	0.87	.	11.6863	0.51487	0.0:0.9101:0.0:0.0899	.	301	Q99788	CML1_HUMAN	T	301;301;299;299;301	ENSP00000311733:A301T;ENSP00000401293:A301T;ENSP00000380803:A299T;ENSP00000447579:A299T;ENSP00000449716:A301T	ENSP00000311733:A301T	A	-	1	0	CMKLR1	107209969	1.000000	0.71417	1.000000	0.80357	0.098000	0.18820	3.985000	0.56930	2.563000	0.86464	0.550000	0.68814	GCC		0.557	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1		
SSH1	54434	broad.mit.edu	37	12	109201464	109201464	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:109201464C>T	ENST00000326495.5	-	8	769	c.676G>A	c.(676-678)Gcc>Acc	p.A226T	SSH1_ENST00000326470.5_Missense_Mutation_p.A237T|SSH1_ENST00000551165.1_Missense_Mutation_p.A226T|SSH1_ENST00000360239.3_5'UTR	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	226					actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A226T(1)		breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCCTGCATGGCGTTCCACTCG	0.607																																					p.A237T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G709A	12						.						97.0	98.0	98.0					12																	109201464		2203	4300	6503	107725593	SO:0001583	missense	54434	exon7			BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.676G>A	12.37:g.109201464C>T	ENSP00000315713:p.Ala226Thr	Somatic		Capture	Illumina HiSeq	Phase_I	107725593	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235588	0.79800	.	.	ENSG00000084112	ENST00000326495;ENST00000551165;ENST00000326470;ENST00000303438	T;T;T	0.36520	1.25;1.25;1.25	5.35	5.35	0.76521	.	0.048356	0.85682	D	0.000000	T	0.36744	0.0978	L	0.55103	1.725	0.80722	D	1	P;B;P;B	0.45827	0.867;0.172;0.839;0.416	B;B;B;B	0.43155	0.163;0.031;0.41;0.072	T	0.22068	-1.0227	10	0.56958	D	0.05	-30.3146	11.5122	0.50500	0.0:0.9184:0.0:0.0816	.	237;130;226;226	Q8WYL5-5;Q8WYL5-3;Q8WYL5-2;Q8WYL5	.;.;.;SSH1_HUMAN	T	226;226;237;130	ENSP00000315713:A226T;ENSP00000448824:A226T;ENSP00000326107:A237T	ENSP00000307610:A130T	A	-	1	0	SSH1	107725593	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	4.907000	0.63300	2.488000	0.83962	0.655000	0.94253	GCC		0.607	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	
MYO1H	283446	broad.mit.edu	37	12	109831250	109831250	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:109831250G>A	ENST00000431443.2	+	2	241	c.241G>A	c.(241-243)Gtc>Atc	p.V81I	MYO1H_ENST00000310903.5_Splice_Site_p.V81I	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	81	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.V81I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GCCACCACATGTGTAAGTAGC	0.468																																					p.V81I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G241A	12						.						73.0	73.0	73.0					12																	109831250		1980	4166	6146	108315633	SO:0001630	splice_region_variant	283446	exon2				CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.242+1G>A	12.37:g.109831250G>A		Somatic		Capture	Illumina HiSeq	Phase_I	108315633	NM_001101421	F5H3C6	Missense_Mutation	SNP	ENST00000431443.2	37		.	.	.	.	.	.	.	.	.	.	G	3.011	-0.203852	0.06180	.	.	ENSG00000174527	ENST00000310903;ENST00000431443	D;D	0.86497	-2.13;-2.13	4.86	3.95	0.45737	.	.	.	.	.	T	0.62146	0.2404	N	0.01649	-0.78	0.28326	N	0.922015	B	0.06786	0.001	B	0.04013	0.001	T	0.56366	-0.7991	9	0.02654	T	1	.	6.0732	0.19901	0.1745:0.1676:0.6579:0.0	.	81	F5H3C6	.	I	81	ENSP00000439182:V81I;ENSP00000444076:V81I	ENSP00000439182:V81I	V	+	1	0	MYO1H	108315633	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.911000	0.28584	1.183000	0.42943	0.650000	0.86243	GTC		0.468	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	Missense_Mutation
TAS2R50	259296	broad.mit.edu	37	12	11138694	11138694	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:11138694G>A	ENST00000506868.1	-	1	817	c.766C>T	c.(766-768)Cgg>Tgg	p.R256W	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176890.2	NP_795371.2	P59544	T2R50_HUMAN	taste receptor, type 2, member 50	256					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)	p.R256W(1)		haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(2)|pancreas(1)	17						GGGTCATTCCGCAGCCTCCTA	0.428																																					p.R256W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C766T	12						.						78.0	80.0	79.0					12																	11138694		2203	4300	6503	11029961	SO:0001583	missense	259296	exon1			AF494235	CCDS8638.1	12p13.2	2012-08-22			ENSG00000212126	ENSG00000212126		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18882	protein-coding gene	gene with protein product		609627				12379855, 12584440, 16175505	Standard	NM_176890		Approved	T2R51	uc001qzl.2	P59544	OTTHUMG00000162719	ENST00000506868.1:c.766C>T	12.37:g.11138694G>A	ENSP00000424040:p.Arg256Trp	Somatic		Capture	Illumina HiSeq	Phase_I	11029961	NM_176890	P59545|Q2M255|Q645Y0	Missense_Mutation	SNP	ENST00000506868.1	37	CCDS8638.1	.	.	.	.	.	.	.	.	.	.	G	7.126	0.578884	0.13686	.	.	ENSG00000212126	ENST00000506868	T	0.00776	5.71	2.19	0.0662	0.14360	.	1.518050	0.04751	U	0.424515	T	0.00524	0.0017	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	10	0.87932	D	0	.	3.6885	0.08338	0.1678:0.2556:0.5766:0.0	.	256	P59544	T2R50_HUMAN	W	256	ENSP00000424040:R256W	ENSP00000424040:R256W	R	-	1	2	TAS2R50	11029961	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.561000	0.02158	-0.149000	0.11215	-0.802000	0.03209	CGG		0.428	TAS2R50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370192.2	NM_176890	
TCHP	84260	broad.mit.edu	37	12	110340923	110340923	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:110340923G>A	ENST00000312777.5	+	2	306	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	TCHP_ENST00000405876.4_Missense_Mutation_p.R31Q	NM_032300.4	NP_115676.1			trichoplein, keratin filament binding									p.R31Q(1)		NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(2)	22						GCCCGGCTTCGGCAGCAGTGG	0.592																																					p.R31Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G92A	12						.						71.0	71.0	71.0					12																	110340923		2203	4300	6503	108825306	SO:0001583	missense	84260	exon2			AK092736	CCDS9137.1	12q24.11	2011-08-25	2006-01-27			ENSG00000139437			28135	protein-coding gene	gene with protein product	"""mitostatin"""	612654				15731013, 20930847	Standard	NM_032300		Approved	MGC10854, TpMs	uc001tpn.3	Q9BT92		ENST00000312777.5:c.92G>A	12.37:g.110340923G>A	ENSP00000324404:p.Arg31Gln	Somatic		Capture	Illumina HiSeq	Phase_I	108825306	NM_001143852		Missense_Mutation	SNP	ENST00000312777.5	37	CCDS9137.1	.	.	.	.	.	.	.	.	.	.	G	32	5.159990	0.94727	.	.	ENSG00000139437	ENST00000405876;ENST00000536868;ENST00000312777;ENST00000536408	T;T;T	0.53423	1.3;1.3;0.62	4.7	3.81	0.43845	.	0.129024	0.51477	D	0.000094	T	0.59528	0.2200	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.56438	-0.7979	10	0.13853	T	0.58	-24.2323	10.6465	0.45623	0.095:0.0:0.905:0.0	.	31	Q9BT92	TCHP_HUMAN	Q	31	ENSP00000384520:R31Q;ENSP00000324404:R31Q;ENSP00000441835:R31Q	ENSP00000324404:R31Q	R	+	2	0	TCHP	108825306	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.308000	0.72820	0.999000	0.39023	0.449000	0.29647	CGG		0.592	TCHP-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403289.1	NM_032300	
SH2B3	10019	broad.mit.edu	37	12	111885616	111885616	+	Missense_Mutation	SNP	G	G	A	rs374482426		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:111885616G>A	ENST00000341259.2	+	7	1750	c.1393G>A	c.(1393-1395)Gtc>Atc	p.V465I	SH2B3_ENST00000538307.1_Missense_Mutation_p.V263I	NM_005475.2	NP_005466.1	Q9UQQ2	SH2B3_HUMAN	SH2B adaptor protein 3	465					blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic hemopoiesis (GO:0035162)|intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)	phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)	p.V465I(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(1)|skin(1)	10					Pazopanib(DB06589)	CGTGGTAGTCGTCTCCCAACC	0.632																																					p.V465I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1393A	12						.	G	ILE/VAL	0,4406		0,0,2203	75.0	67.0	70.0		1393	0.8	0.5	12		70	2,8598	2.2+/-6.3	0,2,4298	no	missense	SH2B3	NM_005475.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	465/576	111885616	2,13004	2203	4300	6503	110369999	SO:0001583	missense	10019	exon7			AF055581	CCDS9153.1	12q24.12	2014-09-17				ENSG00000111252		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	29605	protein-coding gene	gene with protein product	"""lymphocyte adaptor protein"""	605093				10799879	Standard	NM_005475		Approved	LNK, IDDM20	uc001tse.3	Q9UQQ2		ENST00000341259.2:c.1393G>A	12.37:g.111885616G>A	ENSP00000345492:p.Val465Ile	Somatic		Capture	Illumina HiSeq	Phase_I	110369999	NM_005475	B9EGG5|O95184	Missense_Mutation	SNP	ENST00000341259.2	37	CCDS9153.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.087551	0.36855	0.0	2.33E-4	ENSG00000111252	ENST00000341259;ENST00000551001;ENST00000538307	T;T	0.34072	1.39;1.38	4.96	0.777	0.18538	.	1.051440	0.07353	N	0.882787	T	0.30634	0.0771	L	0.43152	1.355	0.22213	N	0.999281	P;P;B	0.36412	0.455;0.552;0.326	B;B;B	0.32393	0.145;0.055;0.069	T	0.20338	-1.0278	10	0.37606	T	0.19	-37.0969	12.2861	0.54793	0.0683:0.4806:0.4511:0.0	.	263;329;465	F5GYM4;Q59H48;Q9UQQ2	.;.;SH2B3_HUMAN	I	465;275;263	ENSP00000345492:V465I;ENSP00000440597:V263I	ENSP00000345492:V465I	V	+	1	0	SH2B3	110369999	0.558000	0.26554	0.497000	0.27552	0.834000	0.47266	0.955000	0.29188	-0.055000	0.13244	0.462000	0.41574	GTC		0.632	SH2B3-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000404779.1	NM_005475	
TAS2R46	259292	broad.mit.edu	37	12	11214075	11214075	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:11214075T>C	ENST00000533467.1	-	1	818	c.819A>G	c.(817-819)tcA>tcG	p.S273S	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176887.2	NP_795368.2	P59540	T2R46_HUMAN	taste receptor, type 2, member 46	273					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		ATGGGTGGGTTGAAGGATAGC	0.418																																					p.S273S												.	.	0			c.A819G	12						.						198.0	205.0	202.0					12																	11214075		2151	4282	6433	11105342	SO:0001819	synonymous_variant	259292	exon1			AF494227	CCDS53748.1	12p13.2	2012-08-22				ENSG00000226761		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18877	protein-coding gene	gene with protein product		612774				12379855	Standard	NM_176887		Approved	T2R54	uc001qzp.1	P59540		ENST00000533467.1:c.819A>G	12.37:g.11214075T>C		None		Capture	Illumina HiSeq	Phase_I	11105342	NM_176887	P59548|Q645X6	Silent	SNP	ENST00000533467.1	37	CCDS53748.1																																																																																				0.418	TAS2R46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383559.1	NM_176887	
ATXN2	6311	broad.mit.edu	37	12	111990214	111990214	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:111990214G>A	ENST00000377617.3	-	5	1082	c.921C>T	c.(919-921)gcC>gcT	p.A307A	ATXN2_ENST00000608853.1_Silent_p.A147A|ATXN2_ENST00000389153.4_Silent_p.A42A|ATXN2_ENST00000542287.2_Silent_p.A42A|ATXN2_ENST00000550104.1_Silent_p.A307A|ATXN2_ENST00000549455.1_Intron|ATXN2_ENST00000535949.1_Silent_p.A18A	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	307					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)	p.A307A(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						TCTCATGTGCGGCATCAAGTA	0.353																																					p.A307A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C921T	12						.						77.0	77.0	77.0					12																	111990214		2203	4300	6503	110474597	SO:0001819	synonymous_variant	6311	exon5			U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.921C>T	12.37:g.111990214G>A		Somatic		Capture	Illumina HiSeq	Phase_I	110474597	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	CCDS31902.1																																																																																				0.353	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973	
HECTD4	283450	broad.mit.edu	37	12	112622214	112622214	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:112622214G>C	ENST00000430131.2	-	60	10435	c.9290C>G	c.(9289-9291)cCc>cGc	p.P3097R	HECTD4_ENST00000377560.5_Missense_Mutation_p.P3347R|HECTD4_ENST00000550722.1_Missense_Mutation_p.P3373R			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3097					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.P3347R(1)									CGGAGGGATGGGCAGCTCGAG	0.687																																					p.P3347R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C10040G	12						.						13.0	19.0	17.0					12																	112622214		2123	4237	6360	111106597	SO:0001583	missense	283450	exon60			AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9290C>G	12.37:g.112622214G>C	ENSP00000404379:p.Pro3097Arg	Somatic		Capture	Illumina HiSeq	Phase_I	111106597	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	G	12.49	1.954152	0.34471	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.42900	0.96;0.96;0.96	5.58	5.58	0.84498	.	.	.	.	.	T	0.34978	0.0916	N	0.19112	0.55	0.30771	N	0.743004	B	0.19583	0.037	B	0.15484	0.013	T	0.36553	-0.9743	9	0.87932	D	0	.	19.5799	0.95461	0.0:0.0:1.0:0.0	.	3097	Q9Y4D8	K0614_HUMAN	R	3347;3097;3373	ENSP00000366783:P3347R;ENSP00000404379:P3097R;ENSP00000449784:P3373R	ENSP00000366783:P3347R	P	-	2	0	C12orf51	111106597	1.000000	0.71417	0.999000	0.59377	0.674000	0.39518	5.308000	0.65768	2.642000	0.89623	0.655000	0.94253	CCC		0.687	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
RBM19	9904	broad.mit.edu	37	12	114384271	114384271	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:114384271G>A	ENST00000545145.2	-	12	1495	c.1417C>T	c.(1417-1419)Ctc>Ttc	p.L473F	RBM19_ENST00000392561.3_Missense_Mutation_p.L473F|RBM19_ENST00000261741.5_Missense_Mutation_p.L473F	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	473	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				multicellular organismal development (GO:0007275)|positive regulation of embryonic development (GO:0040019)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.L473F(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(4)	55	Medulloblastoma(191;0.163)|all_neural(191;0.178)					AACACGTGGAGCATCCTGCCC	0.557																																					p.L473F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1417T	12						.						111.0	88.0	96.0					12																	114384271		2203	4300	6503	112868654	SO:0001583	missense	9904	exon12			AL117547	CCDS9172.1	12q24.21	2013-02-12				ENSG00000122965		"""RNA binding motif (RRM) containing"""	29098	protein-coding gene	gene with protein product						9734811, 11230166	Standard	NM_016196		Approved	DKFZp586F1023, KIAA0682	uc009zwi.2	Q9Y4C8	OTTHUMG00000169646	ENST00000545145.2:c.1417C>T	12.37:g.114384271G>A	ENSP00000442053:p.Leu473Phe	Somatic		Capture	Illumina HiSeq	Phase_I	112868654	NM_016196	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	.	.	.	.	.	.	.	.	.	.	G	18.12	3.552882	0.65425	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.22539	1.95;1.95;1.95	4.6	3.7	0.42460	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.071829	0.64402	D	0.000020	T	0.38825	0.1055	M	0.89968	3.075	0.54753	D	0.999988	P	0.44429	0.835	P	0.49477	0.612	T	0.40478	-0.9561	10	0.59425	D	0.04	-26.5486	8.2152	0.31507	0.0864:0.0:0.7455:0.168	.	473	Q9Y4C8	RBM19_HUMAN	F	473	ENSP00000442053:L473F;ENSP00000376344:L473F;ENSP00000261741:L473F	ENSP00000261741:L473F	L	-	1	0	RBM19	112868654	1.000000	0.71417	0.998000	0.56505	0.837000	0.47467	3.644000	0.54381	2.118000	0.64928	0.655000	0.94253	CTC		0.557	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
CIT	11113	broad.mit.edu	37	12	120168378	120168378	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:120168378C>T	ENST00000261833.7	-	26	3334	c.3282G>A	c.(3280-3282)aaG>aaA	p.K1094K	CIT_ENST00000392521.2_Silent_p.K1136K|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1094	Interaction with Rho/Rac.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.K1094K(1)|p.K1137K(1)		breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CCTTGTGCTCCTTCACTGCCA	0.602																																					p.K1094K												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3282A	12						.						66.0	58.0	60.0					12																	120168378		2203	4300	6503	118652761	SO:0001819	synonymous_variant	11113	exon26			AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3282G>A	12.37:g.120168378C>T		Somatic		Capture	Illumina HiSeq	Phase_I	118652761	NM_007174	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	9.930	1.214694	0.22289	.	.	ENSG00000122966	ENST00000392520	.	.	.	5.45	4.56	0.56223	.	.	.	.	.	T	0.62146	0.2404	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60244	-0.7301	4	.	.	.	.	10.7262	0.46070	0.0:0.8011:0.0:0.1989	.	.	.	.	K	722	.	.	R	-	2	0	CIT	118652761	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.474000	0.35398	1.303000	0.44873	0.655000	0.94253	AGG		0.602	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
CCDC64	92558	broad.mit.edu	37	12	120527853	120527853	+	Missense_Mutation	SNP	C	C	T	rs377763632		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:120527853C>T	ENST00000397558.2	+	8	1538	c.1538C>T	c.(1537-1539)tCg>tTg	p.S513L	CCDC64_ENST00000257583.4_Missense_Mutation_p.S210L|CCDC64_ENST00000446727.2_Missense_Mutation_p.S184L	NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	513					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)	p.S513L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CTGAACCTCTCGCAGCAGCTG	0.532																																					p.S513L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1538T	12						.	C	LEU/SER	0,3922		0,0,1961	78.0	79.0	79.0		1538	5.2	1.0	12		79	1,8309		0,1,4154	no	missense	CCDC64	NM_207311.2	145	0,1,6115	TT,TC,CC		0.012,0.0,0.0082	probably-damaging	513/574	120527853	1,12231	1961	4155	6116	119012236	SO:0001583	missense	92558	exon8			U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.1538C>T	12.37:g.120527853C>T	ENSP00000380690:p.Ser513Leu	Somatic		Capture	Illumina HiSeq	Phase_I	119012236	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	37	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	C	34	5.313570	0.95655	0.0	1.2E-4	ENSG00000135127	ENST00000397558;ENST00000446727;ENST00000548673;ENST00000257583	T;T;T	0.51325	0.71;3.53;3.51	5.23	5.23	0.72850	.	0.000000	0.56097	U	0.000028	T	0.65249	0.2673	L	0.51422	1.61	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.87578	0.998;0.99;0.996	T	0.66312	-0.5955	10	0.56958	D	0.05	-0.2499	18.8023	0.92023	0.0:1.0:0.0:0.0	.	210;184;513	B4DWL0;B4DNE7;Q6ZP65	.;.;BICR1_HUMAN	L	513;184;231;210	ENSP00000380690:S513L;ENSP00000399658:S184L;ENSP00000447477:S231L	ENSP00000257583:S210L	S	+	2	0	CCDC64	119012236	1.000000	0.71417	0.979000	0.43373	0.925000	0.55904	6.042000	0.70996	2.422000	0.82143	0.462000	0.41574	TCG		0.532	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311	
GCN1L1	10985	broad.mit.edu	37	12	120565671	120565671	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:120565671G>A	ENST00000300648.6	-	58	8010	c.7998C>T	c.(7996-7998)gaC>gaT	p.D2666D		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2666					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)	p.D2666D(1)		NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGATGGTGTCGTCCACCTGCT	0.537																																					p.D2666D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C7998T	12						.						87.0	95.0	92.0					12																	120565671		2031	4187	6218	119050054	SO:0001819	synonymous_variant	10985	exon58			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7998C>T	12.37:g.120565671G>A		Somatic		Capture	Illumina HiSeq	Phase_I	119050054	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	37	CCDS41847.1																																																																																				0.537	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
GCN1L1	10985	broad.mit.edu	37	12	120572169	120572169	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:120572169C>T	ENST00000300648.6	-	53	7255	c.7243G>A	c.(7243-7245)Gca>Aca	p.A2415T		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	2415					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					TTGGCCCCTGCTCCCTGAATC	0.607																																					p.A2415T												.	.	0			c.G7243A	12						.						106.0	108.0	107.0					12																	120572169		2096	4224	6320	119056552	SO:0001583	missense	10985	exon53			U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.7243G>A	12.37:g.120572169C>T	ENSP00000300648:p.Ala2415Thr	None		Capture	Illumina HiSeq	Phase_I	119056552	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	C	36	5.887374	0.97068	.	.	ENSG00000089154	ENST00000300648	T	0.66280	-0.2	5.5	5.5	0.81552	Armadillo-like helical (1);Armadillo-type fold (1);	0.062499	0.64402	D	0.000006	T	0.81451	0.4825	M	0.90870	3.155	0.80722	D	1	D	0.62365	0.991	P	0.56700	0.804	D	0.85878	0.1420	10	0.87932	D	0	-10.2473	19.3918	0.94585	0.0:1.0:0.0:0.0	.	2415	Q92616	GCN1L_HUMAN	T	2415	ENSP00000300648:A2415T	ENSP00000300648:A2415T	A	-	1	0	GCN1L1	119056552	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.474000	0.81024	2.595000	0.87683	0.511000	0.50034	GCA		0.607	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
ZCCHC8	55596	broad.mit.edu	37	12	122985209	122985209	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:122985209A>G	ENST00000336229.4	-	1	309	c.179T>C	c.(178-180)aTc>aCc	p.I60T	ZCCHC8_ENST00000543897.1_5'Flank|ZCCHC8_ENST00000536306.1_5'Flank	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	60					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.I60T(1)		endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		GAGCTGCTCGATGGTCTCCTC	0.701																																					p.I60T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T179C	12						.						22.0	27.0	26.0					12																	122985209		1920	4099	6019	121551162	SO:0001583	missense	55596	exon1			BC017704		12q24.31	2014-04-14				ENSG00000033030		"""Zinc fingers, CCHC domain containing"""	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.179T>C	12.37:g.122985209A>G	ENSP00000337313:p.Ile60Thr	Somatic		Capture	Illumina HiSeq	Phase_I	121551162	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	A	19.06	3.753465	0.69648	.	.	ENSG00000033030	ENST00000336229	T	0.28895	1.59	5.33	5.33	0.75918	.	0.287377	0.38005	N	0.001860	T	0.31575	0.0801	M	0.61703	1.905	0.42812	D	0.993963	P	0.39665	0.682	B	0.32864	0.154	T	0.30621	-0.9972	10	0.87932	D	0	-4.7453	15.5961	0.76583	1.0:0.0:0.0:0.0	.	60	Q6NZY4	ZCHC8_HUMAN	T	60	ENSP00000337313:I60T	ENSP00000337313:I60T	I	-	2	0	ZCCHC8	121551162	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	5.941000	0.70195	2.137000	0.66172	0.533000	0.62120	ATC		0.701	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612	
KNTC1	9735	broad.mit.edu	37	12	123107100	123107100	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:123107100C>T	ENST00000333479.7	+	62	6638	c.6461C>T	c.(6460-6462)gCg>gTg	p.A2154V	KNTC1_ENST00000537348.1_3'UTR|KNTC1_ENST00000436959.3_Missense_Mutation_p.A75V|KNTC1_ENST00000534995.1_Missense_Mutation_p.A75V|HCAR1_ENST00000356987.2_Intron|KNTC1_ENST00000450485.2_Missense_Mutation_p.A1079V	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	2154					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AAGATGCATGCGATGAATACC	0.294																																					p.A2154V												.	.	0			c.C6461T	12						.						45.0	43.0	43.0					12																	123107100		1850	4086	5936	121673053	SO:0001583	missense	9735	exon62				CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.6461C>T	12.37:g.123107100C>T	ENSP00000328236:p.Ala2154Val	None		Capture	Illumina HiSeq	Phase_I	121673053	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.515614	0.00975	.	.	ENSG00000184445	ENST00000450485;ENST00000333479;ENST00000436959;ENST00000534995	T;T	0.18338	2.22;2.8	5.11	-1.45	0.08828	.	0.776541	0.12726	N	0.444260	T	0.06234	0.0161	N	0.04508	-0.205	0.21604	N	0.999621	B;B	0.27910	0.193;0.0	B;B	0.20384	0.029;0.0	T	0.41893	-0.9483	10	0.14252	T	0.57	-1.0408	10.4792	0.44682	0.0:0.4668:0.0:0.5332	.	1079;2154	E7ES84;P50748	.;KNTC1_HUMAN	V	1079;2154;75;75	ENSP00000397992:A1079V;ENSP00000328236:A2154V	ENSP00000328236:A2154V	A	+	2	0	KNTC1	121673053	0.397000	0.25270	0.040000	0.18447	0.236000	0.25371	0.477000	0.22196	-0.449000	0.07117	-0.416000	0.06073	GCG		0.294	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
HIP1R	9026	broad.mit.edu	37	12	123339665	123339665	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:123339665G>A	ENST00000253083.4	+	10	967	c.842G>A	c.(841-843)cGg>cAg	p.R281Q		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	281					receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)	p.R281Q(1)		breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CAGATCCCCCGGCTGCCCGAG	0.642																																					p.R281Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G842A	12						.						59.0	66.0	63.0					12																	123339665		2203	4300	6503	121905618	SO:0001583	missense	9026	exon10			AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.842G>A	12.37:g.123339665G>A	ENSP00000253083:p.Arg281Gln	Somatic		Capture	Illumina HiSeq	Phase_I	121905618	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.396674	0.42512	.	.	ENSG00000130787	ENST00000253083	T	0.28895	1.59	4.58	2.6	0.31112	ANTH (1);	0.114703	0.56097	D	0.000028	T	0.19927	0.0479	N	0.17082	0.46	0.58432	D	0.999999	B;B;P	0.52061	0.027;0.124;0.95	B;B;P	0.49226	0.013;0.02;0.603	T	0.04041	-1.0982	10	0.09338	T	0.73	-31.3259	8.3946	0.32548	0.0823:0.0:0.7638:0.1539	.	281;281;269	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	Q	281	ENSP00000253083:R281Q	ENSP00000253083:R281Q	R	+	2	0	HIP1R	121905618	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.513000	0.53414	0.926000	0.37118	0.563000	0.77884	CGG		0.642	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
LRP6	4040	broad.mit.edu	37	12	12317346	12317346	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:12317346C>T	ENST00000261349.4	-	9	1989	c.1913G>A	c.(1912-1914)cGg>cAg	p.R638Q	LRP6_ENST00000543091.1_Missense_Mutation_p.R638Q	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	638	Beta-propeller 3.				anterior/posterior pattern specification (GO:0009952)|axis elongation involved in somitogenesis (GO:0090245)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac neural crest cell differentiation involved in heart development (GO:0061310)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration involved in gastrulation (GO:0042074)|cellular response to cholesterol (GO:0071397)|cerebellum morphogenesis (GO:0021587)|cerebral cortex cell migration (GO:0021795)|cerebral cortex development (GO:0021987)|convergent extension (GO:0060026)|dopaminergic neuron differentiation (GO:0071542)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|external genitalia morphogenesis (GO:0035261)|face morphogenesis (GO:0060325)|forebrain radial glial cell differentiation (GO:0021861)|formation of radial glial scaffolds (GO:0021943)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|mammary placode formation (GO:0060596)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of planar cell polarity pathway involved in cardiac muscle tissue morphogenesis (GO:2000151)|negative regulation of planar cell polarity pathway involved in cardiac right atrium morphogenesis (GO:2000162)|negative regulation of planar cell polarity pathway involved in neural tube closure (GO:2000168)|negative regulation of planar cell polarity pathway involved in outflow tract morphogenesis (GO:2000164)|negative regulation of planar cell polarity pathway involved in pericardium morphogenesis (GO:2000166)|negative regulation of planar cell polarity pathway involved in ventricular septum morphogenesis (GO:2000149)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of smooth muscle cell apoptotic process (GO:0034392)|neural crest cell differentiation (GO:0014033)|neural crest formation (GO:0014029)|neural tube closure (GO:0001843)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone resorption (GO:0045780)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell cycle (GO:0045787)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of ossification (GO:0045778)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification (GO:2000055)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of cell development (GO:0060284)|regulation of fat cell differentiation (GO:0045598)|regulation of ossification (GO:0030278)|response to folic acid (GO:0051593)|response to peptide hormone (GO:0043434)|single organismal cell-cell adhesion (GO:0016337)|synaptic transmission (GO:0007268)|thalamus development (GO:0021794)|toxin transport (GO:1901998)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	apolipoprotein binding (GO:0034185)|coreceptor activity involved in Wnt signaling pathway (GO:0071936)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|kinase inhibitor activity (GO:0019210)|low-density lipoprotein receptor activity (GO:0005041)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxin transporter activity (GO:0019534)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.R638Q(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(28)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	85		Prostate(47;0.0865)				ATCTGCTCTCCGTGAAAACAA	0.438																																					p.R638Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1913A	12						.						103.0	101.0	102.0					12																	12317346		2203	4300	6503	12208613	SO:0001583	missense	4040	exon9			AF074264	CCDS8647.1	12p13.2	2013-05-29			ENSG00000070018	ENSG00000070018		"""Low density lipoprotein receptors"""	6698	protein-coding gene	gene with protein product		603507				9704021	Standard	NM_002336		Approved	ADCAD2	uc001rah.4	O75581	OTTHUMG00000168540	ENST00000261349.4:c.1913G>A	12.37:g.12317346C>T	ENSP00000261349:p.Arg638Gln	Somatic		Capture	Illumina HiSeq	Phase_I	12208613	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045719	0.75846	.	.	ENSG00000070018	ENST00000261349;ENST00000543091	D;D	0.91124	-2.79;-2.79	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.56097	D	0.000026	D	0.86285	0.5896	L	0.41124	1.26	0.58432	D	0.999999	D;P	0.63880	0.993;0.755	B;B	0.41299	0.353;0.062	D	0.83751	0.0209	10	0.10111	T	0.7	.	20.0965	0.97849	0.0:1.0:0.0:0.0	.	638;638	F5H7J9;O75581	.;LRP6_HUMAN	Q	638	ENSP00000261349:R638Q;ENSP00000442472:R638Q	ENSP00000261349:R638Q	R	-	2	0	LRP6	12208613	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	4.859000	0.62954	2.824000	0.97209	0.655000	0.94253	CGG		0.438	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1		
ABCB9	23457	broad.mit.edu	37	12	123414591	123414591	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:123414591G>A	ENST00000542678.1	-	12	5006	c.2168C>T	c.(2167-2169)aCc>aTc	p.T723I	ABCB9_ENST00000344275.7_Intron|ABCB9_ENST00000392439.3_Missense_Mutation_p.T723I|ABCB9_ENST00000540285.1_Missense_Mutation_p.T660I|ABCB9_ENST00000442833.2_Intron|ABCB9_ENST00000346530.5_Missense_Mutation_p.T680I|ABCB9_ENST00000280560.8_Missense_Mutation_p.T723I|ABCB9_ENST00000442028.2_Missense_Mutation_p.T726I			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	723	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)	p.T723I(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		CTGCTGGTGGGTGCCCTGCTG	0.667																																					p.T680I	Ovarian(49;786 1333 9175 38236)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2039T	12						.						21.0	18.0	19.0					12																	123414591		2195	4282	6477	121980544	SO:0001583	missense	23457	exon11			U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78		ENST00000542678.1:c.2168C>T	12.37:g.123414591G>A	ENSP00000440288:p.Thr723Ile	Somatic		Capture	Illumina HiSeq	Phase_I	121980544	NM_019624	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.271543	0.80469	.	.	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028;ENST00000546289	T;T;T;T;T;T;T	0.74737	-0.87;-0.87;-0.87;-0.87;-0.87;-0.87;-0.87	4.81	4.81	0.61882	ABC transporter-like (1);	0.415084	0.26496	N	0.024059	D	0.88923	0.6569	H	0.94847	3.59	0.22954	N	0.99852	D;P;P;B	0.59357	0.985;0.807;0.926;0.399	P;B;D;B	0.66979	0.791;0.242;0.948;0.265	T	0.83322	-0.0017	10	0.87932	D	0	-23.1579	13.6197	0.62130	0.0:0.1553:0.8447:0.0	.	660;330;680;723	B4E2J0;B4DFR8;Q9NP78-2;Q9NP78	.;.;.;ABCB9_HUMAN	I	723;660;680;723;723;726;267	ENSP00000280560:T723I;ENSP00000441734:T660I;ENSP00000280559:T680I;ENSP00000376234:T723I;ENSP00000440288:T723I;ENSP00000394898:T726I;ENSP00000442281:T267I	ENSP00000280560:T723I	T	-	2	0	ABCB9	121980544	0.432000	0.25554	0.948000	0.38648	0.998000	0.95712	3.224000	0.51238	2.213000	0.71641	0.561000	0.74099	ACC		0.667	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
ATP6V0A2	23545	broad.mit.edu	37	12	124220121	124220121	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:124220121C>T	ENST00000330342.3	+	8	1023	c.775C>T	c.(775-777)Cgg>Tgg	p.R259W		NM_012463.3	NP_036595.2	Q9Y487	VPP2_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a2	259					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|immune response (GO:0006955)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	hydrogen ion transmembrane transporter activity (GO:0015078)	p.R259W(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000224)|Epithelial(86;0.000625)|all cancers(50;0.00775)		AGCCGAGGAGCGGAGGGAGAT	0.522																																					p.R259W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C775T	12						.						101.0	87.0	92.0					12																	124220121		2203	4300	6503	122786074	SO:0001583	missense	23545	exon8			AF112972	CCDS9254.1	12q24.31	2010-04-21	2006-01-20		ENSG00000185344	ENSG00000185344		"""ATPases / V-type"""	18481	protein-coding gene	gene with protein product	"""infantile malignant osteopetrosis"""	611716	"""infantile malignant osteopetrosis"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 2"", ""ATPase, H+ transporting, lysosomal V0 subunit A2"""			2247090, 18157129	Standard	NM_012463		Approved	TJ6, a2, TJ6s, TJ6M, ATP6a2, J6B7, ATP6N1D, Vph1, Stv1	uc001ufr.3	Q9Y487	OTTHUMG00000168723	ENST00000330342.3:c.775C>T	12.37:g.124220121C>T	ENSP00000332247:p.Arg259Trp	Somatic		Capture	Illumina HiSeq	Phase_I	122786074	NM_012463	A8K026|Q6NUM0	Missense_Mutation	SNP	ENST00000330342.3	37	CCDS9254.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376531	0.61735	.	.	ENSG00000185344	ENST00000330342;ENST00000541854;ENST00000504192	D;D	0.88741	-2.42;-2.42	5.97	3.12	0.35913	.	0.000000	0.85682	D	0.000000	D	0.95348	0.8490	H	0.95679	3.705	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.95	D	0.94067	0.7332	10	0.87932	D	0	-29.149	8.915	0.35576	0.3828:0.552:0.0:0.0651	.	259;259	Q9Y487;Q8TBM3	VPP2_HUMAN;.	W	259;259;129	ENSP00000332247:R259W;ENSP00000443441:R129W	ENSP00000332247:R259W	R	+	1	2	ATP6V0A2	122786074	1.000000	0.71417	0.909000	0.35828	0.370000	0.29829	1.878000	0.39608	0.402000	0.25451	-0.293000	0.09583	CGG		0.522	ATP6V0A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400765.2	NM_012463	
DNAH10	196385	broad.mit.edu	37	12	124325959	124325959	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:124325959A>G	ENST00000409039.3	+	29	4898	c.4873A>G	c.(4873-4875)Atg>Gtg	p.M1625V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1625	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGGAGAAGTCATGGAGTTTCG	0.463																																					p.M1625V												.	.	0			c.A4873G	12						.						222.0	224.0	223.0					12																	124325959		2013	4167	6180	122891912	SO:0001583	missense	196385	exon29			AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.4873A>G	12.37:g.124325959A>G	ENSP00000386770:p.Met1625Val	None		Capture	Illumina HiSeq	Phase_I	122891912	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	A	5.966	0.362253	0.11296	.	.	ENSG00000197653	ENST00000409039	T	0.49139	0.79	5.23	5.23	0.72850	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	U	0.000000	T	0.29749	0.0743	N	0.16037	0.36	0.58432	D	0.999999	P	0.42123	0.771	B	0.41135	0.348	T	0.17837	-1.0356	10	0.02654	T	1	.	15.108	0.72334	1.0:0.0:0.0:0.0	.	1625	Q8IVF4	DYH10_HUMAN	V	1625	ENSP00000386770:M1625V	ENSP00000386770:M1625V	M	+	1	0	DNAH10	122891912	1.000000	0.71417	0.985000	0.45067	0.785000	0.44390	9.105000	0.94246	1.989000	0.58080	0.459000	0.35465	ATG		0.463	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
TMEM132D	121256	broad.mit.edu	37	12	130184472	130184472	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:130184472A>C	ENST00000422113.2	-	2	1177	c.851T>G	c.(850-852)cTg>cGg	p.L284R	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	284					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)		p.L284R(1)		NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		GTCCAGACGCAGTTCTCTCAG	0.532																																					p.L284R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T851G	12						.						102.0	97.0	98.0					12																	130184472		2203	4300	6503	128750425	SO:0001583	missense	121256	exon2			AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.851T>G	12.37:g.130184472A>C	ENSP00000408581:p.Leu284Arg	Somatic		Capture	Illumina HiSeq	Phase_I	128750425	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.622277	0.46840	.	.	ENSG00000151952	ENST00000422113	T	0.12984	2.63	5.17	5.17	0.71159	.	0.218952	0.30285	N	0.009971	T	0.30479	0.0766	M	0.81497	2.545	0.36223	D	0.852105	D	0.53885	0.963	P	0.51385	0.668	T	0.45249	-0.9274	9	.	.	.	-22.3014	15.32	0.74115	1.0:0.0:0.0:0.0	.	284	Q14C87	T132D_HUMAN	R	284	ENSP00000408581:L284R	.	L	-	2	0	TMEM132D	128750425	0.892000	0.30473	0.988000	0.46212	0.031000	0.12232	3.778000	0.55371	2.057000	0.61298	0.528000	0.53228	CTG		0.532	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
RIMBP2	23504	broad.mit.edu	37	12	130926475	130926475	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:130926475T>G	ENST00000261655.4	-	8	1534	c.1371A>C	c.(1369-1371)aaA>aaC	p.K457N	RIMBP2_ENST00000535703.1_Missense_Mutation_p.K365N|RIMBP2_ENST00000536002.1_Missense_Mutation_p.K365N	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	457	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.K457N(1)		NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		TCTGGTGGGGTTTGGCCAGAA	0.567																																					p.K457N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1371C	12						.						72.0	63.0	66.0					12																	130926475		2203	4300	6503	129492428	SO:0001583	missense	23504	exon8			AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.1371A>C	12.37:g.130926475T>G	ENSP00000261655:p.Lys457Asn	Somatic		Capture	Illumina HiSeq	Phase_I	129492428	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	t	15.90	2.968365	0.53614	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.54279	0.58;0.58;0.58	4.23	0.724	0.18236	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.504247	0.20430	N	0.092495	T	0.55273	0.1910	M	0.68593	2.085	0.30090	N	0.808391	P;P;B	0.46706	0.883;0.745;0.361	B;P;B	0.49226	0.444;0.603;0.086	T	0.58375	-0.7647	10	0.72032	D	0.01	-16.4039	9.2531	0.37566	0.0:0.6623:0.0:0.3377	.	365;365;457	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	N	457;365;365;365	ENSP00000261655:K457N;ENSP00000440347:K365N;ENSP00000439159:K365N	ENSP00000261655:K457N	K	-	3	2	RIMBP2	129492428	0.086000	0.21541	0.947000	0.38551	0.969000	0.65631	0.588000	0.23924	0.242000	0.21303	-0.435000	0.05868	AAA		0.567	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
SFSWAP	6433	broad.mit.edu	37	12	132241092	132241092	+	Silent	SNP	G	G	A	rs34225497	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:132241092G>A	ENST00000261674.4	+	11	1764	c.1623G>A	c.(1621-1623)gcG>gcA	p.A541A	SFSWAP_ENST00000541286.1_Silent_p.A541A|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	541					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)	p.A541A(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						AGGATGGCGCGCCTGAAGACG	0.587																																					p.A541A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1623A	12						.	G		0,4406		0,0,2203	65.0	64.0	64.0		1623	-1.2	0.0	12	dbSNP_126	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFSWAP	NM_004592.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		541/952	132241092	1,13005	2203	4300	6503	130807045	SO:0001819	synonymous_variant	6433	exon11			U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1623G>A	12.37:g.132241092G>A		Somatic		Capture	Illumina HiSeq	Phase_I	130807045	NM_004592	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	G	5.555	0.287281	0.10513	0.0	1.16E-4	ENSG00000061936	ENST00000537164	.	.	.	5.34	-1.18	0.09617	.	.	.	.	.	T	0.20536	0.0494	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25187	-1.0139	4	.	.	.	-0.166	2.4091	0.04420	0.1502:0.1072:0.2979:0.4447	.	.	.	.	H	181	.	.	R	+	2	0	SFSWAP	130807045	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.776000	0.04674	-0.178000	0.10672	-0.397000	0.06425	CGC		0.587	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
GALNT9	50614	broad.mit.edu	37	12	132683771	132683771	+	Missense_Mutation	SNP	G	G	A	rs569920280		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:132683771G>A	ENST00000328957.8	-	9	1444	c.1445C>T	c.(1444-1446)gCg>gTg	p.A482V	GALNT9_ENST00000397325.2_Missense_Mutation_p.A116V|GALNT9_ENST00000541995.1_Missense_Mutation_p.A116V|GALNT9_ENST00000535228.1_Missense_Mutation_p.A233V	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	482	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A116V(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		GCCGTCCTCCGCTCCCTGGTC	0.657													g|||	1	0.000199681	0.0008	0.0	5008	,	,		15287	0.0		0.0	False		,,,				2504	0.0				p.A482V	Colon(186;2147 2752 13553 41466)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1445T	12						.						49.0	56.0	54.0					12																	132683771		2013	4152	6165	131249724	SO:0001583	missense	50614	exon9			AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1445C>T	12.37:g.132683771G>A	ENSP00000329846:p.Ala482Val	Somatic		Capture	Illumina HiSeq	Phase_I	131249724	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Missense_Mutation	SNP	ENST00000328957.8	37		.	.	.	.	.	.	.	.	.	.	g	14.12	2.442022	0.43326	.	.	ENSG00000182870	ENST00000397325;ENST00000328957;ENST00000535228;ENST00000541995	T;T;T;T	0.27890	1.64;1.64;1.64;1.64	4.49	4.49	0.54785	Ricin B-related lectin (1);Ricin B lectin (3);	0.305004	0.35615	N	0.003099	T	0.23886	0.0578	L	0.28192	0.835	0.30591	N	0.761558	B;B;B	0.30634	0.288;0.034;0.014	B;B;B	0.27796	0.083;0.023;0.01	T	0.13629	-1.0502	10	0.40728	T	0.16	.	17.1692	0.86825	0.0:0.0:1.0:0.0	.	233;482;339	B3KNR7;Q9HCQ5;B3KP58	.;GALT9_HUMAN;.	V	116;482;233;116	ENSP00000380488:A116V;ENSP00000329846:A482V;ENSP00000439745:A233V;ENSP00000440544:A116V	ENSP00000329846:A482V	A	-	2	0	GALNT9	131249724	1.000000	0.71417	0.093000	0.20910	0.439000	0.31926	7.640000	0.83355	2.025000	0.59659	0.563000	0.77884	GCG		0.657	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
CACNA1C	775	broad.mit.edu	37	12	2614109	2614109	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:2614109C>T	ENST00000347598.4	+	8	1215	c.1215C>T	c.(1213-1215)agC>agT	p.S405S	CACNA1C_ENST00000399638.1_Silent_p.S405S|CACNA1C_ENST00000399621.1_Silent_p.S405S|CACNA1C_ENST00000399595.1_Silent_p.S405S|CACNA1C_ENST00000399591.1_Silent_p.S405S|CACNA1C_ENST00000399637.1_Silent_p.S405S|CACNA1C_ENST00000402845.3_Silent_p.S405S|CACNA1C_ENST00000399655.1_Silent_p.S405S|CACNA1C_ENST00000335762.5_Silent_p.S405S|CACNA1C_ENST00000399649.1_Silent_p.S405S|CACNA1C_ENST00000399629.1_Silent_p.S405S|CACNA1C_ENST00000344100.3_Silent_p.S405S|CACNA1C_ENST00000491104.1_Intron|CACNA1C_ENST00000399606.1_Silent_p.S405S|CACNA1C_ENST00000406454.3_Intron|CACNA1C_ENST00000399634.1_Intron|CACNA1C_ENST00000399601.1_Silent_p.S405S|CACNA1C_ENST00000399641.1_Intron|CACNA1C_ENST00000399603.1_Intron|CACNA1C_ENST00000327702.7_Silent_p.S405S|CACNA1C_ENST00000480911.1_Silent_p.S405S|CACNA1C_ENST00000399644.1_Silent_p.S405S|CACNA1C_ENST00000399597.1_Silent_p.S405S|CACNA1C_ENST00000399617.1_Intron	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	405					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.S435S(1)|p.S405S(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GTGTGCTTAGCGGGTAAGCAG	0.393																																					p.S405S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1215T	12						.						102.0	94.0	96.0					12																	2614109		1867	4124	5991	2484370	SO:0001819	synonymous_variant	775	exon8			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1215C>T	12.37:g.2614109C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2484370	NM_001129842	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Silent	SNP	ENST00000347598.4	37	CCDS44788.1																																																																																				0.393	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
CACNA1C	775	broad.mit.edu	37	12	2621995	2621995	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:2621995G>T	ENST00000347598.4	+	9	1235	c.1235G>T	c.(1234-1236)aGg>aTg	p.R412M	CACNA1C_ENST00000399638.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399637.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R412M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R412M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R412M|CACNA1C_ENST00000491104.1_3'UTR|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R412M|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R412M|CACNA1C_ENST00000480911.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R412M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R412M	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	412					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R442M(1)|p.R412M(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCAAAGAGAGGGAGAAGGCC	0.572																																					p.R412M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1235T	12						.						22.0	26.0	25.0					12																	2621995		2093	4244	6337	2492256	SO:0001583	missense	775	exon9			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.1235G>T	12.37:g.2621995G>T	ENSP00000266376:p.Arg412Met	Somatic		Capture	Illumina HiSeq	Phase_I	2492256	NM_001129842	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.591479	0.86851	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97430	-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38;-4.38	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	D	0.99042	0.9672	H	0.96833	3.89	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0;1.0;0.998;1.0;1.0;0.998;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.998;0.996;0.997;0.996;0.996;0.999;0.997;0.999;1.0;0.997;0.999;0.997;0.99;0.999;0.993;0.997;0.992;0.998;0.999;0.997;0.992;0.999;0.999;0.992;0.997	D	0.99191	1.0870	10	0.87932	D	0	.	18.1293	0.89596	0.0:0.0:1.0:0.0	.	41;412;409;412;412;412;412;412;412;412;412;412;383;412;412;412;412;412;412;412;412;412;412;412;412	Q5V9X8;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	M	412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;412;253	ENSP00000336982:R412M;ENSP00000382563:R412M;ENSP00000437936:R412M;ENSP00000382552:R412M;ENSP00000382547:R412M;ENSP00000382506:R412M;ENSP00000382530:R412M;ENSP00000382546:R412M;ENSP00000382500:R412M;ENSP00000382549:R412M;ENSP00000266376:R412M;ENSP00000382515:R412M;ENSP00000382510:R412M;ENSP00000341092:R412M;ENSP00000382537:R412M;ENSP00000329877:R412M;ENSP00000382557:R412M;ENSP00000385724:R412M;ENSP00000382512:R412M;ENSP00000382542:R412M;ENSP00000382526:R412M;ENSP00000385896:R412M;ENSP00000382504:R412M	ENSP00000323129:R253M	R	+	2	0	CACNA1C	2492256	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.593000	0.98250	2.581000	0.87130	0.655000	0.94253	AGG		0.572	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
CACNA1C	775	broad.mit.edu	37	12	2760900	2760900	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:2760900G>A	ENST00000347598.4	+	34	4184	c.4184G>A	c.(4183-4185)cGg>cAg	p.R1395Q	CACNA1C_ENST00000399638.1_Missense_Mutation_p.R1375Q|CACNA1C_ENST00000399621.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399595.1_Missense_Mutation_p.R1336Q|CACNA1C_ENST00000399591.1_Missense_Mutation_p.R1336Q|CACNA1C_ENST00000399637.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000402845.3_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399655.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000335762.5_Missense_Mutation_p.R1372Q|CACNA1C_ENST00000399649.1_Missense_Mutation_p.R1334Q|CACNA1C_ENST00000399629.1_Missense_Mutation_p.R1364Q|CACNA1C_ENST00000344100.3_Missense_Mutation_p.R1369Q|CACNA1C_ENST00000399606.1_Missense_Mutation_p.R1367Q|CACNA1C_ENST00000406454.3_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399634.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399601.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399641.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399603.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000327702.7_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399644.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399597.1_Missense_Mutation_p.R1347Q|CACNA1C_ENST00000399617.1_Missense_Mutation_p.R1347Q	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1395					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R1369Q(1)|p.R1425Q(1)|p.R882Q(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GAGGGCATCCGGACGCTGCTG	0.632																																					p.R1347Q												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G4040A	12						.						51.0	61.0	57.0					12																	2760900		2200	4299	6499	2631161	SO:0001583	missense	775	exon32			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4184G>A	12.37:g.2760900G>A	ENSP00000266376:p.Arg1395Gln	Somatic		Capture	Illumina HiSeq	Phase_I	2631161	NM_001129842	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	36	5.798973	0.96960	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98792	-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14;-5.14	5.17	5.17	0.71159	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99205	0.9724	M	0.86028	2.79	0.58432	D	0.999999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;0.999;1.0;0.999;1.0;1.0;0.999;1.0;1.0;0.999;0.999;0.999;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.999;0.988;0.964;0.998;0.988;0.964;0.964;0.973;0.998;0.981;0.964;0.964;0.988;0.997;0.994;0.984;0.975;0.997;0.996;0.992;0.964;0.996;0.996;0.964;0.964	D	0.99593	1.0976	10	0.87932	D	0	.	18.6538	0.91441	0.0:0.0:1.0:0.0	.	38;1369;1344;1395;1347;1347;1347;1364;1375;1347;1367;1347;1307;1395;1347;1347;1347;1336;1334;1336;1336;1347;1347;1347;1347	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	Q	1372;1347;1347;1375;1347;1347;1347;1336;1347;1395;1367;1347;1369;1364;1347;1334;1347;1347;1347;1347;1347;1336;1177	ENSP00000336982:R1372Q;ENSP00000382563:R1347Q;ENSP00000382552:R1347Q;ENSP00000382547:R1375Q;ENSP00000382506:R1347Q;ENSP00000382530:R1347Q;ENSP00000382546:R1347Q;ENSP00000382500:R1336Q;ENSP00000382549:R1347Q;ENSP00000266376:R1395Q;ENSP00000382515:R1367Q;ENSP00000382510:R1347Q;ENSP00000341092:R1369Q;ENSP00000382537:R1364Q;ENSP00000329877:R1347Q;ENSP00000382557:R1334Q;ENSP00000385724:R1347Q;ENSP00000382512:R1347Q;ENSP00000382542:R1347Q;ENSP00000382526:R1347Q;ENSP00000385896:R1347Q;ENSP00000382504:R1336Q	ENSP00000323129:R1177Q	R	+	2	0	CACNA1C	2631161	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	9.805000	0.99149	2.412000	0.81896	0.491000	0.48974	CGG		0.632	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
KCNA1	3736	broad.mit.edu	37	12	5020763	5020763	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:5020763C>T	ENST00000382545.3	+	2	1326	c.219C>T	c.(217-219)ttC>ttT	p.F73F	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	73					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)	p.F73F(1)		NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	TGCGCTACTTCGACCCCCTGA	0.627																																					p.F73F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C219T	12						.						66.0	67.0	66.0					12																	5020763		2203	4300	6503	4891024	SO:0001819	synonymous_variant	3736	exon2			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.219C>T	12.37:g.5020763C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4891024	NM_000217	A6NM83|Q3MIQ9	Silent	SNP	ENST00000382545.3	37	CCDS8535.1																																																																																				0.627	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
KCNA1	3736	broad.mit.edu	37	12	5021006	5021006	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:5021006G>A	ENST00000382545.3	+	2	1569	c.462G>A	c.(460-462)tgG>tgA	p.W154*	KCNA1_ENST00000543874.2_Intron	NM_000217.2	NP_000208.2	Q09470	KCNA1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 1 (episodic ataxia with myokymia)	154					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|juxtaparanode region of axon (GO:0044224)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|potassium ion transmembrane transporter activity (GO:0015079)	p.W154*(1)		NS(1)|breast(3)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(23)|ovary(3)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63					Amitriptyline(DB00321)|Dalfampridine(DB06637)|Desflurane(DB01189)|Enflurane(DB00228)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Nifedipine(DB01115)|Sevoflurane(DB01236)	GCCAGGTGTGGCTGCTCTTCG	0.622																																					p.W154X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G462A	12						.						65.0	69.0	68.0					12																	5021006		2203	4300	6503	4891267	SO:0001587	stop_gained	3736	exon2			L02750	CCDS8535.1	12p13	2012-07-05			ENSG00000111262	ENSG00000111262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6218	protein-coding gene	gene with protein product		176260		AEMK		1349297, 8821794, 16382104	Standard	NM_000217		Approved	Kv1.1, RBK1, HUK1, MBK1	uc001qnh.3	Q09470	OTTHUMG00000044398	ENST00000382545.3:c.462G>A	12.37:g.5021006G>A	ENSP00000371985:p.Trp154*	Somatic		Capture	Illumina HiSeq	Phase_I	4891267	NM_000217	A6NM83|Q3MIQ9	Nonsense_Mutation	SNP	ENST00000382545.3	37	CCDS8535.1	.	.	.	.	.	.	.	.	.	.	G	47	13.011115	0.99713	.	.	ENSG00000111262	ENST00000382545;ENST00000228858	.	.	.	4.5	4.5	0.54988	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.7323	0.85438	0.0:0.0:1.0:0.0	.	.	.	.	X	154	.	ENSP00000228858:W154X	W	+	3	0	KCNA1	4891267	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.531000	0.98054	2.496000	0.84212	0.655000	0.94253	TGG		0.622	KCNA1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103343.2	NM_000217	
LAG3	3902	broad.mit.edu	37	12	6882418	6882418	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:6882418C>T	ENST00000203629.2	+	2	452	c.119C>T	c.(118-120)gCc>gTc	p.A40V	LAG3_ENST00000441671.2_Missense_Mutation_p.A40V	NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	40	Ig-like V-type.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)	p.A40V(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GGGGCTCCTGCCCAGCTCCCC	0.652																																					p.A40V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C119T	12						.						44.0	47.0	46.0					12																	6882418		2203	4300	6503	6752679	SO:0001583	missense	3902	exon2				CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.119C>T	12.37:g.6882418C>T	ENSP00000203629:p.Ala40Val	Somatic		Capture	Illumina HiSeq	Phase_I	6752679	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	.	.	.	.	.	.	.	.	.	.	C	10.14	1.267508	0.23136	.	.	ENSG00000089692	ENST00000441671;ENST00000203629	T;T	0.23147	1.92;1.92	4.84	-0.37	0.12530	Immunoglobulin subtype (1);	0.616792	0.14404	N	0.321706	T	0.12475	0.0303	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.11235	0.002;0.004	B;B	0.15052	0.003;0.012	T	0.28202	-1.0051	10	0.27082	T	0.32	-6.4947	7.443	0.27194	0.0:0.3297:0.0:0.6703	.	40;40	P18627;Q7Z643	LAG3_HUMAN;.	V	40	ENSP00000413825:A40V;ENSP00000203629:A40V	ENSP00000203629:A40V	A	+	2	0	LAG3	6752679	0.002000	0.14202	0.804000	0.32291	0.947000	0.59692	0.028000	0.13644	-0.104000	0.12154	0.462000	0.41574	GCC		0.652	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
USP5	8078	broad.mit.edu	37	12	6970186	6970186	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:6970186C>A	ENST00000229268.8	+	12	1466	c.1414C>A	c.(1414-1416)Ctg>Atg	p.L472M	USP5_ENST00000541969.1_3'UTR|USP5_ENST00000389231.5_Missense_Mutation_p.L472M	NM_001098536.1	NP_001092006.1	P45974	UBP5_HUMAN	ubiquitin specific peptidase 5 (isopeptidase T)	472	USP.				positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)	lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin thiolesterase activity (GO:0004221)|zinc ion binding (GO:0008270)	p.L472M(1)		breast(6)|endometrium(4)|kidney(2)|large_intestine(6)|lung(14)|skin(2)|urinary_tract(2)	36						GATCAAGTGCCTGGCCACAGA	0.522																																					p.L472M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1414A	12						.						190.0	182.0	185.0					12																	6970186		2203	4300	6503	6840447	SO:0001583	missense	8078	exon12			U35116	CCDS31733.1, CCDS41743.1	12p13	2007-03-02	2005-08-08		ENSG00000111667	ENSG00000111667		"""Ubiquitin-specific peptidases"""	12628	protein-coding gene	gene with protein product		601447	"""ubiquitin specific protease 5 (isopeptidase T)"""			12838346, 8723724	Standard	NM_003481		Approved	IsoT	uc001qri.4	P45974	OTTHUMG00000169233	ENST00000229268.8:c.1414C>A	12.37:g.6970186C>A	ENSP00000229268:p.Leu472Met	Somatic		Capture	Illumina HiSeq	Phase_I	6840447	NM_003481	D3DUS7|D3DUS8|Q96J22	Missense_Mutation	SNP	ENST00000229268.8	37	CCDS41743.1	.	.	.	.	.	.	.	.	.	.	C	13.53	2.266202	0.40095	.	.	ENSG00000111667	ENST00000229268;ENST00000389231	T;T	0.33865	1.39;1.39	5.04	2.26	0.28386	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.065127	0.64402	D	0.000006	T	0.41236	0.1150	L	0.32530	0.975	0.47584	D	0.999461	D;B	0.55385	0.971;0.05	P;B	0.62491	0.903;0.037	T	0.09773	-1.0659	10	0.44086	T	0.13	-4.3774	9.2919	0.37791	0.0:0.7152:0.0:0.2848	.	472;472	P45974;P45974-2	UBP5_HUMAN;.	M	472	ENSP00000229268:L472M;ENSP00000373883:L472M	ENSP00000229268:L472M	L	+	1	2	USP5	6840447	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.223000	0.51231	0.313000	0.23062	0.561000	0.74099	CTG		0.522	USP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402982.1		
ENO2	2026	broad.mit.edu	37	12	7025671	7025671	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:7025671G>A	ENST00000535366.1	+	2	802	c.176G>A	c.(175-177)gGc>gAc	p.G59D	ENO2_ENST00000538763.1_Missense_Mutation_p.G59D|ENO2_ENST00000541477.1_Missense_Mutation_p.G59D|ENO2_ENST00000545045.2_Missense_Mutation_p.G59D|ENO2_ENST00000229277.1_Missense_Mutation_p.G59D|ENO2_ENST00000544774.1_Missense_Mutation_p.G59D			P09104	ENOG_HUMAN	enolase 2 (gamma, neuronal)	59					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perikaryon (GO:0043204)|phosphopyruvate hydratase complex (GO:0000015)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)	p.G59D(1)		endometrium(3)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						CGTTACTTAGGCAAAGGTGAG	0.577																																					p.G59D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G176A	12						.						171.0	136.0	148.0					12																	7025671		2203	4300	6503	6895932	SO:0001583	missense	2026	exon3			M22349	CCDS8570.1	12p13	2012-10-02				ENSG00000111674	4.2.1.11		3353	protein-coding gene	gene with protein product		131360					Standard	NM_001975		Approved		uc001qru.1	P09104		ENST00000535366.1:c.176G>A	12.37:g.7025671G>A	ENSP00000437402:p.Gly59Asp	Somatic		Capture	Illumina HiSeq	Phase_I	6895932	NM_001975	B7Z2X9|Q96J33	Missense_Mutation	SNP	ENST00000535366.1	37	CCDS8570.1	.	.	.	.	.	.	.	.	.	.	g	35	5.491822	0.96339	.	.	ENSG00000111674	ENST00000537688;ENST00000540580;ENST00000541477;ENST00000229277;ENST00000538763;ENST00000544774;ENST00000539713;ENST00000535366;ENST00000545045;ENST00000544430	T;T;T;T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82;0.82	5.02	5.02	0.67125	Enolase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85652	0.5746	H	0.99977	5.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93340	0.6709	10	0.87932	D	0	-22.8407	18.6946	0.91596	0.0:0.0:1.0:0.0	.	59;59	B7Z2X9;P09104	.;ENOG_HUMAN	D	59	ENSP00000445788:G59D;ENSP00000443117:G59D;ENSP00000438873:G59D;ENSP00000229277:G59D;ENSP00000441490:G59D;ENSP00000446195:G59D;ENSP00000441740:G59D;ENSP00000437402:G59D;ENSP00000438062:G59D	ENSP00000229277:G59D	G	+	2	0	ENO2	6895932	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.546000	0.98097	2.479000	0.83701	0.556000	0.70494	GGC		0.577	ENO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401786.1		
CD163	9332	broad.mit.edu	37	12	7636248	7636248	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:7636248G>A	ENST00000359156.4	-	12	3005	c.2803C>T	c.(2803-2805)Ccc>Tcc	p.P935S	CD163_ENST00000539632.1_5'UTR|CD163_ENST00000541972.1_Missense_Mutation_p.P923S|CD163_ENST00000396620.3_Missense_Mutation_p.P968S|CD163_ENST00000432237.2_Missense_Mutation_p.P935S	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	935	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)	p.P935S(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	CAGGAAGTGGGTCCTTCCTGA	0.468																																					p.P935S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2803T	12						.						77.0	65.0	69.0					12																	7636248		2203	4300	6503	7527515	SO:0001583	missense	9332	exon12			Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.2803C>T	12.37:g.7636248G>A	ENSP00000352071:p.Pro935Ser	Somatic		Capture	Illumina HiSeq	Phase_I	7527515	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Missense_Mutation	SNP	ENST00000359156.4	37	CCDS8578.1	.	.	.	.	.	.	.	.	.	.	G	9.429	1.085166	0.20390	.	.	ENSG00000177575	ENST00000359156;ENST00000541972;ENST00000396620;ENST00000432237	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	4.78	-7.4	0.01397	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	2.173550	0.01477	N	0.016516	T	0.11452	0.0279	N	0.02973	-0.45	0.09310	N	1	B;B;B	0.25351	0.12;0.0;0.124	B;B;B	0.27500	0.08;0.001;0.08	T	0.29640	-1.0005	10	0.07030	T	0.85	.	9.9994	0.41920	0.0:0.3789:0.476:0.1451	.	968;935;935	C9JHR8;Q86VB7-3;Q86VB7	.;.;C163A_HUMAN	S	935;923;968;935	ENSP00000352071:P935S;ENSP00000444071:P923S;ENSP00000379863:P968S;ENSP00000403885:P935S	ENSP00000352071:P935S	P	-	1	0	CD163	7527515	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.842000	0.04354	-1.165000	0.02786	-0.410000	0.06199	CCC		0.468	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
ATF7IP	55729	broad.mit.edu	37	12	14613682	14613682	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:14613682T>C	ENST00000540793.1	+	8	2567	c.2412T>C	c.(2410-2412)acT>acC	p.T804T	ATF7IP_ENST00000543189.1_Silent_p.T803T|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000261168.4_Silent_p.T804T|ATF7IP_ENST00000544627.1_Silent_p.T812T|ATF7IP_ENST00000536444.1_Silent_p.T803T			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	804	Interaction with SETDB1.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.T804T(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						ATCCAGGGACTTTGGTGACTA	0.468																																					p.T804T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2412C	12						.						102.0	101.0	101.0					12																	14613682		2203	4300	6503	14504949	SO:0001819	synonymous_variant	55729	exon9			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.2412T>C	12.37:g.14613682T>C		Somatic		Capture	Illumina HiSeq	Phase_I	14504949	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																				0.468	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
ATF7IP	55729	broad.mit.edu	37	12	14650995	14650995	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:14650995C>A	ENST00000540793.1	+	14	3956	c.3801C>A	c.(3799-3801)acC>acA	p.T1267T	ATF7IP_ENST00000261168.4_Silent_p.T1267T|ATF7IP_ENST00000544627.1_Silent_p.T1275T|ATF7IP_ENST00000536444.1_Silent_p.T1266T			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	1267	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Interaction with MBD1.				DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)		p.T1267T(1)		cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						TCTCTTCTACCCAGAGCAGTT	0.388																																					p.T1267T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3801A	12						.						150.0	158.0	155.0					12																	14650995		2203	4300	6503	14542262	SO:0001819	synonymous_variant	55729	exon15			AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.3801C>A	12.37:g.14650995C>A		Somatic		Capture	Illumina HiSeq	Phase_I	14542262	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																				0.388	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
PLEKHA5	54477	broad.mit.edu	37	12	19514518	19514518	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:19514518delA	ENST00000299275.6	+	23	2994	c.2988delA	c.(2986-2988)ttafs	p.L996fs	PLEKHA5_ENST00000429027.2_Frame_Shift_Del_p.L1162fs|PLEKHA5_ENST00000317589.4_Frame_Shift_Del_p.L1059fs|PLEKHA5_ENST00000359180.3_Frame_Shift_Del_p.L940fs|PLEKHA5_ENST00000424268.1_Frame_Shift_Del_p.L985fs|PLEKHA5_ENST00000355397.3_Frame_Shift_Del_p.L1054fs|PLEKHA5_ENST00000543806.1_Frame_Shift_Del_p.L978fs|PLEKHA5_ENST00000538714.1_Frame_Shift_Del_p.L1054fs|PLEKHA5_ENST00000539256.1_Frame_Shift_Del_p.L754fs	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	996					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)	p.T1160fs*17(1)|p.T999fs*17(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					TTCTACAGTTAAAAAAAACTG	0.244																																					p.L996fs	Pancreas(196;329 2193 11246 14234 19524)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2988delA	12						.						22.0	24.0	23.0					12																	19514518		2190	4292	6482	19405785	SO:0001589	frameshift_variant	54477	exon23			AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.2988delA	12.37:g.19514518delA	ENSP00000299275:p.Leu996fs	Somatic		Capture	Illumina HiSeq	Phase_I	19405785	NM_019012	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Frame_Shift_Del	DEL	ENST00000299275.6	37	CCDS8682.1																																																																																				0.244	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
GYS2	2998	broad.mit.edu	37	12	21713339	21713339	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:21713339C>T	ENST00000261195.2	-	8	1404	c.1150G>A	c.(1150-1152)Gca>Aca	p.A384T		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	384					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)	p.A384T(1)		NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						TTTCGCACTGCTTGTCCTTTC	0.383																																					p.A384T	Colon(149;9 1820 3690 10544 50424)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1150A	12						.						206.0	184.0	191.0					12																	21713339		2203	4300	6503	21604606	SO:0001583	missense	2998	exon8				CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1150G>A	12.37:g.21713339C>T	ENSP00000261195:p.Ala384Thr	Somatic		Capture	Illumina HiSeq	Phase_I	21604606	NM_021957	A0AVD8	Missense_Mutation	SNP	ENST00000261195.2	37	CCDS8690.1	.	.	.	.	.	.	.	.	.	.	C	31	5.104624	0.94245	.	.	ENSG00000111713	ENST00000261195	T	0.72167	-0.63	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	D	0.87038	0.6078	M	0.92833	3.35	0.80722	D	1	D	0.57899	0.981	P	0.62435	0.902	D	0.90286	0.4319	10	0.87932	D	0	-22.8457	18.4086	0.90543	0.0:1.0:0.0:0.0	.	384	P54840	GYS2_HUMAN	T	384	ENSP00000261195:A384T	ENSP00000261195:A384T	A	-	1	0	GYS2	21604606	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.638000	0.83328	2.577000	0.86979	0.563000	0.77884	GCA		0.383	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
C2CD5	9847	broad.mit.edu	37	12	22677557	22677557	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:22677557C>T	ENST00000333957.4	-	6	705	c.450G>A	c.(448-450)acG>acA	p.T150T	C2CD5_ENST00000446597.1_Silent_p.T150T|C2CD5_ENST00000545552.1_Silent_p.T150T|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000536386.1_Silent_p.T150T|C2CD5_ENST00000540703.1_5'UTR|C2CD5_ENST00000542676.1_Silent_p.T150T|C2CD5_ENST00000396028.2_Silent_p.T150T	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	150					cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)	p.T150T(1)									TTGGAATAGACGTTGCTGTTA	0.308																																					p.T150T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G450A	12						.						92.0	86.0	88.0					12																	22677557		2203	4300	6503	22568824	SO:0001819	synonymous_variant	9847	exon6			AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.450G>A	12.37:g.22677557C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22568824	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																				0.308	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
FAR2	55711	broad.mit.edu	37	12	29423429	29423429	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:29423429C>T	ENST00000536681.3	+	2	293	c.47C>T	c.(46-48)aCg>aTg	p.T16M	FAR2_ENST00000182377.4_Missense_Mutation_p.T16M|FAR2_ENST00000547116.1_Intron	NM_001271783.1|NM_001271784.1	NP_001258712.1|NP_001258713.1	Q96K12	FACR2_HUMAN	fatty acyl CoA reductase 2	16					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	fatty-acyl-CoA reductase (alcohol-forming) activity (GO:0080019)|long-chain-fatty-acyl-CoA reductase activity (GO:0050062)	p.T16M(1)		central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(15)|prostate(1)|stomach(1)	29						ATTCTCATCACGGGGGCCACA	0.502																																					p.T16M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C47T	12						.						70.0	70.0	70.0					12																	29423429		2203	4300	6503	29314696	SO:0001583	missense	55711	exon2			AL136843	CCDS8717.1, CCDS61084.1	12p11.23	2013-07-30	2008-06-06	2008-06-06	ENSG00000064763	ENSG00000064763	1.2.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	25531	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 10E, member 2"""		"""male sterility domain containing 1"""	MLSTD1		15220348, 15220349, 19027726	Standard	NM_001271783		Approved	FLJ10462, SDR10E2	uc001ris.5	Q96K12	OTTHUMG00000169320	ENST00000536681.3:c.47C>T	12.37:g.29423429C>T	ENSP00000443291:p.Thr16Met	Somatic		Capture	Illumina HiSeq	Phase_I	29314696	NM_018099	F8VV73|Q9H0D5|Q9NVW8	Missense_Mutation	SNP	ENST00000536681.3	37	CCDS8717.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.967951	0.53507	.	.	ENSG00000064763	ENST00000536681;ENST00000182377	T;T	0.77620	-1.11;-1.11	5.3	5.3	0.74995	NAD(P)-binding domain (1);Male sterility, NAD-binding (1);	0.000000	0.85682	D	0.000000	D	0.92407	0.7590	H	0.97365	3.99	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94913	0.8066	10	0.87932	D	0	6.3963	16.4532	0.83998	0.0:1.0:0.0:0.0	.	16	Q96K12	FACR2_HUMAN	M	16	ENSP00000443291:T16M;ENSP00000182377:T16M	ENSP00000182377:T16M	T	+	2	0	FAR2	29314696	1.000000	0.71417	0.943000	0.38184	0.028000	0.11728	7.367000	0.79558	2.474000	0.83562	0.561000	0.74099	ACG		0.502	FAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403479.2	NM_018099	
DENND5B	160518	broad.mit.edu	37	12	31600513	31600513	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:31600513C>T	ENST00000389082.5	-	6	2084	c.1820G>A	c.(1819-1821)cGg>cAg	p.R607Q	DENND5B_ENST00000306833.6_Missense_Mutation_p.R642Q|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000536562.1_Missense_Mutation_p.R642Q|DENND5B_ENST00000354285.4_Missense_Mutation_p.R629Q	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	607					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R607Q(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						TATAGATGTCCGCAAGGTGGG	0.373																																					p.R607Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1820A	12						.						62.0	58.0	59.0					12																	31600513		1847	4098	5945	31491780	SO:0001583	missense	160518	exon6			AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1820G>A	12.37:g.31600513C>T	ENSP00000373734:p.Arg607Gln	Somatic		Capture	Illumina HiSeq	Phase_I	31491780	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	C	33	5.236584	0.95240	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	T	0.66655	0.2811	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.997;1.0	D;P;D	0.73708	0.981;0.873;0.973	T	0.69654	-0.5087	10	0.59425	D	0.04	-18.2443	18.59	0.91206	0.0:1.0:0.0:0.0	.	629;607;642	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	Q	607;642;642;629	ENSP00000373734:R607Q;ENSP00000306482:R642Q;ENSP00000444889:R642Q;ENSP00000346238:R629Q	ENSP00000306482:R642Q	R	-	2	0	DENND5B	31491780	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.452000	0.80683	2.628000	0.89032	0.563000	0.77884	CGG		0.373	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
KIF21A	55605	broad.mit.edu	37	12	39724054	39724054	+	Silent	SNP	G	G	A	rs139033996		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:39724054G>A	ENST00000361418.5	-	24	3345	c.3330C>T	c.(3328-3330)agC>agT	p.S1110S	KIF21A_ENST00000544797.2_Intron|KIF21A_ENST00000361961.3_Silent_p.S1097S|KIF21A_ENST00000541463.2_Silent_p.S1074S|KIF21A_ENST00000395670.3_Intron			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1110					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S1097S(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				CTAATGGTACGCTATCTAGAT	0.313																																					p.S1074S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.C3222T	12						.	G	,,,	0,4406		0,0,2203	93.0	81.0	85.0		,3330,3222,3291	5.9	1.0	12	dbSNP_134	85	1,8597	1.2+/-3.3	0,1,4298	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	,,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,,	,1110/1675,1074/1622,1097/1662	39724054	1,13003	2203	4299	6502	38010321	SO:0001819	synonymous_variant	55605	exon22			AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.3330C>T	12.37:g.39724054G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38010321	NM_001173465	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	G	8.490	0.861864	0.17178	0.0	1.16E-4	ENSG00000139116	ENST00000552961	.	.	.	5.95	5.95	0.96441	.	.	.	.	.	T	0.77075	0.4077	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73990	-0.3808	4	.	.	.	.	20.3812	0.98933	0.0:0.0:1.0:0.0	.	.	.	.	V	458	.	.	A	-	2	0	KIF21A	38010321	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.915000	0.87484	2.821000	0.97095	0.650000	0.86243	GCG		0.313	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
LRRK2	120892	broad.mit.edu	37	12	40758799	40758799	+	Missense_Mutation	SNP	G	G	A	rs200795955		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:40758799G>A	ENST00000298910.7	+	49	7395	c.7337G>A	c.(7336-7338)cGt>cAt	p.R2446H		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	2446					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|autophagy (GO:0006914)|cellular protein localization (GO:0034613)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to oxidative stress (GO:0034599)|determination of adult lifespan (GO:0008340)|endocytosis (GO:0006897)|exploration behavior (GO:0035640)|GTP catabolic process (GO:0006184)|intracellular distribution of mitochondria (GO:0048312)|intracellular signal transduction (GO:0035556)|locomotory exploration behavior (GO:0035641)|MAPK cascade (GO:0000165)|negative regulation of GTPase activity (GO:0034260)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|negative regulation of late endosome to lysosome transport (GO:1902823)|negative regulation of peroxidase activity (GO:2000469)|negative regulation of protein binding (GO:0032091)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein processing (GO:0010955)|negative regulation of protein processing involved in protein targeting to mitochondrion (GO:1903217)|negative regulation of protein targeting to mitochondrion (GO:1903215)|negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation (GO:1903125)|neuromuscular junction development (GO:0007528)|neuron death (GO:0070997)|neuron projection morphogenesis (GO:0048812)|olfactory bulb development (GO:0021772)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of autophagy (GO:0010508)|positive regulation of dopamine receptor signaling pathway (GO:0060161)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of programmed cell death (GO:0043068)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein autoubiquitination (GO:1902499)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of kidney size (GO:0035564)|regulation of locomotion (GO:0040012)|regulation of membrane potential (GO:0042391)|regulation of mitochondrial depolarization (GO:0051900)|regulation of neuroblast proliferation (GO:1902692)|regulation of neuron death (GO:1901214)|regulation of neuron maturation (GO:0014041)|regulation of protein kinase A signaling (GO:0010738)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of synaptic vesicle exocytosis (GO:2000300)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic side of mitochondrial outer membrane (GO:0032473)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)|ATP binding (GO:0005524)|clathrin binding (GO:0030276)|glycoprotein binding (GO:0001948)|GTP binding (GO:0005525)|GTP-dependent protein kinase activity (GO:0034211)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|kinase activity (GO:0016301)|MAP kinase kinase activity (GO:0004708)|peroxidase inhibitor activity (GO:0036479)|protein homodimerization activity (GO:0042803)|protein kinase A binding (GO:0051018)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rho GTPase binding (GO:0017048)|SNARE binding (GO:0000149)|syntaxin-1 binding (GO:0017075)|tubulin binding (GO:0015631)	p.R2446H(2)|p.R2453H(2)		NS(3)|biliary_tract(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(23)|large_intestine(31)|lung(55)|ovary(15)|pancreas(2)|prostate(4)|skin(4)|stomach(9)|upper_aerodigestive_tract(7)|urinary_tract(2)	181	all_cancers(12;0.00108)|Breast(8;0.218)	Lung NSC(34;0.0942)|all_lung(34;0.11)				CGACTTATACGTGTAATTTAC	0.388																																					p.R2446H												.	.	4	Substitution - Missense(4)	large_intestine(2)|stomach(2)	c.G7337A	12						.						96.0	89.0	91.0					12																	40758799		2203	4299	6502	39045066	SO:0001583	missense	120892	exon49			AK026776	CCDS31774.1	12q12	2011-07-21			ENSG00000188906	ENSG00000188906		"""Parkinson disease"""	18618	protein-coding gene	gene with protein product		609007	"""Parkinson disease (autosomal dominant) 8"""	PARK8		15541308	Standard	NM_198578		Approved	ROCO2, DKFZp434H2111, FLJ45829, RIPK7	uc001rmg.4	Q5S007	OTTHUMG00000059742	ENST00000298910.7:c.7337G>A	12.37:g.40758799G>A	ENSP00000298910:p.Arg2446His	Somatic		Capture	Illumina HiSeq	Phase_I	39045066	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	13.42	2.231484	0.39399	.	.	ENSG00000188906	ENST00000298910	T	0.35973	1.28	5.29	4.2	0.49525	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.236644	0.44902	D	0.000415	T	0.29882	0.0747	L	0.35723	1.085	0.34748	D	0.731508	B;B	0.12013	0.005;0.005	B;B	0.08055	0.003;0.003	T	0.34900	-0.9810	10	0.41790	T	0.15	.	14.8045	0.69942	0.0814:0.0:0.9186:0.0	.	2446;2446	Q17RV3;Q5S007	.;LRRK2_HUMAN	H	2446	ENSP00000298910:R2446H	ENSP00000298910:R2446H	R	+	2	0	LRRK2	39045066	0.570000	0.26651	0.700000	0.30305	0.737000	0.42083	3.398000	0.52579	2.466000	0.83321	0.585000	0.79938	CGT		0.388	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	
GXYLT1	283464	broad.mit.edu	37	12	42481686	42481686	+	Frame_Shift_Del	DEL	T	T	-	rs200923104		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:42481686delT	ENST00000398675.3	-	8	1457	c.1225delA	c.(1225-1227)acafs	p.T409fs	GXYLT1_ENST00000280876.6_Frame_Shift_Del_p.T378fs	NM_001099650.1|NM_173601.1	NP_001093120.1|NP_775872.1	Q4G148	GXLT1_HUMAN	glucoside xylosyltransferase 1	409					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|O-glycan processing (GO:0016266)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)	p.T409fs*17(1)|p.T378fs*17(1)		kidney(2)|large_intestine(4)|liver(3)|lung(8)	17						GTATGCACTGTTTTTTGTAGT	0.279																																					p.T409fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1225delA	12						.						72.0	65.0	67.0					12																	42481686		1799	4071	5870	40767953	SO:0001589	frameshift_variant	283464	exon8			BC015597	CCDS41771.1, CCDS41772.1	12q12	2013-10-11	2009-11-17	2009-11-17	ENSG00000151233	ENSG00000151233		"""Glycosyltransferase family 8 domain containing"""	27482	protein-coding gene	gene with protein product		613321	"""glycosyltransferase 8 domain containing 3"""	GLT8D3		19940119	Standard	NM_001099650		Approved	FLJ43151	uc001rms.4	Q4G148	OTTHUMG00000169379	ENST00000398675.3:c.1225delA	12.37:g.42481686delT	ENSP00000381666:p.Thr409fs	Somatic		Capture	Illumina HiSeq	Phase_I	40767953	NM_173601	B3KWJ2|Q8IXV1|Q96BH4	Frame_Shift_Del	DEL	ENST00000398675.3	37	CCDS41772.1																																																																																				0.279	GXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403778.1	XM_290597	
PPHLN1	51535	broad.mit.edu	37	12	42792658	42792658	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:42792658G>A	ENST00000395568.2	+	9	855	c.771G>A	c.(769-771)gcG>gcA	p.A257A	PPHLN1_ENST00000337898.6_Silent_p.A202A|PPHLN1_ENST00000395580.3_Silent_p.A264A|PPHLN1_ENST00000432191.2_Silent_p.A202A|PPHLN1_ENST00000256678.8_Silent_p.A137A|PPHLN1_ENST00000552761.1_Silent_p.A209A|PPHLN1_ENST00000449194.2_Silent_p.A238A|PPHLN1_ENST00000317560.9_Silent_p.A190A|PPHLN1_ENST00000549190.1_Silent_p.A275A|RNU6-249P_ENST00000363016.1_RNA|PPHLN1_ENST00000358314.7_Silent_p.A257A	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	257					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A257A(2)		breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		TTTTCAAGGCGGGATCCACAG	0.378																																					p.A209A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G627A	12						.						75.0	70.0	72.0					12																	42792658		2203	4300	6503	41078925	SO:0001819	synonymous_variant	51535	exon9			AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.771G>A	12.37:g.42792658G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41078925	NM_201438	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Silent	SNP	ENST00000395568.2	37	CCDS31777.1																																																																																				0.378	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	
ADAMTS20	80070	broad.mit.edu	37	12	43826230	43826230	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:43826230A>C	ENST00000389420.3	-	21	2972	c.2973T>G	c.(2971-2973)tcT>tcG	p.S991S	ADAMTS20_ENST00000395541.2_Silent_p.S145S|ADAMTS20_ENST00000553158.1_Silent_p.S991S	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	991	TSP type-1 4. {ECO:0000255|PROSITE- ProRule:PRU00210}.				extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.S991S(1)|p.C991W(1)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		TCATACAATAAGATTCTCGAG	0.378																																					p.S991S												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(2)	c.T2973G	12						.						118.0	117.0	118.0					12																	43826230		2203	4300	6503	42112497	SO:0001819	synonymous_variant	80070	exon21			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.2973T>G	12.37:g.43826230A>C		Somatic		Capture	Illumina HiSeq	Phase_I	42112497	NM_025003	A6NNC9|J3QT00	Silent	SNP	ENST00000389420.3	37	CCDS31778.2																																																																																				0.378	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
ADAMTS20	80070	broad.mit.edu	37	12	43945028	43945028	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:43945028T>G	ENST00000389420.3	-	2	136	c.137A>C	c.(136-138)gAg>gCg	p.E46A	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.E46A	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	46					extracellular matrix organization (GO:0030198)|negative regulation of apoptotic process (GO:0043066)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of signal transduction (GO:0009967)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.E46A(2)		breast(1)|central_nervous_system(6)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(43)|ovary(4)|pancreas(3)|prostate(5)|skin(12)|upper_aerodigestive_tract(1)|urinary_tract(1)	95	all_cancers(12;2.6e-05)|Lung SC(27;0.184)	Lung NSC(34;0.0569)|all_lung(34;0.129)		GBM - Glioblastoma multiforme(48;0.0473)		ATTGACCCGCTCGGGGATCAC	0.587																																					p.E46A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A137C	12						.						69.0	60.0	63.0					12																	43945028		2203	4300	6503	42231295	SO:0001583	missense	80070	exon2			AF488804	CCDS31778.2	12q12	2005-08-19	2005-08-19			ENSG00000173157		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17178	protein-coding gene	gene with protein product		611681	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 20"""			12514189, 12562771	Standard	NM_025003		Approved	GON-1	uc010skx.2	P59510		ENST00000389420.3:c.137A>C	12.37:g.43945028T>G	ENSP00000374071:p.Glu46Ala	Somatic		Capture	Illumina HiSeq	Phase_I	42231295	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	T	5.380	0.255438	0.10185	.	.	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.07327	3.2;3.2	3.01	-0.0925	0.13656	Peptidase M12B, propeptide (1);	0.772775	0.10621	N	0.653369	T	0.03053	0.0090	N	0.03608	-0.345	0.19300	N	0.999973	B	0.06786	0.001	B	0.11329	0.006	T	0.47548	-0.9109	10	0.20046	T	0.44	.	4.6682	0.12676	0.1879:0.0:0.4992:0.3128	.	46	P59510	ATS20_HUMAN	A	46	ENSP00000374071:E46A;ENSP00000448341:E46A	ENSP00000374068:E46A	E	-	2	0	ADAMTS20	42231295	0.982000	0.34865	0.863000	0.33907	0.906000	0.53458	1.903000	0.39858	-0.026000	0.13895	-0.213000	0.12676	GAG		0.587	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003	
PCED1B	91523	broad.mit.edu	37	12	47472644	47472644	+	5'Flank	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:47472644C>T	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Missense_Mutation_p.A48T|AMIGO2_ENST00000266581.4_Missense_Mutation_p.A48T|AMIGO2_ENST00000321382.3_Missense_Mutation_p.A48T|AMIGO2_ENST00000550413.1_Missense_Mutation_p.A48T			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)	p.A48T(1)									ATGTCAGTGGCACAGATGCAA	0.552																																					p.A48T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G142A	12						.						78.0	77.0	78.0					12																	47472644		2203	4300	6503	45758911	SO:0001631	upstream_gene_variant	347902	exon2			BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617		12.37:g.47472644C>T	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	45758911	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	C	32	5.179980	0.94846	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.02369	4.32;4.32;4.32;4.32	4.75	4.75	0.60458	Leucine-rich repeat-containing N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.08447	0.0210	L	0.28608	0.87	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.53187	-0.8474	10	0.23302	T	0.38	-16.2949	17.6266	0.88095	0.0:1.0:0.0:0.0	.	48	Q86SJ2	AMGO2_HUMAN	T	48	ENSP00000266581:A48T;ENSP00000449034:A48T;ENSP00000406020:A48T;ENSP00000320848:A48T	ENSP00000266581:A48T	A	-	1	0	AMIGO2	45758911	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.713000	0.84693	2.580000	0.87095	0.655000	0.94253	GCC		0.552	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
LALBA	3906	broad.mit.edu	37	12	48963683	48963683	+	Missense_Mutation	SNP	C	C	T	rs558586421		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:48963683C>T	ENST00000301046.2	-	1	146	c.121G>A	c.(121-123)Gct>Act	p.A41T	LALBA_ENST00000549817.1_Missense_Mutation_p.A41T	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-	41					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)	p.A41T(1)		large_intestine(1)|stomach(2)	3						TCAGGCAAAGCGATGCCTCCA	0.512													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.A41T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	12						.						146.0	118.0	127.0					12																	48963683		2203	4300	6503	47249950	SO:0001583	missense	3906	exon1				CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.121G>A	12.37:g.48963683C>T	ENSP00000301046:p.Ala41Thr	None		Capture	Illumina HiSeq	Phase_I	47249950	NM_002289	Q6FGX0|Q9UDK4	Missense_Mutation	SNP	ENST00000301046.2	37	CCDS8765.1	.	.	.	.	.	.	.	.	.	.	C	11.09	1.537366	0.27475	.	.	ENSG00000167531	ENST00000301046;ENST00000549817	T;T	0.68903	1.05;-0.36	5.03	-10.1	0.00402	Lysozyme-like domain (1);	1.580710	0.03950	N	0.288296	T	0.25344	0.0616	N	0.00855	-1.145	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.23691	-1.0181	10	0.48119	T	0.1	-2.197	0.1309	0.00073	0.2746:0.1765:0.2039:0.345	.	41	P00709	LALBA_HUMAN	T	41	ENSP00000301046:A41T;ENSP00000449780:A41T	ENSP00000301046:A41T	A	-	1	0	LALBA	47249950	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	-0.837000	0.04377	-1.455000	0.01923	-0.493000	0.04662	GCT		0.512	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289	
PRKAG1	5571	broad.mit.edu	37	12	49398782	49398782	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:49398782G>T	ENST00000548065.1	-	7	831	c.375C>A	c.(373-375)tcC>tcA	p.S125S	RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|PRKAG1_ENST00000316299.5_Silent_p.S134S|PRKAG1_ENST00000552212.1_Silent_p.S93S|RP11-386G11.5_ENST00000547866.1_RNA|PRKAG1_ENST00000395170.3_Silent_p.S41S|RP11-386G11.5_ENST00000547395.1_RNA|PRKAG1_ENST00000547306.1_Silent_p.S74S			P54619	AAKG1_HUMAN	protein kinase, AMP-activated, gamma 1 non-catalytic subunit	125	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|insulin receptor signaling pathway (GO:0008286)|membrane organization (GO:0061024)|positive regulation of gene expression (GO:0010628)|positive regulation of protein kinase activity (GO:0045860)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of glycolytic process (GO:0006110)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)	p.S125S(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	9					Acetylsalicylic acid(DB00945)	GCGGTTTAAAGGAGTCCTGGA	0.458																																					p.S125S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C375A	12						.						129.0	128.0	128.0					12																	49398782		2203	4300	6503	47685049	SO:0001819	synonymous_variant	5571	exon7			U42412	CCDS8777.1, CCDS55824.1, CCDS55825.1	12q12-q14	1998-07-16				ENSG00000181929			9385	protein-coding gene	gene with protein product		602742				8557660, 8621499	Standard	NM_002733		Approved		uc001rsz.3	P54619	OTTHUMG00000170406	ENST00000548065.1:c.375C>A	12.37:g.49398782G>T		Somatic		Capture	Illumina HiSeq	Phase_I	47685049	NM_002733	B4DDT7|Q8N7V9	Silent	SNP	ENST00000548065.1	37	CCDS8777.1																																																																																				0.458	PRKAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408946.1	NM_002733	
KCNH3	23416	broad.mit.edu	37	12	49934840	49934840	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:49934840G>A	ENST00000257981.6	+	2	495	c.235G>A	c.(235-237)Gtc>Atc	p.V79I		NM_012284.1	NP_036416.1	Q9ULD8	KCNH3_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 3	79	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	36						CAGTGAGCTCGTCCGCCAACA	0.632																																					p.V79I												.	.	0			c.G235A	12						.						59.0	58.0	58.0					12																	49934840		2203	4300	6503	48221107	SO:0001583	missense	23416	exon2			AB022696	CCDS8786.1	12q13	2012-07-05				ENSG00000135519		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6252	protein-coding gene	gene with protein product		604527				10455180, 16382104	Standard	NM_012284		Approved	Kv12.2, BEC1, elk2	uc001ruh.1	Q9ULD8	OTTHUMG00000169517	ENST00000257981.6:c.235G>A	12.37:g.49934840G>A	ENSP00000257981:p.Val79Ile	None		Capture	Illumina HiSeq	Phase_I	48221107	NM_012284	Q9UQ06	Missense_Mutation	SNP	ENST00000257981.6	37	CCDS8786.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.233597	0.58886	.	.	ENSG00000135519	ENST00000257981	D	0.99563	-6.17	5.05	5.05	0.67936	PAS (3);PAS fold-4 (1);	0.000000	0.41194	D	0.000932	D	0.97882	0.9304	L	0.29908	0.895	0.30487	N	0.771747	B	0.31435	0.323	B	0.34824	0.19	D	0.96448	0.9332	10	0.24483	T	0.36	.	9.6343	0.39798	0.0927:0.0:0.9073:0.0	.	79	Q9ULD8	KCNH3_HUMAN	I	79	ENSP00000257981:V79I	ENSP00000257981:V79I	V	+	1	0	KCNH3	48221107	0.097000	0.21791	0.984000	0.44739	0.998000	0.95712	0.572000	0.23684	2.808000	0.96608	0.650000	0.86243	GTC		0.632	KCNH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404571.2	NM_012284	
SLC11A2	4891	broad.mit.edu	37	12	51384621	51384621	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:51384621G>T	ENST00000262051.7	-	15	1619	c.1532C>A	c.(1531-1533)gCt>gAt	p.A511D	SLC11A2_ENST00000541174.2_Missense_Mutation_p.A511D|SLC11A2_ENST00000547688.1_Missense_Mutation_p.A540D|SLC11A2_ENST00000546743.1_Missense_Mutation_p.A432D|SLC11A2_ENST00000547198.1_Missense_Mutation_p.A511D|SLC11A2_ENST00000545993.2_Missense_Mutation_p.A507D|SLC11A2_ENST00000262052.5_Missense_Mutation_p.A511D|SLC11A2_ENST00000394904.3_Missense_Mutation_p.A540D	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	511					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						GACCACAGCAGCCACCACATA	0.488																																					p.A540D												.	.	0			c.C1619A	12						.						127.0	103.0	111.0					12																	51384621		2203	4300	6503	49670888	SO:0001583	missense	4891	exon15			AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1532C>A	12.37:g.51384621G>T	ENSP00000262051:p.Ala511Asp	None		Capture	Illumina HiSeq	Phase_I	49670888	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.736597	0.89482	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.32515	1.84;1.84;1.84;1.82;1.82;1.84;1.84;1.45	5.91	5.91	0.95273	.	0.047783	0.85682	D	0.000000	T	0.50326	0.1609	M	0.83603	2.65	0.80722	D	1	P;P;P;P;P;P	0.47762	0.84;0.9;0.812;0.9;0.84;0.84	B;P;P;P;B;B	0.48454	0.374;0.578;0.578;0.578;0.374;0.374	T	0.55431	-0.8142	10	0.66056	D	0.02	-10.0439	19.0571	0.93070	0.0:0.0:1.0:0.0	.	474;507;540;511;360;511	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	D	511;511;511;540;540;511;507;432	ENSP00000262051:A511D;ENSP00000446769:A511D;ENSP00000262052:A511D;ENSP00000378364:A540D;ENSP00000449200:A540D;ENSP00000444542:A511D;ENSP00000442810:A507D;ENSP00000446914:A432D	ENSP00000262051:A511D	A	-	2	0	SLC11A2	49670888	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	8.624000	0.90961	2.803000	0.96430	0.650000	0.86243	GCT		0.488	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
SCN8A	6334	broad.mit.edu	37	12	52078073	52078073	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:52078073A>G	ENST00000354534.6	+	3	570	c.392A>G	c.(391-393)cAt>cGt	p.H131R	SCN8A_ENST00000545061.1_Missense_Mutation_p.H131R|SCN8A_ENST00000550891.1_Missense_Mutation_p.H131R	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	131					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)	p.H131R(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	ATTTTGATACATTCATATCCT	0.353																																					p.H131R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A392G	12						.						58.0	59.0	59.0					12																	52078073		1873	4109	5982	50364340	SO:0001583	missense	6334	exon3			AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.392A>G	12.37:g.52078073A>G	ENSP00000346534:p.His131Arg	Somatic		Capture	Illumina HiSeq	Phase_I	50364340	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	.	.	.	.	.	.	.	.	.	.	A	17.19	3.326678	0.60743	.	.	ENSG00000196876	ENST00000550891;ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	D	0.97306	0.9119	M	0.92077	3.27	0.80722	D	1	D	0.55385	0.971	B	0.42462	0.388	D	0.98122	1.0426	10	0.87932	D	0	.	14.9233	0.70856	1.0:0.0:0.0:0.0	.	131	Q9UQD0	SCN8A_HUMAN	R	131;131;131;131;44	ENSP00000448415:H131R;ENSP00000346534:H131R;ENSP00000440360:H131R;ENSP00000347255:H131R	ENSP00000346534:H131R	H	+	2	0	SCN8A	50364340	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.120000	0.94369	2.178000	0.69098	0.533000	0.62120	CAT		0.353	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
FIGNL2	401720	broad.mit.edu	37	12	52216051	52216051	+	lincRNA	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:52216051G>A	ENST00000562343.2	+	0	4188				RP11-923I11.4_ENST00000567167.1_lincRNA																							CTGAGATGTCGTCGTGTGCCC	0.642																																					p.D49D												.	.	0			c.C147T	12						.						63.0	67.0	66.0					12																	52216051		2163	4257	6420	50502318			401720	exon1																															12.37:g.52216051G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50502318	NM_001013690		Silent	SNP	ENST00000562343.2	37																																																																																					0.642	RP11-923I11.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000430848.2		
SP7	121340	broad.mit.edu	37	12	53723095	53723095	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:53723095G>A	ENST00000536324.2	-	3	414	c.131C>T	c.(130-132)aCa>aTa	p.T44I	SP7_ENST00000537210.2_Missense_Mutation_p.T26I|SP7_ENST00000303846.3_Missense_Mutation_p.T44I	NM_001173467.1	NP_001166938.1	Q8TDD2	SP7_HUMAN	Sp7 transcription factor	44					hematopoietic stem cell differentiation (GO:0060218)|osteoblast differentiation (GO:0001649)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T44I(1)		cervix(2)|large_intestine(3)|lung(7)|skin(1)|urinary_tract(1)	14						CGGCTTCTTTGTGCCTGCTTT	0.562																																					p.T44I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C131T	12						.						137.0	141.0	140.0					12																	53723095		2087	4224	6311	52009362	SO:0001583	missense	121340	exon2			AF477981	CCDS44897.1, CCDS73475.1	12q13.13	2013-01-08				ENSG00000170374		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	17321	protein-coding gene	gene with protein product		606633				11792318	Standard	NM_152860		Approved	osterix, OSX	uc001sct.3	Q8TDD2		ENST00000536324.2:c.131C>T	12.37:g.53723095G>A	ENSP00000443827:p.Thr44Ile	Somatic		Capture	Illumina HiSeq	Phase_I	52009362	NM_152860	B3KY26|Q3MJ72|Q7Z718	Missense_Mutation	SNP	ENST00000536324.2	37	CCDS44897.1	.	.	.	.	.	.	.	.	.	.	G	5.492	0.275727	0.10403	.	.	ENSG00000170374	ENST00000536324;ENST00000303846;ENST00000537210;ENST00000547755	T;T;T;T	0.42513	3.36;3.36;3.36;0.97	3.95	3.95	0.45737	.	0.404453	0.25250	N	0.032034	T	0.16471	0.0396	N	0.02011	-0.69	0.28338	N	0.921467	B	0.13145	0.007	B	0.11329	0.006	T	0.10474	-1.0628	10	0.23302	T	0.38	.	9.6257	0.39750	0.1008:0.0:0.8992:0.0	.	44	Q8TDD2	SP7_HUMAN	I	44;44;26;26	ENSP00000443827:T44I;ENSP00000302812:T44I;ENSP00000441367:T26I;ENSP00000449355:T26I	ENSP00000302812:T44I	T	-	2	0	SP7	52009362	0.037000	0.19845	0.833000	0.33012	0.738000	0.42128	2.406000	0.44557	2.497000	0.84241	0.313000	0.20887	ACA		0.562	SP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406917.1		
HOXC12	3228	broad.mit.edu	37	12	54348768	54348768	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:54348768C>T	ENST00000243103.3	+	1	151	c.55C>T	c.(55-57)Cac>Tac	p.H19Y	AC012531.23_ENST00000603432.1_lincRNA	NM_173860.1	NP_776272.1	P31275	HXC12_HUMAN	homeobox C12	19					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.H19Y(1)		large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	12						GGTAAACATCCACACGGGAGA	0.617																																					p.H19Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C55T	12						.						43.0	53.0	50.0					12																	54348768		2203	4300	6503	52635035	SO:0001583	missense	3228	exon1			AF328962	CCDS8866.1	12q13.13	2011-06-20	2005-12-22		ENSG00000123407	ENSG00000123407		"""Homeoboxes / ANTP class : HOXL subclass"""	5124	protein-coding gene	gene with protein product		142975	"""homeo box C12"""	HOX3, HOX3F, HOC3F		1973146, 1358459	Standard	NM_173860		Approved		uc010soq.2	P31275	OTTHUMG00000160010	ENST00000243103.3:c.55C>T	12.37:g.54348768C>T	ENSP00000243103:p.His19Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	52635035	NM_173860	Q9BXJ6	Missense_Mutation	SNP	ENST00000243103.3	37	CCDS8866.1	.	.	.	.	.	.	.	.	.	.	C	19.74	3.883104	0.72410	.	.	ENSG00000123407	ENST00000243103	D	0.93133	-3.17	2.71	2.71	0.32032	.	0.000000	0.85682	D	0.000000	D	0.95462	0.8526	M	0.81682	2.555	0.58432	D	0.999999	D	0.67145	0.996	D	0.66196	0.942	D	0.93826	0.7123	10	0.19590	T	0.45	.	13.2251	0.59911	0.0:1.0:0.0:0.0	.	19	P31275	HXC12_HUMAN	Y	19	ENSP00000243103:H19Y	ENSP00000243103:H19Y	H	+	1	0	HOXC12	52635035	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.080000	0.76837	1.820000	0.53075	0.455000	0.32223	CAC		0.617	HOXC12-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358868.2	NM_173860	
OR9K2	441639	broad.mit.edu	37	12	55523721	55523721	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:55523721T>G	ENST00000305377.5	+	1	257	c.169T>G	c.(169-171)Ttg>Gtg	p.L57V		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	57						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L57V(1)		NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CCTGCTATTTTTGTTTGTTTA	0.448																																					p.L57V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T169G	12						.						177.0	169.0	172.0					12																	55523721		2203	4300	6503	53809988	SO:0001583	missense	441639	exon1			BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.169T>G	12.37:g.55523721T>G	ENSP00000307598:p.Leu57Val	Somatic		Capture	Illumina HiSeq	Phase_I	53809988	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	.	.	.	.	.	.	.	.	.	.	T	10.67	1.415810	0.25552	.	.	ENSG00000170605	ENST00000305377	T	0.01902	4.57	4.98	0.995	0.19838	.	0.185506	0.26065	N	0.026547	T	0.09905	0.0243	M	0.86573	2.825	0.30391	N	0.780957	D	0.89917	1.0	D	0.87578	0.998	T	0.06215	-1.0839	10	0.66056	D	0.02	-0.937	2.7749	0.05345	0.129:0.5314:0.1251:0.2144	.	57	Q8NGE7	OR9K2_HUMAN	V	57	ENSP00000307598:L57V	ENSP00000307598:L57V	L	+	1	2	OR9K2	53809988	0.000000	0.05858	0.050000	0.19076	0.107000	0.19398	-0.970000	0.03810	0.084000	0.17077	-0.872000	0.02987	TTG		0.448	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
OR6C65	403282	broad.mit.edu	37	12	55794610	55794610	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:55794610delT	ENST00000379665.2	+	1	397	c.298delT	c.(298-300)tttfs	p.F101fs		NM_001005518.1	NP_001005518.1	A6NJZ3	O6C65_HUMAN	olfactory receptor, family 6, subfamily C, member 65	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L102fs*1(1)		cervix(1)|endometrium(2)|large_intestine(3)|lung(9)	15						GGCCCAAGTATTTTTTTTAAT	0.358																																					p.F100fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.298delT	12						.						81.0	87.0	85.0					12																	55794610		2203	4300	6503	54080877	SO:0001589	frameshift_variant	403282	exon1				CCDS31821.1	12q13.2	2013-09-23			ENSG00000205328	ENSG00000205328		"""GPCR / Class A : Olfactory receptors"""	31295	protein-coding gene	gene with protein product							Standard	NM_001005518		Approved		uc010spl.2	A6NJZ3	OTTHUMG00000169955	ENST00000379665.2:c.298delT	12.37:g.55794610delT	ENSP00000368986:p.Phe101fs	Somatic		Capture	Illumina HiSeq	Phase_I	54080877	NM_001005518	B2RNH9	Frame_Shift_Del	DEL	ENST00000379665.2	37	CCDS31821.1																																																																																				0.358	OR6C65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406674.1		
OR10P1	121130	broad.mit.edu	37	12	56031446	56031446	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:56031446C>T	ENST00000309675.2	+	1	803	c.771C>T	c.(769-771)agC>agT	p.S257S	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	257						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S257S(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						GAACAGCCAGCATCACCTACA	0.582																																					p.S257S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C771T	12						.						109.0	97.0	101.0					12																	56031446		2203	4300	6503	54317713	SO:0001819	synonymous_variant	121130	exon1			BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.771C>T	12.37:g.56031446C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54317713	NM_206899	B9EGY4	Silent	SNP	ENST00000309675.2	37	CCDS31828.1																																																																																				0.582	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
ITGA7	3679	broad.mit.edu	37	12	56101370	56101370	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:56101370C>T	ENST00000555728.1	-	1	125	c.97G>A	c.(97-99)Gcc>Acc	p.A33T	ITGA7_ENST00000452168.2_Intron|ITGA7_ENST00000394230.2_Missense_Mutation_p.A33T|ITGA7_ENST00000553804.1_Missense_Mutation_p.A33T|ITGA7_ENST00000257879.6_Missense_Mutation_p.A33T|ITGA7_ENST00000257880.7_Missense_Mutation_p.A33T|ITGA7_ENST00000394229.2_Missense_Mutation_p.A33T|ITGA7_ENST00000347027.6_Missense_Mutation_p.A33T			Q13683	ITA7_HUMAN	integrin, alpha 7	33					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.A33T(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						AGATTGAAGGCGACAGCCCGT	0.662																																					p.A33T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G97A	12						.						35.0	41.0	39.0					12																	56101370		2203	4300	6503	54387637	SO:0001583	missense	3679	exon1				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.97G>A	12.37:g.56101370C>T	ENSP00000452387:p.Ala33Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54387637	NM_001144996	B4E3U0|C9JMD3|C9JMZ6|O43197|Q86W93|Q9NY89|Q9UET0|Q9UEV2	Missense_Mutation	SNP	ENST00000555728.1	37		.	.	.	.	.	.	.	.	.	.	C	34	5.317275	0.95682	.	.	ENSG00000135424	ENST00000553804;ENST00000257879;ENST00000347027;ENST00000257880;ENST00000394230;ENST00000394229;ENST00000353687;ENST00000555728	D;D;D;D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65;-2.65;-2.65;-2.65	4.37	4.37	0.52481	.	0.096826	0.42172	D	0.000747	D	0.95242	0.8457	M	0.85462	2.755	0.39171	D	0.962588	D;D	0.89917	0.997;1.0	D;D	0.71870	0.923;0.975	D	0.96422	0.9312	10	0.87932	D	0	.	14.8188	0.70055	0.0:1.0:0.0:0.0	.	33;96	Q13683-3;Q4LE35	.;.	T	33	ENSP00000452120:A33T;ENSP00000257879:A33T;ENSP00000343009:A33T;ENSP00000257880:A33T;ENSP00000377777:A33T;ENSP00000377776:A33T;ENSP00000452387:A33T	ENSP00000257879:A33T	A	-	1	0	ITGA7	54387637	0.999000	0.42202	0.996000	0.52242	0.973000	0.67179	4.262000	0.58847	2.449000	0.82847	0.462000	0.41574	GCC		0.662	ITGA7-014	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000410138.1	NM_002206	
STAT2	6773	broad.mit.edu	37	12	56749969	56749969	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:56749969G>T	ENST00000314128.4	-	3	255	c.232C>A	c.(232-234)Cca>Aca	p.P78T	STAT2_ENST00000418572.2_Missense_Mutation_p.P78T|STAT2_ENST00000557235.1_Missense_Mutation_p.P78T			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	78					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P78T(1)		NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						AAGGACTCTGGGTCCTGGCTG	0.532																																					p.P78T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C232A	12						.						89.0	86.0	87.0					12																	56749969		2203	4300	6503	55036236	SO:0001583	missense	6773	exon3			BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.232C>A	12.37:g.56749969G>T	ENSP00000315768:p.Pro78Thr	Somatic		Capture	Illumina HiSeq	Phase_I	55036236	NM_198332	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	G	8.705	0.910713	0.17833	.	.	ENSG00000170581	ENST00000314128;ENST00000557235;ENST00000553337;ENST00000418572	D;D;T	0.85955	-2.04;-2.05;-1.47	5.08	-0.0375	0.13884	STAT transcription factor, protein interaction (4);	1.068790	0.07313	N	0.876233	T	0.77412	0.4126	L	0.34521	1.04	0.09310	N	1	B;B;P	0.40000	0.202;0.128;0.698	B;B;B	0.40825	0.129;0.098;0.341	T	0.63812	-0.6552	10	0.29301	T	0.29	0.0561	7.2771	0.26290	0.536:0.0:0.464:0.0	.	78;78;78	B4DLC8;G3V2M6;P52630	.;.;STAT2_HUMAN	T	78	ENSP00000315768:P78T;ENSP00000450751:P78T;ENSP00000387354:P78T	ENSP00000315768:P78T	P	-	1	0	STAT2	55036236	0.006000	0.16342	0.093000	0.20910	0.265000	0.26407	-0.740000	0.04861	0.093000	0.17368	0.655000	0.94253	CCA		0.532	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	
TIMELESS	8914	broad.mit.edu	37	12	56825292	56825292	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:56825292C>T	ENST00000553532.1	-	8	934	c.784G>A	c.(784-786)Gca>Aca	p.A262T	TIMELESS_ENST00000229201.4_Missense_Mutation_p.A261T|TIMELESS_ENST00000554616.1_Missense_Mutation_p.A262T					timeless circadian clock									p.A262T(1)		NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						TTCTTTTCTGCCATCTCTCGC	0.562																																					p.A262T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G784A	12						.						130.0	110.0	116.0					12																	56825292		2203	4300	6503	55111559	SO:0001583	missense	8914	exon8			AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.784G>A	12.37:g.56825292C>T	ENSP00000450607:p.Ala262Thr	Somatic		Capture	Illumina HiSeq	Phase_I	55111559	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.568503	0.65651	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.48522	0.81;0.81;0.81	5.42	5.42	0.78866	Timeless protein (1);	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.70595	2.14	0.58432	D	0.999999	P;P	0.43857	0.783;0.819	B;B	0.40066	0.212;0.318	T	0.40757	-0.9546	10	0.25106	T	0.35	-12.8548	12.5003	0.55952	0.0:0.9189:0.0:0.0811	.	261;262	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	T	261;262;262	ENSP00000229201:A261T;ENSP00000450607:A262T;ENSP00000450848:A262T	ENSP00000229201:A262T	A	-	1	0	TIMELESS	55111559	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.471000	0.66762	2.715000	0.92844	0.655000	0.94253	GCA		0.562	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
AGAP2-AS1	100130776	broad.mit.edu	37	12	58121322	58121322	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:58121322G>T	ENST00000542466.2	+	2	683	c.547G>T	c.(547-549)Gat>Tat	p.D183Y	AGAP2_ENST00000547588.1_Silent_p.I967I|RP11-571M6.8_ENST00000548410.2_RNA|AGAP2_ENST00000257897.3_Silent_p.I611I					AGAP2 antisense RNA 1									p.I611I(1)									CAGAACACTCGATGCAGATGA	0.672																																					p.I611I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1833A	12						.						73.0	69.0	71.0					12																	58121322		2203	4300	6503	56407589	SO:0001583	missense	116986	exon16			BC039697, BC069024		12q14.1	2013-05-30			ENSG00000255737	ENSG00000255737		"""Long non-coding RNAs"""	48633	non-coding RNA	RNA, long non-coding							Standard	NR_027032		Approved				OTTHUMG00000170286	ENST00000542466.2:c.547G>T	12.37:g.58121322G>T	ENSP00000437523:p.Asp183Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	56407589	NM_014770		Silent	SNP	ENST00000542466.2	37		.	.	.	.	.	.	.	.	.	.	G	12.90	2.075623	0.36662	.	.	ENSG00000255737	ENST00000542466	.	.	.	5.0	4.09	0.47781	.	.	.	.	.	T	0.71091	0.3299	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.73072	-0.4098	7	0.87932	D	0	.	7.323	0.26539	0.2383:0.0:0.7617:0.0	.	183	B7Z718	.	Y	183	.	ENSP00000437523:D183Y	D	+	1	0	RP11-571M6.6	56407589	0.999000	0.42202	1.000000	0.80357	0.984000	0.73092	0.505000	0.22642	2.480000	0.83734	0.655000	0.94253	GAT		0.672	AGAP2-AS1-001	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000408368.1		
AVIL	10677	broad.mit.edu	37	12	58200173	58200173	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:58200173A>G	ENST00000257861.3	-	13	2071	c.1641T>C	c.(1639-1641)acT>acC	p.T547T	TSFM_ENST00000548851.1_Intron|AVIL_ENST00000537081.1_Silent_p.T540T|AVIL_ENST00000550083.1_5'UTR|RP11-571M6.17_ENST00000602802.1_lincRNA|RNU6-1083P_ENST00000384022.1_RNA	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	547	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)	p.T547T(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					GCTCTGCCTGAGTTCGCAGCA	0.547																																					p.T547T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1641C	12						.						139.0	117.0	125.0					12																	58200173		2203	4300	6503	56486440	SO:0001819	synonymous_variant	10677	exon13			AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.1641T>C	12.37:g.58200173A>G		Somatic		Capture	Illumina HiSeq	Phase_I	56486440	NM_006576	B2RAU7|Q2NKM9	Silent	SNP	ENST00000257861.3	37	CCDS8959.1																																																																																				0.547	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576	
SRGAP1	57522	broad.mit.edu	37	12	64521873	64521873	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:64521873G>A	ENST00000355086.3	+	21	3297	c.2773G>A	c.(2773-2775)Gac>Aac	p.D925N	SRGAP1_ENST00000357825.3_Missense_Mutation_p.D902N|SRGAP1_ENST00000543397.1_Missense_Mutation_p.D862N	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	925					axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)	p.D925N(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CAGCCGGCACGACTCCCTCAA	0.602																																					p.D925N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2773A	12						.						53.0	49.0	50.0					12																	64521873		2203	4300	6503	62808140	SO:0001583	missense	57522	exon21			AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.2773G>A	12.37:g.64521873G>A	ENSP00000347198:p.Asp925Asn	Somatic		Capture	Illumina HiSeq	Phase_I	62808140	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.624000	0.87560	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.20069	3.13;2.69;2.1	5.65	5.65	0.86999	.	0.000000	0.36303	U	0.002669	T	0.17874	0.0429	L	0.38175	1.15	0.80722	D	1	P;B	0.35700	0.516;0.006	B;B	0.26864	0.074;0.005	T	0.02991	-1.1085	9	.	.	.	.	20.1057	0.97893	0.0:0.0:1.0:0.0	.	925;862	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	N	925;902;862	ENSP00000347198:D925N;ENSP00000350480:D902N;ENSP00000437948:D862N	.	D	+	1	0	SRGAP1	62808140	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	7.625000	0.83145	2.827000	0.97445	0.650000	0.86243	GAC		0.602	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
HELB	92797	broad.mit.edu	37	12	66731839	66731839	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:66731839T>C	ENST00000247815.4	+	13	3280	c.3221T>C	c.(3220-3222)aTt>aCt	p.I1074T		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	1074					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)	p.I1074T(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		AATAATTTAATTCCCAGGCAA	0.313																																					p.I1074T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3221C	12						.						68.0	71.0	70.0					12																	66731839		2203	4299	6502	65018106	SO:0001583	missense	92797	exon13			AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.3221T>C	12.37:g.66731839T>C	ENSP00000247815:p.Ile1074Thr	Somatic		Capture	Illumina HiSeq	Phase_I	65018106	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	T	0.025	-1.380640	0.01204	.	.	ENSG00000127311	ENST00000247815	T	0.10382	2.88	5.5	-4.88	0.03113	.	1.169440	0.06547	N	0.744314	T	0.02156	0.0067	N	0.00246	-1.78	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48758	-0.9007	9	.	.	.	0.0402	9.3403	0.38076	0.1699:0.6558:0.0:0.1743	.	1074	Q8NG08	HELB_HUMAN	T	1074	ENSP00000247815:I1074T	.	I	+	2	0	HELB	65018106	0.000000	0.05858	0.000000	0.03702	0.149000	0.21700	-0.541000	0.06099	-0.912000	0.03837	-0.290000	0.09829	ATT		0.313	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
OSBPL8	114882	broad.mit.edu	37	12	76791624	76791624	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:76791624C>T	ENST00000261183.3	-	8	1001	c.522G>A	c.(520-522)ggG>ggA	p.G174G	OSBPL8_ENST00000393250.4_Silent_p.G132G|OSBPL8_ENST00000393249.2_Silent_p.G132G	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	174	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)	p.G174G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TCAGTAGCACCCCAGGTTTCA	0.388																																					p.G174G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G522A	12						.						100.0	91.0	94.0					12																	76791624		2203	4300	6503	75315755	SO:0001819	synonymous_variant	114882	exon8			AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.522G>A	12.37:g.76791624C>T		Somatic		Capture	Illumina HiSeq	Phase_I	75315755	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Silent	SNP	ENST00000261183.3	37	CCDS31862.1																																																																																				0.388	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
METTL25	84190	broad.mit.edu	37	12	82752583	82752583	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:82752583T>C	ENST00000248306.3	+	1	308	c.239T>C	c.(238-240)gTg>gCg	p.V80A	CCDC59_ENST00000256151.7_5'Flank|METTL25_ENST00000547357.1_3'UTR|CCDC59_ENST00000548126.1_5'Flank	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	80							methyltransferase activity (GO:0008168)										CGCCCCCTAGTGGAAGCAGAG	0.687											OREG0022008	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V80A												.	.	0			c.T239C	12						.						23.0	25.0	25.0					12																	82752583		2202	4299	6501	81276714	SO:0001583	missense	84190	exon1			BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.239T>C	12.37:g.82752583T>C	ENSP00000248306:p.Val80Ala	None	1216	Capture	Illumina HiSeq	Phase_I	81276714	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.743324	0.30865	.	.	ENSG00000127720	ENST00000248306;ENST00000548200	T	0.30448	1.53	5.4	-4.48	0.03515	.	1.823960	0.02713	N	0.113037	T	0.15003	0.0362	N	0.21448	0.665	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11397	-1.0589	10	0.15952	T	0.53	2.8041	0.2832	0.00248	0.2922:0.1503:0.2048:0.3527	.	80	Q8N6Q8	CL026_HUMAN	A	80	ENSP00000248306:V80A	ENSP00000248306:V80A	V	+	2	0	C12orf26	81276714	0.000000	0.05858	0.052000	0.19188	0.176000	0.22953	-1.631000	0.02026	-0.256000	0.09473	0.528000	0.53228	GTG		0.687	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
TMTC2	160335	broad.mit.edu	37	12	83424610	83424610	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:83424610A>G	ENST00000321196.3	+	9	2811	c.2104A>G	c.(2104-2106)Aag>Gag	p.K702E	TMTC2_ENST00000549919.1_Missense_Mutation_p.K696E	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	702					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						GCTCTTCTTGAAGGCTATTGA	0.418																																					p.K702E												.	.	0			c.A2104G	12						.						198.0	179.0	186.0					12																	83424610		2203	4300	6503	81948741	SO:0001583	missense	160335	exon9			AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.2104A>G	12.37:g.83424610A>G	ENSP00000322300:p.Lys702Glu	None		Capture	Illumina HiSeq	Phase_I	81948741	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.629645	0.87660	.	.	ENSG00000179104	ENST00000321196;ENST00000549919;ENST00000546590	D;D	0.89050	-2.46;-2.46	5.53	5.53	0.82687	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.90259	0.6954	M	0.62209	1.925	0.80722	D	1	P	0.50819	0.939	P	0.51453	0.67	D	0.88655	0.3185	10	0.27785	T	0.31	-18.2458	14.7775	0.69740	1.0:0.0:0.0:0.0	.	702	Q8N394	TMTC2_HUMAN	E	702;696;457	ENSP00000322300:K702E;ENSP00000447609:K696E	ENSP00000322300:K702E	K	+	1	0	TMTC2	81948741	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.257000	0.89851	2.231000	0.72958	0.455000	0.32223	AAG		0.418	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
SLC6A15	55117	broad.mit.edu	37	12	85260839	85260839	+	Silent	SNP	A	A	G	rs112560925		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:85260839A>G	ENST00000266682.5	-	10	2170	c.1629T>C	c.(1627-1629)gcT>gcC	p.A543A	SLC6A15_ENST00000552192.1_Silent_p.A436A|SLC6A15_ENST00000309283.7_Silent_p.A251A	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	543					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.A543A(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CAAAGCATACAGCAATATTCT	0.299																																					p.A543A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1629C	12						.						86.0	82.0	84.0					12																	85260839		2203	4298	6501	83784970	SO:0001819	synonymous_variant	55117	exon10			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.1629T>C	12.37:g.85260839A>G		Somatic		Capture	Illumina HiSeq	Phase_I	83784970	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																				0.299	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
SLC6A15	55117	broad.mit.edu	37	12	85270339	85270339	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:85270339G>A	ENST00000266682.5	-	6	1345	c.804C>T	c.(802-804)ttC>ttT	p.F268F	SLC6A15_ENST00000551388.1_5'UTR|SLC6A15_ENST00000552192.1_Silent_p.F161F	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	268					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)	p.F268F(1)		kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						CTCTGATGAGGAAGCAAATAA	0.308																																					p.F268F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C804T	12						.						84.0	85.0	85.0					12																	85270339		2203	4296	6499	83794470	SO:0001819	synonymous_variant	55117	exon6			AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.804C>T	12.37:g.85270339G>A		Somatic		Capture	Illumina HiSeq	Phase_I	83794470	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Silent	SNP	ENST00000266682.5	37	CCDS9026.1																																																																																				0.308	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
LRRIQ1	84125	broad.mit.edu	37	12	85517951	85517951	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:85517951A>T	ENST00000393217.2	+	17	3722	c.3661A>T	c.(3661-3663)Act>Tct	p.T1221S		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1221								p.T1221S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		AGGGGATGTAACTATCACCAA	0.398																																					p.T1221S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3661T	12						.						100.0	103.0	102.0					12																	85517951		2203	4300	6503	84042082	SO:0001583	missense	84125	exon17			AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3661A>T	12.37:g.85517951A>T	ENSP00000376910:p.Thr1221Ser	Somatic		Capture	Illumina HiSeq	Phase_I	84042082	NM_032165	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	0.007	-1.936551	0.00484	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.51071	0.72	5.52	3.11	0.35812	.	1.125150	0.06671	N	0.766140	T	0.22666	0.0547	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.22800	-1.0206	10	0.06099	T	0.92	.	6.7685	0.23581	0.6355:0.2896:0.0749:0.0	.	1221;1196	Q96JM4;C9JI57	LRIQ1_HUMAN;.	S	1221;1196;1221	ENSP00000376910:T1221S	ENSP00000256007:T1221S	T	+	1	0	LRRIQ1	84042082	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.436000	0.21526	0.363000	0.24346	0.477000	0.44152	ACT		0.398	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
CEP290	80184	broad.mit.edu	37	12	88471051	88471051	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:88471051T>C	ENST00000552810.1	-	41	6000	c.5657A>G	c.(5656-5658)aAc>aGc	p.N1886S	CEP290_ENST00000397838.3_Missense_Mutation_p.N946S|CEP290_ENST00000547691.2_Missense_Mutation_p.N946S|CEP290_ENST00000309041.7_Missense_Mutation_p.N1888S	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1886					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						CTCTAATTGGTTCTCTAGTTT	0.323																																					p.N1886S												.	.	0			c.A5657G	12						.						116.0	104.0	108.0					12																	88471051		1806	4064	5870	86995182	SO:0001583	missense	80184	exon41			AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.5657A>G	12.37:g.88471051T>C	ENSP00000448012:p.Asn1886Ser	None		Capture	Illumina HiSeq	Phase_I	86995182	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.984393	0.00443	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.61859	0.65;0.07;0.07;0.65	5.31	4.42	0.53409	.	0.515620	0.24788	N	0.035588	T	0.20740	0.0499	N	0.00926	-1.1	0.20074	N	0.999932	B	0.02656	0.0	B	0.04013	0.001	T	0.23476	-1.0187	10	0.08179	T	0.78	.	4.9352	0.13937	0.1322:0.5547:0.2338:0.0792	.	1886	O15078	CE290_HUMAN	S	946;1886;1888;946	ENSP00000446905:N946S;ENSP00000448012:N1886S;ENSP00000308021:N1888S;ENSP00000380938:N946S	ENSP00000308021:N1888S	N	-	2	0	CEP290	86995182	0.988000	0.35896	1.000000	0.80357	0.058000	0.15608	0.101000	0.15251	1.245000	0.43885	-0.221000	0.12465	AAC		0.323	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
ATP2B1	490	broad.mit.edu	37	12	90015377	90015377	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:90015377G>T	ENST00000428670.3	-	10	1992	c.1536C>A	c.(1534-1536)tcC>tcA	p.S512S	ATP2B1_ENST00000359142.3_Silent_p.S512S|ATP2B1_ENST00000348959.3_Silent_p.S512S|ATP2B1_ENST00000393164.2_Silent_p.S255S|ATP2B1_ENST00000261173.2_Silent_p.S512S			P20020	AT2B1_HUMAN	ATPase, Ca++ transporting, plasma membrane 1	512					blood coagulation (GO:0007596)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)	p.S512S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	45						TTACAAGATAGGACAAAATAT	0.274																																					p.S512S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1536A	12						.						79.0	82.0	81.0					12																	90015377		2201	4297	6498	88539508	SO:0001819	synonymous_variant	490	exon9			J04027	CCDS9035.1, CCDS41817.1	12q21.33	2010-04-20			ENSG00000070961	ENSG00000070961	3.6.3.8	"""ATPases / P-type"""	814	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 1"""	108731				1674727	Standard	NM_001682		Approved	PMCA1	uc001tbh.3	P20020		ENST00000428670.3:c.1536C>A	12.37:g.90015377G>T		Somatic		Capture	Illumina HiSeq	Phase_I	88539508	NM_001001323	Q12992|Q12993|Q13819|Q13820|Q13821|Q16504|Q93082	Silent	SNP	ENST00000428670.3	37	CCDS9035.1																																																																																				0.274	ATP2B1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406653.1	NM_001682	
KERA	11081	broad.mit.edu	37	12	91449970	91449970	+	Missense_Mutation	SNP	T	T	C	rs569894609		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:91449970T>C	ENST00000266719.3	-	2	336	c.89A>G	c.(88-90)cAt>cGt	p.H30R		NM_007035.3	NP_008966.1	O60938	KERA_HUMAN	keratocan	30					carbohydrate metabolic process (GO:0005975)|cornea development in camera-type eye (GO:0061303)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|response to stimulus (GO:0050896)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.H30R(1)		breast(2)|large_intestine(8)|lung(5)|prostate(2)|skin(2)	19						ATCTGAATCATGTACTTCATA	0.423													T|||	1	0.000199681	0.0	0.0	5008	,	,		18417	0.0		0.0	False		,,,				2504	0.001				p.H30R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A89G	12						.						99.0	79.0	86.0					12																	91449970		2203	4300	6503	89974101	SO:0001583	missense	11081	exon2			AF063301	CCDS9037.1	12q21.3-q22	2014-09-17				ENSG00000139330		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	6309	protein-coding gene	gene with protein product	"""keratocan proteoglycan"""	603288		CNA2		10565548, 10802664	Standard	NM_007035		Approved	SLRR2B	uc001tbl.3	O60938		ENST00000266719.3:c.89A>G	12.37:g.91449970T>C	ENSP00000266719:p.His30Arg	Somatic		Capture	Illumina HiSeq	Phase_I	89974101	NM_007035		Missense_Mutation	SNP	ENST00000266719.3	37	CCDS9037.1	.	.	.	.	.	.	.	.	.	.	T	0.033	-1.322897	0.01320	.	.	ENSG00000139330	ENST00000266719	T	0.20069	2.1	5.93	0.984	0.19773	.	1.525430	0.03294	N	0.188097	T	0.09379	0.0231	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.23048	-1.0199	10	0.12103	T	0.63	-0.6242	1.3698	0.02208	0.1189:0.2435:0.2358:0.4018	.	30	O60938	KERA_HUMAN	R	30	ENSP00000266719:H30R	ENSP00000266719:H30R	H	-	2	0	KERA	89974101	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.030000	0.12308	0.158000	0.19367	0.529000	0.55759	CAT		0.423	KERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407149.2	NM_007035	
EEA1	8411	broad.mit.edu	37	12	93170685	93170685	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:93170685C>T	ENST00000322349.8	-	28	4312	c.4048G>A	c.(4048-4050)Gcc>Acc	p.A1350T		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1350					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)	p.A1350T(1)		endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TTGTCTTCGGCCCACTTTCTA	0.328																																					p.A1350T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4048A	12						.						216.0	209.0	211.0					12																	93170685		2203	4300	6503	91694816	SO:0001583	missense	8411	exon28			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.4048G>A	12.37:g.93170685C>T	ENSP00000317955:p.Ala1350Thr	Somatic		Capture	Illumina HiSeq	Phase_I	91694816	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	C	15.66	2.897751	0.52227	.	.	ENSG00000102189	ENST00000322349	T	0.71817	-0.6	5.48	3.64	0.41730	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-type (2);Zinc finger, FYVE/PHD-type (1);	0.116092	0.38058	N	0.001834	T	0.52058	0.1711	N	0.11673	0.155	0.39543	D	0.968842	P	0.41978	0.767	P	0.44732	0.459	T	0.48647	-0.9017	10	0.18710	T	0.47	.	9.5191	0.39124	0.0:0.7816:0.0:0.2184	.	1350	Q15075	EEA1_HUMAN	T	1350	ENSP00000317955:A1350T	ENSP00000317955:A1350T	A	-	1	0	EEA1	91694816	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.669000	0.46825	1.305000	0.44909	0.650000	0.86243	GCC		0.328	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
TMCC3	57458	broad.mit.edu	37	12	94976064	94976064	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:94976064C>T	ENST00000261226.4	-	2	460	c.329G>A	c.(328-330)cGt>cAt	p.R110H	TMCC3_ENST00000551457.1_Missense_Mutation_p.R79H	NM_020698.2	NP_065749	Q9ULS5	TMCC3_HUMAN	transmembrane and coiled-coil domain family 3	110						integral component of membrane (GO:0016021)		p.R110H(2)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	29						TTGCTTGATACGTCCCGCCTG	0.463																																					p.R110H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G329A	12						.						136.0	122.0	127.0					12																	94976064		2203	4300	6503	93500195	SO:0001583	missense	57458	exon2			AB032971	CCDS31877.1, CCDS73506.1	12q22	2005-01-21	2005-07-13			ENSG00000057704		"""Transmembrane and coiled-coil domain containing"""	29199	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 3"""			10574461	Standard	XM_005269039		Approved	KIAA1145	uc001tdj.2	Q9ULS5	OTTHUMG00000170225	ENST00000261226.4:c.329G>A	12.37:g.94976064C>T	ENSP00000261226:p.Arg110His	Somatic		Capture	Illumina HiSeq	Phase_I	93500195	NM_020698	Q8IWB2	Missense_Mutation	SNP	ENST00000261226.4	37	CCDS31877.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114813	0.94339	.	.	ENSG00000057704	ENST00000261226;ENST00000551457;ENST00000548918	T;T;T	0.54866	0.55;0.55;0.55	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.72260	0.3438	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	T	0.69446	-0.5143	10	0.45353	T	0.12	-26.4066	20.2825	0.98528	0.0:1.0:0.0:0.0	.	110	Q9ULS5	TMCC3_HUMAN	H	110;79;79	ENSP00000261226:R110H;ENSP00000449888:R79H;ENSP00000450078:R79H	ENSP00000261226:R110H	R	-	2	0	TMCC3	93500195	1.000000	0.71417	0.285000	0.24819	0.945000	0.59286	7.634000	0.83273	2.873000	0.98535	0.561000	0.74099	CGT		0.463	TMCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408113.1	NM_020698	
FGD6	55785	broad.mit.edu	37	12	95604775	95604775	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:95604775A>G	ENST00000343958.4	-	2	508	c.285T>C	c.(283-285)tgT>tgC	p.C95C	FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Silent_p.C95C|FGD6_ENST00000546711.1_Silent_p.C95C	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	95					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.C95C(1)		breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						CTTCATATTTACAATTAAAGT	0.408																																					p.C95C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T285C	12						.						190.0	203.0	199.0					12																	95604775		2203	4300	6503	94128906	SO:0001819	synonymous_variant	55785	exon2			AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.285T>C	12.37:g.95604775A>G		Somatic		Capture	Illumina HiSeq	Phase_I	94128906	NM_018351	Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Silent	SNP	ENST00000343958.4	37	CCDS31878.1																																																																																				0.408	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351	
NR1H4	9971	broad.mit.edu	37	12	100904617	100904617	+	Silent	SNP	G	G	A	rs148156024		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:100904617G>A	ENST00000551379.1	+	2	199	c.171G>A	c.(169-171)tcG>tcA	p.S57S	NR1H4_ENST00000188403.7_Silent_p.S57S|NR1H4_ENST00000392986.3_Silent_p.S47S|NR1H4_ENST00000549996.1_Silent_p.S47S|NR1H4_ENST00000548884.1_Silent_p.S47S			Q96RI1	NR1H4_HUMAN	nuclear receptor subfamily 1, group H, member 4	57					bile acid metabolic process (GO:0008206)|cellular response to acid chemical (GO:0071229)|cellular response to organonitrogen compound (GO:0071417)|digestive tract development (GO:0048565)|gene expression (GO:0010467)|intracellular bile acid receptor signaling pathway (GO:0038185)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitrogen catabolite activation of transcription from RNA polymerase II promoter (GO:0001080)|positive regulation of ammonia assimilation cycle (GO:2001250)|positive regulation of glutamate metabolic process (GO:2000213)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of carbohydrate metabolic process (GO:0006109)|regulation of cholesterol metabolic process (GO:0090181)|regulation of urea metabolic process (GO:0034255)|response to glucose (GO:0009749)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)	bile acid binding (GO:0032052)|bile acid receptor activity (GO:0038181)|chenodeoxycholic acid binding (GO:1902122)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|ligand-dependent nuclear receptor binding (GO:0016922)|peptide binding (GO:0042277)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.S47S(1)		NS(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(23)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	44					Chenodeoxycholic acid(DB06777)	AACCATACTCGCAATACAGCA	0.458																																					p.S47S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G141A	12						.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	84.0	75.0	78.0		141,141,141,171,171,141	-9.2	0.0	12	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NR1H4	NM_001206977.1,NM_001206978.1,NM_001206979.1,NM_001206992.1,NM_001206993.1,NM_005123.3	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	47/477,47/426,47/477,57/483,57/487,47/473	100904617	1,13005	2203	4300	6503	99428748	SO:0001819	synonymous_variant	9971	exon4			U68233	CCDS9078.1, CCDS55873.1, CCDS55874.1, CCDS55875.1, CCDS55876.1	12q23.1	2013-01-16				ENSG00000012504		"""Nuclear hormone receptors"""	7967	protein-coding gene	gene with protein product		603826				7774010, 9223286	Standard	NM_001206977		Approved	FXR, RIP14, HRR1, HRR-1	uc001tht.2	Q96RI1	OTTHUMG00000170359	ENST00000551379.1:c.171G>A	12.37:g.100904617G>A		Somatic		Capture	Illumina HiSeq	Phase_I	99428748	NM_005123	A1L4K5|B7Z412|B7ZM06|F8VYG8|Q8NFP5|Q8NFP6|Q92943	Silent	SNP	ENST00000551379.1	37	CCDS55876.1																																																																																				0.458	NR1H4-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409140.1	NM_005123	
MYO1H	283446	broad.mit.edu	37	12	109858795	109858795	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:109858795delA	ENST00000431443.2	+	15	1589	c.1589delA	c.(1588-1590)gaafs	p.E530fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.E520fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	530	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.N522fs*9(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(17)|prostate(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	47						GGATTCTTGGAAAAAAACAAT	0.303																																					p.E520fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1559delA	12						.						66.0	64.0	64.0					12																	109858795		1793	4065	5858	108343178	SO:0001589	frameshift_variant	283446	exon15				CCDS53826.1	12q24.11	2011-09-27			ENSG00000174527	ENSG00000174527		"""Myosins / Myosin superfamily : Class I"""	13879	protein-coding gene	gene with protein product		614636					Standard	NM_001101421		Approved	FLJ37587	uc010sxn.1	Q8N1T3	OTTHUMG00000169252	ENST00000431443.2:c.1589delA	12.37:g.109858795delA	ENSP00000444076:p.Glu530fs	Somatic		Capture	Illumina HiSeq	Phase_I	108343178	NM_001101421	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	37																																																																																					0.303	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597	
GIT2	9815	broad.mit.edu	37	12	110429529	110429529	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:110429529delA	ENST00000355312.3	-	2	88	c.89delT	c.(88-90)ttafs	p.L30fs	GIT2_ENST00000551209.1_Frame_Shift_Del_p.L30fs|GIT2_ENST00000360185.4_Frame_Shift_Del_p.L30fs|GIT2_ENST00000553118.1_Frame_Shift_Del_p.L30fs|GIT2_ENST00000338373.5_Frame_Shift_Del_p.L30fs|GIT2_ENST00000356259.4_Frame_Shift_Del_p.L30fs|GIT2_ENST00000547815.1_Frame_Shift_Del_p.L30fs|GIT2_ENST00000457474.2_Frame_Shift_Del_p.L30fs|GIT2_ENST00000320063.9_Frame_Shift_Del_p.L30fs|GIT2_ENST00000361006.5_Frame_Shift_Del_p.L30fs|GIT2_ENST00000343646.5_Frame_Shift_Del_p.L30fs|GIT2_ENST00000354574.4_Frame_Shift_Del_p.L30fs	NM_057169.3	NP_476510.1	Q14161	GIT2_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 2	30	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				behavioral response to pain (GO:0048266)|regulation of ARF GTPase activity (GO:0032312)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.L30fs*12(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(8)|skin(4)	27						CTCATCACATAAAAACGTTCC	0.512																																					p.L30fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.89delT	12						.						117.0	101.0	106.0					12																	110429529		2203	4300	6503	108913912	SO:0001589	frameshift_variant	9815	exon2			AF124491	CCDS9138.1, CCDS9139.1, CCDS44968.1, CCDS44969.1, CCDS55884.1	12q24.1	2013-01-10	2008-09-05			ENSG00000139436		"""ADP-ribosylation factor GTPase activating proteins"", ""Ankyrin repeat domain containing"""	4273	protein-coding gene	gene with protein product		608564	"""G protein-coupled receptor kinase interactor 2"""			9826657, 10896954	Standard	NM_139201		Approved	KIAA0148	uc001tps.2	Q14161	OTTHUMG00000169313	ENST00000355312.3:c.89delT	12.37:g.110429529delA	ENSP00000347464:p.Leu30fs	Somatic		Capture	Illumina HiSeq	Phase_I	108913912	NM_001135214	Q86U59|Q96CI2|Q9BV91|Q9Y5V2	Frame_Shift_Del	DEL	ENST00000355312.3	37	CCDS9138.1																																																																																				0.512	GIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403407.1	NM_057169	
GOLGA3	2802	broad.mit.edu	37	12	133384809	133384809	+	Silent	SNP	G	G	A	rs7299219	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr12:133384809G>A	ENST00000450791.2	-	4	1029	c.846C>T	c.(844-846)tcC>tcT	p.S282S	GOLGA3_ENST00000545875.1_Silent_p.S282S|GOLGA3_ENST00000456883.2_Silent_p.S282S|GOLGA3_ENST00000204726.3_Silent_p.S282S|GOLGA3_ENST00000537452.1_Silent_p.S282S			Q08378	GOGA3_HUMAN	golgin A3	282					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)	p.S282S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CAGACACAACGGACGCCGCAC	0.567													G|||	12	0.00239617	0.0091	0.0	5008	,	,		13037	0.0		0.0	False		,,,				2504	0.0				p.S282S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C846T	12						.	G	,	51,4355	52.3+/-87.9	0,51,2152	122.0	126.0	125.0		846,846	-10.6	0.0	12	dbSNP_116	125	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GOLGA3	NM_001172557.1,NM_005895.3	,	0,51,6452	AA,AG,GG		0.0,1.1575,0.3921	,	282/1135,282/1499	133384809	51,12955	2203	4300	6503	131894882	SO:0001819	synonymous_variant	2802	exon5			AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.846C>T	12.37:g.133384809G>A		Somatic		Capture	Illumina HiSeq	Phase_I	131894882	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																				0.567	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
ERCC5	2073	broad.mit.edu	37	13	103528097	103528097	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:103528097A>G	ENST00000355739.4	+	15	4828	c.3405A>G	c.(3403-3405)gaA>gaG	p.E1135E	ERCC5_ENST00000375954.1_Silent_p.E368E|ERCC5_ENST00000472247.1_3'UTR	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	1135					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)	p.E1135E(1)		breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CAGTGAAGGAAGCTCCCGTGA	0.483			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E1135E		yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3405G	13						.						48.0	48.0	48.0					13																	103528097		2203	4300	6503	102326098	SO:0001819	synonymous_variant	2073	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.3405A>G	13.37:g.103528097A>G		Somatic		Capture	Illumina HiSeq	Phase_I	102326098	NM_000123	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																				0.483	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
MCF2L	23263	broad.mit.edu	37	13	113724384	113724384	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:113724384A>G	ENST00000375608.3	+	10	1041	c.983A>G	c.(982-984)cAg>cGg	p.Q328R	MCF2L_ENST00000375597.4_Missense_Mutation_p.Q296R|MCF2L_ENST00000375604.2_Missense_Mutation_p.Q355R|MCF2L_ENST00000442652.2_Missense_Mutation_p.Q328R|MCF2L_ENST00000535094.2_Missense_Mutation_p.Q298R|MCF2L_ENST00000375601.3_Missense_Mutation_p.Q302R|MCF2L_ENST00000423482.2_Missense_Mutation_p.Q296R|MCF2L_ENST00000434480.2_Missense_Mutation_p.Q304R|MCF2L_ENST00000421756.1_Missense_Mutation_p.Q302R|MCF2L_ENST00000397030.1_Missense_Mutation_p.Q331R			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	328					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.Q302R(1)|p.Q296R(1)		kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CTCCTGGCCCAGCTGAACGAA	0.622																																					p.Q302R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A905G	13						.						125.0	99.0	108.0					13																	113724384		2203	4300	6503	112772385	SO:0001583	missense	23263	exon9			AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.983A>G	13.37:g.113724384A>G	ENSP00000364758:p.Gln328Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112772385	NM_024979	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	A	32	5.121318	0.94385	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	T;T;T;T;T;T;T;T;T;T	0.53640	0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	M	0.90870	3.155	0.51482	D	0.999924	D;D;D;D;P;D	0.59767	0.986;0.986;0.986;0.975;0.913;0.975	P;P;P;P;P;P	0.61201	0.885;0.885;0.885;0.77;0.823;0.77	T	0.80491	-0.1359	10	0.87932	D	0	.	15.7443	0.77926	1.0:0.0:0.0:0.0	.	296;298;355;260;296;328	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	R	328;328;355;331;298;302;302;304;296;296;139	ENSP00000364758:Q328R;ENSP00000401422:Q328R;ENSP00000364754:Q355R;ENSP00000380225:Q331R;ENSP00000440374:Q298R;ENSP00000397285:Q302R;ENSP00000364751:Q302R;ENSP00000407722:Q304R;ENSP00000405639:Q296R;ENSP00000364747:Q296R	ENSP00000364747:Q296R	Q	+	2	0	MCF2L	112772385	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	8.684000	0.91242	2.118000	0.64928	0.533000	0.62120	CAG		0.622	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
TPTE2	93492	broad.mit.edu	37	13	20024243	20024243	+	Missense_Mutation	SNP	C	C	T	rs374764694		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:20024243C>T	ENST00000400230.2	-	13	990	c.946G>A	c.(946-948)Gta>Ata	p.V316I	TPTE2_ENST00000255310.6_Missense_Mutation_p.V239I|TPTE2_ENST00000457266.2_Missense_Mutation_p.V205I|TPTE2_ENST00000382977.4_Missense_Mutation_p.V316I|TPTE2_ENST00000382978.1_Missense_Mutation_p.V276I|TPTE2_ENST00000400103.2_Missense_Mutation_p.V205I|TPTE2_ENST00000390680.2_Missense_Mutation_p.V239I|TPTE2_ENST00000382975.4_Missense_Mutation_p.V276I			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	316	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.V239I(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		TGAATCGCTACGATGTTTTCA	0.313																																					p.V205I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G613A	13						.	C	ILE/VAL,ILE/VAL,ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	45.0	48.0	47.0		613,715,946	-0.1	0.0	13		47	0,8584		0,0,4292	no	missense,missense,missense	TPTE2	NM_001141968.1,NM_130785.3,NM_199254.2	29,29,29	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign	205/412,239/446,316/523	20024243	1,12989	2203	4292	6495	18922243	SO:0001583	missense	93492	exon12			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.946G>A	13.37:g.20024243C>T	ENSP00000383089:p.Val316Ile	Somatic		Capture	Illumina HiSeq	Phase_I	18922243	NM_001141968	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Missense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	c	0.171	-1.071190	0.01918	2.27E-4	0.0	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266;ENST00000343548;ENST00000419256	D;D;D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	2.68	-0.0981	0.13630	Phosphatase tensin type (1);Dual specificity phosphatase, catalytic domain (1);	0.112361	0.56097	N	0.000027	T	0.72301	0.3443	N	0.11651	0.15	0.09310	N	1	B;B;B	0.20164	0.001;0.042;0.018	B;B;B	0.19391	0.009;0.012;0.025	T	0.58059	-0.7703	9	.	.	.	-10.4341	6.0803	0.19938	0.0:0.4655:0.0:0.5345	.	205;239;316	A8MX64;Q6XPS3-3;Q6XPS3	.;.;TPTE2_HUMAN	I	276;205;316;239;239;316;276;205;316;185	ENSP00000372438:V276I;ENSP00000382974:V205I;ENSP00000383089:V316I;ENSP00000255310:V239I;ENSP00000375098:V239I;ENSP00000372437:V316I;ENSP00000372435:V276I;ENSP00000442218:V205I	.	V	-	1	0	TPTE2	18922243	0.058000	0.20735	0.000000	0.03702	0.001000	0.01503	0.072000	0.14617	-0.062000	0.13088	-0.300000	0.09419	GTA		0.313	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_199254	
ZDHHC20	253832	broad.mit.edu	37	13	21987888	21987888	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:21987888C>A	ENST00000400590.3	-	4	471	c.273G>T	c.(271-273)aaG>aaT	p.K91N	ZDHHC20_ENST00000542645.1_Missense_Mutation_p.K28N|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.K91N|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.K91N|ZDHHC20_ENST00000422251.1_Missense_Mutation_p.K91N|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.K91N			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	91					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.K91N(1)		central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		CATAACGTTCCTTTTCAGAAT	0.308																																					p.K91N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G273T	13						.						97.0	81.0	86.0					13																	21987888		1794	4061	5855	20885888	SO:0001583	missense	253832	exon4			AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.273G>T	13.37:g.21987888C>A	ENSP00000383433:p.Lys91Asn	Somatic		Capture	Illumina HiSeq	Phase_I	20885888	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	C	17.07	3.295178	0.60086	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724;ENST00000422251	T;T;T;T;T	0.54675	0.79;0.82;0.78;0.56;0.79	5.59	2.89	0.33648	.	0.082390	0.85682	D	0.000000	T	0.53562	0.1804	M	0.65975	2.015	0.58432	D	0.999991	B;P	0.35527	0.009;0.507	B;B	0.43386	0.099;0.418	T	0.53585	-0.8418	10	0.40728	T	0.16	-6.6982	8.4459	0.32841	0.0:0.7092:0.0:0.2908	.	28;91	B4DRN8;Q5W0Z9-3	.;.	N	91;91;91;28;91;91	ENSP00000383433:K91N;ENSP00000313583:K91N;ENSP00000371905:K91N;ENSP00000443236:K28N;ENSP00000401232:K91N	ENSP00000313583:K91N	K	-	3	2	ZDHHC20	20885888	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.804000	0.27098	1.373000	0.46208	0.491000	0.48974	AAG		0.308	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
SACS	26278	broad.mit.edu	37	13	23905530	23905530	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:23905530G>A	ENST00000382292.3	-	9	12758	c.12485C>T	c.(12484-12486)gCt>gTt	p.A4162V	SACS_ENST00000382298.3_Missense_Mutation_p.A4162V|SACS_ENST00000402364.1_Missense_Mutation_p.A3412V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4162					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.A4015V(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		ATGAATTTCAGCAGGAATTGG	0.418																																					p.A4162V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12485T	13						.						145.0	146.0	145.0					13																	23905530		2203	4300	6503	22803530	SO:0001583	missense	26278	exon10			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.12485C>T	13.37:g.23905530G>A	ENSP00000371729:p.Ala4162Val	Somatic		Capture	Illumina HiSeq	Phase_I	22803530	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	11.38	1.620255	0.28801	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87729	-2.14;-2.29;-2.14	5.0	4.12	0.48240	.	0.048610	0.85682	D	0.000000	T	0.79015	0.4375	L	0.29908	0.895	0.42100	D	0.991339	B	0.19200	0.034	B	0.17979	0.02	T	0.71573	-0.4552	10	0.10902	T	0.67	.	14.7512	0.69528	0.0:0.0:0.8542:0.1458	.	4162	Q9NZJ4	SACS_HUMAN	V	4162;3412;4162	ENSP00000371729:A4162V;ENSP00000385844:A3412V;ENSP00000371735:A4162V	ENSP00000371729:A4162V	A	-	2	0	SACS	22803530	1.000000	0.71417	0.846000	0.33378	0.078000	0.17371	4.781000	0.62389	1.151000	0.42436	0.650000	0.86243	GCT		0.418	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SACS	26278	broad.mit.edu	37	13	23929928	23929928	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:23929928G>T	ENST00000382292.3	-	7	1096	c.823C>A	c.(823-825)Ctt>Att	p.L275I	SACS_ENST00000382298.3_Missense_Mutation_p.L275I|SACS_ENST00000476776.1_5'Flank|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	275					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)	p.L128I(1)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TGTAGGCGAAGAGGGAAACGG	0.413																																					p.L275I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C823A	13						.						111.0	106.0	107.0					13																	23929928		2203	4300	6503	22827928	SO:0001583	missense	26278	exon8			AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.823C>A	13.37:g.23929928G>T	ENSP00000371729:p.Leu275Ile	Somatic		Capture	Illumina HiSeq	Phase_I	22827928	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.4|28.4	4.918857|4.918857	0.92249|0.92249	.|.	.|.	ENSG00000151835|ENSG00000151835	ENST00000382292;ENST00000382298|ENST00000455470	D;D|.	0.94000|.	-3.33;-3.33|.	5.64|5.64	5.64|5.64	0.86602|0.86602	ATPase-like, ATP-binding domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.82953|0.82953	0.5149|0.5149	M|M	0.84326|0.84326	2.69|2.69	0.54753|0.54753	D|D	0.999985|0.999985	D;D;D|.	0.89917|.	0.997;0.999;1.0|.	D;D;D|.	0.91635|.	0.955;0.99;0.999|.	T|T	0.83180|0.83180	-0.0089|-0.0089	10|5	0.66056|.	D|.	0.02|.	.|.	20.0769|20.0769	0.97748|0.97748	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	174;62;275|.	B2REB1;E9PAL4;Q9NZJ4|.	.;.;SACS_HUMAN|.	I|Y	275|174	ENSP00000371729:L275I;ENSP00000371735:L275I|.	ENSP00000371729:L275I|.	L|S	-|-	1|2	0|0	SACS|SACS	22827928|22827928	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.912000|0.912000	0.54170|0.54170	9.813000|9.813000	0.99286|0.99286	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CTT|TCT		0.413	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
SPATA13	221178	broad.mit.edu	37	13	24868997	24868997	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:24868997G>T	ENST00000382095.4	+	9	1733	c.1326G>T	c.(1324-1326)gtG>gtT	p.V442V	SPATA13_ENST00000382108.3_Silent_p.V1067V|RP11-307N16.6_ENST00000382141.4_Silent_p.V945V|SPATA13_ENST00000399949.2_Silent_p.V364V|SPATA13_ENST00000409126.1_Silent_p.V302V|SPATA13_ENST00000424834.2_Silent_p.V1067V|SPATA13_ENST00000343003.6_Silent_p.V386V	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13	442					cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.V442V(1)		breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		TGTCTATCGTGGGCTGGGAGG	0.542																																					p.V1067V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3201T	13						.						94.0	79.0	84.0					13																	24868997		2203	4300	6503	23766997	SO:0001819	synonymous_variant	221178	exon10			AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.1326G>T	13.37:g.24868997G>T		Somatic		Capture	Illumina HiSeq	Phase_I	23766997	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Silent	SNP	ENST00000382095.4	37	CCDS9305.1	.	.	.	.	.	.	.	.	.	.	G	10.80	1.453620	0.26161	.	.	ENSG00000182957	ENST00000424834	.	.	.	5.64	-0.524	0.11920	.	.	.	.	.	T	0.52645	0.1747	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39313	-0.9620	4	.	.	.	.	6.8204	0.23855	0.5456:0.0:0.3329:0.1215	.	.	.	.	W	1105	.	.	G	+	1	0	SPATA13	23766997	0.185000	0.23213	0.979000	0.43373	0.995000	0.86356	-0.455000	0.06762	-0.483000	0.06772	0.561000	0.74099	GGG		0.542	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
ATP12A	479	broad.mit.edu	37	13	25283890	25283890	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:25283890G>A	ENST00000381946.3	+	19	2854	c.2687G>A	c.(2686-2688)cGc>cAc	p.R896H	ATP12A_ENST00000218548.6_Missense_Mutation_p.R902H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	896					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)	p.R896H(1)		breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTTCTGCCCCGCACTCTCATT	0.527																																					p.R902H	Pancreas(156;1582 1935 18898 22665 26498)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2705A	13						.						136.0	134.0	134.0					13																	25283890		2203	4300	6503	24181890	SO:0001583	missense	479	exon19			L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.2687G>A	13.37:g.25283890G>A	ENSP00000371372:p.Arg896His	Somatic		Capture	Illumina HiSeq	Phase_I	24181890	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	.	.	.	.	.	.	.	.	.	.	G	1.603	-0.526076	0.04141	.	.	ENSG00000075673	ENST00000218548;ENST00000381946	D;D	0.88741	-2.42;-2.42	6.03	-3.41	0.04839	ATPase, P-type cation-transporter, C-terminal (1);ATPase, P-type,  transmembrane domain (1);	1.216330	0.05322	N	0.526781	T	0.71031	0.3292	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.59899	-0.7367	10	0.15066	T	0.55	.	9.6025	0.39612	0.3765:0.4958:0.1277:0.0	.	902;896	P54707-2;P54707	.;AT12A_HUMAN	H	902;896	ENSP00000218548:R902H;ENSP00000371372:R896H	ENSP00000218548:R902H	R	+	2	0	ATP12A	24181890	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.215000	0.17562	-0.305000	0.08831	-0.885000	0.02943	CGC		0.527	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
RNF17	56163	broad.mit.edu	37	13	25439048	25439048	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:25439048A>G	ENST00000255324.5	+	29	4065	c.4013A>G	c.(4012-4014)cAc>cGc	p.H1338R	RNF17_ENST00000381921.1_Intron|RNF17_ENST00000339524.3_Intron	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	1338					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.H1338R(1)		NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		TTGTCTATTCACCTCTATTTT	0.299																																					p.H1334R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4001G	13						.						93.0	96.0	95.0					13																	25439048		2201	4288	6489	24337048	SO:0001583	missense	56163	exon29			AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.4013A>G	13.37:g.25439048A>G	ENSP00000255324:p.His1338Arg	Somatic		Capture	Illumina HiSeq	Phase_I	24337048	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Missense_Mutation	SNP	ENST00000255324.5	37	CCDS9308.2	.	.	.	.	.	.	.	.	.	.	A	9.852	1.193894	0.22037	.	.	ENSG00000132972	ENST00000255324;ENST00000418120	T;T	0.11277	3.56;2.79	5.04	3.83	0.44106	.	0.100234	0.44097	D	0.000500	T	0.09774	0.0240	L	0.54323	1.7	0.80722	D	1	B;B;B	0.32302	0.309;0.16;0.363	B;B;B	0.28232	0.058;0.087;0.054	T	0.17107	-1.0380	10	0.20046	T	0.44	-7.077	8.8196	0.35018	0.8169:0.0:0.0:0.1831	.	1334;1332;1338	B7Z7S1;Q9BXT8-5;Q9BXT8	.;.;RNF17_HUMAN	R	1338;662	ENSP00000255324:H1338R;ENSP00000388892:H662R	ENSP00000255324:H1338R	H	+	2	0	RNF17	24337048	1.000000	0.71417	0.995000	0.50966	0.569000	0.35902	1.349000	0.33998	0.826000	0.34661	0.459000	0.35465	CAC		0.299	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
HSPH1	10808	broad.mit.edu	37	13	31732974	31732974	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:31732974delT	ENST00000320027.5	-	2	478	c.134delA	c.(133-135)aatfs	p.N45fs	HSPH1_ENST00000380406.5_Frame_Shift_Del_p.N45fs|HSPH1_ENST00000445273.2_Frame_Shift_Del_p.N47fs|HSPH1_ENST00000429785.2_5'UTR|HSPH1_ENST00000380405.4_Frame_Shift_Del_p.N45fs	NM_006644.2	NP_006635.2	Q92598	HS105_HUMAN	heat shock 105kDa/110kDa protein 1	45					chaperone mediated protein folding requiring cofactor (GO:0051085)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of NK T cell activation (GO:0051135)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)	p.N45fs*43(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27		Lung SC(185;0.0257)		all cancers(112;0.00385)|Epithelial(112;0.0328)|OV - Ovarian serous cystadenocarcinoma(117;0.0375)|GBM - Glioblastoma multiforme(144;0.125)		GATTGTTCTATTTTTTGATCC	0.294																																					p.N45fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.134delA	13						.						62.0	62.0	62.0					13																	31732974		2202	4298	6500	30630974	SO:0001589	frameshift_variant	10808	exon2			AB003333	CCDS9340.1, CCDS66525.1, CCDS73559.1	13q12.2-q13.3	2011-09-02			ENSG00000120694	ENSG00000120694		"""Heat shock proteins / HSP70"""	16969	protein-coding gene	gene with protein product		610703				9610721, 9931472	Standard	XM_005266236		Approved	HSP105B, KIAA0201, HSP105A, NY-CO-25	uc001utj.3	Q92598	OTTHUMG00000016685	ENST00000320027.5:c.134delA	13.37:g.31732974delT	ENSP00000318687:p.Asn45fs	Somatic		Capture	Illumina HiSeq	Phase_I	30630974	NM_006644	B4DYH1|O95739|Q5TBM6|Q5TBM7|Q5TBM8|Q9UPC4	Frame_Shift_Del	DEL	ENST00000320027.5	37	CCDS9340.1																																																																																				0.294	HSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044384.1		
FRY	10129	broad.mit.edu	37	13	32805408	32805408	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:32805408T>A	ENST00000380250.3	+	41	5994	c.5498T>A	c.(5497-5499)gTt>gAt	p.V1833D		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1833						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.V1833D(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CTACGTCACGTTGTATCTGTA	0.373																																					p.V1833D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5498A	13						.						165.0	150.0	155.0					13																	32805408		1894	4102	5996	31703408	SO:0001583	missense	10129	exon41			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5498T>A	13.37:g.32805408T>A	ENSP00000369600:p.Val1833Asp	Somatic		Capture	Illumina HiSeq	Phase_I	31703408	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.684708	0.88639	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.33654	1.4	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.63977	0.2557	M	0.82517	2.595	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.69760	-0.5058	10	0.87932	D	0	.	16.0668	0.80887	0.0:0.0:0.0:1.0	.	1833	Q5TBA9	FRY_HUMAN	D	1833;670	ENSP00000369600:V1833D	ENSP00000369600:V1833D	V	+	2	0	FRY	31703408	1.000000	0.71417	0.869000	0.34112	0.980000	0.70556	7.694000	0.84235	2.191000	0.70037	0.477000	0.44152	GTT		0.373	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
FRY	10129	broad.mit.edu	37	13	32811688	32811688	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:32811688T>A	ENST00000380250.3	+	44	6479	c.5983T>A	c.(5983-5985)Tct>Act	p.S1995T		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1995						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.S1995T(1)		NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		CGACCGATCCTCTGACCCACC	0.557																																					p.S1995T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5983A	13						.						74.0	79.0	78.0					13																	32811688		2041	4196	6237	31709688	SO:0001583	missense	10129	exon44			AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.5983T>A	13.37:g.32811688T>A	ENSP00000369600:p.Ser1995Thr	Somatic		Capture	Illumina HiSeq	Phase_I	31709688	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.823948	0.50739	.	.	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.24151	1.87	6.17	5.0	0.66597	.	0.061993	0.64402	N	0.000002	T	0.21427	0.0516	L	0.38175	1.15	0.80722	D	1	B	0.32051	0.354	B	0.34301	0.179	T	0.03534	-1.1027	10	0.21540	T	0.41	.	12.3147	0.54948	0.0:0.0655:0.0:0.9345	.	1995	Q5TBA9	FRY_HUMAN	T	1995;832	ENSP00000369600:S1995T	ENSP00000369600:S1995T	S	+	1	0	FRY	31709688	1.000000	0.71417	0.930000	0.37139	0.991000	0.79684	4.261000	0.58841	1.155000	0.42497	0.533000	0.62120	TCT		0.557	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
N4BP2L1	90634	broad.mit.edu	37	13	32972538	32972538	+	IGR	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:32972538G>T	ENST00000380130.2	-	0	3046				BRCA2_ENST00000544455.1_Missense_Mutation_p.K3296N|BRCA2_ENST00000380152.3_Missense_Mutation_p.K3296N	NM_052818.2	NP_438169.2	Q5TBK1	N42L1_HUMAN	NEDD4 binding protein 2-like 1											large_intestine(1)|lung(2)|ovary(1)|skin(1)	5		Lung SC(185;0.0262)		all cancers(112;6.3e-06)|Epithelial(112;3.51e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00607)|BRCA - Breast invasive adenocarcinoma(63;0.0171)		CTGCACAGAAGGCATTTCAGC	0.413																																					p.K3296N												.	.	0			c.G9888T	13						.						131.0	131.0	131.0					13																	32972538		2203	4300	6503	31870538	SO:0001628	intergenic_variant	675	exon27			U50527	CCDS9345.2, CCDS41877.1	13q13.1	2008-11-05			ENSG00000139597	ENSG00000139597			25037	protein-coding gene	gene with protein product	"""hypothetical gene CG018"""					8812419	Standard	NM_052818		Approved	CG018	uc001uuc.3	Q5TBK1	OTTHUMG00000016697		13.37:g.32972538G>T		None		Capture	Illumina HiSeq	Phase_I	31870538	NM_000059	A4QN21|Q5TBK0	Missense_Mutation	SNP	ENST00000380130.2	37	CCDS9345.2	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759961	0.69763	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.01313	5.02;5.02	5.74	1.23	0.21249	.	0.000000	0.85682	D	0.000000	T	0.06371	0.0164	M	0.76328	2.33	0.45015	D	0.998038	D	0.89917	1.0	D	0.72075	0.976	T	0.03910	-1.0993	10	0.87932	D	0	.	10.4426	0.44474	0.4295:0.0:0.5705:0.0	.	3296	P51587	BRCA2_HUMAN	N	3296	ENSP00000369497:K3296N;ENSP00000439902:K3296N	ENSP00000369497:K3296N	K	+	3	2	BRCA2	31870538	0.994000	0.37717	0.998000	0.56505	0.995000	0.86356	0.166000	0.16583	0.254000	0.21573	0.591000	0.81541	AAG		0.413	N4BP2L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_052818	
DCLK1	9201	broad.mit.edu	37	13	36686022	36686022	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:36686022G>A	ENST00000360631.3	-	3	918	c.707C>T	c.(706-708)aCg>aTg	p.T236M	DCLK1_ENST00000255448.4_Missense_Mutation_p.T236M|DCLK1_ENST00000379892.4_Missense_Mutation_p.T236M			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	236	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.T236M(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		CCCATCCAACGTGTACAGGCG	0.478																																					p.T236M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C707T	13						.						107.0	92.0	97.0					13																	36686022		2203	4300	6503	35584022	SO:0001583	missense	9201	exon3			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.707C>T	13.37:g.36686022G>A	ENSP00000353846:p.Thr236Met	Somatic		Capture	Illumina HiSeq	Phase_I	35584022	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	21.9	4.215237	0.79352	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	D;D;D	0.95272	-3.66;-3.66;-3.66	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.97592	0.9211	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.97885	1.0294	10	0.87932	D	0	.	19.8703	0.96847	0.0:0.0:1.0:0.0	.	236	O15075-2	.	M	236	ENSP00000255448:T236M;ENSP00000353846:T236M;ENSP00000369222:T236M	ENSP00000255448:T236M	T	-	2	0	DCLK1	35584022	1.000000	0.71417	0.962000	0.40283	0.711000	0.40976	9.592000	0.98245	2.770000	0.95276	0.650000	0.86243	ACG		0.478	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
DCLK1	9201	broad.mit.edu	37	13	36686179	36686179	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:36686179G>A	ENST00000360631.3	-	3	761	c.550C>T	c.(550-552)Cgg>Tgg	p.R184W	DCLK1_ENST00000255448.4_Missense_Mutation_p.R184W|DCLK1_ENST00000379892.4_Missense_Mutation_p.R184W			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	184					axon extension (GO:0048675)|central nervous system development (GO:0007417)|central nervous system projection neuron axonogenesis (GO:0021952)|dendrite morphogenesis (GO:0048813)|endosomal transport (GO:0016197)|forebrain development (GO:0030900)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|response to virus (GO:0009615)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein activity (GO:0005057)	p.R184W(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(18)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(6)|urinary_tract(1)	64		Breast(139;0.0147)|Lung SC(185;0.0685)|Prostate(109;0.122)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.72e-06)|Epithelial(112;4.24e-05)|BRCA - Breast invasive adenocarcinoma(63;0.00159)|OV - Ovarian serous cystadenocarcinoma(117;0.0158)|GBM - Glioblastoma multiforme(144;0.0638)		AGCTTGGGCCGAATGAAATCC	0.537																																					p.R184W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C550T	13						.						153.0	144.0	147.0					13																	36686179		2203	4300	6503	35584179	SO:0001583	missense	9201	exon3			AB002367	CCDS9354.1, CCDS55895.1, CCDS73561.1	13q13.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000133083	ENSG00000133083			2700	protein-coding gene	gene with protein product		604742	"""doublecortin and CaM kinase-like 1"""	DCAMKL1		9747029, 10036192	Standard	NM_004734		Approved	KIAA0369, DCLK, DCDC3A	uc001uvf.3	O15075	OTTHUMG00000016729	ENST00000360631.3:c.550C>T	13.37:g.36686179G>A	ENSP00000353846:p.Arg184Trp	Somatic		Capture	Illumina HiSeq	Phase_I	35584179	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Missense_Mutation	SNP	ENST00000360631.3	37		.	.	.	.	.	.	.	.	.	.	G	25.8	4.675435	0.88445	.	.	ENSG00000133083	ENST00000255448;ENST00000360631;ENST00000539451;ENST00000379892	D;D;D	0.93953	-3.32;-3.32;-3.32	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.95928	0.8674	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	D	0.95971	0.8970	10	0.87932	D	0	.	15.5654	0.76287	0.0:0.0:0.8539:0.1461	.	184	O15075-2	.	W	184	ENSP00000255448:R184W;ENSP00000353846:R184W;ENSP00000369222:R184W	ENSP00000255448:R184W	R	-	1	2	DCLK1	35584179	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.563000	0.53784	2.770000	0.95276	0.650000	0.86243	CGG		0.537	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	
SPG20	23111	broad.mit.edu	37	13	36905624	36905624	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:36905624A>G	ENST00000451493.1	-	3	1137	c.920T>C	c.(919-921)gTg>gCg	p.V307A	SPG20_ENST00000495510.1_5'UTR|SPG20_ENST00000355182.4_Missense_Mutation_p.V307A|SPG20_ENST00000438666.2_Missense_Mutation_p.V307A|SPG20_ENST00000494062.2_Missense_Mutation_p.V307A	NM_001142295.1	NP_001135767.1	Q8N0X7	SPG20_HUMAN	spastic paraplegia 20 (Troyer syndrome)	307					abscission (GO:0009838)|adipose tissue development (GO:0060612)|cell death (GO:0008219)|cell division (GO:0051301)|lipid particle organization (GO:0034389)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of collateral sprouting in absence of injury (GO:0048698)|neuromuscular process (GO:0050905)|regulation of mitochondrial membrane potential (GO:0051881)	cytoplasm (GO:0005737)|lipid particle (GO:0005811)|midbody (GO:0030496)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ubiquitin protein ligase binding (GO:0031625)	p.V307A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	27		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;2.42e-08)|Epithelial(112;1.58e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00128)|BRCA - Breast invasive adenocarcinoma(63;0.0125)|GBM - Glioblastoma multiforme(144;0.026)		GACGACCCCCACAAAGCATCC	0.478																																					p.V307A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T920C	13						.						116.0	109.0	111.0					13																	36905624		2203	4300	6503	35803624	SO:0001583	missense	23111	exon3			AB011182	CCDS9356.1	13q13.1	2008-07-04	2007-04-23		ENSG00000133104	ENSG00000133104			18514	protein-coding gene	gene with protein product	"""spartin"""	607111				6022528, 12134148	Standard	NM_001142294		Approved	KIAA0610, TAHCCP1	uc001uvm.3	Q8N0X7	OTTHUMG00000016730	ENST00000451493.1:c.920T>C	13.37:g.36905624A>G	ENSP00000414147:p.Val307Ala	Somatic		Capture	Illumina HiSeq	Phase_I	35803624	NM_001142295	O60349|Q86Y67|Q9H1T2|Q9H1T3	Missense_Mutation	SNP	ENST00000451493.1	37	CCDS9356.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958187	0.92726	.	.	ENSG00000133104	ENST00000438666;ENST00000355182;ENST00000451493;ENST00000423217	D;D;D	0.94650	-3.48;-3.48;-3.48	5.67	5.67	0.87782	.	0.064282	0.64402	D	0.000009	D	0.96470	0.8848	M	0.64404	1.975	0.49915	D	0.999831	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.77004	0.938;0.989;0.938	D	0.96189	0.9136	10	0.44086	T	0.13	-18.7454	15.9024	0.79392	1.0:0.0:0.0:0.0	.	307;307;307	A8K6Q9;B3KMI3;Q8N0X7	.;.;SPG20_HUMAN	A	307	ENSP00000406061:V307A;ENSP00000347314:V307A;ENSP00000414147:V307A	ENSP00000347314:V307A	V	-	2	0	SPG20	35803624	1.000000	0.71417	0.925000	0.36789	0.939000	0.58152	8.705000	0.91357	2.157000	0.67596	0.482000	0.46254	GTG		0.478	SPG20-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044494.2		
CCNA1	8900	broad.mit.edu	37	13	37006802	37006802	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:37006802T>C	ENST00000255465.4	+	1	308	c.44T>C	c.(43-45)aTt>aCt	p.I15T	CCNA1_ENST00000449823.1_Intron|CCNA1_ENST00000463403.1_Intron|CCNA1_ENST00000440264.1_Intron|CCNA1_ENST00000418263.1_Missense_Mutation_p.I15T			P78396	CCNA1_HUMAN	cyclin A1	15					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)		p.I15T(1)		breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		GGATCTTTTATTGGGGGCTGG	0.592																																					p.I15T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T44C	13						.						48.0	48.0	48.0					13																	37006802		2203	4300	6503	35904802	SO:0001583	missense	8900	exon1			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.44T>C	13.37:g.37006802T>C	ENSP00000255465:p.Ile15Thr	Somatic		Capture	Illumina HiSeq	Phase_I	35904802	NM_003914	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Missense_Mutation	SNP	ENST00000255465.4	37	CCDS9357.1	.	.	.	.	.	.	.	.	.	.	T	7.420	0.636476	0.14386	.	.	ENSG00000133101	ENST00000418263;ENST00000255465	T;T	0.16457	2.34;2.34	3.11	-6.23	0.02052	.	.	.	.	.	T	0.06142	0.0159	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.72032	D	0.01	.	1.4527	0.02378	0.1481:0.3186:0.3012:0.2321	.	15;15	P78396-2;P78396	.;CCNA1_HUMAN	T	15	ENSP00000396479:I15T;ENSP00000255465:I15T	ENSP00000255465:I15T	I	+	2	0	CCNA1	35904802	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.765000	0.04730	-1.978000	0.00993	-0.361000	0.07541	ATT		0.592	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2	NM_003914	
FREM2	341640	broad.mit.edu	37	13	39450493	39450493	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:39450493T>C	ENST00000280481.7	+	20	8734	c.8518T>C	c.(8518-8520)Ttt>Ctt	p.F2840L		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2840					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F2840L(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACCTGTCACCTTTGACCTTGA	0.443																																					p.F2840L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T8518C	13						.						125.0	103.0	110.0					13																	39450493		2203	4300	6503	38348493	SO:0001583	missense	341640	exon20			BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8518T>C	13.37:g.39450493T>C	ENSP00000280481:p.Phe2840Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38348493	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	T	34	5.367165	0.95900	.	.	ENSG00000150893	ENST00000280481	T	0.65916	-0.18	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.82490	0.5048	M	0.88105	2.93	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.86099	0.1555	10	0.87932	D	0	.	15.9477	0.79806	0.0:0.0:0.0:1.0	.	2840	Q5SZK8	FREM2_HUMAN	L	2840	ENSP00000280481:F2840L	ENSP00000280481:F2840L	F	+	1	0	FREM2	38348493	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.967000	0.87967	2.179000	0.69175	0.460000	0.39030	TTT		0.443	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
DGKH	160851	broad.mit.edu	37	13	42783190	42783190	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:42783190G>A	ENST00000337343.4	+	22	2718	c.2697G>A	c.(2695-2697)caG>caA	p.Q899Q	DGKH_ENST00000261491.5_Silent_p.Q899Q|DGKH_ENST00000536612.1_Silent_p.Q763Q|DGKH_ENST00000379274.2_Silent_p.Q763Q|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000540693.1_Silent_p.Q899Q|DGKH_ENST00000538674.1_Silent_p.Q654Q	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	899					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.Q899Q(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TTAAACTGCAGCATCATCGAA	0.428																																					p.Q899Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2697A	13						.						98.0	81.0	87.0					13																	42783190		2203	4300	6503	41681190	SO:0001819	synonymous_variant	160851	exon22			AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.2697G>A	13.37:g.42783190G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41681190	NM_178009	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																				0.428	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
ZC3H13	23091	broad.mit.edu	37	13	46549942	46549942	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:46549942C>A	ENST00000242848.4	-	12	2292	c.1944G>T	c.(1942-1944)caG>caT	p.Q648H	ZC3H13_ENST00000282007.3_Missense_Mutation_p.Q648H			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	648	Arg/Ser-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q648H(1)		cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		CATTCCTTCCCTGATGTCGAA	0.423																																					p.Q648H	Esophageal Squamous(187;747 2077 11056 31291 44172)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1944T	13						.						200.0	140.0	160.0					13																	46549942		2203	4300	6503	45447943	SO:0001583	missense	23091	exon12			AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.1944G>T	13.37:g.46549942C>A	ENSP00000242848:p.Gln648His	Somatic		Capture	Illumina HiSeq	Phase_I	45447943	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	De_novo_Start_OutOfFrame	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	C	9.639	1.138461	0.21123	.	.	ENSG00000123200	ENST00000242848;ENST00000282007;ENST00000431251	T;T	0.34667	2.35;1.35	5.27	4.41	0.53225	.	0.000000	0.56097	D	0.000022	T	0.45617	0.1351	L	0.36672	1.1	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.81914	0.99;0.995	T	0.21793	-1.0235	10	0.40728	T	0.16	.	9.9361	0.41552	0.0:0.8399:0.0:0.1601	.	648;648	Q5T200;Q5T200-2	ZC3HD_HUMAN;.	H	648;648;464	ENSP00000242848:Q648H;ENSP00000282007:Q648H	ENSP00000242848:Q648H	Q	-	3	2	ZC3H13	45447943	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.616000	0.36933	2.607000	0.88179	0.557000	0.71058	CAG		0.423	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
LCP1	3936	broad.mit.edu	37	13	46701726	46701726	+	Nonstop_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:46701726T>G	ENST00000398576.2	-	19	2272	c.1884A>C	c.(1882-1884)tgA>tgC	p.*628C	LCP1_ENST00000435666.2_Nonstop_Mutation_p.*197C|LCP1_ENST00000323076.2_Nonstop_Mutation_p.*628C			P13796	PLSL_HUMAN	lymphocyte cytosolic protein 1 (L-plastin)	0					actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|organ regeneration (GO:0031100)|protein kinase A signaling (GO:0010737)|regulation of intracellular protein transport (GO:0033157)|T cell activation involved in immune response (GO:0002286)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|actin filament bundle (GO:0032432)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)	p.*628C(1)		breast(2)|kidney(1)|large_intestine(6)|lung(18)|ovary(4)|prostate(2)|skin(1)	34		Lung NSC(96;1.27e-05)|Breast(56;8.04e-05)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;5.39e-05)		CCATTGGGCCTCACACCCTCT	0.552			T	BCL6	NHL																																p.X628C			Dom	yes		13	13q14.1-q14.3	3936	lymphocyte cytosolic protein 1 (L-plastin)		L	.	.	1	Nonstop extension(1)	large_intestine(1)	c.A1884C	13						.						134.0	117.0	123.0					13																	46701726		2203	4300	6503	45599727	SO:0001578	stop_lost	3936	exon16			M22300	CCDS9403.1	13q14.3	2013-01-10			ENSG00000136167	ENSG00000136167		"""EF-hand domain containing"""	6528	protein-coding gene	gene with protein product	"""plastin 2"""	153430				2111166	Standard	NM_002298		Approved	PLS2, CP64, L-PLASTIN, LC64P	uc001vba.4	P13796	OTTHUMG00000016864	ENST00000398576.2:c.1884A>C	13.37:g.46701726T>G	ENSP00000381581:p.*628Trpext*14	Somatic		Capture	Illumina HiSeq	Phase_I	45599727	NM_002298	B2R613|B4DUA0|Q5TBN4	Nonstop_Mutation	SNP	ENST00000398576.2	37	CCDS9403.1	.	.	.	.	.	.	.	.	.	.	T	17.84	3.488139	0.64074	.	.	ENSG00000136167	ENST00000323076;ENST00000398576;ENST00000435666	.	.	.	5.39	4.22	0.49857	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2602	0.37608	0.0:0.0819:0.0:0.9181	.	.	.	.	C	628;628;197	.	.	X	-	3	0	LCP1	45599727	0.999000	0.42202	0.135000	0.22099	0.632000	0.37999	5.388000	0.66249	0.988000	0.38734	0.533000	0.62120	TGA		0.552	LCP1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044800.3	NM_002298	
ATP7B	540	broad.mit.edu	37	13	52516578	52516578	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:52516578G>T	ENST00000242839.4	-	15	3512	c.3356C>A	c.(3355-3357)cCt>cAt	p.P1119H	ATP7B_ENST00000417240.2_Missense_Mutation_p.P330H|ATP7B_ENST00000418097.2_Missense_Mutation_p.P1054H|ATP7B_ENST00000400366.3_Missense_Mutation_p.P1008H|ATP7B_ENST00000344297.5_Missense_Mutation_p.P912H|ATP7B_ENST00000400370.3_Missense_Mutation_p.P689H|ATP7B_ENST00000448424.2_Missense_Mutation_p.P1041H|ATP7B_ENST00000482841.1_5'UTR	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1119					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)	p.P1119H(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCACTCAAAGGGCGCTCACT	0.562									Wilson disease																												p.P1119H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3356A	13						.						81.0	85.0	83.0					13																	52516578		2039	4188	6227	51414579	SO:0001583	missense	540	exon15	Familial Cancer Database		U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.3356C>A	13.37:g.52516578G>T	ENSP00000242839:p.Pro1119His	Somatic		Capture	Illumina HiSeq	Phase_I	51414579	NM_000053	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	G	7.895	0.733062	0.15507	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.98060	-3.9;-3.89;-4.03;-4.69;-3.82;-4.31;-3.94	4.23	-3.68	0.04463	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	2.804860	0.01678	N	0.025976	D	0.92176	0.7519	N	0.08118	0	0.09310	N	1	P;B;B;B;B;B;B;B	0.42203	0.773;0.0;0.199;0.018;0.199;0.028;0.199;0.259	B;B;B;B;B;B;B;B	0.43274	0.414;0.0;0.079;0.272;0.079;0.093;0.079;0.385	D	0.88231	0.2903	10	0.44086	T	0.13	.	0.5185	0.00608	0.3445:0.1283:0.2765:0.2508	.	1041;1071;1054;330;689;1008;912;1119	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	H	1119;1008;912;330;1041;689;1054	ENSP00000242839:P1119H;ENSP00000383217:P1008H;ENSP00000342559:P912H;ENSP00000390360:P330H;ENSP00000416738:P1041H;ENSP00000383221:P689H;ENSP00000393343:P1054H	ENSP00000242839:P1119H	P	-	2	0	ATP7B	51414579	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.227000	0.02950	-1.106000	0.03008	0.491000	0.48974	CCT		0.562	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
PCDH17	27253	broad.mit.edu	37	13	58208642	58208642	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:58208642C>T	ENST00000377918.3	+	1	1988	c.1962C>T	c.(1960-1962)gaC>gaT	p.D654D		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	654	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D654D(1)		breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TCTGGGAGGACGTGACGCCCG	0.647																																					p.D654D	Melanoma(72;952 1291 1619 12849 33676)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1962T	13						.						101.0	99.0	100.0					13																	58208642		2203	4300	6503	57106643	SO:0001819	synonymous_variant	27253	exon1			AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1962C>T	13.37:g.58208642C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57106643	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																				0.647	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
PCDH20	64881	broad.mit.edu	37	13	61987430	61987430	+	Missense_Mutation	SNP	G	G	A	rs150237018	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:61987430G>A	ENST00000409186.1	-	5	2907	c.802C>T	c.(802-804)Cgc>Tgc	p.R268C	PCDH20_ENST00000409204.4_Missense_Mutation_p.R268C			Q8N6Y1	PCD20_HUMAN	protocadherin 20	268	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)	p.R241C(1)		breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(14)|liver(1)|lung(23)|ovary(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	58		Breast(118;0.195)|Prostate(109;0.229)		GBM - Glioblastoma multiforme(99;0.000118)		TAGGGGGTGCGCTCCCCATTC	0.517													G|||	6	0.00119808	0.0	0.0	5008	,	,		17718	0.0		0.0	False		,,,				2504	0.0061				p.R268C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C802T	13						.						96.0	83.0	87.0					13																	61987430		2203	4300	6503	60885431	SO:0001583	missense	64881	exon2			AF169693	CCDS9442.2	13q21	2010-01-26			ENSG00000197991	ENSG00000197991		"""Cadherins / Protocadherins : Non-clustered"""	14257	protein-coding gene	gene with protein product		614449					Standard	NM_022843		Approved	PCDH13, FLJ22218	uc001vid.4	Q8N6Y1	OTTHUMG00000017012	ENST00000409186.1:c.802C>T	13.37:g.61987430G>A	ENSP00000386653:p.Arg268Cys	Somatic		Capture	Illumina HiSeq	Phase_I	60885431	NM_022843	A8K1K9|B1AQU2|Q8NDN4|Q9NRT9	Missense_Mutation	SNP	ENST00000409186.1	37	CCDS9442.2	.	.	.	.	.	.	.	.	.	.	G	13.69	2.312482	0.40895	.	.	ENSG00000197991	ENST00000409204;ENST00000409186;ENST00000358674	T;T	0.68624	-0.34;-0.34	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000003	T	0.75982	0.3924	L	0.55481	1.735	0.51767	D	0.999937	D	0.89917	1.0	P	0.61658	0.892	T	0.77373	-0.2612	10	0.87932	D	0	.	14.5378	0.67973	0.0:0.0:0.734:0.266	.	268	A8K1K9	.	C	268;268;14	ENSP00000387250:R268C;ENSP00000386653:R268C	ENSP00000351500:R14C	R	-	1	0	PCDH20	60885431	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	2.682000	0.46934	2.813000	0.96785	0.655000	0.94253	CGC		0.517	PCDH20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333054.2	NM_022843	
KLF5	688	broad.mit.edu	37	13	73636718	73636718	+	Silent	SNP	C	C	A	rs144202002		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:73636718C>A	ENST00000377687.4	+	2	1517	c.981C>A	c.(979-981)tcC>tcA	p.S327S	KLF5_ENST00000477333.1_3'UTR|KLF5_ENST00000539231.1_Silent_p.S236S	NM_001730.3	NP_001721.2	Q13887	KLF5_HUMAN	Kruppel-like factor 5 (intestinal)	327	Interaction with WWP1.				angiogenesis (GO:0001525)|cellular response to organic cyclic compound (GO:0071407)|cellular response to peptide (GO:1901653)|intestinal epithelial cell development (GO:0060576)|microvillus assembly (GO:0030033)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of microvillus assembly (GO:0032534)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|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)			breast(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(6;0.00187)|Breast(118;0.0735)		GBM - Glioblastoma multiforme(99;0.0011)		CACCTCCATCCTATGCTGCTA	0.468																																					p.S327S												.	.	0			c.C981A	13						.						151.0	135.0	140.0					13																	73636718		2203	4300	6503	72534719	SO:0001819	synonymous_variant	688	exon2			D14520	CCDS9448.1, CCDS66562.1	13q21.3	2013-01-08			ENSG00000102554	ENSG00000102554		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6349	protein-coding gene	gene with protein product		602903		BTEB2		8479902, 9973612	Standard	NM_001730		Approved	IKLF, CKLF	uc001vje.3	Q13887	OTTHUMG00000017074	ENST00000377687.4:c.981C>A	13.37:g.73636718C>A		None		Capture	Illumina HiSeq	Phase_I	72534719	NM_001730	L0R3U5|L0R4T9|Q9UHP8	Silent	SNP	ENST00000377687.4	37	CCDS9448.1																																																																																				0.468	KLF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045263.1		
MYCBP2	23077	broad.mit.edu	37	13	77742582	77742582	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:77742582G>A	ENST00000544440.2	-	40	5998	c.5981C>T	c.(5980-5982)gCc>gTc	p.A1994V	MYCBP2_ENST00000357337.6_Missense_Mutation_p.A1994V|MYCBP2_ENST00000360084.5_5'UTR|MYCBP2_ENST00000407578.2_Missense_Mutation_p.A2032V					MYC binding protein 2, E3 ubiquitin protein ligase									p.A1994V(1)|p.A2032V(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(51)|ovary(5)|pancreas(2)|prostate(5)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	118		Breast(118;0.212)|Acute lymphoblastic leukemia(28;0.22)		GBM - Glioblastoma multiforme(99;0.109)		CATCACACAGGCAGGTTTATA	0.473																																					p.A2032V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C6095T	13						.						196.0	172.0	180.0					13																	77742582		2203	4300	6503	76640583	SO:0001583	missense	23077	exon40			AB020723		13q22	2012-02-23	2012-02-23		ENSG00000005810	ENSG00000005810			23386	protein-coding gene	gene with protein product		610392	"""MYC binding protein 2"""			9689053, 15057823	Standard	NM_015057		Approved	PAM, KIAA0916, FLJ10106	uc021rks.1	O75592	OTTHUMG00000017105	ENST00000544440.2:c.5981C>T	13.37:g.77742582G>A	ENSP00000444596:p.Ala1994Val	Somatic		Capture	Illumina HiSeq	Phase_I	76640583	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	G	33	5.276679	0.95459	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.38887	1.12;1.11;1.12	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.63153	0.2487	L	0.60455	1.87	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.63747	-0.6567	10	0.87932	D	0	.	19.8949	0.96954	0.0:0.0:1.0:0.0	.	1994	O75592	MYCB2_HUMAN	V	1994;2032;1994	ENSP00000349892:A1994V;ENSP00000384288:A2032V;ENSP00000444596:A1994V	ENSP00000349892:A1994V	A	-	2	0	MYCBP2	76640583	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.704000	0.92352	0.650000	0.86243	GCC		0.473	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057	
EDNRB	1910	broad.mit.edu	37	13	78492479	78492479	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:78492479G>A	ENST00000334286.5	-	1	466	c.230C>T	c.(229-231)aCg>aTg	p.T77M	EDNRB_ENST00000475537.1_5'UTR|RNF219-AS1_ENST00000607862.1_RNA|EDNRB_ENST00000377211.4_Missense_Mutation_p.T167M|EDNRB_ENST00000446573.1_Missense_Mutation_p.T77M	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	77					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)	p.T77M(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AGATCCTGCCGTCCTGTCTCC	0.582																																					p.T77M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C230T	13						.						105.0	104.0	104.0					13																	78492479		2203	4300	6503	77390480	SO:0001583	missense	1910	exon1			L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"""GPCR / Class A : Endothelin receptors"""	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.230C>T	13.37:g.78492479G>A	ENSP00000335311:p.Thr77Met	Somatic		Capture	Illumina HiSeq	Phase_I	77390480	NM_001122659	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Missense_Mutation	SNP	ENST00000334286.5	37	CCDS9461.1	.	.	.	.	.	.	.	.	.	.	G	10.93	1.489112	0.26686	.	.	ENSG00000136160	ENST00000377211;ENST00000446573;ENST00000334286	T;T;T	0.72282	-0.64;-0.46;-0.59	4.33	1.39	0.22231	.	1.833440	0.02504	N	0.090808	T	0.50292	0.1607	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.25772	0.134;0.119;0.003	B;B;B	0.20577	0.021;0.03;0.006	T	0.43426	-0.9392	10	0.46703	T	0.11	0.7521	5.878	0.18840	0.1824:0.1561:0.6614:0.0	.	77;167;77	P24530-2;P24530-3;P24530	.;.;EDNRB_HUMAN	M	167;77;77	ENSP00000366416:T167M;ENSP00000403401:T77M;ENSP00000335311:T77M	ENSP00000335311:T77M	T	-	2	0	EDNRB	77390480	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	0.123000	0.15708	0.119000	0.18210	0.591000	0.81541	ACG		0.582	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1		
SLITRK1	114798	broad.mit.edu	37	13	84455509	84455509	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:84455509delT	ENST00000377084.2	-	1	1019	c.134delA	c.(133-135)aagfs	p.K45fs		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	45	LRRNT 1.				adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.K45fs*64(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)		TGTGAAGCCCTTTTTTTCACA	0.463																																					p.K45fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.134delA	13						.						90.0	89.0	89.0					13																	84455509		2203	4300	6503	83353510	SO:0001589	frameshift_variant	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.134delA	13.37:g.84455509delT	ENSP00000366288:p.Lys45fs	Somatic		Capture	Illumina HiSeq	Phase_I	83353510	NM_052910	Q5U5I6|Q96SF9	Frame_Shift_Del	DEL	ENST00000377084.2	37	CCDS9464.1																																																																																				0.463	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
DZIP1	22873	broad.mit.edu	37	13	96237160	96237160	+	Missense_Mutation	SNP	G	G	A	rs138276983		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:96237160G>A	ENST00000376829.2	-	22	3205	c.2354C>T	c.(2353-2355)gCg>gTg	p.A785V	DZIP1_ENST00000361396.2_Missense_Mutation_p.A766V|DZIP1_ENST00000347108.3_Missense_Mutation_p.A785V|DZIP1_ENST00000361156.3_Missense_Mutation_p.A766V	NM_198968.3	NP_945319.1	Q86YF9	DZIP1_HUMAN	DAZ interacting zinc finger protein 1	785					cilium assembly (GO:0042384)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.A766V(1)		endometrium(1)|kidney(1)|large_intestine(20)|lung(11)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	38	all_neural(89;0.0878)|Breast(111;0.148)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.141)			CTCCACATCCGCACACTAAAA	0.403																																					p.A766V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2297T	13						.	G	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	65.0	62.0	63.0		2297,2354	4.5	0.8	13	dbSNP_134	63	0,8600		0,0,4300	no	missense,missense	DZIP1	NM_014934.3,NM_198968.2	64,64	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	766/849,785/868	96237160	1,13005	2203	4300	6503	95035161	SO:0001583	missense	22873	exon21			AB023213	CCDS9477.1, CCDS9478.1	13q32.1	2013-05-22	2013-05-22		ENSG00000134874	ENSG00000134874		"""Zinc fingers, C2H2-type"""	20908	protein-coding gene	gene with protein product		608671	"""DAZ interacting protein 1"""				Standard	NM_014934		Approved	KIAA0996, DZIP	uc001vmk.4	Q86YF9	OTTHUMG00000017224	ENST00000376829.2:c.2354C>T	13.37:g.96237160G>A	ENSP00000366025:p.Ala785Val	Somatic		Capture	Illumina HiSeq	Phase_I	95035161	NM_014934	Q5W078|Q5W079|Q8WY45|Q8WY46|Q9UGA5|Q9Y2K0	Missense_Mutation	SNP	ENST00000376829.2	37	CCDS9478.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.251683	0.22880	2.27E-4	0.0	ENSG00000134874	ENST00000347108;ENST00000361156;ENST00000361396;ENST00000376829	T;T;T;T	0.08807	3.05;3.05;3.05;3.05	5.38	4.54	0.55810	.	1.569350	0.03349	N	0.195883	T	0.10252	0.0251	L	0.41824	1.3	0.24437	N	0.994547	B;B	0.23591	0.083;0.088	B;B	0.14023	0.01;0.007	T	0.27434	-1.0074	10	0.48119	T	0.1	1.9469	8.0403	0.30517	0.0797:0.0:0.7626:0.1577	.	766;785	Q86YF9-2;Q86YF9	.;DZIP1_HUMAN	V	785;766;766;785	ENSP00000257312:A785V;ENSP00000355018:A766V;ENSP00000355175:A766V;ENSP00000366025:A785V	ENSP00000257312:A785V	A	-	2	0	DZIP1	95035161	0.933000	0.31639	0.751000	0.31187	0.154000	0.21943	1.768000	0.38511	1.280000	0.44463	0.448000	0.29417	GCG		0.403	DZIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045496.3	NM_014934	
RNF113B	140432	broad.mit.edu	37	13	98828976	98828976	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:98828976G>A	ENST00000267291.6	-	1	543	c.515C>T	c.(514-516)gCg>gTg	p.A172V	FARP1_ENST00000319562.6_Intron|FARP1_ENST00000376586.2_Intron|FARP1_ENST00000376581.5_Intron|FARP1_ENST00000595437.1_Intron	NM_178861.4	NP_849192.1	Q8IZP6	R113B_HUMAN	ring finger protein 113B	172							zinc ion binding (GO:0008270)	p.A172V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)			GCCCTTCCTCGCCATCCCCGA	0.622																																					p.A172V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C515T	13						.						80.0	68.0	72.0					13																	98828976		2203	4300	6503	97626977	SO:0001583	missense	140432	exon1			AF539427	CCDS9486.1	13q32.2	2006-08-22	2005-03-22	2005-03-22	ENSG00000139797	ENSG00000139797		"""RING-type (C3HC4) zinc fingers"""	17267	protein-coding gene	gene with protein product			"""zinc finger protein 183-like 1"""	ZNF183L1			Standard	NM_178861		Approved	RNF161	uc001vnk.3	Q8IZP6	OTTHUMG00000017245	ENST00000267291.6:c.515C>T	13.37:g.98828976G>A	ENSP00000267291:p.Ala172Val	None		Capture	Illumina HiSeq	Phase_I	97626977	NM_178861	Q8WWF9|Q96QY9	Missense_Mutation	SNP	ENST00000267291.6	37	CCDS9486.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.172681	0.00315	.	.	ENSG00000139797	ENST00000267291	T	0.27890	1.64	1.16	-0.143	0.13444	.	0.074349	0.53938	N	0.000060	T	0.04497	0.0123	N	0.00254	-1.765	0.22648	N	0.998891	B	0.09022	0.002	B	0.09377	0.004	T	0.36625	-0.9740	10	0.02654	T	1	.	3.0076	0.06033	0.6569:0.0:0.3431:0.0	.	172	Q8IZP6	R113B_HUMAN	V	172	ENSP00000267291:A172V	ENSP00000267291:A172V	A	-	2	0	RNF113B	97626977	1.000000	0.71417	0.976000	0.42696	0.243000	0.25628	2.097000	0.41748	-0.045000	0.13468	-0.350000	0.07774	GCG		0.622	RNF113B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045536.3	NM_178861	
FARP1	10160	broad.mit.edu	37	13	99061770	99061770	+	Silent	SNP	C	C	T	rs560567728		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:99061770C>T	ENST00000319562.6	+	14	1858	c.1593C>T	c.(1591-1593)ggC>ggT	p.G531G	FARP1_ENST00000376586.2_Silent_p.G531G|FARP1_ENST00000595437.1_Silent_p.G531G	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	531					dendrite morphogenesis (GO:0048813)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|synapse assembly (GO:0007416)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|synapse (GO:0045202)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.G531G(1)		breast(3)|endometrium(6)|kidney(6)|large_intestine(13)|lung(16)|ovary(1)|skin(3)|urinary_tract(1)	49	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.233)			AGGATGAGGGCCGGAGGAAGG	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		17362	0.001		0.0	False		,,,				2504	0.0				p.G531G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1593T	13						.						26.0	19.0	21.0					13																	99061770		2203	4299	6502	97859771	SO:0001819	synonymous_variant	10160	exon14			AB008430	CCDS9487.1, CCDS32000.1, CCDS66572.1	13q32.2	2013-01-10			ENSG00000152767	ENSG00000152767		"""Rho guanine nucleotide exchange factors"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Pleckstrin homology (PH) domain containing"""	3591	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 75"""	602654				9425278	Standard	NM_005766		Approved	CDEP, PLEKHC2, MGC87400, PPP1R75	uc001vnj.3	Q9Y4F1	OTTHUMG00000017248	ENST00000319562.6:c.1593C>T	13.37:g.99061770C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97859771	NM_005766	Q5JVI9|Q6IQ29	Silent	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	C	8.853	0.945057	0.18356	.	.	ENSG00000152767	ENST00000457029	.	.	.	5.57	4.7	0.59300	.	.	.	.	.	T	0.69762	0.3147	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68625	-0.5359	4	.	.	.	.	13.8629	0.63571	0.1528:0.8472:0.0:0.0	.	.	.	.	V	60	.	.	A	+	2	0	FARP1	97859771	1.000000	0.71417	0.985000	0.45067	0.716000	0.41182	1.007000	0.29860	1.279000	0.44446	0.655000	0.94253	GCC		0.557	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766	
ARHGEF7	8874	broad.mit.edu	37	13	111767934	111767934	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:111767934delA	ENST00000375741.2	+	1	311	c.61delA	c.(61-63)aaafs	p.K22fs	ARHGEF7_ENST00000317133.5_Frame_Shift_Del_p.K22fs|ARHGEF7-AS2_ENST00000425094.2_RNA|ARHGEF7_ENST00000370623.3_Frame_Shift_Del_p.K22fs|ARHGEF7_ENST00000375739.2_Frame_Shift_Del_p.K22fs	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	22	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T23fs*13(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GGAGTCGCCCAAAAAAACCAT	0.672																																					p.K21fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.61delA	13						.						25.0	25.0	25.0					13																	111767934		2201	4300	6501	110565935	SO:0001589	frameshift_variant	8874	exon1			D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.61delA	13.37:g.111767934delA	ENSP00000364893:p.Lys22fs	Somatic		Capture	Illumina HiSeq	Phase_I	110565935	NM_001113512	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Frame_Shift_Del	DEL	ENST00000375741.2	37	CCDS45068.1																																																																																				0.672	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
ATP4B	496	broad.mit.edu	37	13	114307230	114307230	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr13:114307230G>A	ENST00000335288.4	-	4	554	c.513C>T	c.(511-513)ggC>ggT	p.G171G		NM_000705.3	NP_000696.1	P51164	ATP4B_HUMAN	ATPase, H+/K+ exchanging, beta polypeptide	171					cell adhesion (GO:0007155)|hydrogen ion transmembrane transport (GO:1902600)|ion transmembrane transport (GO:0034220)|response to lipopolysaccharide (GO:0032496)|response to organonitrogen compound (GO:0010243)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	hydrogen:potassium-exchanging ATPase activity (GO:0008900)	p.G171G(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Lung NSC(43;0.0113)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.00696)|all_epithelial(44;0.00347)|all_lung(25;0.0221)|Breast(118;0.0411)|Lung NSC(25;0.0839)	all cancers(43;0.171)			CTTCTTCAAAGCCGAAGTTGG	0.517																																					p.G171G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C513T	13						.						74.0	73.0	74.0					13																	114307230		2203	4300	6503	113355231	SO:0001819	synonymous_variant	496	exon4				CCDS9539.1	13q34	2011-08-01			ENSG00000186009	ENSG00000186009	3.6.3.10	"""ATPases / P-type"""	820	protein-coding gene	gene with protein product		137217				1330887, 15057823	Standard	NM_000705		Approved	ATP6B	uc001vtz.3	P51164	OTTHUMG00000140234	ENST00000335288.4:c.513C>T	13.37:g.114307230G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113355231	NM_000705	B1B0N8	Silent	SNP	ENST00000335288.4	37	CCDS9539.1																																																																																				0.517	ATP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276703.2	NM_000705	
AHNAK2	113146	broad.mit.edu	37	14	105406342	105406343	+	Frame_Shift_Ins	INS	-	-	C	rs538236789		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:105406342_105406343insC	ENST00000333244.5	-	7	15564_15565	c.15445_15446insG	c.(15445-15447)gagfs	p.E5149fs	AHNAK2_ENST00000557457.1_Frame_Shift_Ins_p.E147fs	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	5149						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.E5149fs*8(1)|p.E119fs*8(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCTATCCCCTCCCCACAAGGC	0.579																																					p.E5149fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.15446_15447insG	14						.																																			104477388	SO:0001589	frameshift_variant	113146	exon7			AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.15446dupG	14.37:g.105406346_105406346dupC	ENSP00000353114:p.Glu5149fs	Somatic		Capture	Illumina HiSeq	Phase_I	104477387	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Ins	INS	ENST00000333244.5	37	CCDS45177.1																																																																																				0.579	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
PPP2R5C	5527	broad.mit.edu	37	14	102384282	102384282	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:102384282C>T	ENST00000334743.5	+	13	1489	c.1441C>T	c.(1441-1443)Cag>Tag	p.Q481*	PPP2R5C_ENST00000328724.5_Intron|PPP2R5C_ENST00000422945.2_Nonsense_Mutation_p.Q512*|PPP2R5C_ENST00000350249.3_Intron	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	481					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.Q481*(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CGAGGCTCATCAGGTAAAAGT	0.473																																					p.Q481X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1441T	14						.						123.0	105.0	111.0					14																	102384282		2203	4300	6503	101454035	SO:0001587	stop_gained	5527	exon13			L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9311	protein-coding gene	gene with protein product		601645	"""protein phosphatase 2, regulatory subunit B (B56), gamma isoform"", ""protein phosphatase 2, regulatory subunit B', gamma isoform"""			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1441C>T	14.37:g.102384282C>T	ENSP00000333905:p.Gln481*	Somatic		Capture	Illumina HiSeq	Phase_I	101454035	NM_002719	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Nonsense_Mutation	SNP	ENST00000334743.5	37	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	35	5.460753	0.96240	.	.	ENSG00000078304	ENST00000422945;ENST00000557268;ENST00000334743	.	.	.	5.83	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	16.8303	0.85942	0.0:0.8712:0.1288:0.0	.	.	.	.	X	512;510;481	.	ENSP00000333905:Q481X	Q	+	1	0	PPP2R5C	101454035	1.000000	0.71417	0.900000	0.35374	0.839000	0.47603	5.931000	0.70113	1.440000	0.47531	0.555000	0.69702	CAG		0.473	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	
OR4K5	79317	broad.mit.edu	37	14	20389150	20389150	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:20389150C>T	ENST00000315915.4	+	1	410	c.385C>T	c.(385-387)Ccc>Tcc	p.P129S		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	129						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P129S(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CATATGCAAACCCTTATACTA	0.448																																					p.P129S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C385T	14						.						226.0	224.0	225.0					14																	20389150		2203	4300	6503	19458990	SO:0001583	missense	79317	exon1			BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"""GPCR / Class A : Olfactory receptors"""	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.385C>T	14.37:g.20389150C>T	ENSP00000319511:p.Pro129Ser	Somatic		Capture	Illumina HiSeq	Phase_I	19458990	NM_001005483	Q6IFA7	Missense_Mutation	SNP	ENST00000315915.4	37	CCDS32024.1	.	.	.	.	.	.	.	.	.	.	.	18.33	3.599277	0.66332	.	.	ENSG00000176281	ENST00000315915	T	0.01838	4.61	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.000000	0.49916	D	0.000126	T	0.22360	0.0539	H	0.98133	4.155	0.50171	D	0.999852	D	0.76494	0.999	D	0.72625	0.978	T	0.40270	-0.9572	10	0.87932	D	0	.	14.5138	0.67807	0.0:1.0:0.0:0.0	.	129	Q8NGD3	OR4K5_HUMAN	S	129	ENSP00000319511:P129S	ENSP00000319511:P129S	P	+	1	0	OR4K5	19458990	1.000000	0.71417	0.976000	0.42696	0.383000	0.30230	6.964000	0.76061	2.269000	0.75478	0.655000	0.94253	CCC		0.448	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483	
TEP1	7011	broad.mit.edu	37	14	20840909	20840909	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:20840909C>T	ENST00000262715.5	-	49	7099	c.7059G>A	c.(7057-7059)tcG>tcA	p.S2353S	TEP1_ENST00000556935.1_Silent_p.S2245S|TEP1_ENST00000545983.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	2353					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.S2353S(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TTCCGGGTGCCGAACCCTTCC	0.498																																					p.S2353S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G7059A	14						.						128.0	123.0	124.0					14																	20840909		2203	4300	6503	19910749	SO:0001819	synonymous_variant	7011	exon49				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.7059G>A	14.37:g.20840909C>T		Somatic		Capture	Illumina HiSeq	Phase_I	19910749	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	37	CCDS9548.1																																																																																				0.498	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
TEP1	7011	broad.mit.edu	37	14	20876271	20876271	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:20876271G>A	ENST00000262715.5	-	2	368	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W	TEP1_ENST00000556935.1_Missense_Mutation_p.R110W	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	110					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)	p.R110W(1)		NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GCCAGGCACCGGTTCTCCAAG	0.532																																					p.R110W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C328T	14						.						105.0	107.0	107.0					14																	20876271		2203	4300	6503	19946111	SO:0001583	missense	7011	exon2				CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.328C>T	14.37:g.20876271G>A	ENSP00000262715:p.Arg110Trp	Somatic		Capture	Illumina HiSeq	Phase_I	19946111	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.379408	0.61845	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000556549	T;T;T	0.60424	0.19;0.19;0.19	5.08	2.05	0.26809	.	1.118780	0.06745	N	0.778993	T	0.60715	0.2290	L	0.32530	0.975	0.09310	N	0.999997	D;D	0.76494	0.998;0.999	P;P	0.57846	0.736;0.828	T	0.49437	-0.8940	10	0.87932	D	0	-3.7545	7.6614	0.28404	0.0:0.1622:0.5028:0.335	.	110;110	G3V5X7;Q99973	.;TEP1_HUMAN	W	110	ENSP00000262715:R110W;ENSP00000452574:R110W;ENSP00000452240:R110W	ENSP00000262715:R110W	R	-	1	2	TEP1	19946111	0.013000	0.17824	0.313000	0.25210	0.943000	0.58893	0.449000	0.21744	0.324000	0.23333	0.650000	0.86243	CGG		0.532	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
RNASE7	84659	broad.mit.edu	37	14	21511542	21511542	+	Missense_Mutation	SNP	G	G	A	rs371662364		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:21511542G>A	ENST00000298690.4	+	2	648	c.391G>A	c.(391-393)Gta>Ata	p.V131I	NDRG2_ENST00000403829.3_Intron	NM_032572.3	NP_115961	Q9H1E1	RNAS7_HUMAN	ribonuclease, RNase A family, 7	131					antibacterial humoral response (GO:0019731)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|membrane disruption in other organism (GO:0051673)|response to bacterium (GO:0009617)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|lipopolysaccharide binding (GO:0001530)|nucleic acid binding (GO:0003676)|peptidoglycan binding (GO:0042834)|ribonuclease activity (GO:0004540)	p.V131I(1)		endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	6	all_cancers(95;0.000759)		OV - Ovarian serous cystadenocarcinoma(11;3.42e-11)|Epithelial(56;5.57e-09)|all cancers(55;2.36e-08)	GBM - Glioblastoma multiforme(265;0.0191)		CAAGTCTTACGTAGTGGCCTG	0.537																																					p.V131I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G391A	14						.						136.0	132.0	134.0					14																	21511542		2200	4300	6500	20581382	SO:0001583	missense	84659	exon2			AJ131212	CCDS41914.1	14q11.1	2013-02-15			ENSG00000165799	ENSG00000165799		"""Ribonucleases, RNase A"""	19278	protein-coding gene	gene with protein product		612484				12244054, 12527768	Standard	NM_032572		Approved		uc001vzk.4	Q9H1E1	OTTHUMG00000171358	ENST00000298690.4:c.391G>A	14.37:g.21511542G>A	ENSP00000298690:p.Val131Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20581382	NM_032572	P80927|P83685|Q546N3	Missense_Mutation	SNP	ENST00000298690.4	37	CCDS41914.1	.	.	.	.	.	.	.	.	.	.	G	10.85	1.466309	0.26335	.	.	ENSG00000165799	ENST00000298690	T	0.73152	-0.72	5.19	-2.96	0.05547	Ribonuclease A, domain (4);	1.006700	0.07996	N	0.988009	T	0.29914	0.0748	N	0.00823	-1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37619	-0.9698	10	0.02654	T	1	-9.9228	5.6914	0.17831	0.4536:0.0:0.4095:0.1369	.	131	Q9H1E1	RNAS7_HUMAN	I	131	ENSP00000298690:V131I	ENSP00000298690:V131I	V	+	1	0	RNASE7	20581382	0.000000	0.05858	0.001000	0.08648	0.495000	0.33615	0.085000	0.14912	-0.392000	0.07751	-0.294000	0.09567	GTA		0.537	RNASE7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313936.1	NM_032572	
CHD8	57680	broad.mit.edu	37	14	21860938	21860938	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:21860938C>T	ENST00000557364.1	-	34	6762	c.6499G>A	c.(6499-6501)Gtc>Atc	p.V2167I	CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Missense_Mutation_p.V1888I|CHD8_ENST00000399982.2_Missense_Mutation_p.V2167I|SNORD9_ENST00000362566.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	2167					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|canonical Wnt signaling pathway (GO:0060070)|DNA duplex unwinding (GO:0032508)|in utero embryonic development (GO:0001701)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	MLL1 complex (GO:0071339)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|beta-catenin binding (GO:0008013)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|p53 binding (GO:0002039)	p.V2167F(1)|p.V2167I(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(33)|ovary(6)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	85	all_cancers(95;0.00121)		Epithelial(56;2.55e-06)|all cancers(55;1.73e-05)	GBM - Glioblastoma multiforme(265;0.00424)		GCCTGGCAGACGAGGTCAATA	0.483																																					p.V1888I												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G5662A	14						.						137.0	135.0	135.0					14																	21860938		1967	4176	6143	20930778	SO:0001583	missense	57680	exon34			AB046784	CCDS45081.1, CCDS53885.1	14q11.2	2008-02-05	2004-06-22	2004-06-23		ENSG00000100888			20153	protein-coding gene	gene with protein product		610528	"""helicase with SNF2 domain 1"""	HELSNF1		10997877	Standard	NM_020920		Approved	KIAA1564, DUPLIN	uc001war.2	Q9HCK8		ENST00000557364.1:c.6499G>A	14.37:g.21860938C>T	ENSP00000451601:p.Val2167Ile	Somatic		Capture	Illumina HiSeq	Phase_I	20930778	NM_020920	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	0.597	-0.830594	0.02734	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364;ENST00000553870	D;D;D;T	0.84298	-1.83;-1.82;-1.82;2.44	5.34	4.45	0.53987	.	0.146062	0.46442	N	0.000294	T	0.61073	0.2318	N	0.01505	-0.83	0.35838	D	0.825829	B	0.02656	0.0	B	0.04013	0.001	T	0.62329	-0.6877	10	0.02654	T	1	-8.1465	13.3506	0.60599	0.0:0.9219:0.0:0.078	.	1888	Q9HCK8-2	.	I	1888;2167;1887;2167;4	ENSP00000406288:V1888I;ENSP00000382863:V2167I;ENSP00000451601:V2167I;ENSP00000451071:V4I	ENSP00000262707:V1887I	V	-	1	0	CHD8	20930778	0.638000	0.27225	1.000000	0.80357	0.999000	0.98932	0.991000	0.29654	1.449000	0.47699	0.655000	0.94253	GTC		0.483	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920	
SALL2	6297	broad.mit.edu	37	14	21992735	21992735	+	Missense_Mutation	SNP	C	C	T	rs145077959		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:21992735C>T	ENST00000327430.3	-	2	1421	c.1127G>A	c.(1126-1128)cGc>cAc	p.R376H	SALL2_ENST00000317492.5_Intron|SALL2_ENST00000538754.1_Intron|SALL2_ENST00000450879.2_Missense_Mutation_p.R239H|AE000658.22_ENST00000535893.1_RNA	NM_005407.1	NP_005398.1	Q9Y467	SALL2_HUMAN	spalt-like transcription factor 2	376					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R376H(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|lung(12)|ovary(2)|skin(6)|urinary_tract(2)	43	all_cancers(95;0.000662)			GBM - Glioblastoma multiforme(265;0.0151)		GGCACAGAAGCGGCATTTGTG	0.557													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20416	0.0		0.0	False		,,,				2504	0.0				p.R376H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1127A	14						.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	92.0	83.0	86.0		1127	3.4	1.0	14	dbSNP_134	86	0,8600		0,0,4300	no	missense	SALL2	NM_005407.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	376/1008	21992735	1,13005	2203	4300	6503	21062575	SO:0001583	missense	6297	exon2			AB002358	CCDS32045.1	14q11.1-q12.1	2013-10-17	2013-10-17		ENSG00000165821	ENSG00000165821		"""Zinc fingers, C2H2-type"""	10526	protein-coding gene	gene with protein product		602219	"""sal (Drosophila)-like 2"", ""sal-like 2 (Drosophila)"""			8975705	Standard	XM_005267983		Approved	KIAA0360, Hsal2, ZNF795	uc001wbe.3	Q9Y467	OTTHUMG00000168826	ENST00000327430.3:c.1127G>A	14.37:g.21992735C>T	ENSP00000333537:p.Arg376His	Somatic		Capture	Illumina HiSeq	Phase_I	21062575	NM_005407	B2RMX6|B9EGK8|Q8N656|Q9Y4G1	Missense_Mutation	SNP	ENST00000327430.3	37	CCDS32045.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	17.60|17.60	3.430737|3.430737	0.62844|0.62844	2.27E-4|2.27E-4	0.0|0.0	ENSG00000165821|ENSG00000165821	ENST00000546363|ENST00000327430;ENST00000450879;ENST00000541876	.|T;T	.|0.03920	.|3.76;3.76	4.3|4.3	3.42|3.42	0.39159|0.39159	.|Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.|0.000000	.|0.37761	.|N	.|0.001949	T|T	0.12774|0.12774	0.0310|0.0310	L|L	0.43152|0.43152	1.355|1.355	0.48452|0.48452	D|D	0.999654|0.999654	.|D;D;B;D	.|0.76494	.|0.998;0.998;0.417;0.999	.|D;D;B;D	.|0.76071	.|0.976;0.976;0.048;0.987	T|T	0.01143|0.01143	-1.1438|-1.1438	5|10	.|0.59425	.|D	.|0.04	-15.6073|-15.6073	9.89|9.89	0.41285|0.41285	0.0:0.8995:0.0:0.1005|0.0:0.8995:0.0:0.1005	.|.	.|239;239;374;376	.|B4DK65;E7EW59;B4DFD9;Q9Y467	.|.;.;.;SALL2_HUMAN	T|H	235|376;239;376	.|ENSP00000333537:R376H;ENSP00000396773:R239H	.|ENSP00000333537:R376H	A|R	-|-	1|2	0|0	SALL2|SALL2	21062575|21062575	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.960000|0.960000	0.62799|0.62799	4.802000|4.802000	0.62539|0.62539	1.031000|1.031000	0.39867|0.39867	-0.136000|-0.136000	0.14681|0.14681	GCT|CGC		0.557	SALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401242.1	NM_005407	
SLC7A7	9056	broad.mit.edu	37	14	23240753	23240753	+	IGR	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:23240753G>A	ENST00000397532.3	-	0	2447				OXA1L_ENST00000604262.1_Missense_Mutation_p.D432N|OXA1L_ENST00000412791.1_Missense_Mutation_p.D405N|SLC7A7_ENST00000554061.1_5'Flank|OXA1L_ENST00000285848.5_Missense_Mutation_p.D492N|OXA1L_ENST00000358043.5_Missense_Mutation_p.D416N			Q9UM01	YLAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, y+L system), member 7						amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)	p.D492N(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(2)	20	all_cancers(95;8.44e-05)			GBM - Glioblastoma multiforme(265;0.00741)		TCCCTGGCACGACACACTTGG	0.493																																					p.D492N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1474A	14						.						183.0	160.0	168.0					14																	23240753		2203	4300	6503	22310593	SO:0001628	intergenic_variant	5018	exon10			AF092032	CCDS9574.1	14q11.2	2014-09-17	2011-07-12		ENSG00000155465	ENSG00000155465		"""Solute carriers"""	11065	protein-coding gene	gene with protein product		603593		LPI		9829974	Standard	NM_001126106		Approved	y+LAT-1	uc001wgs.4	Q9UM01	OTTHUMG00000028692		14.37:g.23240753G>A		Somatic		Capture	Illumina HiSeq	Phase_I	22310593	NM_005015	B2RAU0|D3DS26|O95984|Q53XC1|Q86U07|Q9P2V5	Missense_Mutation	SNP	ENST00000397532.3	37	CCDS9574.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475327	0.84640	.	.	ENSG00000155463	ENST00000285848;ENST00000412791;ENST00000358043	T;T;T	0.55588	0.9;0.51;1.09	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.73768	0.3629	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.76149	-0.3065	10	0.72032	D	0.01	-21.5701	18.2754	0.90081	0.0:0.0:1.0:0.0	.	405;432	E7EVY0;Q15070	.;OXA1L_HUMAN	N	492;405;416	ENSP00000285848:D492N;ENSP00000387601:D405N;ENSP00000350740:D416N	ENSP00000285848:D492N	D	+	1	0	OXA1L	22310593	1.000000	0.71417	0.904000	0.35570	0.453000	0.32348	7.037000	0.76531	2.600000	0.87896	0.609000	0.83330	GAC		0.493	SLC7A7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071636.3		
REM2	161253	broad.mit.edu	37	14	23355274	23355274	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:23355274C>T	ENST00000267396.4	+	4	684	c.561C>T	c.(559-561)acC>acT	p.T187T	REM2_ENST00000536884.1_Missense_Mutation_p.R163W	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	187					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.T177T(1)		breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		GCCTTCAGACCGGGGACGCCT	0.622																																					p.T187T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C561T	14						.						60.0	65.0	63.0					14																	23355274		2011	4176	6187	22425114	SO:0001819	synonymous_variant	161253	exon4				CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"""RAS (RAD and GEM) like GTP binding 2"""			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.561C>T	14.37:g.23355274C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22425114	NM_173527	B7Z5P1|Q8N8R8	Silent	SNP	ENST00000267396.4	37	CCDS45082.1	.	.	.	.	.	.	.	.	.	.	C	17.22	3.333583	0.60853	.	.	ENSG00000139890	ENST00000536884	T	0.38401	1.14	5.48	-7.33	0.01431	.	.	.	.	.	T	0.22742	0.0549	.	.	.	0.27372	N	0.95568	B	0.16396	0.017	B	0.09377	0.004	T	0.39522	-0.9610	8	0.87932	D	0	.	8.9879	0.36005	0.0767:0.1199:0.6061:0.1974	.	163	B7Z5P1	.	W	163	ENSP00000442774:R163W	ENSP00000442774:R163W	R	+	1	2	REM2	22425114	0.041000	0.20044	0.927000	0.36925	0.994000	0.84299	-0.901000	0.04093	-0.944000	0.03686	0.563000	0.77884	CGG		0.622	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527	
JPH4	84502	broad.mit.edu	37	14	24041120	24041120	+	Silent	SNP	G	G	A	rs143339999	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24041120G>A	ENST00000397118.3	-	5	2063	c.1161C>T	c.(1159-1161)gaC>gaT	p.D387D	JPH4_ENST00000544177.1_Silent_p.D52D|JPH4_ENST00000356300.4_Silent_p.D387D	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	387					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)		p.D387D(1)		endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		TTAGGAGGGCGTCTGCTGCCC	0.612																																					p.D387D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1161T	14						.	G	,	1,4405	2.1+/-5.4	0,1,2202	50.0	46.0	48.0		1161,1161	-5.8	0.9	14	dbSNP_134	48	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	JPH4	NM_001146028.1,NM_032452.2	,	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	,	387/629,387/629	24041120	4,13002	2203	4300	6503	23110960	SO:0001819	synonymous_variant	84502	exon5			AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"""junctophilin like 1"""	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1161C>T	14.37:g.24041120G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23110960	NM_032452	D3DS53|Q8ND44|Q96DQ0	Silent	SNP	ENST00000397118.3	37	CCDS9603.1																																																																																				0.612	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452	
LRRC16B	90668	broad.mit.edu	37	14	24528350	24528350	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24528350G>A	ENST00000342740.5	+	20	1732	c.1578G>A	c.(1576-1578)ctG>ctA	p.L526L	LRRC16B_ENST00000334420.7_5'UTR	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	526						cytoplasm (GO:0005737)		p.L526L(1)		breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCAGGACCCTGGAGGAGATCC	0.632																																					p.L526L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1578A	14						.						32.0	33.0	33.0					14																	24528350		2199	4300	6499	23598190	SO:0001819	synonymous_variant	90668	exon20			AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.1578G>A	14.37:g.24528350G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23598190	NM_138360	Q8TEF7|Q96HS9	Silent	SNP	ENST00000342740.5	37	CCDS32054.1																																																																																				0.632	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
ADCY4	196883	broad.mit.edu	37	14	24793300	24793300	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24793300G>T	ENST00000310677.4	-	17	2127	c.2014C>A	c.(2014-2016)Ctc>Atc	p.L672I	ADCY4_ENST00000396747.3_Missense_Mutation_p.L365I|ADCY4_ENST00000418030.2_Missense_Mutation_p.L672I|ADCY4_ENST00000554068.2_Missense_Mutation_p.L672I	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	672					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.L672I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		AAGACAAGGAGGATGGTGGCG	0.607																																					p.L672I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2014A	14						.						72.0	64.0	67.0					14																	24793300		2203	4300	6503	23863140	SO:0001583	missense	196883	exon17			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.2014C>A	14.37:g.24793300G>T	ENSP00000312126:p.Leu672Ile	Somatic		Capture	Illumina HiSeq	Phase_I	23863140	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261129	0.59431	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030;ENST00000396747	T;T;T;T	0.79749	-1.04;-1.04;-1.04;-1.3	4.84	3.95	0.45737	.	0.000000	0.40302	N	0.001137	T	0.75221	0.3820	M	0.62723	1.935	0.31247	N	0.694447	B	0.25390	0.125	B	0.24006	0.05	T	0.71321	-0.4628	10	0.23891	T	0.37	.	10.7523	0.46216	0.093:0.0:0.907:0.0	.	672	Q8NFM4	ADCY4_HUMAN	I	672;672;672;365	ENSP00000312126:L672I;ENSP00000452250:L672I;ENSP00000393177:L672I;ENSP00000379971:L365I	ENSP00000312126:L672I	L	-	1	0	ADCY4	23863140	1.000000	0.71417	0.999000	0.59377	0.826000	0.46750	2.625000	0.46452	1.273000	0.44346	0.563000	0.77884	CTC		0.607	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
ADCY4	196883	broad.mit.edu	37	14	24800480	24800480	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24800480T>C	ENST00000310677.4	-	6	865	c.752A>G	c.(751-753)cAg>cGg	p.Q251R	ADCY4_ENST00000396747.3_5'UTR|ADCY4_ENST00000418030.2_Missense_Mutation_p.Q251R|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000554068.2_Missense_Mutation_p.Q251R	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	251					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.Q251R(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CCGTGACCCCTGTCCTGCCTG	0.577																																					p.Q251R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A752G	14						.						115.0	93.0	101.0					14																	24800480		2203	4300	6503	23870320	SO:0001583	missense	196883	exon6			AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.752A>G	14.37:g.24800480T>C	ENSP00000312126:p.Gln251Arg	Somatic		Capture	Illumina HiSeq	Phase_I	23870320	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	T	7.086	0.571106	0.13623	.	.	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	T;T;T	0.76186	-1.0;-1.0;-1.0	4.89	3.71	0.42584	Adenylyl cyclase class-3/4/guanylyl cyclase (1);	0.146358	0.31949	N	0.006801	T	0.50803	0.1637	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.46748	-0.9169	10	0.27785	T	0.31	.	8.9203	0.35607	0.0:0.0912:0.0:0.9088	.	251	Q8NFM4	ADCY4_HUMAN	R	251	ENSP00000312126:Q251R;ENSP00000452250:Q251R;ENSP00000393177:Q251R	ENSP00000312126:Q251R	Q	-	2	0	ADCY4	23870320	0.726000	0.28059	1.000000	0.80357	0.958000	0.62258	1.479000	0.35453	2.056000	0.61249	0.459000	0.35465	CAG		0.577	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
NYNRIN	57523	broad.mit.edu	37	14	24877358	24877358	+	Missense_Mutation	SNP	G	G	A	rs572906859		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24877358G>A	ENST00000382554.3	+	3	800	c.482G>A	c.(481-483)cGg>cAg	p.R161Q		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	161					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)	p.R161Q(1)		breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						GAGGTGACCCGGGCCTTTGGG	0.692													G|||	1	0.000199681	0.0	0.0	5008	,	,		14505	0.0		0.0	False		,,,				2504	0.001				p.R161Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G482A	14						.						14.0	17.0	16.0					14																	24877358		1929	4107	6036	23947198	SO:0001583	missense	57523	exon3			AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.482G>A	14.37:g.24877358G>A	ENSP00000371994:p.Arg161Gln	Somatic		Capture	Illumina HiSeq	Phase_I	23947198	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.525820	0.85600	.	.	ENSG00000205978	ENST00000382554	T	0.19532	2.14	4.93	4.04	0.47022	.	0.123230	0.29473	N	0.012048	T	0.22322	0.0538	M	0.71581	2.175	0.28798	N	0.89892	B	0.31503	0.326	B	0.20955	0.032	T	0.19910	-1.0291	10	0.87932	D	0	.	10.9735	0.47452	0.0911:0.0:0.9089:0.0	.	161	Q9P2P1	NYNRI_HUMAN	Q	161	ENSP00000371994:R161Q	ENSP00000371994:R161Q	R	+	2	0	NYNRIN	23947198	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.247000	0.58750	1.288000	0.44600	0.563000	0.77884	CGG		0.692	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
HECTD1	25831	broad.mit.edu	37	14	31605847	31605847	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:31605847G>A	ENST00000399332.1	-	20	3492	c.3004C>T	c.(3004-3006)Cgg>Tgg	p.R1002W	HECTD1_ENST00000553700.1_Missense_Mutation_p.R1002W	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1002					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.R1002W(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		CGTTCCAACCGAAATCGTAAT	0.398																																					p.R1002W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3004T	14						.						141.0	132.0	135.0					14																	31605847		1915	4124	6039	30675598	SO:0001583	missense	25831	exon20			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.3004C>T	14.37:g.31605847G>A	ENSP00000382269:p.Arg1002Trp	Somatic		Capture	Illumina HiSeq	Phase_I	30675598	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	G	33	5.253001	0.95336	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.51574	0.7;0.7;1.18	4.95	4.95	0.65309	.	0.000000	0.64402	U	0.000001	T	0.72285	0.3441	M	0.84082	2.675	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.973	T	0.77509	-0.2561	10	0.87932	D	0	-6.9311	18.5549	0.91080	0.0:0.0:1.0:0.0	.	1002;1002	D3DS86;Q9ULT8	.;HECD1_HUMAN	W	1002;1004;1002;476	ENSP00000450697:R1002W;ENSP00000382269:R1002W;ENSP00000451860:R476W	ENSP00000261312:R1004W	R	-	1	2	HECTD1	30675598	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.789000	0.99068	2.447000	0.82792	0.557000	0.71058	CGG		0.398	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1		
FBXO33	254170	broad.mit.edu	37	14	39870630	39870630	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:39870630T>C	ENST00000298097.7	-	3	1483	c.1146A>G	c.(1144-1146)gaA>gaG	p.E382E	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	382					protein ubiquitination (GO:0016567)			p.E382E(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		TTAACATATCTTCACTCTTGA	0.393																																					p.E382E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1146G	14						.						89.0	86.0	87.0					14																	39870630		2203	4300	6503	38940381	SO:0001819	synonymous_variant	254170	exon3			BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1146A>G	14.37:g.39870630T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38940381	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	37	CCDS9677.1																																																																																				0.393	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
LRFN5	145581	broad.mit.edu	37	14	42360818	42360818	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:42360818C>T	ENST00000298119.4	+	4	2940	c.1751C>T	c.(1750-1752)aCg>aTg	p.T584M	LRFN5_ENST00000554171.1_Intron|LRFN5_ENST00000554120.1_Intron	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	584						integral component of membrane (GO:0016021)		p.T584M(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(67)|ovary(5)|pancreas(3)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(2)	120			LUAD - Lung adenocarcinoma(50;0.0223)|Lung(238;0.0728)	GBM - Glioblastoma multiforme(112;0.00847)		TGTAGTGTAACGCTGCCCCAG	0.453										HNSCC(30;0.082)																											p.T584M												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C1751T	14						.						108.0	94.0	99.0					14																	42360818		2203	4300	6503	41430568	SO:0001583	missense	145581	exon4			AK055365	CCDS9678.1	14q21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000165379	ENSG00000165379		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	20360	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 8"""	612811	"""chromosome 14 open reading frame 146"""	C14orf146		16828986	Standard	NM_152447		Approved	FIGLER8, SALM5	uc001wvm.3	Q96NI6	OTTHUMG00000140261	ENST00000298119.4:c.1751C>T	14.37:g.42360818C>T	ENSP00000298119:p.Thr584Met	Somatic		Capture	Illumina HiSeq	Phase_I	41430568	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	C	9.892	1.204457	0.22205	.	.	ENSG00000165379	ENST00000298119	T	0.47528	0.84	5.95	5.95	0.96441	.	0.278342	0.27544	N	0.018891	T	0.32346	0.0826	N	0.08118	0	0.46185	D	0.998912	B	0.19200	0.034	B	0.11329	0.006	T	0.09596	-1.0667	10	0.49607	T	0.09	.	17.875	0.88822	0.0:1.0:0.0:0.0	.	584	Q96NI6	LRFN5_HUMAN	M	584	ENSP00000298119:T584M	ENSP00000298119:T584M	T	+	2	0	LRFN5	41430568	0.000000	0.05858	0.107000	0.21349	0.670000	0.39368	0.787000	0.26858	2.821000	0.97095	0.650000	0.86243	ACG		0.453	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447	
MDGA2	161357	broad.mit.edu	37	14	47426727	47426727	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:47426727A>T	ENST00000399232.2	-	9	2096	c.1732T>A	c.(1732-1734)Ttg>Atg	p.L578M	MDGA2_ENST00000439988.3_Missense_Mutation_p.L647M|SNORA25_ENST00000515926.1_RNA|MDGA2_ENST00000357362.3_Missense_Mutation_p.L349M|MDGA2_ENST00000426342.1_Missense_Mutation_p.L349M	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	578	Ig-like 6.				pattern specification process (GO:0007389)|spinal cord motor neuron differentiation (GO:0021522)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.L349M(1)|p.L647M(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(14)|lung(41)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(5)	76						TTATTGCCCAAGCGCCACTCA	0.453																																					p.L349M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T1045A	14						.						95.0	96.0	96.0					14																	47426727		1971	4156	6127	46496477	SO:0001583	missense	161357	exon9			AI859192	CCDS41948.1, CCDS45098.1, CCDS45098.2, CCDS45098.3	14q21.2	2013-01-29	2007-04-03	2007-04-03	ENSG00000139915	ENSG00000139915		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19835	protein-coding gene	gene with protein product		611128	"""MAM domain containing 1"""	MAMDC1		15019943	Standard	NM_001113498		Approved		uc001wwj.4	Q7Z553	OTTHUMG00000029429	ENST00000399232.2:c.1732T>A	14.37:g.47426727A>T	ENSP00000382178:p.Leu578Met	Somatic		Capture	Illumina HiSeq	Phase_I	46496477	NM_182830	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.	.	.	.	.	.	.	.	.	.	A	17.52	3.409580	0.62399	.	.	ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362	T;T;T;T	0.14144	2.53;2.53;2.53;2.53	5.54	0.361	0.16107	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.170955	0.26286	U	0.025244	T	0.23249	0.0562	L	0.57536	1.79	0.80722	D	1	B;D	0.53151	0.24;0.958	P;P	0.62649	0.495;0.905	T	0.01666	-1.1300	10	0.42905	T	0.14	.	5.7465	0.18122	0.394:0.1682:0.4378:0.0	.	349;578	F6W3S7;Q7Z553	.;MDGA2_HUMAN	M	578;349;647;349	ENSP00000400011:L578M;ENSP00000405456:L349M;ENSP00000382178:L647M;ENSP00000349925:L349M	ENSP00000349925:L349M	L	-	1	2	MDGA2	46496477	0.025000	0.19082	0.932000	0.37286	0.993000	0.82548	0.256000	0.18351	0.095000	0.17434	0.528000	0.53228	TTG		0.453	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830	
TRIM9	114088	broad.mit.edu	37	14	51467558	51467558	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:51467558G>A	ENST00000298355.3	-	6	2428	c.1307C>T	c.(1306-1308)gCt>gTt	p.A436V	TRIM9_ENST00000338969.5_Intron|TRIM9_ENST00000360392.4_Splice_Site_p.A436V	NM_015163.5	NP_055978.4	Q9C026	TRIM9_HUMAN	tripartite motif containing 9	436					negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of SNARE complex assembly (GO:0035544)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|synaptic vesicle (GO:0008021)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A436V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_epithelial(31;0.00418)|Breast(41;0.148)					TGGAGAGGAAGCTAAACAGAA	0.473																																					p.A436V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1307T	14						.						126.0	119.0	121.0					14																	51467558		2203	4300	6503	50537308	SO:0001630	splice_region_variant	114088	exon6			AF220036	CCDS9703.1, CCDS45105.1	14q21.3	2013-02-11	2011-01-25		ENSG00000100505	ENSG00000100505		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16288	protein-coding gene	gene with protein product		606555	"""tripartite motif-containing 9"""			11331580, 11524423	Standard	NM_015163		Approved	SPRING, RNF91	uc001wyx.4	Q9C026	OTTHUMG00000140291	ENST00000298355.3:c.1307-1C>T	14.37:g.51467558G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50537308	NM_052978	D3DSB7|D3DSB8|Q92557|Q96D24|Q96NI4|Q9C025|Q9C027	Missense_Mutation	SNP	ENST00000298355.3	37	CCDS9703.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.717027	0.48622	.	.	ENSG00000100505	ENST00000298355;ENST00000360392	T;T	0.68903	-0.36;1.6	5.49	4.6	0.57074	Fibronectin, type III (1);	.	.	.	.	T	0.31295	0.0792	N	0.00642	-1.3	0.23089	N	0.99831	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.20140	-1.0284	9	0.19147	T	0.46	.	7.1348	0.25523	0.265:0.0:0.735:0.0	.	436;436	Q9C026-5;Q9C026	.;TRIM9_HUMAN	V	436	ENSP00000298355:A436V;ENSP00000353561:A436V	ENSP00000298355:A436V	A	-	2	0	TRIM9	50537308	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.083000	0.50136	1.333000	0.45449	0.591000	0.81541	GCT		0.473	TRIM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276874.1	NM_015163	Missense_Mutation
NID2	22795	broad.mit.edu	37	14	52473336	52473336	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:52473336C>T	ENST00000216286.5	-	20	3922	c.3923G>A	c.(3922-3924)cGg>cAg	p.R1308Q	NID2_ENST00000541773.1_Missense_Mutation_p.R1207Q	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	1308					basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)	p.R1308Q(1)		NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					AATGACACGCCGTCCAGTTCC	0.458																																					p.R1308Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3923A	14						.						275.0	238.0	250.0					14																	52473336		2203	4300	6503	51543086	SO:0001583	missense	22795	exon20			AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.3923G>A	14.37:g.52473336C>T	ENSP00000216286:p.Arg1308Gln	Somatic		Capture	Illumina HiSeq	Phase_I	51543086	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	.	.	.	.	.	.	.	.	.	.	C	36	5.833223	0.97003	.	.	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773	T;T	0.32023	1.47;1.47	5.99	5.99	0.97316	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.65481	0.2695	M	0.88704	2.975	0.45216	D	0.998227	D;D;D	0.89917	0.995;1.0;0.991	P;D;P	0.83275	0.508;0.996;0.605	T	0.69273	-0.5188	10	0.66056	D	0.02	.	20.4777	0.99188	0.0:1.0:0.0:0.0	.	902;1207;1308	E7EPP3;Q14112-2;Q14112	.;.;NID2_HUMAN	Q	1308;902;1207	ENSP00000216286:R1308Q;ENSP00000443730:R1207Q	ENSP00000216286:R1308Q	R	-	2	0	NID2	51543086	1.000000	0.71417	0.974000	0.42286	0.987000	0.75469	7.546000	0.82137	2.840000	0.97914	0.655000	0.94253	CGG		0.458	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
KTN1	3895	broad.mit.edu	37	14	56130759	56130759	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:56130759G>A	ENST00000395314.3	+	33	3245	c.3177G>A	c.(3175-3177)aaG>aaA	p.K1059K	KTN1_ENST00000416613.1_Splice_Site_p.K1059K|KTN1_ENST00000395308.1_Splice_Site_p.K1036K|KTN1_ENST00000554507.1_Intron|KTN1_ENST00000555573.1_Splice_Site_p.K64K|KTN1_ENST00000395311.1_Splice_Site_p.K1036K|KTN1_ENST00000395309.3_Splice_Site_p.K1059K|KTN1_ENST00000413890.2_Splice_Site_p.K1036K|KTN1_ENST00000438792.2_Intron	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1059					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.K1059K(2)		breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AGACTTCCAAGGTTGTAATGC	0.368			T	RET	papillary thryoid																																p.K1059K			Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G3177A	14						.						67.0	61.0	63.0					14																	56130759		2203	4300	6503	55200512	SO:0001630	splice_region_variant	3895	exon33				CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3177+1G>A	14.37:g.56130759G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55200512	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																				0.368	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		Silent
PSMA3	5684	broad.mit.edu	37	14	58738593	58738593	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:58738593T>C	ENST00000216455.4	+	11	838	c.748T>C	c.(748-750)Tca>Cca	p.S250P	RP11-349A22.5_ENST00000554360.1_RNA|CTD-2002H8.2_ENST00000557322.1_RNA|RP11-349A22.5_ENST00000556400.1_RNA|RP11-349A22.5_ENST00000555275.1_RNA|RP11-349A22.5_ENST00000557660.1_RNA|RP11-349A22.5_ENST00000556002.1_RNA|RP11-349A22.5_ENST00000553657.1_RNA|RP11-349A22.5_ENST00000555162.1_RNA|RP11-349A22.5_ENST00000555707.1_RNA|PSMA3_ENST00000557508.1_Missense_Mutation_p.S175P|RP11-349A22.5_ENST00000556225.1_RNA|RP11-349A22.5_ENST00000554378.1_RNA|PSMA3_ENST00000412908.2_Missense_Mutation_p.S243P	NM_002788.3|NM_152132.2	NP_002779.1|NP_687033.1	P25788	PSA3_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 3	250					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|proteasome core complex, alpha-subunit complex (GO:0019773)	threonine-type endopeptidase activity (GO:0004298)	p.S250P(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(2)	12						AGAAGATGAATCAGATGATGA	0.323																																					p.S250P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T748C	14						.						75.0	73.0	74.0					14																	58738593		2200	4297	6497	57808346	SO:0001583	missense	5684	exon11				CCDS9731.1, CCDS45113.1	14q23	2008-08-29			ENSG00000100567	ENSG00000100567		"""Proteasome (prosome, macropain) subunits"""	9532	protein-coding gene	gene with protein product		176843				2025653, 8811196	Standard	NM_002788		Approved	HC8	uc001xdj.2	P25788	OTTHUMG00000140319	ENST00000216455.4:c.748T>C	14.37:g.58738593T>C	ENSP00000216455:p.Ser250Pro	Somatic		Capture	Illumina HiSeq	Phase_I	57808346	NM_002788	B2RCK6|Q86U83|Q8N1D8|Q9BS70	Missense_Mutation	SNP	ENST00000216455.4	37	CCDS9731.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.399093	0.62177	.	.	ENSG00000100567	ENST00000216455;ENST00000412908;ENST00000557508;ENST00000553677	T;T	0.46063	0.88;0.88	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.54822	0.1882	M	0.83483	2.645	0.80722	D	1	P;P	0.42518	0.782;0.676	P;B	0.46110	0.504;0.307	T	0.61860	-0.6976	10	0.52906	T	0.07	-21.0515	14.8513	0.70297	0.0:0.0:0.0:1.0	.	243;250	P25788-2;P25788	.;PSA3_HUMAN	P	250;243;175;78	ENSP00000216455:S250P;ENSP00000390491:S243P	ENSP00000216455:S250P	S	+	1	0	PSMA3	57808346	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.596000	0.67570	2.225000	0.72522	0.528000	0.53228	TCA		0.323	PSMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276923.1	NM_002788	
PPM1A	5494	broad.mit.edu	37	14	60756575	60756575	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:60756575G>A	ENST00000395076.4	+	4	1434	c.1004G>A	c.(1003-1005)cGc>cAc	p.R335H	PPM1A_ENST00000529574.1_Missense_Mutation_p.R335H|PPM1A_ENST00000325642.3_Missense_Mutation_p.R408H	NM_021003.4	NP_066283.1	P35813	PPM1A_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1A	335					cell cycle arrest (GO:0007050)|dephosphorylation (GO:0016311)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|N-terminal protein myristoylation (GO:0006499)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-threonine dephosphorylation (GO:0035970)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|protein dephosphorylation (GO:0006470)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|voltage-gated calcium channel complex (GO:0005891)	calmodulin-dependent protein phosphatase activity (GO:0033192)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)|R-SMAD binding (GO:0070412)|signal transducer activity (GO:0004871)	p.R335H(1)		cervix(1)|endometrium(1)|large_intestine(8)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(108;0.046)		CATGTGATGCGCACATTAGCG	0.433																																					p.R335H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1004A	14						.						68.0	68.0	68.0					14																	60756575		2203	4300	6503	59826328	SO:0001583	missense	5494	exon4			S87759	CCDS9744.1, CCDS9745.1, CCDS45120.1	14q23.1	2013-01-24	2010-03-05		ENSG00000100614	ENSG00000100614	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9275	protein-coding gene	gene with protein product	"""phosphatase 2C alpha"", ""protein phosphatase 2C, alpha isoform"""	606108	"""protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform"""			1311954	Standard	NM_177952		Approved	MGC9201, PP2Calpha, PP2CA	uc001xew.4	P35813	OTTHUMG00000140333	ENST00000395076.4:c.1004G>A	14.37:g.60756575G>A	ENSP00000378514:p.Arg335His	Somatic		Capture	Illumina HiSeq	Phase_I	59826328	NM_021003	B5BU11|J3KNM0|O75551	Missense_Mutation	SNP	ENST00000395076.4	37	CCDS9744.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255178	0.59321	.	.	ENSG00000100614	ENST00000325642;ENST00000529574;ENST00000395076	T;T;T	0.34275	1.37;1.41;1.41	5.36	5.36	0.76844	Protein serine/threonine phosphatase 2C, C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.34308	0.0893	L	0.39326	1.205	0.80722	D	1	B;B	0.12630	0.001;0.006	B;B	0.06405	0.002;0.002	T	0.05370	-1.0889	10	0.39692	T	0.17	.	19.4366	0.94798	0.0:0.0:1.0:0.0	.	335;335	P35813;B2R8E4	PPM1A_HUMAN;.	H	408;335;335	ENSP00000327255:R408H;ENSP00000432966:R335H;ENSP00000378514:R335H	ENSP00000327255:R408H	R	+	2	0	PPM1A	59826328	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.970000	0.88000	2.669000	0.90835	0.585000	0.79938	CGC		0.433	PPM1A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276949.2	NM_021003	
PLEKHH1	57475	broad.mit.edu	37	14	68028699	68028699	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:68028699G>A	ENST00000329153.5	+	6	584	c.452G>A	c.(451-453)aGc>aAc	p.S151N		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	151						cytoskeleton (GO:0005856)		p.S151N(1)		endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CATCTGAAAAGCCATAATCAG	0.468																																					p.S151N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G452A	14						.						64.0	66.0	66.0					14																	68028699		1997	4173	6170	67098452	SO:0001583	missense	57475	exon6			AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.452G>A	14.37:g.68028699G>A	ENSP00000330278:p.Ser151Asn	Somatic		Capture	Illumina HiSeq	Phase_I	67098452	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	G	5.546	0.285658	0.10513	.	.	ENSG00000054690	ENST00000329153	T	0.42513	0.97	5.15	1.17	0.20885	.	0.414397	0.30930	N	0.008591	T	0.19406	0.0466	N	0.17474	0.49	0.28550	N	0.911676	B	0.02656	0.0	B	0.06405	0.002	T	0.13980	-1.0489	10	0.14656	T	0.56	-5.7304	4.4824	0.11773	0.3494:0.1682:0.4823:0.0	.	151	Q9ULM0	PKHH1_HUMAN	N	151	ENSP00000330278:S151N	ENSP00000330278:S151N	S	+	2	0	PLEKHH1	67098452	1.000000	0.71417	0.985000	0.45067	0.484000	0.33280	1.069000	0.30641	0.326000	0.23384	0.455000	0.32223	AGC		0.468	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
ZFYVE26	23503	broad.mit.edu	37	14	68228112	68228112	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:68228112G>A	ENST00000347230.4	-	35	6697	c.6559C>T	c.(6559-6561)Cgg>Tgg	p.R2187W	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.R2187W|ZFYVE26_ENST00000557306.1_Missense_Mutation_p.R33W	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2187					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.R2187W(1)		NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		AGAGCTTCCCGCAGGCAGCTG	0.522																																					p.R2187W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6559T	14						.						138.0	108.0	118.0					14																	68228112		2203	4300	6503	67297865	SO:0001583	missense	23503	exon35			AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.6559C>T	14.37:g.68228112G>A	ENSP00000251119:p.Arg2187Trp	Somatic		Capture	Illumina HiSeq	Phase_I	67297865	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.146289	0.77888	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000557306;ENST00000555452	T;T;T	0.47528	1.68;0.84;1.57	6.16	5.21	0.72293	.	0.108018	0.64402	D	0.000017	T	0.65606	0.2707	L	0.57536	1.79	0.40422	D	0.979853	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.77004	0.989;0.93;0.965	T	0.67078	-0.5761	10	0.72032	D	0.01	-28.6173	16.6951	0.85333	0.0:0.0:0.8297:0.1703	.	2187;33;2187	G3V2D8;Q96H43;Q68DK2	.;.;ZFY26_HUMAN	W	2187;2166;33;2187	ENSP00000251119:R2187W;ENSP00000452142:R33W;ENSP00000450603:R2187W	ENSP00000251119:R2187W	R	-	1	2	ZFYVE26	67297865	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.372000	0.44257	2.937000	0.99478	0.650000	0.86243	CGG		0.522	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
TSHR	7253	broad.mit.edu	37	14	81610641	81610641	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:81610641C>A	ENST00000541158.2	+	11	2561	c.2239C>A	c.(2239-2241)Cta>Ata	p.L747I	RP11-114N19.3_ENST00000557775.1_RNA|TSHR_ENST00000298171.2_Missense_Mutation_p.L747I			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	747					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)	p.L747I(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	AAACTCCCATCTAACCCCAAA	0.408			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.L747I		yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2239A	14						.						108.0	101.0	103.0					14																	81610641		2203	4300	6503	80680394	SO:0001583	missense	7253	exon10			AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.2239C>A	14.37:g.81610641C>A	ENSP00000441235:p.Leu747Ile	Somatic		Capture	Illumina HiSeq	Phase_I	80680394	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	C	16.27	3.077142	0.55753	.	.	ENSG00000165409	ENST00000541158;ENST00000412429;ENST00000298171	T;T	0.75367	-0.93;-0.93	5.1	4.19	0.49359	.	0.748660	0.12424	N	0.470175	T	0.77525	0.4143	L	0.57536	1.79	0.25676	N	0.985845	P	0.46784	0.884	P	0.50270	0.636	T	0.68693	-0.5341	10	0.56958	D	0.05	.	11.6271	0.51151	0.0:0.9176:0.0:0.0824	.	747	F5GYU5	.	I	747;394;747	ENSP00000441235:L747I;ENSP00000298171:L747I	ENSP00000298171:L747I	L	+	1	2	TSHR	80680394	0.857000	0.29778	0.966000	0.40874	0.944000	0.59088	2.322000	0.43814	2.536000	0.85505	0.561000	0.74099	CTA		0.408	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
FLRT2	23768	broad.mit.edu	37	14	86087996	86087996	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:86087996T>C	ENST00000330753.4	+	2	905	c.138T>C	c.(136-138)ttT>ttC	p.F46F	FLRT2_ENST00000554746.1_Silent_p.F46F	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	46	LRRNT.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.F46F(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		ACAGGAACTTTGTCTACTGTA	0.502																																					p.F46F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T138C	14						.						130.0	120.0	123.0					14																	86087996		2203	4300	6503	85157749	SO:0001819	synonymous_variant	23768	exon2			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.138T>C	14.37:g.86087996T>C		Somatic		Capture	Illumina HiSeq	Phase_I	85157749	NM_013231	A0AV84|B7ZLP3	Silent	SNP	ENST00000330753.4	37	CCDS9877.1																																																																																				0.502	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
SERPINA9	327657	broad.mit.edu	37	14	94929495	94929495	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:94929495T>C	ENST00000380365.3	-	5	1267	c.1189A>G	c.(1189-1191)Att>Gtt	p.I397V	RP11-349I1.2_ENST00000536735.1_RNA|SERPINA9_ENST00000424550.2_Missense_Mutation_p.I266V|SERPINA9_ENST00000337425.5_Missense_Mutation_p.I415V|SERPINA9_ENST00000448305.2_Missense_Mutation_p.I317V|SERPINA9_ENST00000298845.7_Missense_Mutation_p.I315V			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	397					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TTATTTGTAATCATCATCAGG	0.468																																					p.I315V												.	.	0			c.A943G	14						.						138.0	132.0	134.0					14																	94929495		1977	4158	6135	93999248	SO:0001583	missense	327657	exon6			AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.1189A>G	14.37:g.94929495T>C	ENSP00000369723:p.Ile397Val	None		Capture	Illumina HiSeq	Phase_I	93999248	NM_001042518	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		.	.	.	.	.	.	.	.	.	.	T	13.51	2.260176	0.39995	.	.	ENSG00000170054	ENST00000448305;ENST00000298845;ENST00000424550;ENST00000337425;ENST00000380365	D;D;D;D;D	0.91407	-2.84;-2.84;-2.84;-2.84;-2.84	4.21	-6.95	0.01628	.	0.540328	0.15841	N	0.242032	D	0.86851	0.6032	L	0.60067	1.865	0.21697	N	0.999582	B;B;P	0.36378	0.35;0.387;0.55	B;B;B	0.43658	0.126;0.121;0.426	T	0.80562	-0.1327	10	0.62326	D	0.03	.	7.4136	0.27032	0.0:0.2118:0.4553:0.333	.	317;415;315	Q86WD7-6;Q86WD7-7;Q86WD7-2	.;.;.	V	317;315;266;415;397	ENSP00000414092:I317V;ENSP00000298845:I315V;ENSP00000409012:I266V;ENSP00000337133:I415V;ENSP00000369723:I397V	ENSP00000298845:I315V	I	-	1	0	SERPINA9	93999248	0.316000	0.24580	0.000000	0.03702	0.007000	0.05969	0.658000	0.24979	-1.421000	0.02007	-0.466000	0.05196	ATT		0.468	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
SYNE3	161176	broad.mit.edu	37	14	95932532	95932532	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:95932532G>A	ENST00000334258.5	-	3	377	c.363C>T	c.(361-363)gcC>gcT	p.A121A	SYNE3_ENST00000553340.1_Silent_p.A121A|SYNE3_ENST00000557275.1_Silent_p.A121A	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	121					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)	p.A121A(1)		breast(1)|endometrium(2)|lung(25)	28						ACTCATCTCGGGCCAGCAGGT	0.617																																					p.A121A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C363T	14						.						55.0	59.0	58.0					14																	95932532		2203	4300	6503	95002285	SO:0001819	synonymous_variant	161176	exon3			AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.363C>T	14.37:g.95932532G>A		Somatic		Capture	Illumina HiSeq	Phase_I	95002285	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Silent	SNP	ENST00000334258.5	37	CCDS9935.1																																																																																				0.617	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
TRAF3	7187	broad.mit.edu	37	14	103336612	103336612	+	Missense_Mutation	SNP	G	G	T	rs370955205		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:103336612G>T	ENST00000560371.1	+	2	291	c.74G>T	c.(73-75)cGc>cTc	p.R25L	TRAF3_ENST00000392745.2_Missense_Mutation_p.R25L|TRAF3_ENST00000539721.1_Missense_Mutation_p.R25L|TRAF3_ENST00000351691.5_Missense_Mutation_p.R25L|TRAF3_ENST00000347662.4_Missense_Mutation_p.R25L	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	25					apoptotic process (GO:0006915)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|regulation of apoptotic process (GO:0042981)|regulation of cytokine production (GO:0001817)|regulation of defense response to virus (GO:0050688)|regulation of interferon-beta production (GO:0032648)|regulation of proteolysis (GO:0030162)|signal transduction (GO:0007165)|Toll signaling pathway (GO:0008063)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome (GO:0005768)|mitochondrion (GO:0005739)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R25L(1)		breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|liver(2)|lung(7)|ovary(1)|prostate(2)	30		all_cancers(154;7.87e-06)|all_epithelial(191;0.0024)		Epithelial(152;9.92e-24)|all cancers(159;2.23e-21)|OV - Ovarian serous cystadenocarcinoma(161;7.85e-12)|Colorectal(3;0.0971)		CACACTGACCGCAGTGCTGGG	0.517													G|||	1	0.000199681	0.0	0.0	5008	,	,		17271	0.0		0.0	False		,,,				2504	0.001				p.R25L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G74T	14						.						91.0	87.0	88.0					14																	103336612		2203	4300	6503	102406365	SO:0001583	missense	7187	exon3			U21092	CCDS9975.1, CCDS9976.1, CCDS55946.1	14q32.32	2014-09-17				ENSG00000131323			12033	protein-coding gene	gene with protein product		601896				7530216, 7859281	Standard	NM_145725		Approved	CAP-1, CD40bp, CRAF1, LAP1	uc001ymd.2	Q13114		ENST00000560371.1:c.74G>T	14.37:g.103336612G>T	ENSP00000454207:p.Arg25Leu	Somatic		Capture	Illumina HiSeq	Phase_I	102406365	NM_145725	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Missense_Mutation	SNP	ENST00000560371.1	37	CCDS9975.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.161888	0.57368	.	.	ENSG00000131323	ENST00000392745;ENST00000347662;ENST00000351691;ENST00000539721	T;T;T;T	0.44482	2.27;2.25;2.25;0.92	5.44	4.55	0.56014	.	0.801389	0.12332	N	0.478247	T	0.45538	0.1347	N	0.12182	0.205	0.53005	D	0.999969	D;D;D	0.63046	0.988;0.975;0.992	D;P;P	0.63793	0.918;0.677;0.76	T	0.42965	-0.9420	10	0.48119	T	0.1	-37.3151	14.1474	0.65360	0.072:0.0:0.928:0.0	.	25;25;25	Q13114-2;A6NHG8;Q13114	.;.;TRAF3_HUMAN	L	25	ENSP00000376500:R25L;ENSP00000328003:R25L;ENSP00000332468:R25L;ENSP00000445998:R25L	ENSP00000328003:R25L	R	+	2	0	TRAF3	102406365	1.000000	0.71417	0.300000	0.25030	0.009000	0.06853	4.479000	0.60236	1.302000	0.44855	-0.136000	0.14681	CGC		0.517	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725	
CDC42BPB	9578	broad.mit.edu	37	14	103447237	103447237	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:103447237delT	ENST00000361246.2	-	8	1301	c.1013delA	c.(1012-1014)aagfs	p.K338fs		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)									p.K338fs*8(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		AAACGCATGCTTTTTGAAATC	0.453																																					p.K338fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1013delA	14						.						108.0	103.0	105.0					14																	103447237		2203	4300	6503	102516990	SO:0001589	frameshift_variant	9578	exon8			AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.1013delA	14.37:g.103447237delT	ENSP00000355237:p.Lys338fs	Somatic		Capture	Illumina HiSeq	Phase_I	102516990	NM_006035		Frame_Shift_Del	DEL	ENST00000361246.2	37	CCDS9978.1																																																																																				0.453	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
DHRS2	10202	broad.mit.edu	37	14	24108490	24108490	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:24108490delG	ENST00000250383.6	+	3	719	c.243delG	c.(241-243)cagfs	p.Q81fs	DHRS2_ENST00000344777.7_Frame_Shift_Del_p.Q81fs|DHRS2_ENST00000553896.1_3'UTR	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	81					C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)	p.E83fs*3(1)		endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		CCAAGCTGCAGGGGGAGGGGC	0.697																																					p.Q81fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.243delG	14						.						36.0	40.0	39.0					14																	24108490		2202	4298	6500	23178330	SO:0001589	frameshift_variant	10202	exon3				CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.243delG	14.37:g.24108490delG	ENSP00000250383:p.Gln81fs	Somatic		Capture	Illumina HiSeq	Phase_I	23178330	NM_005794	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Frame_Shift_Del	DEL	ENST00000250383.6	37	CCDS9604.1																																																																																				0.697	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
ARHGAP5	394	broad.mit.edu	37	14	32562696	32562696	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr14:32562696delA	ENST00000345122.3	+	2	3136	c.2821delA	c.(2821-2823)aaafs	p.K942fs	ARHGAP5_ENST00000396582.2_Intron|ARHGAP5_ENST00000432921.1_Frame_Shift_Del_p.K942fs|ARHGAP5_ENST00000433497.1_Intron|ARHGAP5_ENST00000539826.2_Frame_Shift_Del_p.K942fs|ARHGAP5_ENST00000556611.1_Frame_Shift_Del_p.K942fs	NM_001030055.1	NP_001025226.1	Q13017	RHG05_HUMAN	Rho GTPase activating protein 5	942					cell adhesion (GO:0007155)|GTP catabolic process (GO:0006184)|mammary gland development (GO:0030879)|positive regulation of cell migration (GO:0030335)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell size (GO:0008361)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)	p.N943fs*2(1)		NS(2)|breast(10)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(12)|ovary(4)|skin(1)|stomach(1)|urinary_tract(4)	55	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.186)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0952)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00566)		TGTTCTAGAGAAAAAAAATAT	0.343																																					p.K941fs	NSCLC(9;77 350 3443 29227 41353)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2821delA	14						.						48.0	48.0	48.0					14																	32562696		2203	4297	6500	31632447	SO:0001589	frameshift_variant	394	exon2			U17032	CCDS32062.1, CCDS45095.1	14q12	2010-02-05						"""Rho GTPase activating proteins"""	675	protein-coding gene	gene with protein product		602680	"""growth factor independent 2"""	GFI2		8537347	Standard	XM_005267635		Approved	RhoGAP5, p190-B, p190BRhoGAP	uc001wrn.3	Q13017		ENST00000345122.3:c.2821delA	14.37:g.32562696delA	ENSP00000371897:p.Lys942fs	Somatic		Capture	Illumina HiSeq	Phase_I	31632447	NM_001030055	A1L375|A1L376|A8KAA1|D3DS89|D3DS90|Q05BE8|Q05BU8|Q59ER0|Q6DHZ3	Frame_Shift_Del	DEL	ENST00000345122.3	37	CCDS32062.1																																																																																				0.343	ARHGAP5-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409735.1	NM_001030055	
POTEB2	100287399	broad.mit.edu	37	15	21040785	21040785	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:21040785C>A	ENST00000454856.4	-	11	1602	c.1570G>T	c.(1570-1572)Gta>Tta	p.V524L	MIR3118-4_ENST00000584700.1_RNA	NM_001277303.1	NP_001264232.1	H3BUK9	POTB2_HUMAN	POTE ankyrin domain family, member B2	524								p.V524L(1)									TTTTCTTTTACACTTTCAATT	0.348																																					p.V561L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1681T	15						.																																			19305337	SO:0001583	missense	339010	exon11				CCDS59248.1	15q11.2	2014-01-29			ENSG00000230031	ENSG00000230031		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	48327	protein-coding gene	gene with protein product							Standard	NM_001277303		Approved			H3BUK9	OTTHUMG00000185829	ENST00000454856.4:c.1570G>T	15.37:g.21040785C>A	ENSP00000456953:p.Val524Leu	Somatic		Capture	Illumina HiSeq	Phase_I	19305337	NM_207355		Missense_Mutation	SNP	ENST00000454856.4	37	CCDS59248.1																																																																																				0.348	POTEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471435.1		
ATP10A	57194	broad.mit.edu	37	15	25963468	25963468	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:25963468C>T	ENST00000356865.6	-	8	1553	c.1442G>A	c.(1441-1443)cGc>cAc	p.R481H		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	481					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R481H(1)		NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GATGCTGCCGCGCTGGGACAC	0.716																																					p.R481H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1442A	15						.						27.0	25.0	26.0					15																	25963468		2200	4295	6495	23514561	SO:0001583	missense	57194	exon8			AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1442G>A	15.37:g.25963468C>T	ENSP00000349325:p.Arg481His	Somatic		Capture	Illumina HiSeq	Phase_I	23514561	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974156	0.53720	.	.	ENSG00000206190	ENST00000356865	T	0.67345	-0.26	5.14	5.14	0.70334	HAD-like domain (1);	0.062016	0.64402	D	0.000003	T	0.61438	0.2347	L	0.43923	1.385	0.58432	D	0.999996	B	0.25850	0.136	B	0.21546	0.035	T	0.59053	-0.7526	10	0.41790	T	0.15	-17.0868	18.6071	0.91271	0.0:1.0:0.0:0.0	.	481	O60312	AT10A_HUMAN	H	481	ENSP00000349325:R481H	ENSP00000349325:R481H	R	-	2	0	ATP10A	23514561	0.993000	0.37304	0.124000	0.21820	0.340000	0.28889	3.146000	0.50631	2.382000	0.81193	0.655000	0.94253	CGC		0.716	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
OCA2	4948	broad.mit.edu	37	15	28171292	28171292	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:28171292G>A	ENST00000354638.3	-	19	2215	c.2060C>T	c.(2059-2061)gCg>gTg	p.A687V	OCA2_ENST00000353809.5_Missense_Mutation_p.A663V	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	687					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)	p.A687V(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		AACAAAGAGCGCTGCAAAAAA	0.368									Oculocutaneous Albinism																												p.A687V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2060T	15						.						105.0	110.0	108.0					15																	28171292		2203	4300	6503	25844887	SO:0001583	missense	4948	exon19	Familial Cancer Database			CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2060C>T	15.37:g.28171292G>A	ENSP00000346659:p.Ala687Val	Somatic		Capture	Illumina HiSeq	Phase_I	25844887	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.751862	0.69533	.	.	ENSG00000104044	ENST00000354638;ENST00000353809	D;D	0.94793	-3.52;-3.52	5.75	5.75	0.90469	Divalent ion symporter (1);	0.163308	0.52532	D	0.000067	D	0.97056	0.9038	M	0.86097	2.795	0.80722	D	1	D;D	0.65815	0.995;0.988	P;P	0.59889	0.847;0.865	D	0.97437	1.0019	10	0.87932	D	0	-10.7247	17.446	0.87579	0.0:0.0:1.0:0.0	.	663;687	Q04671-2;Q04671	.;P_HUMAN	V	687;663	ENSP00000346659:A687V;ENSP00000261276:A663V	ENSP00000261276:A663V	A	-	2	0	OCA2	25844887	1.000000	0.71417	0.896000	0.35187	0.919000	0.55068	5.261000	0.65496	2.725000	0.93324	0.655000	0.94253	GCG		0.368	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
HERC2	8924	broad.mit.edu	37	15	28447529	28447529	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:28447529G>T	ENST00000261609.7	-	46	7552	c.7444C>A	c.(7444-7446)Ctc>Atc	p.L2482I		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.L2482I(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GCACCAGTGAGAGACTTCAGG	0.562																																					p.L2482I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C7444A	15						.						49.0	38.0	41.0					15																	28447529		2203	4300	6503	26121124	SO:0001583	missense	8924	exon46			AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.7444C>A	15.37:g.28447529G>T	ENSP00000261609:p.Leu2482Ile	Somatic		Capture	Illumina HiSeq	Phase_I	26121124	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	G	14.80	2.642234	0.47153	.	.	ENSG00000128731	ENST00000261609	T	0.57273	0.41	3.99	3.03	0.35002	.	0.071147	0.56097	D	0.000025	T	0.48572	0.1507	L	0.52905	1.665	0.58432	D	0.999998	D	0.53885	0.963	P	0.44359	0.447	T	0.49753	-0.8906	10	0.46703	T	0.11	.	11.021	0.47718	0.0965:0.0:0.9035:0.0	.	2482	O95714	HERC2_HUMAN	I	2482	ENSP00000261609:L2482I	ENSP00000261609:L2482I	L	-	1	0	HERC2	26121124	1.000000	0.71417	0.013000	0.15412	0.395000	0.30598	5.608000	0.67654	0.971000	0.38288	0.456000	0.33151	CTC		0.562	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
NDNL2	56160	broad.mit.edu	37	15	29561225	29561225	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:29561225G>A	ENST00000332303.4	-	1	808	c.685C>T	c.(685-687)Cga>Tga	p.R229*	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	229	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)		p.R229*(1)		breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		TAACGCTGTCGCACAAAGTCC	0.532																																					p.R229X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C685T	15						.						68.0	75.0	73.0					15																	29561225		2203	4300	6503	27348517	SO:0001587	stop_gained	56160	exon1			AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.685C>T	15.37:g.29561225G>A	ENSP00000330694:p.Arg229*	Somatic		Capture	Illumina HiSeq	Phase_I	27348517	NM_138704	Q8IW16|Q8TEI6|Q9H214	Nonsense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	G	37	6.068962	0.97256	.	.	ENSG00000185115	ENST00000332303	.	.	.	4.1	3.16	0.36331	.	0.069228	0.56097	D	0.000039	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	.	9.1001	0.36662	0.0:0.0:0.7819:0.2181	.	.	.	.	X	229	.	ENSP00000330694:R229X	R	-	1	2	NDNL2	27348517	0.989000	0.36119	0.984000	0.44739	0.885000	0.51271	1.680000	0.37607	1.262000	0.44165	0.563000	0.77884	CGA		0.532	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704	
FMN1	342184	broad.mit.edu	37	15	33192314	33192314	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:33192314C>T	ENST00000559047.1	-	11	3519	c.3520G>A	c.(3520-3522)Gtg>Atg	p.V1174M	FMN1_ENST00000334528.9_Missense_Mutation_p.V951M|FMN1_ENST00000561249.1_Missense_Mutation_p.V1076M			Q68DA7	FMN1_HUMAN	formin 1	1174	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.V951M(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		ACGCTCTTCACGTGCAGCAAG	0.423																																					p.V951M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2851A	15						.						86.0	84.0	85.0					15																	33192314		1923	4154	6077	30979606	SO:0001583	missense	342184	exon10			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.3520G>A	15.37:g.33192314C>T	ENSP00000454047:p.Val1174Met	Somatic		Capture	Illumina HiSeq	Phase_I	30979606	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	T	11.87	1.769050	0.31320	.	.	ENSG00000248905	ENST00000334528	T	0.62941	-0.01	5.87	5.87	0.94306	.	0.202357	0.64402	N	0.000019	T	0.33556	0.0867	N	0.01352	-0.895	.	.	.	B	0.24258	0.1	B	0.09377	0.004	T	0.42766	-0.9432	9	0.48119	T	0.1	.	12.3288	0.55026	0.0:0.0658:0.0:0.9342	.	951	Q68DA7-5	.	M	951	ENSP00000333950:V951M	ENSP00000333950:V951M	V	-	1	0	FMN1	30979606	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.730000	0.47335	1.158000	0.42547	-0.254000	0.11334	GTG		0.423	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
THBS1	7057	broad.mit.edu	37	15	39880733	39880733	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:39880733G>A	ENST00000260356.5	+	10	1643	c.1478G>A	c.(1477-1479)gGa>gAa	p.G493E		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	493	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)	p.G493E(1)		breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		ACAGTCAATGGAGGCTGGGGT	0.498																																					p.G493E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1478A	15						.						61.0	61.0	61.0					15																	39880733		2200	4297	6497	37668025	SO:0001583	missense	7057	exon10				CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.1478G>A	15.37:g.39880733G>A	ENSP00000260356:p.Gly493Glu	Somatic		Capture	Illumina HiSeq	Phase_I	37668025	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	.	.	.	.	.	.	.	.	.	.	G	33	5.271007	0.95429	.	.	ENSG00000137801	ENST00000260356	T	0.62364	0.03	5.87	5.87	0.94306	.	0.000000	0.35262	N	0.003326	D	0.86464	0.5939	H	0.95780	3.72	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89582	0.3821	10	0.87932	D	0	-11.7385	20.1976	0.98245	0.0:0.0:1.0:0.0	.	493	P07996	TSP1_HUMAN	E	493	ENSP00000260356:G493E	ENSP00000260356:G493E	G	+	2	0	THBS1	37668025	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.864000	0.99589	2.772000	0.95346	0.655000	0.94253	GGA		0.498	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
DISP2	85455	broad.mit.edu	37	15	40661290	40661290	+	Missense_Mutation	SNP	G	G	A	rs149430916	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:40661290G>A	ENST00000267889.3	+	8	3064	c.2977G>A	c.(2977-2979)Gtg>Atg	p.V993M	LINC00594_ENST00000561261.1_lincRNA|RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	993					smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)		p.V993M(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCTATTCTCCGTGGCAGCTGT	0.622													G|||	3	0.000599042	0.0008	0.0	5008	,	,		21275	0.0		0.001	False		,,,				2504	0.001				p.V993M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2977A	15						.	G	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	70.0	59.0	63.0		2977	4.1	0.8	15	dbSNP_134	63	8,8592	5.7+/-21.5	0,8,4292	yes	missense	DISP2	NM_033510.1	21	0,10,6493	AA,AG,GG		0.093,0.0454,0.0769	probably-damaging	993/1402	40661290	10,12996	2203	4300	6503	38448582	SO:0001583	missense	85455	exon8			AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.2977G>A	15.37:g.40661290G>A	ENSP00000267889:p.Val993Met	Somatic		Capture	Illumina HiSeq	Phase_I	38448582	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	14.60	2.585170	0.46110	4.54E-4	9.3E-4	ENSG00000140323	ENST00000267889	D	0.92099	-2.97	5.03	4.1	0.47936	.	0.334872	0.32244	N	0.006378	D	0.90549	0.7038	L	0.54323	1.7	0.26563	N	0.973702	P	0.52170	0.951	B	0.44224	0.444	D	0.85287	0.1065	10	0.54805	T	0.06	-5.7383	15.4868	0.75573	0.0:0.139:0.8609:0.0	.	993	A7MBM2	DISP2_HUMAN	M	993	ENSP00000267889:V993M	ENSP00000267889:V993M	V	+	1	0	DISP2	38448582	1.000000	0.71417	0.775000	0.31657	0.880000	0.50808	3.720000	0.54933	1.323000	0.45263	0.505000	0.49811	GTG		0.622	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
RHOV	171177	broad.mit.edu	37	15	41166149	41166149	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:41166149A>G	ENST00000220507.4	-	1	338	c.189T>C	c.(187-189)acT>acC	p.T63T	AC025166.1_ENST00000582049.1_RNA	NM_133639.3	NP_598378.3			ras homolog family member V									p.T63T(1)		central_nervous_system(1)|large_intestine(1)	2		all_cancers(109;1.42e-13)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.58e-05)|COAD - Colon adenocarcinoma(120;0.149)|BRCA - Breast invasive adenocarcinoma(123;0.163)		TGTCCAGCGCAGTGGGCCGGT	0.706																																					p.T63T	Pancreas(13;103 483 3593 12123 44457)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T189C	15						.						30.0	29.0	30.0					15																	41166149		2202	4298	6500	38953441	SO:0001819	synonymous_variant	171177	exon1			AY059636	CCDS10068.1	15q13.3	2012-02-27	2012-02-27	2004-03-24	ENSG00000104140	ENSG00000104140			18313	protein-coding gene	gene with protein product			"""ras homolog gene family, member V"""	ARHV		11839775	Standard	NM_133639		Approved	Chp, WRCH2	uc001znd.3	Q96L33	OTTHUMG00000130134	ENST00000220507.4:c.189T>C	15.37:g.41166149A>G		Somatic		Capture	Illumina HiSeq	Phase_I	38953441	NM_133639		Silent	SNP	ENST00000220507.4	37	CCDS10068.1																																																																																				0.706	RHOV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252442.1		
MAPKBP1	23005	broad.mit.edu	37	15	42067544	42067544	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:42067544G>A	ENST00000456763.2	+	2	267	c.71G>A	c.(70-72)cGc>cAc	p.R24H	MAPKBP1_ENST00000457542.2_Missense_Mutation_p.R24H|MAPKBP1_ENST00000260357.7_5'UTR|RP11-107F6.3_ENST00000562063.1_lincRNA|MAPKBP1_ENST00000507762.1_3'UTR|MAPKBP1_ENST00000221214.6_Missense_Mutation_p.R24H|MAPKBP1_ENST00000514566.1_Missense_Mutation_p.R24H	NM_001128608.1	NP_001122080.1	O60336	MABP1_HUMAN	mitogen-activated protein kinase binding protein 1	24								p.R24H(1)		breast(6)|central_nervous_system(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_cancers(109;7.71e-14)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.95e-17)|GBM - Glioblastoma multiforme(94;5.71e-07)|Lung(196;0.0436)|BRCA - Breast invasive adenocarcinoma(123;0.203)|LUSC - Lung squamous cell carcinoma(244;0.225)		ATCAAACTGCGCAGGAGTAAG	0.537																																					p.R24H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G71A	15						.						109.0	96.0	100.0					15																	42067544		2203	4300	6503	39854836	SO:0001583	missense	23005	exon2			AB011168	CCDS32201.1, CCDS45239.1, CCDS58359.1	15q15.1	2013-01-10	2008-01-30		ENSG00000137802	ENSG00000137802		"""WD repeat domain containing"""	29536	protein-coding gene	gene with protein product			"""mitogen activated protein kinase binding protein 1"""			9628581, 10471813	Standard	NM_014994		Approved	KIAA0596	uc001zok.4	O60336	OTTHUMG00000160227	ENST00000456763.2:c.71G>A	15.37:g.42067544G>A	ENSP00000393099:p.Arg24His	Somatic		Capture	Illumina HiSeq	Phase_I	39854836	NM_014994	A6NM93|A8K8P9|Q14CB5|Q14CD8|Q49AJ8|Q5W9G9	Missense_Mutation	SNP	ENST00000456763.2	37	CCDS45239.1	.	.	.	.	.	.	.	.	.	.	G	33	5.254297	0.95336	.	.	ENSG00000137802	ENST00000457542;ENST00000221214;ENST00000456763;ENST00000514566;ENST00000510535	T;T;T;T;T	0.60171	0.9;1.25;0.95;1.12;0.21	6.13	6.13	0.99165	.	0.059805	0.64402	D	0.000011	T	0.72104	0.3419	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;0.97;0.999	D;B;D	0.67900	0.931;0.367;0.954	T	0.71471	-0.4583	10	0.62326	D	0.03	-10.6019	17.7569	0.88451	0.0:0.0:1.0:0.0	.	24;24;24	O60336-2;O60336;O60336-6	.;MABP1_HUMAN;.	H	24	ENSP00000397570:R24H;ENSP00000221214:R24H;ENSP00000393099:R24H;ENSP00000426154:R24H;ENSP00000422132:R24H	ENSP00000221214:R24H	R	+	2	0	MAPKBP1	39854836	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	6.310000	0.72830	2.932000	0.99384	0.644000	0.83932	CGC		0.537	MAPKBP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000359745.1	NM_014994	
ZNF106	64397	broad.mit.edu	37	15	42742266	42742266	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:42742266G>A	ENST00000263805.4	-	2	2461	c.2135C>T	c.(2134-2136)tCg>tTg	p.S712L	ZNF106_ENST00000565611.1_Intron|ZNF106_ENST00000565380.1_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	712					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.S712L(1)									GAGAGGGCCCGAGGGCTGACT	0.458																																					p.S712L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2135T	15						.						104.0	105.0	105.0					15																	42742266		2203	4299	6502	40529558	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.2135C>T	15.37:g.42742266G>A	ENSP00000263805:p.Ser712Leu	Somatic		Capture	Illumina HiSeq	Phase_I	40529558	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.832938	0.50951	.	.	ENSG00000103994	ENST00000263805	T	0.53640	0.61	5.52	4.61	0.57282	.	0.328689	0.29565	N	0.011789	T	0.41213	0.1149	L	0.53249	1.67	0.80722	D	1	B;B	0.28667	0.219;0.032	B;B	0.18871	0.023;0.004	T	0.30297	-0.9983	10	0.38643	T	0.18	-0.7422	12.4362	0.55600	0.0822:0.0:0.9178:0.0	.	495;712	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	L	712	ENSP00000263805:S712L	ENSP00000263805:S712L	S	-	2	0	ZFP106	40529558	0.604000	0.26932	0.921000	0.36526	0.905000	0.53344	2.991000	0.49409	1.466000	0.48025	0.650000	0.86243	TCG		0.458	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473	
SPG11	80208	broad.mit.edu	37	15	44887652	44887652	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:44887652G>T	ENST00000261866.7	-	26	4456	c.4440C>A	c.(4438-4440)gcC>gcA	p.A1480A	SPG11_ENST00000558319.1_Silent_p.A1480A|SPG11_ENST00000535302.2_Silent_p.A1480A|SPG11_ENST00000427534.2_Silent_p.A1480A	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1480					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.A1480A(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		AAATGGCACTGGCACCCTGCC	0.428																																					p.A1480A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4440A	15						.						69.0	62.0	65.0					15																	44887652		2198	4298	6496	42674944	SO:0001819	synonymous_variant	80208	exon26				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.4440C>A	15.37:g.44887652G>T		Somatic		Capture	Illumina HiSeq	Phase_I	42674944	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	37	CCDS10112.1																																																																																				0.428	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
SPG11	80208	broad.mit.edu	37	15	44891016	44891016	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:44891016A>G	ENST00000261866.7	-	22	3721	c.3705T>C	c.(3703-3705)aaT>aaC	p.N1235N	SPG11_ENST00000558319.1_Silent_p.N1235N|SPG11_ENST00000535302.2_Silent_p.N1235N|SPG11_ENST00000427534.2_Silent_p.N1235N	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1235					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.N1235N(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		CATAGGCTTCATTGCCTACTT	0.408																																					p.N1235N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T3705C	15						.						81.0	71.0	75.0					15																	44891016		2198	4298	6496	42678308	SO:0001819	synonymous_variant	80208	exon22				CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3705T>C	15.37:g.44891016A>G		Somatic		Capture	Illumina HiSeq	Phase_I	42678308	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Silent	SNP	ENST00000261866.7	37	CCDS10112.1																																																																																				0.408	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
DUOX1	53905	broad.mit.edu	37	15	45454098	45454098	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:45454098G>T	ENST00000321429.4	+	31	4426	c.4019G>T	c.(4018-4020)gGg>gTg	p.G1340V	DUOX1_ENST00000561166.1_Missense_Mutation_p.G986V|CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Missense_Mutation_p.G1340V	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1340	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)	p.G1340V(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CGGGCAGCAGGGCCCTGGACC	0.632																																					p.G1340V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4019T	15						.						69.0	61.0	63.0					15																	45454098		2198	4298	6496	43241390	SO:0001583	missense	53905	exon31			AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.4019G>T	15.37:g.45454098G>T	ENSP00000317997:p.Gly1340Val	Somatic		Capture	Illumina HiSeq	Phase_I	43241390	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.346933	0.82022	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	T;T	0.26373	1.74;1.74	4.22	4.22	0.49857	Riboflavin synthase-like beta-barrel (1);FAD-binding 8 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.65228	0.2671	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78760	-0.2078	10	0.87932	D	0	-31.3357	14.4433	0.67333	0.0:0.0:1.0:0.0	.	1340	Q9NRD9	DUOX1_HUMAN	V	1340	ENSP00000317997:G1340V;ENSP00000373689:G1340V	ENSP00000317997:G1340V	G	+	2	0	DUOX1	43241390	1.000000	0.71417	0.987000	0.45799	0.931000	0.56810	9.625000	0.98406	2.345000	0.79718	0.555000	0.69702	GGG		0.632	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
CEP152	22995	broad.mit.edu	37	15	49090225	49090225	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:49090225A>G	ENST00000380950.2	-	3	298	c.111T>C	c.(109-111)ctT>ctC	p.L37L	CEP152_ENST00000399334.3_Silent_p.L37L|CEP152_ENST00000325747.5_Silent_p.L37L	NM_001194998.1|NM_014985.3	NP_001181927.1|NP_055800.2	O94986	CE152_HUMAN	centrosomal protein 152kDa	37					cell projection organization (GO:0030030)|centriole replication (GO:0007099)|centrosome duplication (GO:0051298)|de novo centriole assembly (GO:0098535)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|deuterosome (GO:0098536)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)	p.L37L(1)		breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(16)|lung(30)|ovary(1)|prostate(2)|skin(2)	63		all_lung(180;0.0428)		all cancers(107;1.08e-07)|GBM - Glioblastoma multiforme(94;2.32e-06)		TGTCATGGGGAAGGTCTGTGA	0.502																																					p.L37L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T111C	15						.						76.0	79.0	78.0					15																	49090225		2068	4212	6280	46877517	SO:0001819	synonymous_variant	22995	exon3			AB020719	CCDS42033.1, CCDS58361.1	15q21.1	2014-02-20							29298	protein-coding gene	gene with protein product	"""asterless"""	613529	"""microcephaly, primary autosomal recessive 4"""	MCPH4		14654843, 21131973	Standard	NM_014985		Approved	KIAA0912, SCKL5	uc001zwz.3	O94986		ENST00000380950.2:c.111T>C	15.37:g.49090225A>G		Somatic		Capture	Illumina HiSeq	Phase_I	46877517	NM_001194998	E7ER66|Q17RV1|Q6NTA0	Silent	SNP	ENST00000380950.2	37	CCDS58361.1																																																																																				0.502	CEP152-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417365.1	NM_014985	
FGF7	2252	broad.mit.edu	37	15	49716603	49716603	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:49716603C>G	ENST00000267843.4	+	2	720	c.109C>G	c.(109-111)Cca>Gca	p.P37A	FGF7_ENST00000560270.1_Missense_Mutation_p.P37A|FAM227B_ENST00000299338.6_Intron|FAM227B_ENST00000561064.1_Intron	NM_002009.3	NP_002000.1	P21781	FGF7_HUMAN	fibroblast growth factor 7	37					actin cytoskeleton reorganization (GO:0031532)|branching involved in salivary gland morphogenesis (GO:0060445)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle morphogenesis (GO:0031069)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|protein localization to cell surface (GO:0034394)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)|response to wounding (GO:0009611)|secretion by lung epithelial cell involved in lung growth (GO:0061033)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)	p.P37A(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		all_lung(180;0.00391)		all cancers(107;3.61e-08)|GBM - Glioblastoma multiforme(94;4.06e-05)		TGACATGACTCCAGAGCAAAT	0.423																																					p.P37A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C109G	15						.						163.0	143.0	150.0					15																	49716603		2196	4295	6491	47503895	SO:0001583	missense	2252	exon2			M60828	CCDS10131.1	15q21.2	2014-01-30	2010-08-18		ENSG00000140285	ENSG00000140285		"""Endogenous ligands"""	3685	protein-coding gene	gene with protein product	"""keratinocyte growth factor"""	148180	"""fibroblast growth factor 7 (keratinocyte growth factor)"""			7749227, 1409637	Standard	NM_002009		Approved	KGF	uc001zxn.3	P21781	OTTHUMG00000131517	ENST00000267843.4:c.109C>G	15.37:g.49716603C>G	ENSP00000267843:p.Pro37Ala	Somatic		Capture	Illumina HiSeq	Phase_I	47503895	NM_002009	H0YNY5|Q6FGV5|Q96FG5	Missense_Mutation	SNP	ENST00000267843.4	37	CCDS10131.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223158	0.58668	.	.	ENSG00000140285	ENST00000267843	T	0.39056	1.1	5.7	4.76	0.60689	.	0.000000	0.64402	D	0.000002	T	0.53997	0.1831	.	.	.	0.48452	D	0.999659	D	0.76494	0.999	D	0.78314	0.991	T	0.49224	-0.8962	9	0.08179	T	0.78	.	16.4886	0.84191	0.0:0.8688:0.1312:0.0	.	37	P21781	FGF7_HUMAN	A	37	ENSP00000267843:P37A	ENSP00000267843:P37A	P	+	1	0	FGF7	47503895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.488000	0.60300	1.381000	0.46364	0.655000	0.94253	CCA		0.423	FGF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254374.3	NM_002009	
TRPM7	54822	broad.mit.edu	37	15	50903457	50903457	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:50903457C>A	ENST00000313478.7	-	17	2394	c.2113G>T	c.(2113-2115)Gct>Tct	p.A705S	TRPM7_ENST00000560955.1_Missense_Mutation_p.A705S	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	705					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.A705S(1)		breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		AATTTCATAGCCATGGTTTCA	0.363																																					p.A705S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2113T	15						.						107.0	96.0	99.0					15																	50903457		1826	4087	5913	48690749	SO:0001583	missense	54822	exon17			AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.2113G>T	15.37:g.50903457C>A	ENSP00000320239:p.Ala705Ser	Somatic		Capture	Illumina HiSeq	Phase_I	48690749	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	Missense_Mutation	SNP	ENST00000313478.7	37	CCDS42035.1	.	.	.	.	.	.	.	.	.	.	C	34	5.388269	0.95988	.	.	ENSG00000092439	ENST00000313478	D	0.92752	-3.1	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.93093	0.7801	M	0.67700	2.07	0.80722	D	1	P	0.43314	0.803	P	0.45449	0.481	D	0.93711	0.7024	10	0.87932	D	0	-16.8137	19.4944	0.95065	0.0:1.0:0.0:0.0	.	705	Q96QT4	TRPM7_HUMAN	S	705	ENSP00000320239:A705S	ENSP00000320239:A705S	A	-	1	0	TRPM7	48690749	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.045000	0.71020	2.597000	0.87782	0.655000	0.94253	GCT		0.363	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
BCL2L10	10017	broad.mit.edu	37	15	52404729	52404729	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:52404729G>A	ENST00000561198.1	-	1	236	c.195C>T	c.(193-195)tcC>tcT	p.S65S	BCL2L10_ENST00000260442.3_Silent_p.S65S			Q9HD36	B2L10_HUMAN	BCL2-like 10 (apoptosis facilitator)	55					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|female gamete generation (GO:0007292)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|positive regulation of apoptotic process (GO:0043065)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.S65S(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2				all cancers(107;0.0148)		CGAGGTAGGCGGAGAAAAAGG	0.716																																					p.S65S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C195T	15						.						11.0	14.0	13.0					15																	52404729		2182	4283	6465	50192021	SO:0001819	synonymous_variant	10017	exon1			AF285092	CCDS10148.1	15q21	2007-03-02			ENSG00000137875	ENSG00000137875			993	protein-coding gene	gene with protein product		606910				9829980, 9878060	Standard	NM_020396		Approved	Diva, Boo, BCL-B	uc002abq.3	Q9HD36	OTTHUMG00000131893	ENST00000561198.1:c.195C>T	15.37:g.52404729G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50192021	NM_020396	Q3SX80|Q52LQ9|Q8TCS9	Silent	SNP	ENST00000561198.1	37																																																																																					0.716	BCL2L10-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000419386.1		
RSL24D1	51187	broad.mit.edu	37	15	55484982	55484982	+	Missense_Mutation	SNP	C	C	T	rs572620938		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:55484982C>T	ENST00000260443.4	-	2	307	c.131G>A	c.(130-132)cGc>cAc	p.R44H	RSL24D1_ENST00000565854.1_5'UTR	NM_016304.2	NP_057388.1	Q9UHA3	RLP24_HUMAN	ribosomal L24 domain containing 1	44					ribosome biogenesis (GO:0042254)	nucleus (GO:0005634)		p.R44H(1)		central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	7						GCGAGGATTGCGCTTCTTTTT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		17007	0.0		0.0	False		,,,				2504	0.001				p.R44H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G131A	15						.						91.0	87.0	89.0					15																	55484982		2193	4292	6485	53272274	SO:0001583	missense	51187	exon2			AF201949	CCDS10152.1	15q21	2009-02-27	2009-02-27	2009-02-27	ENSG00000137876	ENSG00000137876			18479	protein-coding gene	gene with protein product		613262	"""chromosome 15 open reading frame 15"""	C15orf15		12808088, 11707418	Standard	NM_016304		Approved	HRP-L30-iso, L30, RPL24L, RPL24	uc002acn.3	Q9UHA3	OTTHUMG00000131957	ENST00000260443.4:c.131G>A	15.37:g.55484982C>T	ENSP00000260443:p.Arg44His	Somatic		Capture	Illumina HiSeq	Phase_I	53272274	NM_016304	B2RD72|Q561V8|Q8N6S8|Q96B04|Q96C76|Q96HJ1	Missense_Mutation	SNP	ENST00000260443.4	37	CCDS10152.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.456139	0.63401	.	.	ENSG00000137876	ENST00000260443	.	.	.	5.13	5.13	0.70059	TRASH (1);Ribosomal protein L24e domain (1);	0.000000	0.85682	D	0.000000	T	0.70046	0.3179	M	0.80616	2.505	0.80722	D	1	B	0.18968	0.032	B	0.21708	0.036	T	0.69273	-0.5188	9	0.46703	T	0.11	-6.4889	16.066	0.80870	0.0:1.0:0.0:0.0	.	44	Q9UHA3	RLP24_HUMAN	H	44	.	ENSP00000260443:R44H	R	-	2	0	RSL24D1	53272274	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	6.991000	0.76232	2.364000	0.80123	0.563000	0.77884	CGC		0.348	RSL24D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254916.1	NM_016304	
NEDD4	4734	broad.mit.edu	37	15	56122189	56122189	+	Missense_Mutation	SNP	C	C	T	rs373654655		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:56122189C>T	ENST00000508342.1	-	25	4165	c.3866G>A	c.(3865-3867)cGc>cAc	p.R1289H	NEDD4_ENST00000506154.1_Missense_Mutation_p.R1273H|NEDD4_ENST00000338963.2_Missense_Mutation_p.R1217H|NEDD4_ENST00000435532.3_Missense_Mutation_p.R870H	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	1289	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				adaptive immune response (GO:0002250)|blood vessel morphogenesis (GO:0048514)|cellular response to UV (GO:0034644)|cytokine-mediated signaling pathway (GO:0019221)|development involved in symbiotic interaction (GO:0044111)|endocardial cushion development (GO:0003197)|glucocorticoid receptor signaling pathway (GO:0042921)|lysosomal transport (GO:0007041)|negative regulation of sodium ion transport (GO:0010766)|negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage (GO:0010768)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|neuromuscular junction development (GO:0007528)|neuron projection development (GO:0031175)|outflow tract morphogenesis (GO:0003151)|positive regulation of nucleocytoplasmic transport (GO:0046824)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein catabolic process (GO:0045732)|progesterone receptor signaling pathway (GO:0050847)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein targeting to lysosome (GO:0006622)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|receptor catabolic process (GO:0032801)|receptor internalization (GO:0031623)|regulation of dendrite morphogenesis (GO:0048814)|regulation of ion transmembrane transport (GO:0034765)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|regulation of synapse organization (GO:0050807)|response to calcium ion (GO:0051592)|T cell activation (GO:0042110)|transmission of virus (GO:0019089)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	apicolateral plasma membrane (GO:0016327)|cell cortex (GO:0005938)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	beta-2 adrenergic receptor binding (GO:0031698)|ligase activity (GO:0016874)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)|proline-rich region binding (GO:0070064)|protein domain specific binding (GO:0019904)|RNA polymerase binding (GO:0070063)|sodium channel inhibitor activity (GO:0019871)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)	p.R1217H(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	43				all cancers(107;0.0299)|GBM - Glioblastoma multiforme(80;0.113)		CAAGTCCAGGCGATTAAAACT	0.398																																					p.R870H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2609A	15						.	C	HIS/ARG,HIS/ARG	1,4385	2.1+/-5.4	0,1,2192	69.0	62.0	64.0		2609,3650	5.2	1.0	15		64	0,8584		0,0,4292	no	missense,missense	NEDD4	NM_006154.2,NM_198400.2	29,29	0,1,6484	TT,TC,CC		0.0,0.0228,0.0077	probably-damaging,probably-damaging	870/901,1217/1248	56122189	1,12969	2193	4292	6485	53909481	SO:0001583	missense	4734	exon29			D42055	CCDS10156.1, CCDS45265.1, CCDS61643.1, CCDS61644.1	15q	2012-02-23	2012-02-23		ENSG00000069869	ENSG00000069869			7727	protein-coding gene	gene with protein product	"""receptor-potentiating factor 1"""	602278	"""neural precursor cell expressed, developmentally down-regulated 4"""			9073511, 8649367	Standard	XR_243101		Approved	KIAA0093, MGC176705, NEDD4-1, RPF1	uc002adi.3	P46934	OTTHUMG00000132015	ENST00000508342.1:c.3866G>A	15.37:g.56122189C>T	ENSP00000424827:p.Arg1289His	Somatic		Capture	Illumina HiSeq	Phase_I	53909481	NM_006154	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.647688|4.647688	0.87958|0.87958	2.28E-4|2.28E-4	0.0|0.0	ENSG00000069869|ENSG00000069869	ENST00000508871|ENST00000508342;ENST00000435532;ENST00000338963;ENST00000506154	.|T;T;T;T	.|0.59083	.|0.29;0.29;0.29;0.29	6.08|6.08	5.15|5.15	0.70609|0.70609	.|HECT (4);	.|0.049108	.|0.85682	.|D	.|0.000000	T|T	0.80031|0.80031	0.4549|0.4549	M|M	0.89163|0.89163	3.01|3.01	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0	.|P;D;D;D	.|0.97110	.|0.861;0.998;1.0;1.0	D|D	0.84547|0.84547	0.0642|0.0642	5|10	.|0.87932	.|D	.|0	.|.	15.7703|15.7703	0.78164|0.78164	0.1373:0.8627:0.0:0.0|0.1373:0.8627:0.0:0.0	.|.	.|1273;870;1289;1217	.|P46934-2;P46934-4;P46934;P46934-3	.|.;.;NEDD4_HUMAN;.	T|H	880|1289;870;1217;1273	.|ENSP00000424827:R1289H;ENSP00000410613:R870H;ENSP00000345530:R1217H;ENSP00000422705:R1273H	.|ENSP00000345530:R1217H	A|R	-|-	1|2	0|0	NEDD4|NEDD4	53909481|53909481	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.930000|0.930000	0.56654|0.56654	7.625000|7.625000	0.83145|0.83145	1.549000|1.549000	0.49425|0.49425	0.591000|0.591000	0.81541|0.81541	GCC|CGC		0.398	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400	
TLN2	83660	broad.mit.edu	37	15	63029265	63029265	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:63029265C>T	ENST00000561311.1	+	28	3777	c.3547C>T	c.(3547-3549)Cgt>Tgt	p.R1183C	TLN2_ENST00000306829.6_Missense_Mutation_p.R1183C|TLN2_ENST00000559908.1_3'UTR			Q9Y4G6	TLN2_HUMAN	talin 2	1183	Ala-rich.				cell adhesion (GO:0007155)|cell-cell junction assembly (GO:0007043)|cytoskeletal anchoring at plasma membrane (GO:0007016)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|synapse (GO:0045202)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(3)|breast(6)|central_nervous_system(3)|endometrium(8)|kidney(8)|large_intestine(20)|lung(34)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)	99						AGATGCAGAGCGTCAACAAAG	0.542																																					p.R1183C												.	.	0			c.C3547T	15						.						60.0	55.0	56.0					15																	63029265		2203	4300	6503	60816557	SO:0001583	missense	83660	exon26			AB002318	CCDS32261.1	15q15-q21	2008-07-03			ENSG00000171914	ENSG00000171914			15447	protein-coding gene	gene with protein product		607349				9205841, 11527381	Standard	NM_015059		Approved	KIAA0320, ILWEQ	uc002alb.4	Q9Y4G6	OTTHUMG00000133679	ENST00000561311.1:c.3547C>T	15.37:g.63029265C>T	ENSP00000453508:p.Arg1183Cys	None		Capture	Illumina HiSeq	Phase_I	60816557	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	15.18	2.757019	0.49468	.	.	ENSG00000171914	ENST00000306829	T	0.13901	2.55	5.12	2.76	0.32466	.	0.125811	0.64402	D	0.000001	T	0.07413	0.0187	N	0.08118	0	0.28151	N	0.929382	B	0.21225	0.053	B	0.09377	0.004	T	0.18398	-1.0338	10	0.51188	T	0.08	-1.392	12.3052	0.54898	0.731:0.269:0.0:0.0	.	1183	Q9Y4G6	TLN2_HUMAN	C	1183	ENSP00000303476:R1183C	ENSP00000303476:R1183C	R	+	1	0	TLN2	60816557	1.000000	0.71417	0.985000	0.45067	0.887000	0.51463	7.476000	0.81055	0.352000	0.24053	-0.346000	0.07831	CGT		0.542	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2		
HERC1	8925	broad.mit.edu	37	15	63937724	63937724	+	Missense_Mutation	SNP	C	C	T	rs143508709	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:63937724C>T	ENST00000443617.2	-	56	11123	c.11036G>A	c.(11035-11037)cGc>cAc	p.R3679H		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	3679					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.R3679H(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						CCCTGGAAGGCGGCACCAAGC	0.428													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		19351	0.0		0.0	False		,,,				2504	0.0				p.R3679H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G11036A	15						.	C	HIS/ARG	57,3847		0,57,1895	64.0	63.0	63.0		11036	0.9	1.0	15	dbSNP_134	63	0,8352		0,0,4176	yes	missense	HERC1	NM_003922.3	29	0,57,6071	TT,TC,CC		0.0,1.46,0.4651	benign	3679/4862	63937724	57,12199	1952	4176	6128	61724777	SO:0001583	missense	8925	exon56			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.11036G>A	15.37:g.63937724C>T	ENSP00000390158:p.Arg3679His	Somatic		Capture	Illumina HiSeq	Phase_I	61724777	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	16.48	3.134947	0.56828	0.0146	0.0	ENSG00000103657	ENST00000443617	T	0.63096	-0.02	6.02	0.875	0.19130	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.292091	0.34484	N	0.003932	T	0.28134	0.0694	N	0.08118	0	0.23607	N	0.997305	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	10	0.54805	T	0.06	.	6.994	0.24772	0.0:0.5519:0.2107:0.2374	.	3679	Q15751	HERC1_HUMAN	H	3679	ENSP00000390158:R3679H	ENSP00000390158:R3679H	R	-	2	0	HERC1	61724777	0.502000	0.26107	1.000000	0.80357	0.988000	0.76386	0.292000	0.19011	0.415000	0.25817	0.650000	0.86243	CGC		0.428	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
ZNF609	23060	broad.mit.edu	37	15	64970406	64970406	+	Missense_Mutation	SNP	G	G	A	rs369840470		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:64970406G>A	ENST00000326648.3	+	5	3622	c.3494G>A	c.(3493-3495)cGc>cAc	p.R1165H		NM_015042.1	NP_055857.1	O15014	ZN609_HUMAN	zinc finger protein 609	1165						nucleus (GO:0005634)	metal ion binding (GO:0046872)	p.R1165H(1)		breast(3)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GAGCGGGACCGCAAATTGAAG	0.532																																					p.R1165H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3494A	15						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	74.0	60.0	64.0		3494	5.4	1.0	15		64	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF609	NM_015042.1	29	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	1165/1412	64970406	2,13002	2203	4299	6502	62757459	SO:0001583	missense	23060	exon5			BC014251	CCDS32270.1	15q22.1	2008-05-02				ENSG00000180357		"""Zinc fingers, C2H2-type"""	29003	protein-coding gene	gene with protein product						9205841	Standard	NM_015042		Approved	KIAA0295	uc002ann.3	O15014		ENST00000326648.3:c.3494G>A	15.37:g.64970406G>A	ENSP00000316527:p.Arg1165His	Somatic		Capture	Illumina HiSeq	Phase_I	62757459	NM_015042	Q0D2I2	Missense_Mutation	SNP	ENST00000326648.3	37	CCDS32270.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.945946	0.92593	2.27E-4	1.16E-4	ENSG00000180357	ENST00000326648	T	0.56275	0.47	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.51805	0.1696	L	0.55481	1.735	0.80722	D	1	P	0.50272	0.933	B	0.40009	0.316	T	0.59936	-0.7360	10	0.66056	D	0.02	-11.8951	19.2633	0.93977	0.0:0.0:1.0:0.0	.	1165	O15014	ZN609_HUMAN	H	1165	ENSP00000316527:R1165H	ENSP00000316527:R1165H	R	+	2	0	ZNF609	62757459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.946000	0.87746	2.537000	0.85549	0.650000	0.86243	CGC		0.532	ZNF609-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418130.1	XM_042833	
CILP	8483	broad.mit.edu	37	15	65499138	65499138	+	Missense_Mutation	SNP	G	G	A	rs142891097	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:65499138G>A	ENST00000261883.4	-	4	572	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	136					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)		p.R136C(2)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						CAGAGGAAGCGTACGGTGTAA	0.637																																					p.R136C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C406T	15						.	G	CYS/ARG	0,4402		0,0,2201	74.0	79.0	77.0		406	4.3	1.0	15	dbSNP_134	77	2,8596	2.2+/-6.3	0,2,4297	no	missense	CILP	NM_003613.3	180	0,2,6498	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	136/1185	65499138	2,12998	2201	4299	6500	63286191	SO:0001583	missense	8483	exon4			AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.406C>T	15.37:g.65499138G>A	ENSP00000261883:p.Arg136Cys	Somatic		Capture	Illumina HiSeq	Phase_I	63286191	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	.	.	.	.	.	.	.	.	.	.	G	15.88	2.963210	0.53507	0.0	2.33E-4	ENSG00000138615	ENST00000261883	T	0.25912	1.77	5.3	4.33	0.51752	.	0.108324	0.64402	D	0.000006	T	0.40119	0.1104	M	0.94063	3.49	0.80722	D	1	B	0.29627	0.252	B	0.26614	0.071	T	0.53279	-0.8461	10	0.87932	D	0	-3.6248	12.955	0.58421	0.0:0.0:0.8288:0.1712	.	136	O75339	CILP1_HUMAN	C	136	ENSP00000261883:R136C	ENSP00000261883:R136C	R	-	1	0	CILP	63286191	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.557000	0.82243	2.763000	0.94921	0.561000	0.74099	CGC		0.637	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613	
DENND4A	10260	broad.mit.edu	37	15	65962505	65962505	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:65962505G>A	ENST00000431932.2	-	25	4562	c.4354C>T	c.(4354-4356)Cgg>Tgg	p.R1452W	DENND4A_ENST00000443035.3_Missense_Mutation_p.R1495W	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1452					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1454W(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						GTTCTACACCGAGAGCAACTT	0.378																																					p.R1495W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4483T	15						.						50.0	48.0	49.0					15																	65962505		1869	4103	5972	63749559	SO:0001583	missense	10260	exon26			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.4354C>T	15.37:g.65962505G>A	ENSP00000396830:p.Arg1452Trp	Somatic		Capture	Illumina HiSeq	Phase_I	63749559	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.790393	0.90367	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.06142	3.35;3.34	5.86	4.9	0.64082	.	0.165679	0.53938	D	0.000051	T	0.22666	0.0547	M	0.61703	1.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73708	0.965;0.981	T	0.00028	-1.2298	10	0.66056	D	0.02	.	16.983	0.86333	0.0:0.0:0.8722:0.1278	.	1495;1452	E7EPL3;Q7Z401	.;MYCPP_HUMAN	W	1495;1452	ENSP00000391167:R1495W;ENSP00000396830:R1452W	ENSP00000396830:R1452W	R	-	1	2	DENND4A	63749559	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.437000	0.73421	2.937000	0.99478	0.650000	0.86243	CGG		0.378	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848	
PIAS1	8554	broad.mit.edu	37	15	68378698	68378698	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:68378698G>A	ENST00000249636.6	+	2	227	c.79G>A	c.(79-81)Ggg>Agg	p.G27R	PIAS1_ENST00000545237.1_Missense_Mutation_p.G29R	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	27	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.G27R(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						GGGCTACGCCGGGAGAAACAA	0.403																																					p.G27R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G79A	15						.						33.0	32.0	33.0					15																	68378698		1849	4105	5954	66165752	SO:0001583	missense	8554	exon2			AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"""Zinc fingers, MIZ-type"""	2752	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 3"""	603566	"""DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"""	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.79G>A	15.37:g.68378698G>A	ENSP00000249636:p.Gly27Arg	Somatic		Capture	Illumina HiSeq	Phase_I	66165752	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028744	0.93518	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.46819	0.86;0.86	5.73	5.73	0.89815	DNA-binding SAP (3);	0.000000	0.85682	D	0.000000	T	0.71813	0.3384	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.97110	1.0;0.921	T	0.74228	-0.3733	10	0.87932	D	0	-8.2276	19.49	0.95047	0.0:0.0:1.0:0.0	.	27;27	C5J4B4;O75925	.;PIAS1_HUMAN	R	27;29	ENSP00000249636:G27R;ENSP00000438574:G29R	ENSP00000249636:G27R	G	+	1	0	PIAS1	66165752	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.704000	0.92352	0.650000	0.86243	GGG		0.403	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2		
STOML1	9399	broad.mit.edu	37	15	74277701	74277701	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:74277701T>G	ENST00000316900.5	-	5	872	c.748A>C	c.(748-750)Agc>Cgc	p.S250R	STOML1_ENST00000564777.1_Missense_Mutation_p.S200R|STOML1_ENST00000316911.6_Missense_Mutation_p.S200R|STOML1_ENST00000561656.1_Missense_Mutation_p.S163R|STOML1_ENST00000359750.4_Missense_Mutation_p.S250R|STOML1_ENST00000541638.1_Missense_Mutation_p.S208R	NM_001256672.1|NM_001256675.1|NM_001256677.1|NM_004809.4	NP_001243601.1|NP_001243604.1|NP_001243606.1|NP_004800.2	Q9UBI4	STML1_HUMAN	stomatin (EPB72)-like 1	250						integral component of membrane (GO:0016021)		p.S250R(1)		endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	8						GAGTTCATGCTTCCTCCCAGG	0.682																																					p.S250R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A748C	15						.						21.0	20.0	21.0					15																	74277701		2198	4297	6495	72064754	SO:0001583	missense	9399	exon5			Y16522	CCDS10254.1, CCDS58381.1, CCDS58382.1, CCDS58383.1, CCDS58384.1, CCDS58385.1	15q24-q25	2008-07-18			ENSG00000067221	ENSG00000067221			14560	protein-coding gene	gene with protein product	"""stomatin-like 1"", ""stomatin (EBP72)-like 1"""	608326				9931417	Standard	NM_004809		Approved	hUNC-24, SLP-1, STORP, FLJ36370	uc002awe.4	Q9UBI4	OTTHUMG00000137608	ENST00000316900.5:c.748A>C	15.37:g.74277701T>G	ENSP00000319323:p.Ser250Arg	Somatic		Capture	Illumina HiSeq	Phase_I	72064754	NM_004809	B3KQN0|B4DUU5|B4DXM9|E7ESC0|H3BRP3|O95675|Q4PNR4|Q6FGL8|Q8WYI7|Q9UMB9|Q9UMC0|Q9Y6H9	Missense_Mutation	SNP	ENST00000316900.5	37	CCDS10254.1	.	.	.	.	.	.	.	.	.	.	T	12.11	1.839230	0.32513	.	.	ENSG00000067221	ENST00000316900;ENST00000316911;ENST00000541638;ENST00000359750	D;D;D;D	0.97404	-2.96;-2.56;-2.94;-4.37	4.5	-0.963	0.10330	.	0.574591	0.17781	N	0.162243	D	0.89230	0.6656	N	0.14661	0.345	0.09310	N	1	B;P;B;P;B;B	0.38335	0.066;0.627;0.108;0.627;0.066;0.066	B;B;B;B;B;B	0.34489	0.078;0.184;0.084;0.184;0.042;0.072	D	0.84308	0.0509	10	0.34782	T	0.22	-8.8815	4.9263	0.13894	0.0:0.3282:0.1643:0.5075	.	208;250;200;250;250;250	B4DUU5;E7ESC0;Q9UBI4-2;Q4PNR4;Q53HB6;Q9UBI4	.;.;.;.;.;STML1_HUMAN	R	250;200;208;250	ENSP00000319323:S250R;ENSP00000319384:S200R;ENSP00000442478:S208R;ENSP00000352788:S250R	ENSP00000319323:S250R	S	-	1	0	STOML1	72064754	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	0.046000	0.14035	-0.028000	0.13850	-0.177000	0.13119	AGC		0.682	STOML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269022.1	NM_004809	
ISLR	3671	broad.mit.edu	37	15	74467462	74467462	+	Missense_Mutation	SNP	C	C	T	rs199636609		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:74467462C>T	ENST00000249842.3	+	2	620	c.263C>T	c.(262-264)aCg>aTg	p.T88M	ISLR_ENST00000395118.1_Missense_Mutation_p.T88M|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	88					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)		p.T88M(1)		central_nervous_system(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)	20						GAGATCCGCACGGTGGCCGCC	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		14832	0.001		0.0	False		,,,				2504	0.0				p.T88M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C263T	15						.	C	MET/THR,MET/THR	1,4395	2.1+/-5.4	0,1,2197	38.0	40.0	39.0		263,263	-8.1	0.0	15		39	0,8594		0,0,4297	yes	missense,missense	ISLR	NM_005545.3,NM_201526.1	81,81	0,1,6494	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	88/429,88/429	74467462	1,12989	2198	4297	6495	72254515	SO:0001583	missense	3671	exon2			AB003184	CCDS10260.1	15q23-q24	2013-01-11			ENSG00000129009	ENSG00000129009		"""Immunoglobulin superfamily / I-set domain containing"""	6133	protein-coding gene	gene with protein product		602059				9325048	Standard	NM_005545		Approved	HsT17563	uc002axh.1	O14498	OTTHUMG00000137623	ENST00000249842.3:c.263C>T	15.37:g.74467462C>T	ENSP00000249842:p.Thr88Met	Somatic		Capture	Illumina HiSeq	Phase_I	72254515	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	C	11.49	1.653170	0.29425	2.27E-4	0.0	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.59906	0.23;0.23	4.05	-8.11	0.01082	.	3.975820	0.01371	N	0.012589	T	0.55417	0.1919	M	0.62723	1.935	0.09310	N	1	P	0.52842	0.956	P	0.51266	0.664	T	0.62530	-0.6835	10	0.46703	T	0.11	.	1.7012	0.02873	0.1608:0.1859:0.3269:0.3263	.	88	O14498	ISLR_HUMAN	M	88	ENSP00000249842:T88M;ENSP00000378550:T88M	ENSP00000249842:T88M	T	+	2	0	ISLR	72254515	0.000000	0.05858	0.008000	0.14137	0.493000	0.33554	-1.030000	0.03581	-1.468000	0.01892	-0.671000	0.03813	ACG		0.642	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545	
LMAN1L	79748	broad.mit.edu	37	15	75105270	75105270	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:75105270G>A	ENST00000309664.5	+	1	214	c.75G>A	c.(73-75)acG>acA	p.T25T	LMAN1L_ENST00000379709.3_Silent_p.T25T	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	25						integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.T25T(1)		NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCCCTGAGACGGGGTGTCCTC	0.612																																					p.T25T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G75A	15						.						117.0	108.0	111.0					15																	75105270		2197	4296	6493	72892323	SO:0001819	synonymous_variant	79748	exon1			AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.75G>A	15.37:g.75105270G>A		Somatic		Capture	Illumina HiSeq	Phase_I	72892323	NM_021819	Q6UWN2	Silent	SNP	ENST00000309664.5	37	CCDS10270.1																																																																																				0.612	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
CTSH	1512	broad.mit.edu	37	15	79217759	79217759	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:79217759C>A	ENST00000220166.5	-	10	832	c.723G>T	c.(721-723)gaG>gaT	p.E241D	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	241					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)	p.E241D(1)		central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						GGGCCACAGCCTCCACCATCG	0.537																																					p.E241D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G723T	15						.						94.0	73.0	80.0					15																	79217759		2196	4293	6489	77004814	SO:0001583	missense	1512	exon10			X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.723G>T	15.37:g.79217759C>A	ENSP00000220166:p.Glu241Asp	Somatic		Capture	Illumina HiSeq	Phase_I	77004814	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	.	.	.	.	.	.	.	.	.	.	C	6.485	0.457580	0.12342	.	.	ENSG00000103811	ENST00000220166;ENST00000394758	D	0.87491	-2.26	5.25	4.12	0.48240	Peptidase C1A, papain C-terminal (2);	0.063262	0.64402	D	0.000008	T	0.75693	0.3884	N	0.21142	0.635	0.41888	D	0.990359	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.002	T	0.68447	-0.5406	10	0.18276	T	0.48	.	9.6518	0.39902	0.0:0.888:0.0:0.112	.	241;229	P09668;E9PBP2	CATH_HUMAN;.	D	241;229	ENSP00000220166:E241D	ENSP00000220166:E241D	E	-	3	2	CTSH	77004814	0.782000	0.28689	1.000000	0.80357	0.375000	0.29983	-0.230000	0.09083	2.465000	0.83290	0.467000	0.42956	GAG		0.537	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
FSD2	123722	broad.mit.edu	37	15	83455778	83455778	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:83455778A>T	ENST00000334574.8	-	2	546	c.365T>A	c.(364-366)cTt>cAt	p.L122H	FSD2_ENST00000541889.1_Missense_Mutation_p.L122H			A1L4K1	FSD2_HUMAN	fibronectin type III and SPRY domain containing 2	122								p.L122H(1)		breast(2)|central_nervous_system(1)|large_intestine(5)|lung(10)	18						CTCTCCACTAAGTCTCCAGTC	0.562																																					p.L122H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T365A	15						.						55.0	61.0	59.0					15																	83455778		2038	4190	6228	81252832	SO:0001583	missense	123722	exon2			AK122875	CCDS45332.1, CCDS61738.1	15q25.2	2013-02-11	2006-01-11	2006-01-11		ENSG00000186628		"""Fibronectin type III domain containing"""	18024	protein-coding gene	gene with protein product			"""SPRY domain containing 1"""	SPRYD1			Standard	NM_001007122		Approved	RP11-127F21	uc002bjd.2	A1L4K1		ENST00000334574.8:c.365T>A	15.37:g.83455778A>T	ENSP00000335651:p.Leu122His	Somatic		Capture	Illumina HiSeq	Phase_I	81252832	NM_001007122	B3KVG1|B7ZM02	Missense_Mutation	SNP	ENST00000334574.8	37	CCDS45332.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.195127	0.38806	.	.	ENSG00000186628	ENST00000334574;ENST00000541889	T;T	0.46819	0.86;0.86	5.07	-0.129	0.13502	.	1.060260	0.07438	N	0.896790	T	0.38348	0.1037	L	0.47716	1.5	0.09310	N	1	P;P	0.39216	0.664;0.664	B;B	0.36808	0.233;0.199	T	0.32107	-0.9919	10	0.59425	D	0.04	-1.3573	6.2345	0.20756	0.6763:0.0:0.2108:0.1129	.	122;122	B7ZM02;A1L4K1	.;FSD2_HUMAN	H	122	ENSP00000335651:L122H;ENSP00000444078:L122H	ENSP00000335651:L122H	L	-	2	0	FSD2	81252832	0.000000	0.05858	0.001000	0.08648	0.267000	0.26476	0.251000	0.18257	-0.010000	0.14271	-1.139000	0.01908	CTT		0.562	FSD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418385.1	NM_001007122	
ADAMTSL3	57188	broad.mit.edu	37	15	84639308	84639308	+	Missense_Mutation	SNP	C	C	T	rs146769560	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:84639308C>T	ENST00000286744.5	+	20	2787	c.2563C>T	c.(2563-2565)Cgc>Tgc	p.R855C	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.R855C|ADAMTSL3_ENST00000567716.1_3'UTR	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	855	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.		R -> C (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> H (in dbSNP:rs2277848).			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R855C(2)		NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			CAAAGGTCGGCGCATCCCCCT	0.522																																					p.R855C												ADAMTSL3,large_intestine,colon,Substitution - Missense,0 	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2563T	15						.	C	CYS/ARG	0,4406		0,0,2203	185.0	163.0	171.0		2563	2.2	0.4	15	dbSNP_134	171	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ADAMTSL3	NM_207517.2	180	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	855/1692	84639308	3,13003	2203	4300	6503	82430312	SO:0001583	missense	57188	exon20			AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2563C>T	15.37:g.84639308C>T	ENSP00000286744:p.Arg855Cys	Somatic		Capture	Illumina HiSeq	Phase_I	82430312	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015852	0.54468	0.0	3.49E-4	ENSG00000156218	ENST00000286744	T	0.54071	0.59	4.39	2.23	0.28157	.	0.534882	0.15912	N	0.238571	T	0.58264	0.2110	L	0.60904	1.88	0.09310	N	1	D;D	0.76494	0.989;0.999	P;P	0.57679	0.784;0.825	T	0.44605	-0.9317	10	0.38643	T	0.18	.	8.0926	0.30809	0.3035:0.6088:0.0:0.0878	.	855;855	P82987-2;P82987	.;ATL3_HUMAN	C	855	ENSP00000286744:R855C	ENSP00000286744:R855C	R	+	1	0	ADAMTSL3	82430312	0.915000	0.31059	0.374000	0.26016	0.370000	0.29829	1.198000	0.32223	0.983000	0.38602	0.650000	0.86243	CGC		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ZSCAN2	54993	broad.mit.edu	37	15	85164147	85164147	+	Missense_Mutation	SNP	G	G	A	rs141372598		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:85164147G>A	ENST00000448803.2	+	3	1013	c.721G>A	c.(721-723)Gag>Aag	p.E241K	ZSCAN2_ENST00000546148.1_Missense_Mutation_p.E241K|ZSCAN2_ENST00000358472.3_Missense_Mutation_p.E91K|ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000327179.6_Missense_Mutation_p.E240K|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000485222.2_Intron	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	241					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E241K(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		CATCACACACGAGAGGACCCA	0.502																																					p.E241K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G721A	15						.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	90.0	94.0	93.0		721	4.8	0.9	15	dbSNP_134	93	0,8598		0,0,4299	no	missense	ZSCAN2	NM_181877.3	56	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	241/615	85164147	1,13003	2203	4299	6502	82965151	SO:0001583	missense	54993	exon3			BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"""-"", ""Zinc fingers, C2H2-type"""	20994	protein-coding gene	gene with protein product			"""zinc finger protein 29"""	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.721G>A	15.37:g.85164147G>A	ENSP00000410198:p.Glu241Lys	Somatic		Capture	Illumina HiSeq	Phase_I	82965151	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Missense_Mutation	SNP	ENST00000448803.2	37	CCDS10329.2	.	.	.	.	.	.	.	.	.	.	G	13.15	2.151204	0.38021	2.27E-4	0.0	ENSG00000176371	ENST00000448803;ENST00000546148;ENST00000358472;ENST00000327179;ENST00000379353	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.78	4.78	0.61160	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.335440	0.25610	N	0.029496	T	0.21227	0.0511	N	0.03903	-0.33	0.30529	N	0.767615	P;B	0.35628	0.513;0.06	B;B	0.30179	0.112;0.016	T	0.11867	-1.0570	9	.	.	.	-19.0421	11.5394	0.50657	0.0:0.1814:0.8186:0.0	.	241;241	A8K5A9;Q7Z7L9	.;ZSCA2_HUMAN	K	241;241;91;240;222	ENSP00000410198:E241K;ENSP00000445451:E241K;ENSP00000351257:E91K;ENSP00000325123:E240K	.	E	+	1	0	ZSCAN2	82965151	0.000000	0.05858	0.908000	0.35775	0.704000	0.40688	0.271000	0.18626	2.355000	0.79922	0.655000	0.94253	GAG		0.502	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894	
AGBL1	123624	broad.mit.edu	37	15	86814893	86814893	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:86814893C>T	ENST00000441037.2	+	14	1988	c.1893C>T	c.(1891-1893)ggC>ggT	p.G631G	AGBL1_ENST00000389298.3_Silent_p.G362G|AGBL1_ENST00000421325.2_Silent_p.G631G	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	631					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.G631G(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						CTCTTCTTGGCAAACCCACCT	0.423																																					p.G631G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1893T	15						.						166.0	161.0	163.0					15																	86814893		1867	4092	5959	84615897	SO:0001819	synonymous_variant	123624	exon14			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.1893C>T	15.37:g.86814893C>T		Somatic		Capture	Illumina HiSeq	Phase_I	84615897	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																				0.423	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
AGBL1	123624	broad.mit.edu	37	15	87066096	87066096	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:87066096G>A	ENST00000441037.2	+	18	2568	c.2473G>A	c.(2473-2475)Gct>Act	p.A825T	AGBL1_ENST00000421325.2_Missense_Mutation_p.A825T|AGBL1_ENST00000389298.3_Missense_Mutation_p.A556T	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	825					C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytoplasm (GO:0005737)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.A825T(1)		NS(3)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(2)|lung(28)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	62						TTCTCCCAGTGCTCATCTGCA	0.488																																					p.A825T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2473A	15						.						147.0	145.0	146.0					15																	87066096		2025	4191	6216	84867100	SO:0001583	missense	123624	exon18			AK056872	CCDS58398.1	15q25.3	2014-06-23			ENSG00000166748	ENSG00000166748			26504	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 4"""	615496				21074048, 24094747	Standard	NM_152336		Approved	FLJ32310, CCP4	uc002blz.1	Q96MI9	OTTHUMG00000149978	ENST00000441037.2:c.2473G>A	15.37:g.87066096G>A	ENSP00000413001:p.Ala825Thr	Somatic		Capture	Illumina HiSeq	Phase_I	84867100	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	10.97	1.501890	0.26949	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10573	2.86;2.86	5.84	2.6	0.31112	Peptidase M14, carboxypeptidase A (1);	0.683858	0.13166	N	0.408708	T	0.11623	0.0283	L	0.49126	1.545	0.09310	N	1	P	0.39352	0.669	B	0.43838	0.433	T	0.20874	-1.0262	10	0.48119	T	0.1	-1.8294	2.3342	0.04243	0.1566:0.1195:0.4934:0.2305	.	825	Q96MI9	CBPC4_HUMAN	T	854;825;556	ENSP00000397173:A825T;ENSP00000373949:A556T	ENSP00000373949:A556T	A	+	1	0	AGBL1	84867100	0.001000	0.12720	0.003000	0.11579	0.439000	0.31926	0.736000	0.26130	1.457000	0.47850	0.655000	0.94253	GCT		0.488	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336	
ISG20	3669	broad.mit.edu	37	15	89198655	89198655	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:89198655C>T	ENST00000306072.5	+	4	797	c.439C>T	c.(439-441)Ctt>Ttt	p.L147F	ISG20_ENST00000560741.1_Missense_Mutation_p.L147F|ISG20_ENST00000560746.1_3'UTR	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	147					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)	p.L147F(1)		large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			GAACAGCCTGCTTGGACACAG	0.587																																					p.L147F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C439T	15						.						67.0	67.0	67.0					15																	89198655		2200	4299	6499	86999659	SO:0001583	missense	3669	exon4			X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"""interferon stimulated gene (20kD)"""			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.439C>T	15.37:g.89198655C>T	ENSP00000306565:p.Leu147Phe	Somatic		Capture	Illumina HiSeq	Phase_I	86999659	NM_002201	O00441|O00586	Missense_Mutation	SNP	ENST00000306072.5	37	CCDS10345.1	.	.	.	.	.	.	.	.	.	.	C	8.833	0.940411	0.18281	.	.	ENSG00000172183	ENST00000306072;ENST00000546338	T	0.30448	1.53	4.1	-8.2	0.01045	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	1.596090	0.03507	N	0.218987	T	0.15825	0.0381	N	0.17800	0.525	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.18085	-1.0348	10	0.45353	T	0.12	.	4.4652	0.11685	0.3836:0.4017:0.0:0.2146	.	147	Q96AZ6	ISG20_HUMAN	F	147;155	ENSP00000306565:L147F	ENSP00000306565:L147F	L	+	1	0	ISG20	86999659	0.000000	0.05858	0.000000	0.03702	0.703000	0.40648	-1.324000	0.02690	-1.451000	0.01933	0.467000	0.42956	CTT		0.587	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201	
ANPEP	290	broad.mit.edu	37	15	90347138	90347138	+	Silent	SNP	C	C	T	rs369610508		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:90347138C>T	ENST00000300060.6	-	7	1588	c.1275G>A	c.(1273-1275)gcG>gcA	p.A425A	ANPEP_ENST00000558177.1_5'Flank	NM_001150.2	NP_001141.2	P15144	AMPN_HUMAN	alanyl (membrane) aminopeptidase	425	Metalloprotease.				angiogenesis (GO:0001525)|angiotensin maturation (GO:0002003)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|viral process (GO:0016032)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|receptor activity (GO:0004872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.A425A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	57	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.169)		Ezetimibe(DB00973)|Icatibant(DB06196)	AGGTGGGCTCCGCATAGTCAG	0.632																																					p.A425A	NSCLC(30;827 977 2459 19669 26125)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1275A	15						.	C		0,4400		0,0,2200	62.0	58.0	60.0		1275	-4.6	1.0	15		60	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ANPEP	NM_001150.2		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		425/968	90347138	1,12997	2200	4299	6499	88148142	SO:0001819	synonymous_variant	290	exon7			M22324	CCDS10356.1	15q25-q26	2008-07-31	2008-07-31		ENSG00000166825	ENSG00000166825	3.4.11.2	"""CD molecules"""	500	protein-coding gene	gene with protein product	"""aminopeptidase N"", ""aminopeptidase M"", ""microsomal aminopeptidase"""	151530		CD13, PEPN		2428842, 1977688	Standard	NM_001150		Approved	LAP1, gp150, p150	uc002bop.4	P15144	OTTHUMG00000149814	ENST00000300060.6:c.1275G>A	15.37:g.90347138C>T		Somatic		Capture	Illumina HiSeq	Phase_I	88148142	NM_001150	Q16728|Q6GT90|Q8IUK3|Q8IVH3|Q9UCE0	Silent	SNP	ENST00000300060.6	37	CCDS10356.1																																																																																				0.632	ANPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313425.1		
TTLL13	440307	broad.mit.edu	37	15	90801277	90801277	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:90801277T>C	ENST00000339615.5	+	9	1233	c.943T>C	c.(943-945)Tcg>Ccg	p.S315P	TTLL13_ENST00000438251.1_Missense_Mutation_p.S315P|RP11-697E2.6_ENST00000561573.1_Intron	NM_001029964.2	NP_001025135.2			tubulin tyrosine ligase-like family, member 13									p.S315P(1)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	16	Melanoma(11;0.00551)|Lung NSC(78;0.0178)|all_lung(78;0.0378)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|BRCA - Breast invasive adenocarcinoma(143;0.0323)|Kidney(142;0.0514)			CAGGAAGCTGTCGACACTCAA	0.562																																					p.S315P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T943C	15						.						97.0	82.0	87.0					15																	90801277		2199	4298	6497	88602281	SO:0001583	missense	440307	exon9			BC036668		15q26.1	2013-02-14				ENSG00000213471		"""Tubulin tyrosine ligase-like family"""	32484	protein-coding gene	gene with protein product						15890843	Standard	NR_104604		Approved	FLJ46079, MGC33417	uc002bpd.1	A6NNM8		ENST00000339615.5:c.943T>C	15.37:g.90801277T>C	ENSP00000345294:p.Ser315Pro	Somatic		Capture	Illumina HiSeq	Phase_I	88602281	NM_001029964		Missense_Mutation	SNP	ENST00000339615.5	37	CCDS32328.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.734671	0.89482	.	.	ENSG00000213471	ENST00000438251;ENST00000339615	T;T	0.07021	3.23;3.23	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000003	T	0.29093	0.0723	M	0.75615	2.305	0.53688	D	0.999972	D	0.76494	0.999	D	0.71656	0.974	T	0.01405	-1.1363	10	0.72032	D	0.01	.	15.1803	0.72952	0.0:0.0:0.0:1.0	.	315	A6NNM8-2	.	P	315	ENSP00000413362:S315P;ENSP00000345294:S315P	ENSP00000345294:S315P	S	+	1	0	TTLL13	88602281	1.000000	0.71417	0.998000	0.56505	0.969000	0.65631	7.558000	0.82253	2.170000	0.68504	0.528000	0.53228	TCG		0.562	TTLL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435854.1	NM_001029964	
IQGAP1	8826	broad.mit.edu	37	15	91027453	91027453	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:91027453C>T	ENST00000268182.5	+	30	3914	c.3790C>T	c.(3790-3792)Cgg>Tgg	p.R1264W	IQGAP1_ENST00000560738.1_Splice_Site_p.R692W	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	1264	C1.				cellular response to calcium ion (GO:0071277)|cellular response to epidermal growth factor stimulus (GO:0071364)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerular visceral epithelial cell development (GO:0072015)|negative regulation of catalytic activity (GO:0043086)|negative regulation of dephosphorylation (GO:0035305)|neuron projection extension (GO:1990138)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|regulation of cytokine production (GO:0001817)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	actin filament (GO:0005884)|axon (GO:0030424)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|midbody (GO:0030496)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)|GTPase inhibitor activity (GO:0005095)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|protein serine/threonine kinase activator activity (GO:0043539)|Ras GTPase activator activity (GO:0005099)	p.R1264W(1)		breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	Melanoma(11;0.00551)|Lung NSC(78;0.0237)|all_lung(78;0.0488)		BRCA - Breast invasive adenocarcinoma(143;0.0745)|KIRC - Kidney renal clear cell carcinoma(17;0.138)|Kidney(142;0.194)			TTATTTCAGACGGTTTTTCCA	0.428																																					p.R1264W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3790T	15						.						128.0	123.0	124.0					15																	91027453		2198	4298	6496	88828457	SO:0001630	splice_region_variant	8826	exon30			D29640	CCDS10362.1	15q26.1	2008-07-18			ENSG00000140575	ENSG00000140575			6110	protein-coding gene	gene with protein product	"""RasGAP-like with IQ motifs"""	603379				8051149, 8670801	Standard	XM_005254984		Approved	p195, KIAA0051, SAR1, HUMORFA01	uc002bpl.1	P46940	OTTHUMG00000149832	ENST00000268182.5:c.3789-1C>T	15.37:g.91027453C>T		Somatic		Capture	Illumina HiSeq	Phase_I	88828457	NM_003870	A7MBM3	Missense_Mutation	SNP	ENST00000268182.5	37	CCDS10362.1	.	.	.	.	.	.	.	.	.	.	C	15.10	2.732158	0.48939	.	.	ENSG00000140575	ENST00000268182	D	0.82619	-1.63	5.02	4.09	0.47781	Rho GTPase activation protein (1);Ras GTPase-activating protein (2);	0.000000	0.85682	D	0.000000	T	0.74168	0.3681	L	0.50333	1.59	0.80722	D	1	P	0.49090	0.919	B	0.29862	0.108	T	0.79075	-0.1952	10	0.87932	D	0	-16.6599	14.2879	0.66258	0.1497:0.8503:0.0:0.0	.	1264	P46940	IQGA1_HUMAN	W	1264	ENSP00000268182:R1264W	ENSP00000268182:R1264W	R	+	1	2	IQGAP1	88828457	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.892000	0.48625	1.448000	0.47680	0.650000	0.86243	CGG		0.428	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870	Missense_Mutation
NR2F2	7026	broad.mit.edu	37	15	96877678	96877678	+	Silent	SNP	C	C	A	rs76163938	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:96877678C>A	ENST00000394166.3	+	2	2205	c.816C>A	c.(814-816)gcC>gcA	p.A272A	NR2F2_ENST00000453270.2_Silent_p.A119A|NR2F2_ENST00000394171.2_Silent_p.A119A|NR2F2_ENST00000421109.2_Silent_p.A139A|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	272	Interaction with ZFPM2. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A272A(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			TCCTGGCCGCCGCCGGCCTGC	0.657																																					p.A139A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C417A	15						.						38.0	37.0	37.0					15																	96877678		2195	4297	6492	94678682	SO:0001819	synonymous_variant	7026	exon2			M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"""Nuclear hormone receptors"""	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.816C>A	15.37:g.96877678C>A		Somatic		Capture	Illumina HiSeq	Phase_I	94678682	NM_001145155	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Silent	SNP	ENST00000394166.3	37	CCDS10375.1																																																																																				0.657	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1		
IGF1R	3480	broad.mit.edu	37	15	99250897	99250897	+	Silent	SNP	C	C	T	rs45468203		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:99250897C>T	ENST00000268035.6	+	2	812	c.201C>T	c.(199-201)gcC>gcT	p.A67A	IGF1R_ENST00000558762.1_Silent_p.A67A	NM_000875.3	NP_000866.1	P08069	IGF1R_HUMAN	insulin-like growth factor 1 receptor	67					axonogenesis (GO:0007409)|brain development (GO:0007420)|epidermis development (GO:0008544)|establishment of cell polarity (GO:0030010)|exocrine pancreas development (GO:0031017)|immune response (GO:0006955)|inactivation of MAPKK activity (GO:0051389)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|male sex determination (GO:0030238)|mammary gland development (GO:0030879)|negative regulation of apoptotic process (GO:0043066)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|peptidyl-tyrosine autophosphorylation (GO:0038083)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mitosis (GO:0045840)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|prostate gland epithelium morphogenesis (GO:0060740)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein tetramerization (GO:0051262)|regulation of JNK cascade (GO:0046328)|response to vitamin E (GO:0033197)|signal transduction (GO:0007165)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor binding (GO:0005520)|insulin-like growth factor I binding (GO:0031994)|insulin-like growth factor-activated receptor activity (GO:0005010)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)	p.A67A(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(13)|lung(20)|ovary(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_cancers(4;4.17e-14)|all_epithelial(3;4.34e-15)|Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00505)|Medulloblastoma(229;0.163)		Epithelial(2;1.94e-12)|all cancers(5;6.83e-11)|BRCA - Breast invasive adenocarcinoma(2;2.88e-09)|OV - Ovarian serous cystadenocarcinoma(32;0.00261)		"""""""Insulin(DB00071)|Insulin Glargine(DB00047)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Mecasermin(DB01277)"""	TCTCCAAGGCCGAGGACTACC	0.607																																					p.A67A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C201T	15						.						104.0	73.0	83.0					15																	99250897		2197	4297	6494	97068420	SO:0001819	synonymous_variant	3480	exon2			M69229	CCDS10378.1, CCDS73785.1	15q26.3	2013-02-11			ENSG00000140443	ENSG00000140443		"""CD molecules"", ""Fibronectin type III domain containing"""	5465	protein-coding gene	gene with protein product		147370				1316909	Standard	XM_006720486		Approved	JTK13, CD221, IGFIR, MGC18216, IGFR	uc002bul.3	P08069	OTTHUMG00000149851	ENST00000268035.6:c.201C>T	15.37:g.99250897C>T		Somatic		Capture	Illumina HiSeq	Phase_I	97068420	NM_000875	B1B5Y2|Q14CV2|Q9UCC0	Silent	SNP	ENST00000268035.6	37	CCDS10378.1																																																																																				0.607	IGF1R-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313537.2	NM_000875	
ALDH1A3	220	broad.mit.edu	37	15	101434182	101434182	+	Silent	SNP	G	G	T	rs139865715		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:101434182G>T	ENST00000329841.5	+	6	1093	c.561G>T	c.(559-561)ctG>ctT	p.L187L	ALDH1A3_ENST00000346623.6_Intron|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	187					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)	p.L187L(1)		NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	TGCTGATGCTGGTGTGGAAGC	0.597																																					p.L187L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G561T	15						.						145.0	128.0	134.0					15																	101434182		2203	4300	6503	99251705	SO:0001819	synonymous_variant	220	exon6			U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.561G>T	15.37:g.101434182G>T		Somatic		Capture	Illumina HiSeq	Phase_I	99251705	NM_000693	Q6NT64	Silent	SNP	ENST00000329841.5	37	CCDS10389.1																																																																																				0.597	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		
SPATA5L1	79029	broad.mit.edu	37	15	45702722	45702722	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:45702722delA	ENST00000305560.6	+	3	1527	c.1428delA	c.(1426-1428)ttafs	p.L476fs	SPATA5L1_ENST00000559860.1_Frame_Shift_Del_p.L476fs	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	476						cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.K477fs*8(1)		kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		AACTGAAGTTAAAACAGGTAA	0.393																																					p.L476fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1428delA	15						.						123.0	119.0	120.0					15																	45702722		2198	4298	6496	43490014	SO:0001589	frameshift_variant	79029	exon3			AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.1428delA	15.37:g.45702722delA	ENSP00000305494:p.Leu476fs	Somatic		Capture	Illumina HiSeq	Phase_I	43490014	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Frame_Shift_Del	DEL	ENST00000305560.6	37	CCDS10123.1																																																																																				0.393	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
UNC13C	440279	broad.mit.edu	37	15	54825260	54825260	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:54825260delA	ENST00000260323.11	+	25	5692	c.5692delA	c.(5692-5694)aaafs	p.K1898fs	UNC13C_ENST00000545554.1_Frame_Shift_Del_p.K1898fs|UNC13C_ENST00000537900.1_Frame_Shift_Del_p.K1896fs	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1898	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)	p.T1899fs*2(1)		breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		TTTTTTGGACAAAACGTAAGT	0.343																																					p.K1898fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.5692delA	15						.						67.0	68.0	68.0					15																	54825260		1805	4071	5876	52612552	SO:0001589	frameshift_variant	440279	exon24			AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5692delA	15.37:g.54825260delA	ENSP00000260323:p.Lys1898fs	Somatic		Capture	Illumina HiSeq	Phase_I	52612552	NM_001080534	Q0P613|Q8ND48|Q96NP3	Frame_Shift_Del	DEL	ENST00000260323.11	37	CCDS45264.1																																																																																				0.343	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
PCSK6	5046	broad.mit.edu	37	15	101929722	101929722	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr15:101929722G>T	ENST00000348070.1	-	10	1253	c.1254C>A	c.(1252-1254)acC>acA	p.T418T	PCSK6_ENST00000561177.1_5'UTR|PCSK6_ENST00000358417.3_Silent_p.T418T|PCSK6_ENST00000398181.2_Silent_p.T418T|PCSK6_ENST00000331826.7_Silent_p.T253T|PCSK6_ENST00000344273.2_Silent_p.T418T	NM_002570.3|NM_138320.1	NP_002561.1|NP_612193.1	P29122	PCSK6_HUMAN	proprotein convertase subtilisin/kexin type 6	419	Peptidase S8.				determination of left/right symmetry (GO:0007368)|glycoprotein metabolic process (GO:0009100)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|regulation of BMP signaling pathway (GO:0030510)|secretion by cell (GO:0032940)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|nerve growth factor binding (GO:0048406)|serine-type endopeptidase activity (GO:0004252)	p.T418T(2)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Lung NSC(78;0.00102)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.000803)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			CAGAGACTGAGGTCCCAGTGT	0.517																																					p.L419I												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1255A	15						.						74.0	82.0	79.0					15																	101929722		2111	4236	6347	99747245	SO:0001819	synonymous_variant	5046	exon9				CCDS73789.1, CCDS73790.1, CCDS73791.1, CCDS73792.1, CCDS73793.1	15q26	2008-07-18	2004-06-14	2004-06-16		ENSG00000140479			8569	protein-coding gene	gene with protein product	"""subtilisin-like protease"", ""subtilisin-like proprotein convertase 4"", ""subtilisin/kexin-like protease PACE4"""	167405	"""paired basic amino acid cleaving system 4"""	PACE4		1741956	Standard	NM_002570		Approved	SPC4	uc002bwy.3	P29122		ENST00000348070.1:c.1254C>A	15.37:g.101929722G>T		Somatic		Capture	Illumina HiSeq	Phase_I	99747245	NM_138322	Q15099|Q15100|Q9UEG7|Q9UEJ1|Q9UEJ2|Q9UEJ7|Q9UEJ8|Q9UEJ9|Q9Y4G9|Q9Y4H0|Q9Y4H1	Silent	SNP	ENST00000348070.1	37																																																																																					0.517	PCSK6-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_002570	
NDRG4	65009	broad.mit.edu	37	16	58521731	58521732	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:58521731_58521732insG	ENST00000394282.4	+	2	516_517	c.109_110insG	c.(109-111)cggfs	p.R37fs	NDRG4_ENST00000394279.2_Frame_Shift_Ins_p.R17fs|NDRG4_ENST00000258187.5_Frame_Shift_Ins_p.R17fs	NM_001130487.1	NP_001123959.1	Q9ULP0	NDRG4_HUMAN	NDRG family member 4	0					cell differentiation (GO:0030154)|cell growth (GO:0016049)|response to stress (GO:0006950)	cytoplasm (GO:0005737)		p.Q19fs*24(1)		breast(1)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11						GCCGCTGCTCCGGGGCCAGGAC	0.683											OREG0023842	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R17fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.49_50insG	16						.																																			57079233	SO:0001589	frameshift_variant	65009	exon2			AB044947	CCDS10797.1, CCDS45500.1, CCDS55999.1, CCDS58465.1, CCDS58466.1, CCDS58467.1	16q21-q22.3	2008-07-04			ENSG00000103034	ENSG00000103034			14466	protein-coding gene	gene with protein product		614463				11352569, 16408304	Standard	NM_020465		Approved	KIAA1180, SMAP-8	uc002enk.3	Q9ULP0	OTTHUMG00000133485	ENST00000394282.4:c.113dupG	16.37:g.58521735_58521735dupG	ENSP00000377823:p.Arg37fs	Somatic	1031	Capture	Illumina HiSeq	Phase_I	57079232	NM_022910	B3KNU2|B4DK66|B4DSW5|H7C600|Q6ZNE7|Q6ZTI7|Q96PL9|Q9GZM1|Q9GZN3|Q9GZX0	Frame_Shift_Ins	INS	ENST00000394282.4	37	CCDS45500.1																																																																																				0.683	NDRG4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257383.5		
LOC101060604	101060604	broad.mit.edu	37	16	21531049	21531050	+	IGR	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:21531049_21531050insA								MIR3680-1 (13593 upstream) : SCARNA6 (67897 downstream)																							TCCAGGAACGCAAAAATGTAGA	0.574																																					.												.	.	0			.	16						.																																			21438551	SO:0001628	intergenic_variant	387254	.																															16.37:g.21531054_21531054dupA		Somatic		Capture	Illumina HiSeq	Phase_I	21438550	.		Frame_Shift_Ins	INS		37																																																																																				0	0.574								
CIITA	4261	broad.mit.edu	37	16	11001150	11001150	+	Silent	SNP	C	C	A	rs569634954		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:11001150C>A	ENST00000324288.8	+	11	1934	c.1801C>A	c.(1801-1803)Cgg>Agg	p.R601R	CIITA_ENST00000381835.5_Intron|CIITA_ENST00000537380.1_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	601	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				aging (GO:0007568)|cellular response to electrical stimulus (GO:0071257)|cellular response to exogenous dsRNA (GO:0071360)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to antibiotic (GO:0046677)|response to interferon-gamma (GO:0034341)|transcription, DNA-templated (GO:0006351)	cell surface (GO:0009986)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	activating transcription factor binding (GO:0033613)|ATP binding (GO:0005524)|GTP binding (GO:0005525)|kinase activity (GO:0016301)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|transferase activity, transferring acyl groups (GO:0016746)	p.R601R(1)		central_nervous_system(1)|large_intestine(7)|ovary(1)|skin(1)|stomach(2)	12						CCTCCGGGACCGGCCACTTCT	0.627			T	"""FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"""	"""PMBL, Hodgkin Lymphona, """																																p.R601R			Dom	yes		16	16p13	4261	"""class II, major histocompatibility complex, transactivator"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1801A	16						.						39.0	37.0	38.0					16																	11001150		2196	4300	6496	10908651	SO:0001819	synonymous_variant	4261	exon11			U18259	CCDS10544.1, CCDS66943.1, CCDS73826.1	16p13	2014-09-17	2005-08-12	2005-08-12	ENSG00000179583	ENSG00000179583		"""Nucleotide-binding domain and leucine rich repeat containing"""	7067	protein-coding gene	gene with protein product	"""NLR family, acid domain containing"", ""nucleotide-binding oligomerization domain, leucine rich repeat and acid domain containing"""	600005	"""MHC class II transactivator"""	MHC2TA		8402893	Standard	NM_000246		Approved	C2TA, NLRA	uc002dai.4	P33076	OTTHUMG00000129753	ENST00000324288.8:c.1801C>A	16.37:g.11001150C>A		Somatic		Capture	Illumina HiSeq	Phase_I	10908651	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Silent	SNP	ENST00000324288.8	37	CCDS10544.1																																																																																				0.627	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246	
TXNDC11	51061	broad.mit.edu	37	16	11785637	11785637	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:11785637G>A	ENST00000356957.3	-	9	1597	c.1490C>T	c.(1489-1491)gCa>gTa	p.A497V	TXNDC11_ENST00000570917.1_5'Flank|TXNDC11_ENST00000283033.5_Missense_Mutation_p.A470V			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	497					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)	p.A470V(1)		endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						ATCCAGAGCTGCTGCCATTTC	0.502																																					p.A470V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1409T	16						.						55.0	56.0	56.0					16																	11785637		2197	4300	6497	11693138	SO:0001583	missense	51061	exon8			BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.1490C>T	16.37:g.11785637G>A	ENSP00000349439:p.Ala497Val	Somatic		Capture	Illumina HiSeq	Phase_I	11693138	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Missense_Mutation	SNP	ENST00000356957.3	37		.	.	.	.	.	.	.	.	.	.	G	16.28	3.078359	0.55753	.	.	ENSG00000153066	ENST00000356957;ENST00000283033	T;T	0.23552	1.9;1.9	5.53	4.57	0.56435	.	0.159375	0.53938	D	0.000049	T	0.36552	0.0971	M	0.64997	1.995	0.39326	D	0.965338	B;D	0.55605	0.205;0.972	B;P	0.48840	0.058;0.592	T	0.39121	-0.9629	10	0.62326	D	0.03	-23.1992	15.4904	0.75602	0.0:0.1389:0.8611:0.0	.	497;470	Q6PKC3;Q6PKC3-2	TXD11_HUMAN;.	V	497;470	ENSP00000349439:A497V;ENSP00000283033:A470V	ENSP00000283033:A470V	A	-	2	0	TXNDC11	11693138	1.000000	0.71417	0.534000	0.28014	0.997000	0.91878	4.905000	0.63286	1.322000	0.45245	0.561000	0.74099	GCA		0.502	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
MYH11	4629	broad.mit.edu	37	16	15814127	15814127	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:15814127G>A	ENST00000300036.5	-	34	4943	c.4834C>T	c.(4834-4836)Cgt>Tgt	p.R1612C	MYH11_ENST00000452625.2_Missense_Mutation_p.R1619C|NDE1_ENST00000396355.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.R1619C|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.R1612C	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1612					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)	p.R1612C(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						GCCAGGGCACGTTGCTTTCGC	0.582			T	CBFB	AML																																p.R1619C			Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4855T	16						.						106.0	88.0	94.0					16																	15814127		2197	4300	6497	15721628	SO:0001583	missense	4629	exon35			X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4834C>T	16.37:g.15814127G>A	ENSP00000300036:p.Arg1612Cys	Somatic		Capture	Illumina HiSeq	Phase_I	15721628	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210546	0.58343	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.95	3.96	0.45880	Myosin tail (1);	0.060325	0.64402	D	0.000011	D	0.91002	0.7170	M	0.92412	3.305	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.992;0.992;0.992;0.992	D	0.91888	0.5521	10	0.87932	D	0	.	11.3763	0.49730	0.0:0.0:0.6595:0.3405	.	1619;1612;1619;1612;1619	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	C	1612;1612;1619;1619;1619	ENSP00000300036:R1612C;ENSP00000345136:R1612C;ENSP00000379616:R1619C;ENSP00000407821:R1619C	ENSP00000300036:R1612C	R	-	1	0	MYH11	15721628	0.999000	0.42202	0.934000	0.37439	0.658000	0.38924	2.440000	0.44855	1.015000	0.39444	0.650000	0.86243	CGT		0.582	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
ABCC1	4363	broad.mit.edu	37	16	16235064	16235064	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:16235064T>C	ENST00000399410.3	+	31	4697	c.4522T>C	c.(4522-4524)Tac>Cac	p.Y1508H	ABCC1_ENST00000399408.2_Missense_Mutation_p.Y1518H|ABCC1_ENST00000346370.5_Missense_Mutation_p.Y1452H|ABCC1_ENST00000351154.5_Missense_Mutation_p.Y1449H|ABCC1_ENST00000349029.5_Missense_Mutation_p.Y1393H|ABCC1_ENST00000345148.5_Missense_Mutation_p.Y1443H	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1508	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.Y1508H(1)		breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	AATCCAGGAGTACGGCGCCCC	0.597																																					p.Y1449H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4345C	16						.						140.0	142.0	141.0					16																	16235064		1944	4139	6083	16142565	SO:0001583	missense	4363	exon30			L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4522T>C	16.37:g.16235064T>C	ENSP00000382342:p.Tyr1508His	Somatic		Capture	Illumina HiSeq	Phase_I	16142565	NM_019862	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.816030	0.50527	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	5.26	4.15	0.48705	ABC transporter-like (1);	0.332135	0.35555	N	0.003127	T	0.51483	0.1677	N	0.14661	0.345	0.27607	N	0.948773	B;P;B;B;B;B	0.38078	0.003;0.617;0.001;0.005;0.001;0.001	B;P;B;B;B;B	0.45343	0.016;0.477;0.009;0.008;0.004;0.016	T	0.51348	-0.8717	10	0.72032	D	0.01	-0.4373	10.721	0.46040	0.1427:0.0:0.0:0.8573	.	1393;1443;1452;1449;1508;1518	P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;MRP1_HUMAN;.	H	1508;1518;1452;1449;1443;1393;1192	ENSP00000382342:Y1508H;ENSP00000382340:Y1518H;ENSP00000263019:Y1452H;ENSP00000263017:Y1449H;ENSP00000263014:Y1443H;ENSP00000263016:Y1393H	ENSP00000263014:Y1443H	Y	+	1	0	ABCC1	16142565	1.000000	0.71417	0.473000	0.27253	0.253000	0.25986	2.750000	0.47500	0.807000	0.34208	0.533000	0.62120	TAC		0.597	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
SMG1	23049	broad.mit.edu	37	16	18827724	18827724	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:18827724C>T	ENST00000446231.2	-	58	10614	c.10202G>A	c.(10201-10203)tGt>tAt	p.C3401Y	SMG1_ENST00000389467.3_Missense_Mutation_p.C3402Y			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	3401					DNA repair (GO:0006281)|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)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.C3397Y(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						AATTGTTTCACAGACCGTTTC	0.428																																					p.C3401Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10202A	16						.						122.0	114.0	117.0					16																	18827724		1904	4120	6024	18735225	SO:0001583	missense	23049	exon58			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.10202G>A	16.37:g.18827724C>T	ENSP00000402515:p.Cys3401Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	18735225	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.850587	0.51270	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01043	5.41;5.41	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.01156	0.0038	N	0.14661	0.345	0.34278	D	0.681789	P	0.46277	0.875	B	0.34652	0.187	T	0.66324	-0.5952	10	0.54805	T	0.06	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	3401	Q96Q15	SMG1_HUMAN	Y	3401;3402	ENSP00000402515:C3401Y;ENSP00000374118:C3402Y	ENSP00000374118:C3402Y	C	-	2	0	SMG1	18735225	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.120000	0.41968	2.941000	0.99782	0.655000	0.94253	TGT		0.428	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
TSC2	7249	broad.mit.edu	37	16	2115609	2115609	+	Silent	SNP	C	C	T	rs137854159		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:2115609C>T	ENST00000219476.3	+	16	2319	c.1689C>T	c.(1687-1689)gcC>gcT	p.A563A	TSC2_ENST00000350773.4_Silent_p.A563A|TSC2_ENST00000439673.2_Silent_p.A526A|TSC2_ENST00000353929.4_Silent_p.A563A|TSC2_ENST00000568454.1_Silent_p.A574A|TSC2_ENST00000401874.2_Silent_p.A563A|TSC2_ENST00000382538.6_Silent_p.A514A	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	563					acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)	p.A563A(1)		NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				TGAAGACAGCCGTCCTGGGGC	0.632			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.A563A		yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1689T	16						.						94.0	98.0	96.0					16																	2115609		2198	4300	6498	2055610	SO:0001819	synonymous_variant	7249	exon16	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.1689C>T	16.37:g.2115609C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2055610	NM_001114382	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																				0.632	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
ACSM1	116285	broad.mit.edu	37	16	20634874	20634874	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:20634874C>T	ENST00000307493.4	-	13	1735	c.1668G>A	c.(1666-1668)ctG>ctA	p.L556L	ACSM1_ENST00000219151.4_Silent_p.L207L|ACSM1_ENST00000520010.1_Silent_p.L556L	NM_052956.2	NP_443188.2	Q08AH1	ACSM1_HUMAN	acyl-CoA synthetase medium-chain family member 1	556					benzoate metabolic process (GO:0018874)|butyrate metabolic process (GO:0019605)|cholesterol homeostasis (GO:0042632)|energy derivation by oxidation of organic compounds (GO:0015980)|fatty acid biosynthetic process (GO:0006633)|fatty acid oxidation (GO:0019395)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	blood microparticle (GO:0072562)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	acyl-CoA ligase activity (GO:0003996)|ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty acid ligase activity (GO:0015645)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.L556L(1)		central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(23)|skin(3)|upper_aerodigestive_tract(2)	42						TGGTTTTTGGCAGCTCTGAGA	0.483																																					p.L556L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1668A	16						.						182.0	149.0	160.0					16																	20634874		2201	4300	6501	20542375	SO:0001819	synonymous_variant	116285	exon13			AB059429	CCDS10587.1	16p12.3	2008-02-05	2005-09-08	2005-09-08	ENSG00000166743	ENSG00000166743	6.2.1.2	"""Acyl-CoA synthetase family"""	18049	protein-coding gene	gene with protein product		614357	"""butyryl Coenzyme A synthetase 1"""	BUCS1		11470804, 12654705	Standard	NM_052956		Approved	MACS1	uc002dhm.1	Q08AH1	OTTHUMG00000131550	ENST00000307493.4:c.1668G>A	16.37:g.20634874C>T		Somatic		Capture	Illumina HiSeq	Phase_I	20542375	NM_052956	Q08AH2|Q96A20	Silent	SNP	ENST00000307493.4	37	CCDS10587.1	.	.	.	.	.	.	.	.	.	.	-	0.701	-0.790822	0.02884	.	.	ENSG00000166743	ENST00000524149	.	.	.	4.18	4.18	0.49190	.	.	.	.	.	T	0.59905	0.2228	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57831	-0.7743	4	.	.	.	.	9.5307	0.39191	0.0:0.8982:0.0:0.1018	.	.	.	.	Y	228	.	.	C	-	2	0	ACSM1	20542375	1.000000	0.71417	1.000000	0.80357	0.134000	0.20937	2.222000	0.42926	2.018000	0.59344	0.509000	0.49947	TGC		0.483	ACSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254412.1	NM_052956	
ABCA3	21	broad.mit.edu	37	16	2348433	2348433	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:2348433A>C	ENST00000301732.5	-	15	2550	c.1850T>G	c.(1849-1851)cTg>cGg	p.L617R	ABCA3_ENST00000382381.3_Missense_Mutation_p.L559R	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	617	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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.L617R(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)	GTTGTCAAACAGGATGTCGTG	0.572																																					p.L617R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1850G	16						.						151.0	143.0	146.0					16																	2348433		2198	4300	6498	2288434	SO:0001583	missense	21	exon15			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.1850T>G	16.37:g.2348433A>C	ENSP00000301732:p.Leu617Arg	Somatic		Capture	Illumina HiSeq	Phase_I	2288434	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	A	18.19	3.569242	0.65765	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D;D	0.96168	-3.8;-3.93	6.08	6.08	0.98989	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.85682	D	0.000000	D	0.98232	0.9415	M	0.93016	3.37	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.99257	1.0889	10	0.87932	D	0	.	15.4788	0.75508	1.0:0.0:0.0:0.0	.	617;621;617	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	R	617;621	ENSP00000301732:L617R;ENSP00000371818:L621R	ENSP00000301732:L617R	L	-	2	0	ABCA3	2288434	1.000000	0.71417	0.922000	0.36590	0.015000	0.08874	9.305000	0.96197	2.333000	0.79357	0.533000	0.62120	CTG		0.572	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
ABCA3	21	broad.mit.edu	37	16	2374530	2374530	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:2374530G>A	ENST00000301732.5	-	6	1022	c.322C>T	c.(322-324)Cgc>Tgc	p.R108C	ABCA3_ENST00000567910.1_Missense_Mutation_p.R108C|ABCA3_ENST00000382381.3_Missense_Mutation_p.R108C	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	108					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.R108C(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)	GGAAAGCCGCGCACTGCAAAG	0.567																																					p.R108C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C322T	16						.						53.0	46.0	48.0					16																	2374530		2198	4300	6498	2314531	SO:0001583	missense	21	exon6			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.322C>T	16.37:g.2374530G>A	ENSP00000301732:p.Arg108Cys	Somatic		Capture	Illumina HiSeq	Phase_I	2314531	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.754819	0.89843	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.90620	-2.7	5.42	5.42	0.78866	.	0.302554	0.36932	N	0.002336	D	0.93644	0.7970	L	0.60957	1.885	0.27195	N	0.960316	D;D;D;D	0.76494	0.997;0.997;0.999;0.994	P;P;P;P	0.61722	0.893;0.846;0.861;0.893	D	0.89049	0.3454	10	0.72032	D	0.01	.	17.8302	0.88680	0.0:0.0:1.0:0.0	.	108;170;108;108	A7MBM9;Q4LE27;Q6P5P9;Q99758	.;.;.;ABCA3_HUMAN	C	108;170	ENSP00000301732:R108C	ENSP00000301732:R108C	R	-	1	0	ABCA3	2314531	0.987000	0.35691	0.010000	0.14722	0.062000	0.15995	7.881000	0.87252	2.542000	0.85734	0.655000	0.94253	CGC		0.567	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
DNAH3	55567	broad.mit.edu	37	16	20944669	20944669	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:20944669G>T	ENST00000261383.3	-	62	12157	c.12158C>A	c.(12157-12159)cCt>cAt	p.P4053H	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	4053					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.P4053H(2)		NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GCTCTCCCCAGGTTTCAGCCA	0.522																																					p.P4053H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C12158A	16						.						155.0	152.0	153.0					16																	20944669		2201	4300	6501	20852170	SO:0001583	missense	55567	exon62			U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.12158C>A	16.37:g.20944669G>T	ENSP00000261383:p.Pro4053His	Somatic		Capture	Illumina HiSeq	Phase_I	20852170	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787130	0.70337	.	.	ENSG00000158486	ENST00000261383	T	0.08984	3.03	5.24	5.24	0.73138	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.50701	0.1631	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74423	-0.3670	10	0.87932	D	0	.	18.8244	0.92111	0.0:0.0:1.0:0.0	.	4053	Q8TD57	DYH3_HUMAN	H	4053	ENSP00000261383:P4053H	ENSP00000261383:P4053H	P	-	2	0	DNAH3	20852170	1.000000	0.71417	0.998000	0.56505	0.827000	0.46813	7.961000	0.87903	2.451000	0.82905	0.563000	0.77884	CCT		0.522	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
PALB2	79728	broad.mit.edu	37	16	23634431	23634431	+	Missense_Mutation	SNP	T	T	C	rs373280855		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:23634431T>C	ENST00000261584.4	-	9	3007	c.2855A>G	c.(2854-2856)gAt>gGt	p.D952G	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	952	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.				DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|inner cell mass cell proliferation (GO:0001833)|mesoderm development (GO:0007498)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|post-anal tail morphogenesis (GO:0036342)|somitogenesis (GO:0001756)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.D952G(1)		breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(3)	55				GBM - Glioblastoma multiforme(48;0.0167)		ACTTTCATCATCAGAGGAACA	0.383			"""F, N, Mis"""			"""Wilms tumor, medulloblastoma, AML ,breast"""		Involved in tolerance or repair of DNA crosslinks																													p.D952G		yes	Rec		"""Fanconi anaemia N, breast cancer susceptibility """	16	16p12.1	79728	partner and localizer of BRCA2		"""L, O, E"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2855G	16						.						65.0	59.0	61.0					16																	23634431		2197	4300	6497	23541932	SO:0001583	missense	79728	exon9				CCDS32406.1	16p12.1	2014-09-17				ENSG00000083093		"""Fanconi anemia, complementation groups"""	26144	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group N"""	610355				16793542, 17200672	Standard	NM_024675		Approved	FLJ21816, FANCN	uc002dlx.1	Q86YC2		ENST00000261584.4:c.2855A>G	16.37:g.23634431T>C	ENSP00000261584:p.Asp952Gly	Somatic		Capture	Illumina HiSeq	Phase_I	23541932	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.619607	0.28801	.	.	ENSG00000083093	ENST00000261584	T	0.47528	0.84	5.93	4.63	0.57726	WD40 repeat-like-containing domain (1);	0.629040	0.15730	N	0.247448	T	0.36054	0.0953	L	0.42245	1.32	0.21220	N	0.999751	B	0.17268	0.021	B	0.16722	0.016	T	0.28235	-1.0050	10	0.17369	T	0.5	-3.5962	7.0404	0.25017	0.0:0.1366:0.0:0.8634	.	952	Q86YC2	PALB2_HUMAN	G	952	ENSP00000261584:D952G	ENSP00000261584:D952G	D	-	2	0	PALB2	23541932	0.046000	0.20272	0.073000	0.20177	0.336000	0.28762	2.085000	0.41634	0.865000	0.35603	0.454000	0.30748	GAT		0.383	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675	
PRKCB	5579	broad.mit.edu	37	16	24226061	24226061	+	Intron	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:24226061G>C	ENST00000321728.7	+	17	2038				PRKCB_ENST00000303531.7_Missense_Mutation_p.R649T	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta						apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)	p.R649T(1)		central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	GAAGTCATCAGGAATATTGAC	0.438																																					p.R649T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1946C	16						.						92.0	91.0	91.0					16																	24226061		2197	4300	6497	24133562	SO:0001627	intron_variant	5579	exon17			M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.1864-5221G>C	16.37:g.24226061G>C		Somatic		Capture	Illumina HiSeq	Phase_I	24133562	NM_002738	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	7.856	0.724976	0.15439	.	.	ENSG00000166501	ENST00000303531	T	0.48201	0.82	5.96	5.96	0.96718	.	0.270342	0.37906	N	0.001898	T	0.36220	0.0959	.	.	.	0.41012	D	0.985015	B	0.14012	0.009	B	0.15484	0.013	T	0.16571	-1.0398	9	0.13853	T	0.58	.	18.9646	0.92691	0.0:0.0:1.0:0.0	.	649	P05771-2	.	T	649	ENSP00000305355:R649T	ENSP00000305355:R649T	R	+	2	0	PRKCB	24133562	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.182000	0.32029	2.826000	0.97356	0.655000	0.94253	AGG		0.438	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
TBC1D24	57465	broad.mit.edu	37	16	2548323	2548323	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:2548323G>A	ENST00000293970.5	+	4	1201	c.1068G>A	c.(1066-1068)tgG>tgA	p.W356*	RP11-20I23.1_ENST00000564543.1_Intron|TBC1D24_ENST00000567020.1_Nonsense_Mutation_p.W350*|TBC1D24_ENST00000434757.2_Nonsense_Mutation_p.W356*	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	356					neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)	p.W350*(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						TCTGGTCCTGGGTCCCCGAGC	0.632																																					p.W356X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1068A	16						.						54.0	64.0	60.0					16																	2548323		2111	4224	6335	2488324	SO:0001587	stop_gained	57465	exon4			AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 6"""	613577	"""deafness, autosomal recessive 86"""	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.1068G>A	16.37:g.2548323G>A	ENSP00000293970:p.Trp356*	Somatic		Capture	Illumina HiSeq	Phase_I	2488324	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Nonsense_Mutation	SNP	ENST00000293970.5	37	CCDS55980.1	.	.	.	.	.	.	.	.	.	.	G	41	8.956117	0.99016	.	.	ENSG00000162065	ENST00000293970;ENST00000434757	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-22.2703	18.2004	0.89836	0.0:0.0:1.0:0.0	.	.	.	.	X	350;356	.	ENSP00000293970:W350X	W	+	3	0	TBC1D24	2488324	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.801000	0.99128	2.635000	0.89317	0.650000	0.86243	TGG		0.632	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705	
PRSS21	10942	broad.mit.edu	37	16	2868943	2868943	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:2868943G>T	ENST00000005995.3	+	4	565	c.523G>T	c.(523-525)Ggc>Tgc	p.G175C	PRSS21_ENST00000450020.3_Missense_Mutation_p.G175C|PRSS21_ENST00000575739.1_3'UTR|PRSS21_ENST00000455114.1_Missense_Mutation_p.G173C			Q9Y6M0	TEST_HUMAN	protease, serine, 21 (testisin)	175	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				spermatogenesis (GO:0007283)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G175C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	15						CTGGGTGACTGGCTGGGGGTA	0.557																																					p.G175C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G523T	16						.						74.0	67.0	69.0					16																	2868943		2198	4300	6498	2808944	SO:0001583	missense	10942	exon4			AF058300	CCDS10478.1, CCDS45388.1	16p13.3	2010-05-07			ENSG00000007038	ENSG00000007038		"""Serine peptidases / Serine peptidases"""	9485	protein-coding gene	gene with protein product		608159				10397266, 9826525	Standard	NM_006799		Approved	ESP-1, TEST1, TESTISIN	uc002crt.4	Q9Y6M0	OTTHUMG00000128931	ENST00000005995.3:c.523G>T	16.37:g.2868943G>T	ENSP00000005995:p.Gly175Cys	Somatic		Capture	Illumina HiSeq	Phase_I	2808944	NM_006799	Q9NS34|Q9P2V6	Missense_Mutation	SNP	ENST00000005995.3	37	CCDS10478.1	.	.	.	.	.	.	.	.	.	.	g	17.49	3.403006	0.62288	.	.	ENSG00000007038	ENST00000455114;ENST00000450020;ENST00000005995	D;D;D	0.96885	-4.16;-4.16;-4.16	4.67	4.67	0.58626	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.33438	N	0.004915	D	0.99074	0.9682	H	0.99705	4.715	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98588	1.0653	10	0.87932	D	0	.	15.0995	0.72262	0.0:0.0:1.0:0.0	.	175;173;175	Q9Y6M0;Q9Y6M0-2;Q9Y6M0-3	TEST_HUMAN;.;.	C	173;175;175	ENSP00000400632:G173C;ENSP00000407741:G175C;ENSP00000005995:G175C	ENSP00000005995:G175C	G	+	1	0	PRSS21	2808944	1.000000	0.71417	0.982000	0.44146	0.348000	0.29142	7.108000	0.77055	2.394000	0.81467	0.586000	0.80456	GGC		0.557	PRSS21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250910.1	NM_006799	
SLC5A11	115584	broad.mit.edu	37	16	24918417	24918417	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:24918417G>A	ENST00000347898.3	+	12	1808	c.1186G>A	c.(1186-1188)Gcc>Acc	p.A396T	SLC5A11_ENST00000539472.1_Missense_Mutation_p.A332T|SLC5A11_ENST00000449109.2_Splice_Site_p.A240T|SLC5A11_ENST00000568579.1_Missense_Mutation_p.A326T|SLC5A11_ENST00000545376.1_Missense_Mutation_p.A326T|SLC5A11_ENST00000424767.2_Missense_Mutation_p.A361T|SLC5A11_ENST00000567758.1_Missense_Mutation_p.A361T|SLC5A11_ENST00000565769.1_Missense_Mutation_p.A332T|SLC5A11_ENST00000569071.1_Splice_Site_p.A240T	NM_052944.3	NP_443176.2			solute carrier family 5 (sodium/inositol cotransporter), member 11									p.A396T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(30)|ovary(2)|prostate(2)|urinary_tract(1)	49				GBM - Glioblastoma multiforme(48;0.0365)		CTTTAACAGTGCCAGCACCAT	0.612																																					p.A396T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1186A	16						.						146.0	135.0	139.0					16																	24918417		2197	4300	6497	24825918	SO:0001583	missense	115584	exon12			AF292385	CCDS10625.1, CCDS58437.1, CCDS58438.1, CCDS58439.1, CCDS58440.1	16p12.1	2013-07-19	2013-07-19		ENSG00000158865	ENSG00000158865		"""Solute carriers"""	23091	protein-coding gene	gene with protein product		610238	"""solute carrier family 5 (sodium/glucose cotransporter), member 11"""			12039040, 12133831	Standard	NM_001258414		Approved	KST1, SMIT2, SGLT6	uc002dmu.4	Q8WWX8	OTTHUMG00000097003	ENST00000347898.3:c.1186G>A	16.37:g.24918417G>A	ENSP00000289932:p.Ala396Thr	Somatic		Capture	Illumina HiSeq	Phase_I	24825918	NM_052944		Missense_Mutation	SNP	ENST00000347898.3	37	CCDS10625.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.083753	0.76642	.	.	ENSG00000158865	ENST00000347898;ENST00000449109;ENST00000424767;ENST00000545376;ENST00000539472	D;D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63;-2.63	5.57	2.08	0.27032	.	0.387148	0.31312	N	0.007874	D	0.89371	0.6696	L	0.35542	1.07	0.58432	D	0.999992	P;P;P;P	0.51791	0.537;0.948;0.927;0.805	B;P;P;P	0.54210	0.168;0.628;0.745;0.492	D	0.88447	0.3046	10	0.49607	T	0.09	.	13.9021	0.63812	0.0:0.0:0.602:0.398	.	326;361;396;240	B7Z329;Q8WWX8-2;Q8WWX8;Q05BF1	.;.;SC5AB_HUMAN;.	T	396;240;361;326;332	ENSP00000289932:A396T;ENSP00000389606:A240T;ENSP00000416782:A361T;ENSP00000441384:A326T;ENSP00000441018:A332T	ENSP00000289932:A396T	A	+	1	0	SLC5A11	24825918	0.962000	0.33011	1.000000	0.80357	0.998000	0.95712	-0.042000	0.12063	0.671000	0.31185	0.563000	0.77884	GCC		0.612	SLC5A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214091.3	NM_052944	
APOBR	55911	broad.mit.edu	37	16	28509406	28509406	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:28509406C>T	ENST00000431282.1	+	4	2943	c.2933C>T	c.(2932-2934)cCg>cTg	p.P978L	CLN3_ENST00000569430.1_5'Flank|APOBR_ENST00000328423.5_Missense_Mutation_p.P978L|APOBR_ENST00000564831.1_Missense_Mutation_p.P987L|CLN3_ENST00000567160.1_5'Flank			Q0VD83	APOBR_HUMAN	apolipoprotein B receptor	978					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	chylomicron (GO:0042627)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	very-low-density lipoprotein particle receptor activity (GO:0030229)	p.P978L(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|skin(2)|stomach(1)	29						CTGCAGGCCCCGCTCCCCGGG	0.667																																					p.P978L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2933T	16						.						21.0	27.0	25.0					16																	28509406		2130	4236	6366	28416907	SO:0001583	missense	55911	exon4			AK025123	CCDS58442.1	16p11.2	2011-02-14			ENSG00000184730	ENSG00000184730			24087	protein-coding gene	gene with protein product	"""apolipoprotein B48 receptor"", ""apolipoprotein B100 receptor"""	605220				10852956	Standard	NM_018690		Approved	APOB48R, APOB100R	uc002dqb.2	Q0VD83		ENST00000431282.1:c.2933C>T	16.37:g.28509406C>T	ENSP00000416094:p.Pro978Leu	Somatic		Capture	Illumina HiSeq	Phase_I	28416907	NM_018690	H3BU97|Q0VD81|Q8NC15|Q9NPJ9	Missense_Mutation	SNP	ENST00000431282.1	37		.	.	.	.	.	.	.	.	.	.	C	0.007	-1.979226	0.00448	.	.	ENSG00000184730	ENST00000328423;ENST00000431282	T;T	0.55760	0.5;0.5	4.63	-4.99	0.03010	.	.	.	.	.	T	0.21674	0.0522	N	0.03608	-0.345	0.25829	N	0.984194	B;B	0.19200	0.012;0.034	B;B	0.12837	0.008;0.008	T	0.41197	-0.9522	9	0.02654	T	1	0.6707	12.1897	0.54264	0.0:0.591:0.0:0.409	.	978;978	Q0VD83;Q9NS13	APOBR_HUMAN;.	L	978	ENSP00000327669:P978L;ENSP00000416094:P978L	ENSP00000327669:P978L	P	+	2	0	APOBR	28416907	0.082000	0.21442	0.344000	0.25628	0.052000	0.14988	-0.379000	0.07437	-0.826000	0.04284	-0.689000	0.03729	CCG		0.667	APOBR-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_182804	
ATP2A1	487	broad.mit.edu	37	16	28911985	28911985	+	Silent	SNP	C	C	T	rs199776484		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:28911985C>T	ENST00000357084.3	+	15	2115	c.1848C>T	c.(1846-1848)gaC>gaT	p.D616D	ATP2A1_ENST00000536376.1_Silent_p.D491D|ATP2A1_ENST00000395503.4_Silent_p.D616D	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	616					apoptotic mitochondrial changes (GO:0008637)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|ion transmembrane transport (GO:0034220)|maintenance of mitochondrion location (GO:0051659)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|negative regulation of striated muscle contraction (GO:0045988)|positive regulation of endoplasmic reticulum calcium ion concentration (GO:0032470)|positive regulation of fast-twitch skeletal muscle fiber contraction (GO:0031448)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|regulation of striated muscle contraction (GO:0006942)|relaxation of skeletal muscle (GO:0090076)|response to endoplasmic reticulum stress (GO:0034976)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|H zone (GO:0031673)|I band (GO:0031674)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(10)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	38						TGTGCCGTGACGCCGGGATCC	0.622													C|||	1	0.000199681	0.0	0.0014	5008	,	,		15208	0.0		0.0	False		,,,				2504	0.0				p.D616D												.	.	0			c.C1848T	16						.						86.0	71.0	76.0					16																	28911985		2197	4300	6497	28819486	SO:0001819	synonymous_variant	487	exon15				CCDS10643.1, CCDS42139.1, CCDS66997.1	16p12.1	2012-10-22			ENSG00000196296	ENSG00000196296	3.6.3.8	"""ATPases / P-type"""	811	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 1"", ""calcium pump 1"""	108730		ATP2A			Standard	NM_004320		Approved	SERCA1	uc002dro.1	O14983	OTTHUMG00000131760	ENST00000357084.3:c.1848C>T	16.37:g.28911985C>T		None		Capture	Illumina HiSeq	Phase_I	28819486	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																				0.622	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320	
CD19	930	broad.mit.edu	37	16	28947888	28947888	+	Missense_Mutation	SNP	G	G	A	rs148576690		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:28947888G>A	ENST00000324662.3	+	7	1095	c.1051G>A	c.(1051-1053)Gtg>Atg	p.V351M	CD19_ENST00000538922.1_Missense_Mutation_p.V351M|CD19_ENST00000567541.1_Missense_Mutation_p.V351M			P15391	CD19_HUMAN	CD19 molecule	351					B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)	p.V351M(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						GTACGGGAACGTGCTGTCTCT	0.647																																					p.V351M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1051A	16						.	G	MET/VAL,MET/VAL	1,4393	2.1+/-5.4	0,1,2196	60.0	57.0	58.0		1051,1051	3.6	1.0	16	dbSNP_134	58	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CD19	NM_001178098.1,NM_001770.5	21,21	0,2,6495	AA,AG,GG		0.0116,0.0228,0.0154	probably-damaging,probably-damaging	351/558,351/557	28947888	2,12992	2197	4300	6497	28855389	SO:0001583	missense	930	exon7				CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.1051G>A	16.37:g.28947888G>A	ENSP00000313419:p.Val351Met	Somatic		Capture	Illumina HiSeq	Phase_I	28855389	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Missense_Mutation	SNP	ENST00000324662.3	37	CCDS10644.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406762	0.62399	2.28E-4	1.16E-4	ENSG00000177455	ENST00000538922;ENST00000380673;ENST00000324662;ENST00000537306	T;T	0.54675	0.56;0.56	4.55	3.57	0.40892	.	0.387333	0.19296	N	0.117764	T	0.36413	0.0966	L	0.27053	0.805	0.34206	D	0.673768	D;D	0.62365	0.991;0.984	B;B	0.42030	0.373;0.206	T	0.50415	-0.8831	10	0.42905	T	0.14	-7.4555	8.0776	0.30726	0.1228:0.0:0.8772:0.0	.	351;351	F5H635;P15391	.;CD19_HUMAN	M	351;158;351;200	ENSP00000437940:V351M;ENSP00000313419:V351M	ENSP00000313419:V351M	V	+	1	0	CD19	28855389	0.999000	0.42202	1.000000	0.80357	0.657000	0.38888	0.952000	0.29149	1.180000	0.42898	0.460000	0.39030	GTG		0.647	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
MVP	9961	broad.mit.edu	37	16	29858552	29858552	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:29858552A>C	ENST00000357402.5	+	14	2438	c.2300A>C	c.(2299-2301)gAg>gCg	p.E767A	MVP_ENST00000395353.1_Missense_Mutation_p.E767A	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	767					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)	p.E767A(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						AAGGTCCGAGAGCTGGAACTG	0.542																																					p.E767A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2300C	16						.						63.0	70.0	68.0					16																	29858552		2196	4300	6496	29766053	SO:0001583	missense	9961	exon14			X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.2300A>C	16.37:g.29858552A>C	ENSP00000349977:p.Glu767Ala	Somatic		Capture	Illumina HiSeq	Phase_I	29766053	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.301161	0.40694	.	.	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.34275	1.37;1.37	6.06	6.06	0.98353	.	0.140222	0.64402	D	0.000005	T	0.29556	0.0737	L	0.41415	1.275	0.80722	D	1	B	0.13145	0.007	B	0.13407	0.009	T	0.07790	-1.0754	10	0.33141	T	0.24	-32.0678	10.5917	0.45314	0.8387:0.1613:0.0:0.0	.	767	Q14764	MVP_HUMAN	A	767	ENSP00000349977:E767A;ENSP00000378760:E767A	ENSP00000349977:E767A	E	+	2	0	MVP	29766053	1.000000	0.71417	0.199000	0.23439	0.101000	0.19017	4.685000	0.61693	2.315000	0.78130	0.533000	0.62120	GAG		0.542	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
FAM57B	83723	broad.mit.edu	37	16	30038007	30038007	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:30038007G>A	ENST00000380495.4	-	3	1098	c.367C>T	c.(367-369)Cgt>Tgt	p.R123C	FAM57B_ENST00000279389.4_Missense_Mutation_p.R73C|FAM57B_ENST00000564806.1_Missense_Mutation_p.R73C	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	123	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)	p.R123C(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						AGGTAGCCACGCGCTATGGCC	0.652																																					p.R123C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C367T	16						.						69.0	59.0	63.0					16																	30038007		2197	4300	6497	29945508	SO:0001583	missense	83723	exon3			AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.367C>T	16.37:g.30038007G>A	ENSP00000369863:p.Arg123Cys	Somatic		Capture	Illumina HiSeq	Phase_I	29945508	NM_031478	Q9H0J1	Missense_Mutation	SNP	ENST00000380495.4	37	CCDS10667.2	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179279	0.57800	.	.	ENSG00000149926	ENST00000380495	.	.	.	5.83	5.83	0.93111	TRAM/LAG1/CLN8 homology domain (3);	0.488450	0.22221	N	0.062944	T	0.75170	0.3813	M	0.67397	2.05	0.39210	D	0.963301	D;D	0.89917	1.0;0.974	D;P	0.65773	0.938;0.664	T	0.75266	-0.3378	9	0.41790	T	0.15	-13.4025	13.8092	0.63252	0.0:0.0:0.8466:0.1534	.	123;123	F1T0F5;Q71RH2	.;FA57B_HUMAN	C	123	.	ENSP00000369863:R123C	R	-	1	0	FAM57B	29945508	0.003000	0.15002	0.252000	0.24328	0.198000	0.23893	0.980000	0.29513	2.750000	0.94351	0.655000	0.94253	CGT		0.652	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255142.2	NM_031478	
SRCAP	10847	broad.mit.edu	37	16	30750247	30750247	+	Silent	SNP	C	C	T	rs185172515		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:30750247C>T	ENST00000262518.4	+	34	9271	c.8886C>T	c.(8884-8886)tcC>tcT	p.S2962S	SRCAP_ENST00000395059.2_Silent_p.S2900S|SRCAP_ENST00000344771.4_Silent_p.S2804S|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2962	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.S2962S(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			ATGGCAACTCCGAAAGTCGGA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		17830	0.001		0.0	False		,,,				2504	0.0				p.S2962S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8886T	16						.						122.0	106.0	111.0					16																	30750247		2197	4300	6497	30657748	SO:0001819	synonymous_variant	10847	exon34			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.8886C>T	16.37:g.30750247C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30657748	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Silent	SNP	ENST00000262518.4	37	CCDS10689.2																																																																																				0.582	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
SRCAP	10847	broad.mit.edu	37	16	30750828	30750828	+	Missense_Mutation	SNP	G	G	A	rs371418984		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:30750828G>A	ENST00000262518.4	+	34	9852	c.9467G>A	c.(9466-9468)cGc>cAc	p.R3156H	SRCAP_ENST00000395059.2_Missense_Mutation_p.R3094H|SRCAP_ENST00000344771.4_Missense_Mutation_p.R2998H|RP11-2C24.4_ENST00000483578.1_lincRNA	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	3156					histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)	p.R3156H(1)		NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			AAGCGGGGCCGCCTACAGCCC	0.652																																					p.R3156H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9467A	16						.	G	HIS/ARG	0,4390		0,0,2195	15.0	18.0	17.0		9467	3.9	0.8	16		17	1,8593		0,1,4296	no	missense	SRCAP	NM_006662.2	29	0,1,6491	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	3156/3231	30750828	1,12983	2195	4297	6492	30658329	SO:0001583	missense	10847	exon34			AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.9467G>A	16.37:g.30750828G>A	ENSP00000262518:p.Arg3156His	Somatic		Capture	Illumina HiSeq	Phase_I	30658329	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	7.042	0.562701	0.13498	0.0	1.16E-4	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.92199	-2.96;-2.99;-2.99	4.97	3.94	0.45596	.	0.435286	0.19770	N	0.106441	T	0.81555	0.4847	N	0.08118	0	0.09310	N	1	P;P	0.42039	0.769;0.658	B;B	0.37422	0.249;0.126	T	0.76580	-0.2907	10	0.72032	D	0.01	-1.4195	10.0964	0.42478	0.1065:0.0:0.8935:0.0	.	3094;3156	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	H	3156;3094;2998	ENSP00000262518:R3156H;ENSP00000378499:R3094H;ENSP00000343042:R2998H	ENSP00000262518:R3156H	R	+	2	0	SRCAP	30658329	0.641000	0.27251	0.793000	0.32043	0.985000	0.73830	2.194000	0.42668	2.584000	0.87258	0.462000	0.41574	CGC		0.652	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
FUS	2521	broad.mit.edu	37	16	31202390	31202390	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31202390T>C	ENST00000254108.7	+	14	1605	c.1500T>C	c.(1498-1500)ggT>ggC	p.G500G	FUS_ENST00000474990.1_3'UTR|FUS_ENST00000380244.3_Silent_p.G499G|FUS_ENST00000568685.1_Silent_p.G501G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	500	Arg/Gly-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.G500G(1)	FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		GCCGGGGTGGTGGGGACAGAG	0.582			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""																																p.G499G			Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1497C	16						.						25.0	34.0	31.0					16																	31202390		2117	4231	6348	31109891	SO:0001819	synonymous_variant	2521	exon14			AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.1500T>C	16.37:g.31202390T>C		Somatic		Capture	Illumina HiSeq	Phase_I	31109891	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																				0.582	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
PYDC1	260434	broad.mit.edu	37	16	31228238	31228238	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31228238G>A	ENST00000302964.3	-	1	442	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C	PYDC1_ENST00000568383.1_5'Flank|TRIM72_ENST00000322122.3_Intron	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1	38	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)		p.R38C(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CGCGGGATGCGCTCAAAGCCC	0.647																																					p.R38C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C112T	16						.						66.0	59.0	62.0					16																	31228238		2197	4300	6497	31135739	SO:0001583	missense	260434	exon1				CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"""pyrin domain containing 1"""			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407	ENST00000302964.3:c.112C>T	16.37:g.31228238G>A	ENSP00000304336:p.Arg38Cys	Somatic		Capture	Illumina HiSeq	Phase_I	31135739	NM_152901	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.180941	0.57800	.	.	ENSG00000169900	ENST00000302964	T	0.53206	0.63	4.39	-0.742	0.11108	Pyrin (2);DEATH-like (2);	2.323500	0.02303	U	0.071423	T	0.64057	0.2564	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.72075	0.976	T	0.49698	-0.8912	9	0.87932	D	0	.	6.6099	0.22745	0.0:0.1064:0.5714:0.3222	.	38	Q8WXC3	PYDC1_HUMAN	C	38	ENSP00000304336:R38C	ENSP00000304336:R38C	R	-	1	0	PYDC1	31135739	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.708000	0.05035	0.227000	0.20999	-0.397000	0.06425	CGC		0.647	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901	
PYDC1	260434	broad.mit.edu	37	16	31228342	31228342	+	Missense_Mutation	SNP	G	G	A	rs546281460	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31228342G>A	ENST00000302964.3	-	1	338	c.8C>T	c.(7-9)aCg>aTg	p.T3M	PYDC1_ENST00000568383.1_5'Flank|TRIM72_ENST00000322122.3_Intron	NM_152901.2	NP_690865.1	Q8WXC3	PYDC1_HUMAN	PYD (pyrin domain) containing 1	3	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of interleukin-1 beta secretion (GO:0050718)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|IkappaB kinase complex (GO:0008385)|nucleus (GO:0005634)		p.T3M(1)|p.T3R(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)	5						CTCGCGCTTCGTTCCCATGGC	0.647													G|||	2	0.000399361	0.0	0.0	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.002				p.T3M												.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C8T	16						.						45.0	38.0	40.0					16																	31228342		2197	4300	6497	31135843	SO:0001583	missense	260434	exon1				CCDS10710.1	16p11.2	2008-02-05	2005-12-02		ENSG00000169900	ENSG00000169900			30261	protein-coding gene	gene with protein product		615700	"""pyrin domain containing 1"""			11786556, 16905547	Standard	NM_152901		Approved	ASC2, POP1	uc002ebo.3	Q8WXC3	OTTHUMG00000132407	ENST00000302964.3:c.8C>T	16.37:g.31228342G>A	ENSP00000304336:p.Thr3Met	Somatic		Capture	Illumina HiSeq	Phase_I	31135843	NM_152901	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	G	9.438	1.087433	0.20390	.	.	ENSG00000169900	ENST00000302964	T	0.43688	0.94	3.63	-3.22	0.05125	Pyrin (1);DEATH-like (2);	2.334450	0.02566	U	0.097247	T	0.23210	0.0561	.	.	.	0.09310	N	1	P	0.35745	0.518	B	0.16289	0.015	T	0.19516	-1.0303	9	0.56958	D	0.05	.	4.4689	0.11703	0.0:0.3093:0.3388:0.3519	.	3	Q8WXC3	PYDC1_HUMAN	M	3	ENSP00000304336:T3M	ENSP00000304336:T3M	T	-	2	0	PYDC1	31135843	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.836000	0.01690	-0.510000	0.06523	-1.048000	0.02349	ACG		0.647	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901	
ITGAX	3687	broad.mit.edu	37	16	31373161	31373161	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31373161G>A	ENST00000268296.4	+	10	1138	c.1017G>A	c.(1015-1017)acG>acA	p.T339T	ITGAX_ENST00000562522.1_Silent_p.T339T	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	339	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)	p.T339T(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CCCCAGGTACGGAGACCACAA	0.577																																					p.T339T												.	.	2	Substitution - coding silent(2)	ovary(1)|large_intestine(1)	c.G1017A	16						.						134.0	114.0	121.0					16																	31373161		2197	4300	6497	31280662	SO:0001819	synonymous_variant	3687	exon10			BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1017G>A	16.37:g.31373161G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31280662	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																				0.577	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
ARMC5	79798	broad.mit.edu	37	16	31476037	31476037	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31476037C>T	ENST00000563544.1	+	5	2239	c.1693C>T	c.(1693-1695)Cgt>Tgt	p.R565C	ARMC5_ENST00000457010.2_Missense_Mutation_p.R565C|ARMC5_ENST00000412665.2_Missense_Mutation_p.R209C|ARMC5_ENST00000268314.4_Missense_Mutation_p.R565C|ARMC5_ENST00000408912.3_Missense_Mutation_p.R660C|ARMC5_ENST00000538189.1_Missense_Mutation_p.R597C			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	565								p.R660C(1)		central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GCCCAGCCCACGTGCACTGCG	0.701																																					p.R565C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1693T	16						.						13.0	15.0	14.0					16																	31476037		2117	4231	6348	31383538	SO:0001583	missense	79798	exon4			AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1693C>T	16.37:g.31476037C>T	ENSP00000456877:p.Arg565Cys	Somatic		Capture	Illumina HiSeq	Phase_I	31383538	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.259047	0.59321	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010;ENST00000412665	T;T;T;T;T	0.26223	1.75;1.75;1.75;1.75;1.75	5.97	4.99	0.66335	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	M	0.63843	1.955	0.53688	D	0.999978	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.43032	-0.9416	10	0.87932	D	0	-4.2452	14.4539	0.67404	0.1471:0.8529:0.0:0.0	.	597;597;660;565;565	B4DH27;F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;.;ARMC5_HUMAN;.	C	660;597;565;565;209	ENSP00000386125:R660C;ENSP00000443995:R597C;ENSP00000268314:R565C;ENSP00000399561:R565C;ENSP00000400183:R209C	ENSP00000268314:R565C	R	+	1	0	ARMC5	31383538	0.132000	0.22450	0.267000	0.24556	0.018000	0.09664	1.779000	0.38624	2.837000	0.97791	0.655000	0.94253	CGT		0.701	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
CLUAP1	23059	broad.mit.edu	37	16	3586157	3586157	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:3586157T>A	ENST00000576634.1	+	12	1272	c.1128T>A	c.(1126-1128)gaT>gaA	p.D376E	CLUAP1_ENST00000571025.1_3'UTR|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|CLUAP1_ENST00000572600.1_Missense_Mutation_p.D210E|CLUAP1_ENST00000445795.2_Missense_Mutation_p.D154E|CLUAP1_ENST00000417763.2_Missense_Mutation_p.D210E|NLRC3_ENST00000448023.2_RNA|CLUAP1_ENST00000341633.5_Missense_Mutation_p.D395E|NLRC3_ENST00000301749.7_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	376	Asp-rich.				cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ACATGGAAGATGATGATGACG	0.488																																					p.D210E												.	.	0			c.T630A	16						.						119.0	106.0	110.0					16																	3586157		2197	4300	6497	3526158	SO:0001583	missense	23059	exon8			BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.1128T>A	16.37:g.3586157T>A	ENSP00000460850:p.Asp376Glu	None		Capture	Illumina HiSeq	Phase_I	3526158	NM_024793	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	.	.	.	.	.	.	.	.	.	.	T	9.456	1.091878	0.20471	.	.	ENSG00000103351	ENST00000341633;ENST00000417763;ENST00000445795	T;T	0.52754	0.94;0.65	5.68	-2.08	0.07254	.	0.044115	0.85682	D	0.000000	T	0.32675	0.0837	L	0.54323	1.7	0.36562	D	0.872496	B;B	0.12630	0.006;0.001	B;B	0.12156	0.007;0.003	T	0.48647	-0.9017	10	0.02654	T	1	-24.6758	10.6304	0.45532	0.0:0.4745:0.0:0.5255	.	210;376	Q96AJ1-2;Q96AJ1	.;CLUA1_HUMAN	E	376;210;154	ENSP00000388642:D210E;ENSP00000397710:D154E	ENSP00000344392:D376E	D	+	3	2	CLUAP1	3526158	0.980000	0.34600	0.407000	0.26434	0.833000	0.47200	-0.058000	0.11750	-0.737000	0.04824	0.397000	0.26171	GAT		0.488	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
SLX4	84464	broad.mit.edu	37	16	3639048	3639048	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:3639048G>A	ENST00000294008.3	-	12	5231	c.4591C>T	c.(4591-4593)Cca>Tca	p.P1531S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1531	Interaction with MUS81.|Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)	p.P1531S(1)		breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						CCAGCGCTTGGCATCTGGGCC	0.582								Direct reversal of damage																													p.P1531S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4591T	16						.						89.0	104.0	99.0					16																	3639048		2197	4300	6497	3579049	SO:0001583	missense	84464	exon12			AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.4591C>T	16.37:g.3639048G>A	ENSP00000294008:p.Pro1531Ser	Somatic		Capture	Illumina HiSeq	Phase_I	3579049	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	7.455	0.643519	0.14451	.	.	ENSG00000188827	ENST00000294008	T	0.00976	5.48	5.67	2.63	0.31362	.	1.714020	0.03419	N	0.206091	T	0.00784	0.0026	N	0.16478	0.41	0.09310	N	1	B	0.29341	0.242	B	0.28638	0.092	T	0.46414	-0.9193	10	0.07030	T	0.85	.	5.5527	0.17099	0.2949:0.1413:0.5637:0.0	.	1531	Q8IY92	SLX4_HUMAN	S	1531	ENSP00000294008:P1531S	ENSP00000294008:P1531S	P	-	1	0	SLX4	3579049	0.030000	0.19436	0.004000	0.12327	0.004000	0.04260	1.402000	0.34600	0.871000	0.35750	0.655000	0.94253	CCA		0.582	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CREBBP	1387	broad.mit.edu	37	16	3790470	3790470	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:3790470C>T	ENST00000262367.5	-	24	4872	c.4063G>A	c.(4063-4065)Ggg>Agg	p.G1355R	CREBBP_ENST00000382070.3_Missense_Mutation_p.G1317R	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1355	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.G1355R(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		AAAACCTCCCCGGCTTCAGGG	0.567			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.G1355R			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4063A	16						.						72.0	71.0	71.0					16																	3790470		2197	4300	6497	3730471	SO:0001583	missense	1387	exon24			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4063G>A	16.37:g.3790470C>T	ENSP00000262367:p.Gly1355Arg	Somatic		Capture	Illumina HiSeq	Phase_I	3730471	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	22.4	4.289498	0.80914	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.93189	-3.18;-3.18	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	D	0.96962	0.9008	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96567	0.9420	10	0.42905	T	0.14	-13.5605	18.784	0.91946	0.0:1.0:0.0:0.0	.	1385;1355	Q4LE28;Q92793	.;CBP_HUMAN	R	1355;1385;1317	ENSP00000262367:G1355R;ENSP00000371502:G1317R	ENSP00000262367:G1355R	G	-	1	0	CREBBP	3730471	1.000000	0.71417	0.963000	0.40424	0.990000	0.78478	7.713000	0.84693	2.503000	0.84419	0.555000	0.69702	GGG		0.567	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
CREBBP	1387	broad.mit.edu	37	16	3860748	3860748	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:3860748T>A	ENST00000262367.5	-	3	1640	c.831A>T	c.(829-831)ggA>ggT	p.G277G	CREBBP_ENST00000382070.3_Silent_p.G277G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	277	Interaction with SRCAP.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		TAAAGGGCTGTCCAAATGGAC	0.498			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.G277G			Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	.	0			c.A831T	16						.						100.0	94.0	96.0					16																	3860748		2197	4300	6497	3800749	SO:0001819	synonymous_variant	1387	exon3			U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.831A>T	16.37:g.3860748T>A		None		Capture	Illumina HiSeq	Phase_I	3800749	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Silent	SNP	ENST00000262367.5	37	CCDS10509.1																																																																																				0.498	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
CORO7	79585	broad.mit.edu	37	16	4457556	4457556	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:4457556C>T	ENST00000251166.4	-	5	578	c.433G>A	c.(433-435)Gca>Aca	p.A145T	CORO7_ENST00000574025.1_Intron|CORO7_ENST00000539968.1_Intron|CORO7_ENST00000577144.1_5'UTR|CORO7-PAM16_ENST00000572467.1_Missense_Mutation_p.A145T|CORO7_ENST00000537233.2_Missense_Mutation_p.A127T|CORO7_ENST00000423908.2_Intron	NM_024535.4	NP_078811.3	P57737	CORO7_HUMAN	coronin 7	145					actin filament polymerization (GO:0030041)|Golgi to endosome transport (GO:0006895)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	actin binding (GO:0003779)	p.A145T(1)		breast(3)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|prostate(2)|skin(2)|urinary_tract(2)	23						GTGCCTGCTGCGCTCACCAGA	0.687																																					p.A145T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G433A	16						.						31.0	24.0	26.0					16																	4457556		2193	4297	6490	4397557	SO:0001583	missense	79585	exon5			AK097238	CCDS10513.1, CCDS55982.1, CCDS58417.1	16p13.3	2013-01-10			ENSG00000262246	ENSG00000262246		"""Coronins"", ""WD repeat domain containing"""	26161	protein-coding gene	gene with protein product		611668				15327992	Standard	NM_024535		Approved	FLJ22021		P57737	OTTHUMG00000129465	ENST00000251166.4:c.433G>A	16.37:g.4457556C>T	ENSP00000251166:p.Ala145Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4397557	NM_024535	B4DFD6|B4DL18|I3L416|Q17RK4	Missense_Mutation	SNP	ENST00000251166.4	37	CCDS10513.1	.	.	.	.	.	.	.	.	.	.	C	8.219	0.801977	0.16397	.	.	ENSG00000103426	ENST00000251166	T	0.01265	5.08	5.27	0.247	0.15521	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	1.059930	0.07340	N	0.880564	T	0.01592	0.0051	L	0.44542	1.39	0.53005	D	0.999966	B;B;B	0.16166	0.016;0.002;0.011	B;B;B	0.10450	0.005;0.001;0.003	T	0.39921	-0.9590	10	0.33141	T	0.24	-5.052	4.2194	0.10551	0.1512:0.5366:0.0:0.3122	.	127;145;126	B4DFD6;P57737;B4DKU9	.;CORO7_HUMAN;.	T	145	ENSP00000251166:A145T	ENSP00000251166:A145T	A	-	1	0	CORO7	4397557	0.002000	0.14202	0.203000	0.23512	0.171000	0.22731	0.102000	0.15272	0.051000	0.15978	0.555000	0.69702	GCA		0.687	CORO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251628.2	NM_024535	
C16orf58	64755	broad.mit.edu	37	16	31505238	31505238	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:31505238G>A	ENST00000327237.2	-	7	761	c.722C>T	c.(721-723)gCg>gTg	p.A241V	C16orf58_ENST00000430477.2_Missense_Mutation_p.A99V|C16orf58_ENST00000570164.1_Missense_Mutation_p.A241V|C16orf58_ENST00000567994.1_Missense_Mutation_p.A196V			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	241						integral component of membrane (GO:0016021)|membrane (GO:0016020)		p.A241V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						CAAGAGCCCCGCCAGGTTCAC	0.637																																					p.A241V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C722T	16						.						37.0	38.0	38.0					16																	31505238		2196	4300	6496	31412739	SO:0001583	missense	64755	exon7			AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.722C>T	16.37:g.31505238G>A	ENSP00000317579:p.Ala241Val	Somatic		Capture	Illumina HiSeq	Phase_I	31412739	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Missense_Mutation	SNP	ENST00000327237.2	37	CCDS10715.1	.	.	.	.	.	.	.	.	.	.	G	4.599	0.111297	0.08831	.	.	ENSG00000140688	ENST00000327237;ENST00000452223;ENST00000430477	T;T	0.39056	1.1;1.1	5.39	4.44	0.53790	.	0.048476	0.85682	N	0.000000	T	0.30885	0.0779	L	0.41415	1.275	0.58432	D	0.999991	B;P	0.43662	0.337;0.814	B;B	0.41691	0.091;0.364	T	0.15838	-1.0423	10	0.02654	T	1	-9.4422	12.1837	0.54226	0.0832:0.0:0.9168:0.0	.	99;241	B4DJP2;Q96GQ5	.;CP058_HUMAN	V	241;195;99	ENSP00000317579:A241V;ENSP00000398074:A99V	ENSP00000317579:A241V	A	-	2	0	C16orf58	31412739	1.000000	0.71417	0.993000	0.49108	0.530000	0.34684	5.461000	0.66699	1.279000	0.44446	-0.222000	0.12452	GCG		0.637	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
SNRNP25	79622	broad.mit.edu	37	16	105544	105544	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:105544T>C	ENST00000383018.3	+	2	316	c.155T>C	c.(154-156)gTa>gCa	p.V52A	POLR3K_ENST00000293860.5_5'Flank|SNRNP25_ENST00000493672.1_3'UTR	NM_024571.3	NP_078847.1	Q9BV90	SNR25_HUMAN	small nuclear ribonucleoprotein 25kDa (U11/U12)	52	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|U12-type spliceosomal complex (GO:0005689)				large_intestine(1)|lung(2)	3						GATGGAGAAGTAATGCGTAAG	0.507																																					p.V52A												.	.	0			c.T155C	16						.						234.0	169.0	191.0					16																	105544		2203	4300	6503	45544	SO:0001583	missense	79622	exon2			BC001381	CCDS10396.1	16p13.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000161981	ENSG00000161981			14161	protein-coding gene	gene with protein product	"""U11/U12 snRNP 25K"""		"""chromosome 16 open reading frame 33"""	C16orf33		15146077	Standard	NM_024571		Approved		uc002cfj.4	Q9BV90	OTTHUMG00000060720	ENST00000383018.3:c.155T>C	16.37:g.105544T>C	ENSP00000372482:p.Val52Ala	None		Capture	Illumina HiSeq	Phase_I	45544	NM_024571	Q1W6H3|Q6IEF8|Q9H5W4	Missense_Mutation	SNP	ENST00000383018.3	37	CCDS10396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|.	17.67|17.67	3.447026|3.447026	0.63178|0.63178	.|.	.|.	ENSG00000161981|ENSG00000161981	ENST00000417493|ENST00000293861;ENST00000383018	.|T;T	.|0.11821	.|2.74;2.74	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Ubiquitin supergroup (1);	.|0.218070	.|0.41194	.|D	.|0.000939	.|T	.|0.10551	.|0.0258	L|L	0.41236|0.41236	1.265|1.265	0.39644|0.39644	D|D	0.970363|0.970363	.|B	.|0.25904	.|0.137	.|B	.|0.21708	.|0.036	.|T	.|0.08889	.|-1.0700	.|10	.|0.07990	.|T	.|0.79	.|-3.8168	11.2988|11.2988	0.49294|0.49294	0.0:0.0:0.1522:0.8478|0.0:0.0:0.1522:0.8478	.|.	.|52	.|Q9BV90	.|SNR25_HUMAN	.|A	-1|43;52	.|ENSP00000293861:V43A;ENSP00000372482:V52A	.|ENSP00000293861:V43A	.|V	+|+	.|2	.|0	SNRNP25|SNRNP25	45544|45544	1.000000|1.000000	0.71417|0.71417	0.943000|0.943000	0.38184|0.38184	0.888000|0.888000	0.51559|0.51559	4.198000|4.198000	0.58419|0.58419	2.134000|2.134000	0.65973|0.65973	0.460000|0.460000	0.39030|0.39030	.|GTA		0.507	SNRNP25-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_024571	
ORC6	23594	broad.mit.edu	37	16	46724969	46724969	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:46724969G>T	ENST00000219097.2	+	2	192	c.132G>T	c.(130-132)gaG>gaT	p.E44D	VPS35_ENST00000299138.7_5'Flank|ORC6_ENST00000566860.1_5'UTR|ORC6_ENST00000568364.2_Missense_Mutation_p.E44D	NM_014321.3	NP_055136.1	Q9Y5N6	ORC6_HUMAN	origin recognition complex, subunit 6	44					DNA replication (GO:0006260)|DNA-dependent DNA replication (GO:0006261)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	membrane (GO:0016020)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA binding (GO:0003677)	p.E44D(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	8						GCACCACGGAGACCAGCAGTG	0.557																																					p.E44D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G132T	16						.						121.0	98.0	106.0					16																	46724969		2203	4300	6503	45282470	SO:0001583	missense	23594	exon2			AF139658	CCDS10722.1	16q12	2010-10-12	2010-10-12	2010-10-12	ENSG00000091651	ENSG00000091651			17151	protein-coding gene	gene with protein product		607213	"""origin recognition complex, subunit 6 homolog-like (yeast)"", ""origin recognition complex, subunit 6 like (yeast)"""	ORC6L		10945994	Standard	NM_014321		Approved		uc002eeh.3	Q9Y5N6	OTTHUMG00000132539	ENST00000219097.2:c.132G>T	16.37:g.46724969G>T	ENSP00000219097:p.Glu44Asp	Somatic		Capture	Illumina HiSeq	Phase_I	45282470	NM_014321	B3KN89	Missense_Mutation	SNP	ENST00000219097.2	37	CCDS10722.1	.	.	.	.	.	.	.	.	.	.	G	1.037	-0.680146	0.03353	.	.	ENSG00000091651	ENST00000219097	T	0.66995	-0.24	5.17	-2.92	0.05615	.	0.063173	0.64402	D	0.000015	T	0.50411	0.1614	L	0.43598	1.365	0.80722	D	1	B	0.19445	0.036	B	0.20577	0.03	T	0.14062	-1.0486	10	0.30078	T	0.28	.	8.9554	0.35814	0.3741:0.1771:0.4488:0.0	.	44	Q9Y5N6	ORC6_HUMAN	D	44	ENSP00000219097:E44D	ENSP00000219097:E44D	E	+	3	2	ORC6	45282470	0.994000	0.37717	0.781000	0.31783	0.016000	0.09150	0.293000	0.19029	-0.529000	0.06358	-0.793000	0.03317	GAG		0.557	ORC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255739.3		
ADCY7	113	broad.mit.edu	37	16	50334648	50334648	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:50334648G>A	ENST00000394697.2	+	9	1439	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	ADCY7_ENST00000254235.3_Missense_Mutation_p.V367M|ADCY7_ENST00000566433.2_Missense_Mutation_p.V367M|ADCY7_ENST00000537579.1_Missense_Mutation_p.V367M|ADCY7_ENST00000538642.1_Missense_Mutation_p.V367M			P51828	ADCY7_HUMAN	adenylate cyclase 7	367	Guanylate cyclase 1. {ECO:0000255|PROSITE-ProRule:PRU00099}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)	p.V367M(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		GGCCACGGGCGTGGACATCAA	0.657																																					p.V367M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1099A	16						.						95.0	74.0	81.0					16																	50334648		2072	4094	6166	48892149	SO:0001583	missense	113	exon8			D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.1099G>A	16.37:g.50334648G>A	ENSP00000378187:p.Val367Met	Somatic		Capture	Illumina HiSeq	Phase_I	48892149	NM_001114	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	37	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.766771	0.90020	.	.	ENSG00000121281	ENST00000538642;ENST00000394697;ENST00000537579;ENST00000254235	T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45	4.83	4.83	0.62350	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.000000	0.39985	U	0.001216	D	0.89107	0.6621	M	0.72479	2.2	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.978;0.988	D	0.90481	0.4460	10	0.72032	D	0.01	.	17.906	0.88918	0.0:0.0:1.0:0.0	.	367;367	P51828;F5H4D1	ADCY7_HUMAN;.	M	367	ENSP00000445046:V367M;ENSP00000378187:V367M;ENSP00000437788:V367M;ENSP00000254235:V367M	ENSP00000254235:V367M	V	+	1	0	ADCY7	48892149	1.000000	0.71417	0.995000	0.50966	0.915000	0.54546	7.997000	0.88414	2.209000	0.71365	0.313000	0.20887	GTG		0.657	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
NOD2	64127	broad.mit.edu	37	16	50745613	50745613	+	Silent	SNP	G	G	A	rs140312093		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:50745613G>A	ENST00000300589.2	+	4	1896	c.1791G>A	c.(1789-1791)gcG>gcA	p.A597A	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	597	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|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)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.A597A(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				GGAGTACGGCGCCCCTGGAAT	0.567																																					p.A597A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1791A	16						.	G		5,4391	9.9+/-24.2	0,5,2193	77.0	51.0	59.0		1791	-10.1	0.0	16	dbSNP_134	59	0,8600		0,0,4300	no	coding-synonymous	NOD2	NM_022162.1		0,5,6493	AA,AG,GG		0.0,0.1137,0.0385		597/1041	50745613	5,12991	2198	4300	6498	49303114	SO:0001819	synonymous_variant	64127	exon4			AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.1791G>A	16.37:g.50745613G>A		Somatic		Capture	Illumina HiSeq	Phase_I	49303114	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1																																																																																				0.567	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
FTO	79068	broad.mit.edu	37	16	53922844	53922844	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:53922844G>T	ENST00000471389.1	+	7	1442	c.1220G>T	c.(1219-1221)tGg>tTg	p.W407L	FTO_ENST00000431610.2_Missense_Mutation_p.W8L|FTO_ENST00000460382.1_Missense_Mutation_p.W8L|FTO_ENST00000394647.3_Missense_Mutation_p.W111L	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	407					adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)	p.W407L(1)		endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GAAGCACTGTGGAAGAAGATG	0.498																																					p.W407L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1220T	16						.						287.0	257.0	267.0					16																	53922844		2198	4300	6498	52480345	SO:0001583	missense	79068	exon7			BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.1220G>T	16.37:g.53922844G>T	ENSP00000418823:p.Trp407Leu	Somatic		Capture	Illumina HiSeq	Phase_I	52480345	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.986721	0.74589	.	.	ENSG00000140718	ENST00000471389;ENST00000394647;ENST00000431610;ENST00000460382;ENST00000476894	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.84	5.84	0.93424	Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.75547	0.3864	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77067	-0.2725	10	0.87932	D	0	.	20.1535	0.98095	0.0:0.0:1.0:0.0	.	407	Q9C0B1	FTO_HUMAN	L	407;111;8;8;8	ENSP00000418823:W407L;ENSP00000378142:W111L;ENSP00000415636:W8L;ENSP00000417422:W8L	ENSP00000378142:W111L	W	+	2	0	FTO	52480345	1.000000	0.71417	0.999000	0.59377	0.429000	0.31625	9.379000	0.97198	2.764000	0.94973	0.650000	0.86243	TGG		0.498	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
SLC6A2	6530	broad.mit.edu	37	16	55734144	55734144	+	Missense_Mutation	SNP	G	G	A	rs144701163		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:55734144G>A	ENST00000379906.2	+	12	1939	c.1684G>A	c.(1684-1686)Gcc>Acc	p.A562T	SLC6A2_ENST00000414754.3_Intron|SLC6A2_ENST00000566163.1_Missense_Mutation_p.A517T|SLC6A2_ENST00000567238.1_Missense_Mutation_p.A457T|SLC6A2_ENST00000561820.1_Missense_Mutation_p.A562T|SLC6A2_ENST00000219833.8_Missense_Mutation_p.A562T|SLC6A2_ENST00000568943.1_Missense_Mutation_p.A562T	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	562					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)	p.A562T(4)		breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GTGGGGCATCGCCCTGTCCTC	0.582																																					p.A562T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G1684A	16						.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4396		0,0,2198	123.0	105.0	111.0		1684,1684,1369,1684	3.4	0.9	16	dbSNP_134	111	1,8599		0,1,4299	no	missense,missense,missense,missense	SLC6A2	NM_001043.3,NM_001172501.1,NM_001172502.1,NM_001172504.1	58,58,58,58	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	562/618,562/618,457/513,562/629	55734144	1,12995	2198	4300	6498	54291645	SO:0001583	missense	6530	exon12				CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.1684G>A	16.37:g.55734144G>A	ENSP00000369237:p.Ala562Thr	Somatic		Capture	Illumina HiSeq	Phase_I	54291645	NM_001172504	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.834515	0.71373	0.0	1.16E-4	ENSG00000103546	ENST00000414754;ENST00000537705;ENST00000379906;ENST00000219833	T;T	0.75154	-0.91;-0.91	5.38	3.37	0.38596	.	0.000000	0.85682	D	0.000000	T	0.81064	0.4745	L	0.56769	1.78	0.58432	D	0.999999	D;D;D	0.65815	0.985;0.995;0.988	P;P;P	0.62382	0.793;0.901;0.901	T	0.80197	-0.1482	10	0.48119	T	0.1	.	13.4387	0.61099	0.0:0.0:0.7137:0.2863	.	276;457;562	F5H0T4;B4DX48;P23975	.;.;SC6A2_HUMAN	T	562;276;562;562	ENSP00000369237:A562T;ENSP00000219833:A562T	ENSP00000219833:A562T	A	+	1	0	SLC6A2	54291645	1.000000	0.71417	0.890000	0.34922	0.832000	0.47134	6.211000	0.72182	0.599000	0.29845	-0.152000	0.13540	GCC		0.582	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
NLRC5	84166	broad.mit.edu	37	16	57060140	57060140	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:57060140G>A	ENST00000262510.6	+	6	1510	c.1285G>A	c.(1285-1287)Gtg>Atg	p.V429M	NLRC5_ENST00000308149.7_Missense_Mutation_p.V429M|NLRC5_ENST00000539144.1_Missense_Mutation_p.V429M|NLRC5_ENST00000436936.1_Missense_Mutation_p.V429M	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	429	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.V429M(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				AGGCCAGTCTGTGGCCCTCCT	0.637																																					p.V429M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1285A	16						.						67.0	66.0	66.0					16																	57060140		2198	4300	6498	55617641	SO:0001583	missense	84166	exon6			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1285G>A	16.37:g.57060140G>A	ENSP00000262510:p.Val429Met	Somatic		Capture	Illumina HiSeq	Phase_I	55617641	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.379|4.379	0.069993|0.069993	0.08436|0.08436	.|.	.|.	ENSG00000140853|ENSG00000140853	ENST00000538805|ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	.|T;T;T;T	.|0.73681	.|-0.58;-0.62;-0.77;-0.62	5.21|5.21	0.364|0.364	0.16124|0.16124	.|.	.|0.507764	.|0.14747	.|N	.|0.300838	T|T	0.52980|0.52980	0.1768|0.1768	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B;B;P	.|0.38167	.|0.102;0.098;0.064;0.621	.|B;B;B;B	.|0.39738	.|0.033;0.075;0.098;0.308	T|T	0.48340|0.48340	-0.9044|-0.9044	5|10	.|0.45353	.|T	.|0.12	.|.	8.5028|8.5028	0.33168|0.33168	0.0786:0.0:0.5454:0.3759|0.0786:0.0:0.5454:0.3759	.|.	.|429;429;429;429	.|Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.|.;.;.;NLRC5_HUMAN	Y|M	181|429	.|ENSP00000262510:V429M;ENSP00000308886:V429M;ENSP00000389739:V429M;ENSP00000441727:V429M	.|ENSP00000262510:V429M	C|V	+|+	2|1	0|0	NLRC5|NLRC5	55617641|55617641	0.000000|0.000000	0.05858|0.05858	0.097000|0.097000	0.21041|0.21041	0.142000|0.142000	0.21351|0.21351	0.129000|0.129000	0.15830|0.15830	0.546000|0.546000	0.28920|0.28920	0.561000|0.561000	0.74099|0.74099	TGT|GTG		0.637	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
NLRC5	84166	broad.mit.edu	37	16	57101698	57101698	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:57101698T>C	ENST00000262510.6	+	36	4682	c.4457T>C	c.(4456-4458)cTg>cCg	p.L1486P	NLRC5_ENST00000308149.7_Missense_Mutation_p.L1457P|NLRC5_ENST00000539144.1_Missense_Mutation_p.L1457P|NLRC5_ENST00000436936.1_Missense_Mutation_p.L1486P	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	1486					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.L1486P(1)		NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				TCCCTGCTGCTGCAGAGCCTC	0.522																																					p.L1486P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T4457C	16						.						169.0	145.0	153.0					16																	57101698		2198	4300	6498	55659199	SO:0001583	missense	84166	exon36			AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.4457T>C	16.37:g.57101698T>C	ENSP00000262510:p.Leu1486Pro	Somatic		Capture	Illumina HiSeq	Phase_I	55659199	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	11.91	1.779607	0.31502	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144	T;T;T;T	0.55413	1.41;1.41;0.52;1.41	3.86	3.86	0.44501	.	.	.	.	.	T	0.67887	0.2941	M	0.73217	2.22	0.48452	D	0.99965	D	0.89917	1.0	D	0.87578	0.998	T	0.70641	-0.4816	9	0.87932	D	0	.	9.3555	0.38164	0.0:0.0:0.0:1.0	.	1486	Q86WI3	NLRC5_HUMAN	P	1486;1457;1486;1457	ENSP00000262510:L1486P;ENSP00000308886:L1457P;ENSP00000389739:L1486P;ENSP00000441727:L1457P	ENSP00000262510:L1486P	L	+	2	0	NLRC5	55659199	0.969000	0.33509	0.885000	0.34714	0.050000	0.14768	2.941000	0.49011	1.988000	0.58038	0.372000	0.22366	CTG		0.522	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
CPNE2	221184	broad.mit.edu	37	16	57147337	57147337	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:57147337C>T	ENST00000535318.2	+	4	679	c.318C>T	c.(316-318)gaC>gaT	p.D106D	CPNE2_ENST00000290776.8_Silent_p.D106D|CPNE2_ENST00000537605.1_Silent_p.D4D|CPNE2_ENST00000565874.1_Silent_p.D106D			Q96FN4	CPNE2_HUMAN	copine II	106	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)		p.D106D(1)		central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				TGCGGCTGGACGAGCATGACT	0.602																																					p.D106D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C318T	16						.						87.0	67.0	74.0					16																	57147337		2198	4300	6498	55704838	SO:0001819	synonymous_variant	221184	exon3				CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.318C>T	16.37:g.57147337C>T		Somatic		Capture	Illumina HiSeq	Phase_I	55704838	NM_152727	Q68D19|Q719H8|Q86XP9	Silent	SNP	ENST00000535318.2	37	CCDS10774.1																																																																																				0.602	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
GPR97	222487	broad.mit.edu	37	16	57713197	57713197	+	Missense_Mutation	SNP	G	G	A	rs141398818		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:57713197G>A	ENST00000333493.4	+	5	762	c.601G>A	c.(601-603)Gtc>Atc	p.V201I	RP11-405F3.4_ENST00000563062.1_RNA|GPR97_ENST00000450388.3_Missense_Mutation_p.V81I|GPR97_ENST00000327655.6_5'UTR	NM_170776.4	NP_740746.4	Q86Y34	GPR97_HUMAN	G protein-coupled receptor 97	201					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V201I(2)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						TCTGGAGATCGTCTTCTCTCA	0.647																																					p.V201I												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G601A	16						.	G	ILE/VAL	0,4396		0,0,2198	126.0	115.0	119.0		601	2.9	1.0	16	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR97	NM_170776.4	29	0,1,6497	AA,AG,GG		0.0116,0.0,0.0077	benign	201/550	57713197	1,12995	2198	4300	6498	56270698	SO:0001583	missense	222487	exon5			AY140959	CCDS10786.1	16q13	2014-08-08			ENSG00000182885	ENSG00000182885		"""-"", ""GPCR / Class B : Orphans"""	13728	protein-coding gene	gene with protein product						12435584, 222487	Standard	NM_170776		Approved	Pb99, PGR26	uc002emh.3	Q86Y34	OTTHUMG00000133458	ENST00000333493.4:c.601G>A	16.37:g.57713197G>A	ENSP00000332900:p.Val201Ile	Somatic		Capture	Illumina HiSeq	Phase_I	56270698	NM_170776	Q6ZMF4|Q86SL9|Q8IZF1	Missense_Mutation	SNP	ENST00000333493.4	37	CCDS10786.1	.	.	.	.	.	.	.	.	.	.	G	9.517	1.107283	0.20714	0.0	1.16E-4	ENSG00000182885	ENST00000333493;ENST00000450388	T;T	0.27256	1.68;1.69	5.28	2.89	0.33648	.	0.718495	0.12874	N	0.432005	T	0.10078	0.0247	N	0.02011	-0.69	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.09164	-1.0687	10	0.49607	T	0.09	.	7.5002	0.27513	0.8263:0.0:0.1737:0.0	.	201	Q86Y34	GPR97_HUMAN	I	201;81	ENSP00000332900:V201I;ENSP00000404803:V81I	ENSP00000332900:V201I	V	+	1	0	GPR97	56270698	0.005000	0.15991	0.998000	0.56505	0.089000	0.18198	0.851000	0.27751	0.326000	0.23384	-0.658000	0.03865	GTC		0.647	GPR97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257333.2	NM_170776	
CNOT1	23019	broad.mit.edu	37	16	58577586	58577586	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:58577586A>G	ENST00000317147.5	-	31	4691	c.4359T>C	c.(4357-4359)gcT>gcC	p.A1453A	CNOT1_ENST00000245138.4_Silent_p.A304A|CNOT1_ENST00000569240.1_Silent_p.A1448A|CNOT1_ENST00000441024.2_Silent_p.A1453A	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1453	Interaction with CNOT6, CNOT6L, CNOT7 and CNOT8.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		ATGTAATCATAGCCATTCCAG	0.438																																					p.A1453A												.	.	0			c.T4359C	16						.						155.0	129.0	138.0					16																	58577586		2198	4300	6498	57135087	SO:0001819	synonymous_variant	23019	exon31			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4359T>C	16.37:g.58577586A>G		None		Capture	Illumina HiSeq	Phase_I	57135087	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Silent	SNP	ENST00000317147.5	37	CCDS10799.1																																																																																				0.438	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CDH8	1006	broad.mit.edu	37	16	61689414	61689414	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:61689414G>A	ENST00000577390.1	-	11	2820	c.1866C>T	c.(1864-1866)ggC>ggT	p.G622G	CDH8_ENST00000299345.6_Silent_p.G622G|CDH8_ENST00000577730.1_Silent_p.G622G	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	622					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)	p.G622G(2)		biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CAATTAAGGCGCCCATACTGA	0.448																																					p.G622G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1866T	16						.						113.0	94.0	100.0					16																	61689414		2203	4300	6503	60246915	SO:0001819	synonymous_variant	1006	exon11			L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.1866C>T	16.37:g.61689414G>A		Somatic		Capture	Illumina HiSeq	Phase_I	60246915	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																				0.448	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
EXOC3L1	283849	broad.mit.edu	37	16	67218687	67218687	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:67218687C>T	ENST00000314586.6	-	13	2172	c.1932G>A	c.(1930-1932)gcG>gcA	p.A644A	KIAA0895L_ENST00000290881.7_5'Flank|KIAA0895L_ENST00000561621.1_5'Flank|EXOC3L1_ENST00000562887.1_5'Flank|KIAA0895L_ENST00000563902.1_5'Flank|KIAA0895L_ENST00000563831.2_5'Flank	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	644					exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)		p.A644A(2)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCAGCACCGGCGCGCAGTGCG	0.701																																					p.A644A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1932A	16						.						22.0	28.0	26.0					16																	67218687		2193	4286	6479	65776188	SO:0001819	synonymous_variant	283849	exon13			AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.1932G>A	16.37:g.67218687C>T		Somatic		Capture	Illumina HiSeq	Phase_I	65776188	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	.	.	.	.	.	.	.	.	.	.	C	18.03	3.532942	0.64972	.	.	ENSG00000179044	ENST00000545725;ENST00000314553	T	0.22336	1.96	4.91	0.701	0.18104	.	0.688002	0.15206	N	0.274727	T	0.09468	0.0233	.	.	.	0.25111	N	0.990712	B;B	0.24576	0.086;0.106	B;B	0.17979	0.012;0.02	T	0.38001	-0.9681	9	0.12103	T	0.63	-6.9769	7.9622	0.30079	0.0:0.6528:0.0:0.3472	.	572;572	F5H4W1;B7Z6U0	.;.	T	572;577	ENSP00000439910:A572T	ENSP00000325008:A577T	A	-	1	0	EXOC3L1	65776188	0.001000	0.12720	0.990000	0.47175	0.995000	0.86356	-0.283000	0.08433	0.276000	0.22118	0.561000	0.74099	GCC		0.701	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
LRRC29	26231	broad.mit.edu	37	16	67244005	67244005	+	Silent	SNP	G	G	A	rs373718345		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:67244005G>A	ENST00000409037.1	-	1	983	c.87C>T	c.(85-87)caC>caT	p.H29H	LRRC29_ENST00000341546.3_Silent_p.H29H|LRRC29_ENST00000409509.1_Silent_p.H29H|LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000393992.1_Silent_p.H29H			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	29								p.H29H(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		ATGGAGCCCCGTGCATACAGC	0.637																																					p.H29H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C87T	16						.	G	,	0,4230		0,0,2115	33.0	26.0	28.0		87,87	-6.3	0.0	16		28	1,8283		0,1,4141	no	coding-synonymous,coding-synonymous	LRRC29	NM_001004055.1,NM_012163.2	,	0,1,6256	AA,AG,GG		0.0121,0.0,0.0080	,	29/224,29/224	67244005	1,12513	2115	4142	6257	65801506	SO:0001819	synonymous_variant	26231	exon3			AF176701	CCDS32465.1	16q22.1	2008-02-05	2004-08-23	2004-08-26	ENSG00000125122	ENSG00000125122			13605	protein-coding gene	gene with protein product			"""F-box and leucine-rich repeat protein 9"""	FBXL9		10531037	Standard	NM_012163		Approved	FBL9	uc002esf.3	Q8WV35	OTTHUMG00000154403	ENST00000409037.1:c.87C>T	16.37:g.67244005G>A		Somatic		Capture	Illumina HiSeq	Phase_I	65801506	NM_001004055	B2RE92|Q9UKA0	Silent	SNP	ENST00000409037.1	37	CCDS32465.1																																																																																				0.637	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163	
CLEC18C	283971	broad.mit.edu	37	16	70219800	70219800	+	Silent	SNP	C	C	T	rs375013813		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:70219800C>T	ENST00000569347.2	+	11	1478	c.1224C>T	c.(1222-1224)tgC>tgT	p.C408C	CLEC18C_ENST00000541793.2_Silent_p.C408C|CLEC18C_ENST00000314151.8_Silent_p.C408C|CLEC18C_ENST00000536907.2_Silent_p.C417C	NM_173619.2	NP_775890.2	Q8NCF0	CL18C_HUMAN	C-type lectin domain family 18, member C	408	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)	p.C408C(1)		endometrium(3)|large_intestine(6)|lung(1)	10						TTGGCAACTGCGTGGAGCTGC	0.587																																					p.C408C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1224T	16						.	C		0,4092		0,0,2046	41.0	67.0	59.0		1224	-5.2	1.0	16		59	1,8587		0,1,4293	no	coding-synonymous	CLEC18C	NM_173619.2		0,1,6339	TT,TC,CC		0.0116,0.0,0.0079		408/447	70219800	1,12679	2046	4294	6340	68777301	SO:0001819	synonymous_variant	283971	exon11			AL833339	CCDS32473.1	16q22.1	2010-04-27	2009-03-10	2009-03-10		ENSG00000157335		"""C-type lectin domain containing"""	28538	protein-coding gene	gene with protein product						12477932	Standard	XM_005255906		Approved	MGC34761		Q8NCF0		ENST00000569347.2:c.1224C>T	16.37:g.70219800C>T		Somatic		Capture	Illumina HiSeq	Phase_I	68777301	NM_173619	Q8IUW8	Silent	SNP	ENST00000569347.2	37	CCDS32473.1																																																																																				0.587	CLEC18C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434588.2	NM_173619	
EXOSC6	118460	broad.mit.edu	37	16	70288539	70288539	+	5'Flank	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:70288539G>A	ENST00000435634.1	-	0	0				AARS_ENST00000564359.1_5'Flank|AARS_ENST00000261772.8_Silent_p.I795I	NM_058219.2	NP_478126.1	Q5RKV6	EXOS6_HUMAN	exosome component 6						DNA deamination (GO:0045006)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|isotype switching (GO:0045190)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)	cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I795I(1)									CAAGGTCAGCGATCTCCCTCT	0.547																																					p.I795I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2385T	16						.						161.0	120.0	133.0					16																	70288539		2198	4300	6498	68846040	SO:0001631	upstream_gene_variant	16	exon17			BC052252	CCDS10887.1	16q22.1	2008-02-05			ENSG00000223496	ENSG00000223496			19055	protein-coding gene	gene with protein product	"""Mtr3 (mRNA transport regulator 3)-homolog (yeast)"""	606490				11719186, 12419256	Standard	NM_058219		Approved	MTR3, hMtr3p, Mtr3p, EAP4, p11	uc002eym.1	Q5RKV6	OTTHUMG00000137578		16.37:g.70288539G>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	68846040	NM_001605		Silent	SNP	ENST00000435634.1	37	CCDS10887.1																																																																																				0.547	EXOSC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268966.1	NM_058219	
HYDIN	54768	broad.mit.edu	37	16	70913579	70913579	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:70913579C>A	ENST00000393567.2	-	61	10446	c.10296G>T	c.(10294-10296)acG>acT	p.T3432T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	3432					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.T3431T(1)|p.T3383T(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGAAGGACACCGTGGCAAAGG	0.562																																					p.T3431T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G10293T	16						.																																			69471080	SO:0001819	synonymous_variant	54768	exon61			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.10296G>T	16.37:g.70913579C>A		Somatic		Capture	Illumina HiSeq	Phase_I	69471080	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																				0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HYDIN	54768	broad.mit.edu	37	16	71186562	71186562	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:71186562C>A	ENST00000393567.2	-	7	991	c.841G>T	c.(841-843)Ggt>Tgt	p.G281C	HYDIN_ENST00000538248.1_Splice_Site_p.G308C|HYDIN_ENST00000393550.2_Splice_Site_p.G281C|HYDIN_ENST00000448691.1_Splice_Site_p.G281C|HYDIN_ENST00000288168.10_Splice_Site_p.G298C|HYDIN_ENST00000321489.5_Splice_Site_p.G281C|HYDIN_ENST00000448089.2_Splice_Site_p.G281C|HYDIN_ENST00000541601.1_Splice_Site_p.G298C	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	281					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.G281C(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TACTGCATACCTGTGTCATAA	0.433																																					p.G281C												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G841T	16						.						7.0	6.0	6.0					16																	71186562		2032	4133	6165	69744063	SO:0001630	splice_region_variant	54768	exon7			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.841+1G>T	16.37:g.71186562C>A		Somatic		Capture	Illumina HiSeq	Phase_I	69744063	NM_032821	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	22.6|22.6	4.308926|4.308926	0.81247|0.81247	.|.	.|.	ENSG00000157423|ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089;ENST00000448691;ENST00000321489;ENST00000538248;ENST00000541601;ENST00000288168;ENST00000393550|ENST00000538382	T;T;T;T;T;T;T;T|.	0.20463|.	5.27;3.35;3.35;3.35;3.34;3.33;2.95;2.07|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.31821|.	U|.	0.007010|.	T|T	0.79179|0.79179	0.4402|0.4402	M|M	0.83603|0.83603	2.65|2.65	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;0.999;1.0;1.0|.	D;D;D;D;D;D|.	0.97110|.	1.0;1.0;1.0;0.991;1.0;1.0|.	T|T	0.80786|0.80786	-0.1227|-0.1227	9|5	.|.	.|.	.|.	.|.	17.5881|17.5881	0.87988|0.87988	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	308;298;281;298;281;281|.	B4DRN4;F5H6V3;Q4G0P3;F8WD03;Q4G0P3-5;F8WD23|.	.;.;HYDIN_HUMAN;.;.;.|.	C|H	281;281;281;281;281;308;298;298;281|119	ENSP00000377197:G281C;ENSP00000398544:G281C;ENSP00000394826:G281C;ENSP00000314736:G281C;ENSP00000444970:G308C;ENSP00000437341:G298C;ENSP00000288168:G298C;ENSP00000377181:G281C|.	.|.	G|Q	-|-	1|3	0|2	HYDIN|HYDIN	69744063|69744063	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.890000|0.890000	0.51754|0.51754	5.935000|5.935000	0.70145|0.70145	2.552000|2.552000	0.86080|0.86080	0.552000|0.552000	0.68991|0.68991	GGT|CAG		0.433	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		Missense_Mutation
CMTR2	55783	broad.mit.edu	37	16	71318915	71318915	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:71318915A>G	ENST00000338099.5	-	3	1245	c.909T>C	c.(907-909)ccT>ccC	p.P303P	CMTR2_ENST00000434935.2_Silent_p.P303P			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	303	Adrift-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00946}.				7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)	p.P303P(1)									TGCTAGTAGCAGGTTTGAAAA	0.403																																					p.P303P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T909C	16						.						75.0	75.0	75.0					16																	71318915		2198	4299	6497	69876416	SO:0001819	synonymous_variant	55783	exon3			BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.909T>C	16.37:g.71318915A>G		Somatic		Capture	Illumina HiSeq	Phase_I	69876416	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Silent	SNP	ENST00000338099.5	37	CCDS10898.1																																																																																				0.403	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
ZFHX3	463	broad.mit.edu	37	16	72984473	72984473	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:72984473G>A	ENST00000268489.5	-	3	3783	c.3111C>T	c.(3109-3111)ccC>ccT	p.P1037P	ZFHX3_ENST00000397992.5_Silent_p.P123P	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1037					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P1037P(1)		NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				TGAGGTGCACGGGGTTGCCGA	0.602																																					p.P1037P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3111T	16						.						135.0	102.0	113.0					16																	72984473		2198	4300	6498	71541974	SO:0001819	synonymous_variant	463	exon3			D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.3111C>T	16.37:g.72984473G>A		Somatic		Capture	Illumina HiSeq	Phase_I	71541974	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																				0.602	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
CHST6	4166	broad.mit.edu	37	16	75512725	75512725	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:75512725G>T	ENST00000332272.4	-	3	1181	c.1002C>A	c.(1000-1002)cgC>cgA	p.R334R	RP11-77K12.4_ENST00000530512.3_RNA|CHST6_ENST00000390664.2_Silent_p.R334R	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	334					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)	p.R334R(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						GCAGCGCATGGCGCCAGGCCT	0.642																																					p.R334R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1002A	16						.						63.0	57.0	59.0					16																	75512725		2198	4300	6498	74070226	SO:0001819	synonymous_variant	4166	exon3			AF280086	CCDS10918.1	16q22	2008-02-05			ENSG00000183196	ENSG00000183196		"""Sulfotransferases, membrane-bound"""	6938	protein-coding gene	gene with protein product		605294		MCDC1		8644739, 11017086	Standard	NM_021615		Approved		uc002fef.3	Q9GZX3	OTTHUMG00000137612	ENST00000332272.4:c.1002C>A	16.37:g.75512725G>T		Somatic		Capture	Illumina HiSeq	Phase_I	74070226	NM_021615	D3DUK3	Silent	SNP	ENST00000332272.4	37	CCDS10918.1																																																																																				0.642	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615	
CHST5	23563	broad.mit.edu	37	16	75563240	75563240	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:75563240G>A	ENST00000336257.3	-	3	2437	c.1043C>T	c.(1042-1044)gCg>gTg	p.A348V	CHST5_ENST00000541075.1_Missense_Mutation_p.A354V|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	348					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)	p.A348V(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						GACGTTGCGCGCATTCCTAGA	0.657																																					p.A348V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1043T	16						.						95.0	78.0	84.0					16																	75563240		2198	4299	6497	74120741	SO:0001583	missense	23563	exon3			AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.1043C>T	16.37:g.75563240G>A	ENSP00000338783:p.Ala348Val	Somatic		Capture	Illumina HiSeq	Phase_I	74120741	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758319	0.49468	.	.	ENSG00000135702	ENST00000336257;ENST00000541075	D;D	0.82255	-1.59;-1.59	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	D	0.90981	0.7164	M	0.86651	2.83	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	D	0.91945	0.5566	10	0.59425	D	0.04	.	12.6629	0.56824	0.0:0.0:1.0:0.0	.	354;348	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	V	348;354	ENSP00000338783:A348V;ENSP00000441220:A354V	ENSP00000338783:A348V	A	-	2	0	CHST5	74120741	1.000000	0.71417	0.959000	0.39883	0.018000	0.09664	8.844000	0.92147	1.583000	0.49898	0.313000	0.20887	GCG		0.657	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
CNTNAP4	85445	broad.mit.edu	37	16	76532570	76532570	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:76532570C>T	ENST00000476707.1	+	14	2492	c.2353C>T	c.(2353-2355)Cct>Tct	p.P785S	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.P733S|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.P709S|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.P781S|CNTNAP4_ENST00000469589.1_3'UTR			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	782	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)|regulation of grooming behavior (GO:2000821)|regulation of synaptic transmission, dopaminergic (GO:0032225)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)				breast(4)|central_nervous_system(1)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(33)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	64						TAAACTGGGGCCTCTGCTCTG	0.423																																					p.P709S												.	.	0			c.C2125T	16						.						60.0	55.0	57.0					16																	76532570		2044	4247	6291	75090071	SO:0001583	missense	85445	exon14			AB051550	CCDS10924.1, CCDS10924.2, CCDS73915.1	16q23.1	2008-02-05			ENSG00000152910	ENSG00000152910			18747	protein-coding gene	gene with protein product		610518				12093160	Standard	NM_033401		Approved	CASPR4, KIAA1763	uc010chb.1	Q9C0A0	OTTHUMG00000137617	ENST00000476707.1:c.2353C>T	16.37:g.76532570C>T	ENSP00000417628:p.Pro785Ser	None		Capture	Illumina HiSeq	Phase_I	75090071	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	C	25.7	4.668861	0.88348	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	T;T;T;T	0.52754	0.65;0.65;0.65;0.65	4.93	4.93	0.64822	.	0.000000	0.41294	D	0.000901	T	0.70378	0.3217	.	.	.	0.58432	D	0.999994	D;D;D	0.89917	0.995;0.989;1.0	P;P;D	0.81914	0.882;0.677;0.995	T	0.73668	-0.3910	9	0.66056	D	0.02	.	18.3086	0.90190	0.0:1.0:0.0:0.0	.	709;785;782	E9PFZ6;E9PDN6;Q9C0A0	.;.;CNTP4_HUMAN	S	781;733;709;785	ENSP00000306893:P781S;ENSP00000439733:P733S;ENSP00000418741:P709S;ENSP00000417628:P785S	ENSP00000306893:P781S	P	+	1	0	CNTNAP4	75090071	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.662000	0.61525	2.724000	0.93272	0.650000	0.86243	CCT		0.423	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	
ADAMTS18	170692	broad.mit.edu	37	16	77327136	77327136	+	Missense_Mutation	SNP	C	C	T	rs142167857	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:77327136C>T	ENST00000282849.5	-	20	3444	c.3026G>A	c.(3025-3027)cGa>cAa	p.R1009Q	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1009	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.R1009Q(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CCTCACCCCTCGTCCACAGGT	0.493																																					p.R1009Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3026A	16						.	C	GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	74.0	74.0	74.0		3026	5.2	0.9	16	dbSNP_134	74	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ADAMTS18	NM_199355.2	43	0,3,6495	TT,TC,CC		0.0233,0.0227,0.0231	possibly-damaging	1009/1222	77327136	3,12993	2198	4300	6498	75884637	SO:0001583	missense	170692	exon20			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3026G>A	16.37:g.77327136C>T	ENSP00000282849:p.Arg1009Gln	Somatic		Capture	Illumina HiSeq	Phase_I	75884637	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.735583	0.49045	2.27E-4	2.33E-4	ENSG00000140873	ENST00000282849	T	0.52526	0.66	6.16	5.18	0.71444	.	0.140471	0.46442	N	0.000281	T	0.46151	0.1378	L	0.55103	1.725	0.44702	D	0.997698	P;P	0.52692	0.955;0.69	B;P	0.46796	0.392;0.527	T	0.37174	-0.9717	10	0.25751	T	0.34	.	10.0264	0.42074	0.0:0.8413:0.0:0.1587	.	1009;1009	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	Q	1009	ENSP00000282849:R1009Q	ENSP00000282849:R1009Q	R	-	2	0	ADAMTS18	75884637	1.000000	0.71417	0.950000	0.38849	0.003000	0.03518	4.406000	0.59748	1.530000	0.49136	-0.355000	0.07637	CGA		0.493	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
PLCG2	5336	broad.mit.edu	37	16	81973512	81973512	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:81973512G>A	ENST00000359376.3	+	30	3543	c.3329G>A	c.(3328-3330)aGc>aAc	p.S1110N		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1110	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)	p.S1110N(2)		NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						aatggcctcagccctatctGG	0.473																																					p.S1110N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3329A	16						.						89.0	86.0	87.0					16																	81973512		1893	4123	6016	80531013	SO:0001583	missense	5336	exon30				CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3329G>A	16.37:g.81973512G>A	ENSP00000352336:p.Ser1110Asn	Somatic		Capture	Illumina HiSeq	Phase_I	80531013	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	5.680	0.310128	0.10733	.	.	ENSG00000197943	ENST00000359376	T	0.60797	0.16	5.75	2.67	0.31697	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.165706	0.64402	N	0.000004	T	0.10680	0.0261	N	0.00029	-2.625	0.38831	D	0.955843	B	0.02656	0.0	B	0.04013	0.001	T	0.35773	-0.9775	10	0.02654	T	1	.	5.9626	0.19308	0.5156:0.0:0.4844:0.0	.	1110	P16885	PLCG2_HUMAN	N	1110	ENSP00000352336:S1110N	ENSP00000352336:S1110N	S	+	2	0	PLCG2	80531013	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.684000	0.46951	0.719000	0.32188	0.655000	0.94253	AGC		0.473	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
TAF1C	9013	broad.mit.edu	37	16	84216717	84216717	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:84216717C>G	ENST00000567759.1	-	6	629	c.447G>C	c.(445-447)aaG>aaC	p.K149N	TAF1C_ENST00000570117.1_Intron|TAF1C_ENST00000566732.1_Missense_Mutation_p.K149N|TAF1C_ENST00000341690.6_Missense_Mutation_p.K82N|TAF1C_ENST00000565544.1_5'Flank|TAF1C_ENST00000541676.1_Missense_Mutation_p.K82N|TAF1C_ENST00000378541.4_Missense_Mutation_p.K149N	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	149					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)	p.K149N(1)		endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						CCTGGAGCAGCTTCTTCACAC	0.582																																					p.K82N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G246C	16						.						207.0	184.0	192.0					16																	84216717		2200	4300	6500	82774218	SO:0001583	missense	9013	exon6			L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.447G>C	16.37:g.84216717C>G	ENSP00000455265:p.Lys149Asn	Somatic		Capture	Illumina HiSeq	Phase_I	82774218	NM_139353	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	37	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	3.766	-0.048691	0.07407	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690;ENST00000537450	T;T;T	0.04156	3.79;3.69;3.69	4.63	-1.84	0.07809	.	0.906894	0.09167	N	0.839435	T	0.04543	0.0124	L	0.36672	1.1	0.09310	N	1	P;P;P;P	0.41848	0.557;0.557;0.763;0.557	B;B;B;B	0.42282	0.221;0.215;0.382;0.215	T	0.40346	-0.9568	10	0.31617	T	0.26	-4.3052	5.5632	0.17157	0.1225:0.4351:0.3609:0.0816	.	149;149;149;82	F5H7W6;Q15572-6;Q15572;Q15572-2	.;.;TAF1C_HUMAN;.	N	149;82;82;149	ENSP00000367802:K149N;ENSP00000437900:K82N;ENSP00000345305:K82N	ENSP00000345305:K82N	K	-	3	2	TAF1C	82774218	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	-0.194000	0.09559	-0.399000	0.07668	-2.589000	0.00165	AAG		0.582	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
ADAD2	161931	broad.mit.edu	37	16	84228718	84228718	+	Silent	SNP	C	C	T	rs146515699	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:84228718C>T	ENST00000315906.5	+	4	703	c.651C>T	c.(649-651)agC>agT	p.S217S	RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Silent_p.S289S|RP11-486L19.2_ENST00000536986.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	217					RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.S289S(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CGTTGGTGAGCGCCGGCTTTG	0.657													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		16828	0.0		0.0	False		,,,				2504	0.0				p.S217S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C651T	16						.	C	,	63,4337	57.4+/-93.9	1,61,2138	43.0	45.0	44.0		651,867	-2.8	0.0	16	dbSNP_134	44	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ADAD2	NM_001145400.1,NM_139174.3	,	1,63,6436	TT,TC,CC		0.0233,1.4318,0.5	,	217/584,289/666	84228718	65,12935	2200	4300	6500	82786219	SO:0001819	synonymous_variant	161931	exon4			AF447586	CCDS10944.1, CCDS45536.1	16q24.1	2007-05-31			ENSG00000140955	ENSG00000140955			30714	protein-coding gene	gene with protein product							Standard	NM_139174		Approved	TENRL, FLJ00337	uc002fhr.2	Q8NCV1	OTTHUMG00000137637	ENST00000315906.5:c.651C>T	16.37:g.84228718C>T		Somatic		Capture	Illumina HiSeq	Phase_I	82786219	NM_001145400	B2RCL6|Q8NA94	Silent	SNP	ENST00000315906.5	37	CCDS45536.1																																																																																				0.657	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
FOXF1	2294	broad.mit.edu	37	16	86546652	86546652	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:86546652G>A	ENST00000262426.4	+	2	1144	c.1101G>A	c.(1099-1101)caG>caA	p.Q367Q		NM_001451.2	NP_001442.2	Q12946	FOXF1_HUMAN	forkhead box F1	367					blood vessel development (GO:0001568)|branching involved in open tracheal system development (GO:0060446)|cardiac left ventricle morphogenesis (GO:0003214)|cellular response to cytokine stimulus (GO:0071345)|cellular response to organic cyclic compound (GO:0071407)|detection of wounding (GO:0014822)|determination of left/right symmetry (GO:0007368)|digestive tract development (GO:0048565)|ductus arteriosus closure (GO:0097070)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic ectodermal digestive tract morphogenesis (GO:0048613)|embryonic foregut morphogenesis (GO:0048617)|endocardial cushion development (GO:0003197)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lateral mesodermal cell differentiation (GO:0048371)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|mesenchyme migration (GO:0090131)|midgut development (GO:0007494)|morphogenesis of a branching structure (GO:0001763)|negative regulation of inflammatory response (GO:0050728)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pancreas development (GO:0031016)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|respiratory tube development (GO:0030323)|right lung morphogenesis (GO:0060461)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|smoothened signaling pathway (GO:0007224)|somitogenesis (GO:0001756)|trachea development (GO:0060438)|ureter development (GO:0072189)|vasculogenesis (GO:0001570)|venous blood vessel development (GO:0060841)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)	p.Q342Q(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(1)	12						ACTACCACCAGCAGGTCACCT	0.632																																					p.Q367Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1101A	16						.						53.0	52.0	52.0					16																	86546652		2198	4300	6498	85104153	SO:0001819	synonymous_variant	2294	exon2			U13219	CCDS10957.2	16q24	2008-02-05			ENSG00000103241	ENSG00000103241		"""Forkhead boxes"""	3809	protein-coding gene	gene with protein product		601089		FKHL5		8825632, 7957066	Standard	NM_001451		Approved	FREAC1	uc002fjl.3	Q12946	OTTHUMG00000137651	ENST00000262426.4:c.1101G>A	16.37:g.86546652G>A		Somatic		Capture	Illumina HiSeq	Phase_I	85104153	NM_001451	B2RAF4|Q5FWE5	Silent	SNP	ENST00000262426.4	37	CCDS10957.2																																																																																				0.632	FOXF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000269103.2	NM_001451	
GALNS	2588	broad.mit.edu	37	16	88908373	88908373	+	Missense_Mutation	SNP	G	G	A	rs141340188		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:88908373G>A	ENST00000268695.5	-	3	339	c.251C>T	c.(250-252)gCg>gTg	p.A84V	GALNS_ENST00000565364.1_5'UTR|GALNS_ENST00000542788.1_Intron	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	84	Catalytic domain.		A -> E (in MPS4A; loss of enzymatic activity). {ECO:0000269|PubMed:24726177}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)	p.A84V(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GAGCAGTGCCGCCCTCGCTAT	0.602																																					p.A84V	GBM(129;1929 2344 25209 33204)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C251T	16						.						145.0	113.0	124.0					16																	88908373		2195	4299	6494	87435874	SO:0001583	missense	2588	exon3			D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.251C>T	16.37:g.88908373G>A	ENSP00000268695:p.Ala84Val	Somatic		Capture	Illumina HiSeq	Phase_I	87435874	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.63|14.63	2.592827|2.592827	0.46214|0.46214	.|.	.|.	ENSG00000141012|ENSG00000141012	ENST00000268695|ENST00000439266	D|.	0.95001|.	-3.58|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase, conserved site (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84160|0.84160	0.5411|0.5411	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	0.998;1.0|.	D|D	0.86868|0.86868	0.2034|0.2034	10|6	0.87932|0.87932	D|D	0|0	.|.	19.199|19.199	0.93701|0.93701	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	84;84|.	B2R6P1;P34059|.	.;GALNS_HUMAN|.	V|W	84|43	ENSP00000268695:A84V|.	ENSP00000268695:A84V|ENSP00000402127:R43W	A|R	-|-	2|1	0|2	GALNS|GALNS	87435874|87435874	1.000000|1.000000	0.71417|0.71417	0.469000|0.469000	0.27204|0.27204	0.078000|0.078000	0.17371|0.17371	7.577000|7.577000	0.82486|0.82486	2.620000|2.620000	0.88729|0.88729	0.561000|0.561000	0.74099|0.74099	GCG|CGG		0.602	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
GRIN2A	2903	broad.mit.edu	37	16	9857525	9857525	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:9857525G>A	ENST00000396573.2	-	14	4185	c.3876C>T	c.(3874-3876)taC>taT	p.Y1292Y	GRIN2A_ENST00000562109.1_Intron|GRIN2A_ENST00000535259.1_Intron|GRIN2A_ENST00000404927.2_Intron|GRIN2A_ENST00000330684.3_Silent_p.Y1292Y|GRIN2A_ENST00000396575.2_Silent_p.Y1292Y	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1292					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)	p.Y1292Y(1)		NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAATGTTATCGTAGGAATGCT	0.522																																					p.Y1292Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3876T	16						.						137.0	115.0	122.0					16																	9857525		2197	4300	6497	9765026	SO:0001819	synonymous_variant	2903	exon14				CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.3876C>T	16.37:g.9857525G>A		Somatic		Capture	Illumina HiSeq	Phase_I	9765026	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																				0.522	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
RSL1D1	26156	broad.mit.edu	37	16	11935773	11935773	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:11935773delT	ENST00000571133.1	-	6	792	c.720delA	c.(718-720)aaafs	p.K240fs	RSL1D1_ENST00000542106.1_Frame_Shift_Del_p.K20fs	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	240					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.K240fs*9(1)		NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						CCTCTGGCAATTTTTCTGAAA	0.338																																					p.K240fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.720delA	16						.						60.0	56.0	57.0					16																	11935773		2197	4300	6497	11843274	SO:0001589	frameshift_variant	26156	exon6			AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.720delA	16.37:g.11935773delT	ENSP00000460871:p.Lys240fs	Somatic		Capture	Illumina HiSeq	Phase_I	11843274	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Frame_Shift_Del	DEL	ENST00000571133.1	37	CCDS10551.1																																																																																				0.338	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
CD19	930	broad.mit.edu	37	16	28950039	28950039	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:28950039delC	ENST00000324662.3	+	13	1573	c.1529delC	c.(1528-1530)gccfs	p.A510fs	CD19_ENST00000538922.1_Frame_Shift_Del_p.A511fs|CD19_ENST00000567541.1_Frame_Shift_Del_p.A511fs			P15391	CD19_HUMAN	CD19 molecule	510					B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)	p.Q512fs*>45(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						CTGTATGCAGCCCCCCAGCTC	0.612																																					p.A511fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1532delC	16						.						84.0	80.0	81.0					16																	28950039		2197	4300	6497	28857540	SO:0001589	frameshift_variant	930	exon13				CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.1529delC	16.37:g.28950039delC	ENSP00000313419:p.Ala510fs	Somatic		Capture	Illumina HiSeq	Phase_I	28857540	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Frame_Shift_Del	DEL	ENST00000324662.3	37	CCDS10644.1																																																																																				0.612	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
ZNF629	23361	broad.mit.edu	37	16	30795419	30795419	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:30795419delG	ENST00000262525.4	-	3	437	c.230delC	c.(229-231)ccafs	p.P77fs		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	77					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P77fs*23(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			CAGTGGGGTTGGGGGGTTCTG	0.622																																					p.P77fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.230delC	16						.						15.0	15.0	15.0					16																	30795419		1817	4066	5883	30702920	SO:0001589	frameshift_variant	23361	exon3			AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.230delC	16.37:g.30795419delG	ENSP00000262525:p.Pro77fs	Somatic		Capture	Illumina HiSeq	Phase_I	30702920	NM_001080417	Q15938	Frame_Shift_Del	DEL	ENST00000262525.4	37	CCDS45463.1																																																																																				0.622	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
ZDHHC7	55625	broad.mit.edu	37	16	85010039	85010039	+	Frame_Shift_Del	DEL	G	G	-	rs531874653		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:85010039delG	ENST00000313732.4	-	8	1189	c.837delC	c.(835-837)cccfs	p.P279fs	ZDHHC7_ENST00000564466.1_Frame_Shift_Del_p.P316fs|ZDHHC7_ENST00000569488.1_5'Flank	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	279					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)	p.S280fs*5(1)		large_intestine(6)|lung(4)	10						AGAGGAGTGAGGGGGGCCCCC	0.587																																					p.P279fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.837delC	16						.						48.0	59.0	55.0					16																	85010039		2199	4300	6499	83567540	SO:0001589	frameshift_variant	55625	exon8			AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.837delC	16.37:g.85010039delG	ENSP00000315604:p.Pro279fs	Somatic		Capture	Illumina HiSeq	Phase_I	83567540	NM_017740	D3DUM1|Q8WV42|Q9NVD8	Frame_Shift_Del	DEL	ENST00000313732.4	37	CCDS10950.1																																																																																				0.587	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
FANCA	2175	broad.mit.edu	37	16	89866042	89866042	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr16:89866042G>A	ENST00000389301.3	-	9	827	c.797C>T	c.(796-798)aCg>aTg	p.T266M	FANCA_ENST00000563673.1_Missense_Mutation_p.T266M|FANCA_ENST00000534992.1_Missense_Mutation_p.T266M|FANCA_ENST00000543736.1_Missense_Mutation_p.T234M|FANCA_ENST00000389302.3_Missense_Mutation_p.T266M|FANCA_ENST00000568369.1_Missense_Mutation_p.T266M	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	266			T -> A (in dbSNP:rs7190823). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:9399890, ECO:0000269|Ref.4}.		DNA repair (GO:0006281)|female gonad development (GO:0008585)|male gonad development (GO:0008584)|male meiosis (GO:0007140)|protein complex assembly (GO:0006461)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T266M(1)		breast(5)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|urinary_tract(3)	47		Lung NSC(15;8.48e-06)|all_lung(18;1.31e-05)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.028)		TACATCAACCGTGACCTGTCA	0.358			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.T266M		yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C797T	16						.						147.0	128.0	134.0					16																	89866042		2198	4300	6498	88393543	SO:0001583	missense	2175	exon9	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	Z83067	CCDS32515.1, CCDS42221.1, CCDS67099.1	16q24.3	2014-09-17			ENSG00000187741	ENSG00000187741		"""Fanconi anemia, complementation groups"""	3582	protein-coding gene	gene with protein product		607139		FACA, FANCH		7581462, 9382107	Standard	NM_001286167		Approved	FAA, FA-H, FAH	uc002fou.1	O15360		ENST00000389301.3:c.797C>T	16.37:g.89866042G>A	ENSP00000373952:p.Thr266Met	Somatic		Capture	Illumina HiSeq	Phase_I	88393543	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	.	.	.	.	.	.	.	.	.	.	G	11.18	1.563643	0.27915	.	.	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.1	1.9	0.25705	.	0.674836	0.13063	N	0.416735	T	0.21468	0.0517	N	0.08118	0	0.09310	N	1	B;B;P;P;P;B	0.40660	0.389;0.079;0.726;0.726;0.726;0.389	B;B;B;B;B;B	0.34873	0.057;0.005;0.123;0.191;0.123;0.057	T	0.09662	-1.0664	10	0.72032	D	0.01	-13.3596	10.8279	0.46645	0.0:0.5187:0.4813:0.0	.	266;234;266;266;266;266	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	M	266;266;266;234	ENSP00000373952:T266M;ENSP00000373953:T266M;ENSP00000443675:T266M;ENSP00000443409:T234M	ENSP00000373952:T266M	T	-	2	0	FANCA	88393543	0.012000	0.17670	0.061000	0.19648	0.145000	0.21501	1.720000	0.38022	0.913000	0.36797	0.555000	0.69702	ACG		0.358	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
RAI1	10743	broad.mit.edu	37	17	17699358	17699359	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:17699358_17699359insC	ENST00000353383.1	+	3	3565_3566	c.3096_3097insC	c.(3097-3099)cccfs	p.P1033fs	RAI1_ENST00000261641.6_Frame_Shift_Ins_p.P1033fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1033					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)	p.Q1035fs*31(1)		breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		CCTGCACAGGGCCCCCCCAGGG	0.698																																					p.G1032fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3096_3097insC	17						.																																			17640084	SO:0001589	frameshift_variant	10743	exon3			AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.3103dupC	17.37:g.17699365_17699365dupC	ENSP00000323074:p.Pro1033fs	Somatic		Capture	Illumina HiSeq	Phase_I	17640083	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Ins	INS	ENST00000353383.1	37	CCDS11188.1																																																																																				0.698	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
RNF43	54894	broad.mit.edu	37	17	56435815	56435816	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:56435815_56435816insT	ENST00000584437.1	-	8	3276_3277	c.1321_1322insA	c.(1321-1323)cctfs	p.P441fs	RNF43_ENST00000407977.2_Frame_Shift_Ins_p.P441fs|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000581868.1_Frame_Shift_Ins_p.P314fs|RNF43_ENST00000500597.2_Frame_Shift_Ins_p.P400fs|RNF43_ENST00000577625.1_Frame_Shift_Ins_p.P314fs|RNF43_ENST00000583753.1_Frame_Shift_Ins_p.P400fs|RNF43_ENST00000577716.1_Frame_Shift_Ins_p.P441fs			Q68DV7	RNF43_HUMAN	ring finger protein 43	441					negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.P441fs*2(1)		NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTGCTGTCAGGGGGCCTGGCC	0.634																																					p.P441fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1322_1323insA	17						.																																			53790815	SO:0001589	frameshift_variant	54894	exon9				CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1321_1322insA	17.37:g.56435815_56435816insT	ENSP00000463069:p.Pro441fs	Somatic		Capture	Illumina HiSeq	Phase_I	53790814	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Frame_Shift_Ins	INS	ENST00000584437.1	37	CCDS11607.1																																																																																				0.634	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
CSH1	1442	broad.mit.edu	37	17	61973672	61973673	+	Intron	INS	-	-	T	rs200633741	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:61973672_61973673insT	ENST00000316193.8	-	2	152				CSH1_ENST00000453363.3_Intron|CSH1_ENST00000329882.8_Intron	NM_001317.5	NP_001308.1	P0DML2	CSH1_HUMAN	chorionic somatomammotropin hormone 1 (placental lactogen)							extracellular region (GO:0005576)	metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						GGAGCTGTTTGTTTTTTTTCTC	0.559									Russell-Silver syndrome				TTTTTtt|TTTTTTTT|TTTTTTTTT|cryptic_indel	102	0.0203674	0.0703	0.0043	5008	,	,		21422	0.0		0.001	False		,,,				2504	0.0051				.												.	.	0			.	17						.																																			59327405	SO:0001627	intron_variant	1442	.	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	J00118	CCDS11649.1	17q22-q24	2008-07-18				ENSG00000136488			2440	protein-coding gene	gene with protein product	"""chorionic somatomammotropin A"", ""placental lactogen"", ""choriomammotropin"""	150200				6208192	Standard	NM_001317		Approved	hCS-A, CSA, PL, CSMT, FLJ75407	uc002jcs.2	P0DML2		ENST00000316193.8:c.11-77->A	17.37:g.61973680_61973680dupT		Somatic		Capture	Illumina HiSeq	Phase_I	59327404	.	P01243|Q0VDB1|Q14407	Frame_Shift_Ins	INS	ENST00000316193.8	37	CCDS11649.1																																																																																				0.559	CSH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416040.1	NM_001317	
MYH8	4626	broad.mit.edu	37	17	10315798	10315798	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:10315798G>A	ENST00000403437.2	-	14	1399	c.1305C>T	c.(1303-1305)taC>taT	p.Y435Y	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	435	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)	p.Y435Y(1)		NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						ACATCTTCTCGTAGACGGCTT	0.512									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.Y435Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1305T	17						.						279.0	252.0	261.0					17																	10315798		2203	4300	6503	10256523	SO:0001819	synonymous_variant	4626	exon14	Familial Cancer Database	Carney Complex Variant		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1305C>T	17.37:g.10315798G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10256523	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																				0.512	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
DNAH9	1770	broad.mit.edu	37	17	11778403	11778403	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:11778403G>T	ENST00000262442.4	+	53	10448	c.10380G>T	c.(10378-10380)gaG>gaT	p.E3460D	DNAH9_ENST00000454412.2_Missense_Mutation_p.E3460D|RP11-628O18.1_ENST00000579621.1_RNA	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	3460	AAA 5. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.E3460D(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TCAACTGTGAGCGCTGGCCAC	0.542																																					p.E3460D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10380T	17						.						94.0	83.0	87.0					17																	11778403		2203	4300	6503	11719128	SO:0001583	missense	1770	exon53			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.10380G>T	17.37:g.11778403G>T	ENSP00000262442:p.Glu3460Asp	Somatic		Capture	Illumina HiSeq	Phase_I	11719128	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751402	0.49257	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.25250	1.81;1.81	4.66	2.52	0.30459	.	0.200304	0.42548	D	0.000687	T	0.18800	0.0451	L	0.38733	1.17	0.80722	D	1	B	0.17038	0.02	B	0.25405	0.06	T	0.05402	-1.0887	10	0.26408	T	0.33	.	8.9993	0.36072	0.258:0.0:0.742:0.0	.	3460	Q9NYC9	DYH9_HUMAN	D	3460;3460;2042	ENSP00000262442:E3460D;ENSP00000414874:E3460D	ENSP00000262442:E3460D	E	+	3	2	DNAH9	11719128	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.328000	0.33758	1.189000	0.43028	0.655000	0.94253	GAG		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ARHGAP44	9912	broad.mit.edu	37	17	12832313	12832313	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:12832313G>A	ENST00000379672.5	+	7	832	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.A178T|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.A178T	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	178	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)	p.A178T(1)		NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CAAGGCTGATGCCCTCAGGGA	0.542																																					p.A178T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G532A	17						.						56.0	65.0	62.0					17																	12832313		1875	4110	5985	12773038	SO:0001583	missense	9912	exon7				CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.532G>A	17.37:g.12832313G>A	ENSP00000368994:p.Ala178Thr	Somatic		Capture	Illumina HiSeq	Phase_I	12773038	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.776559	0.49786	.	.	ENSG00000006740	ENST00000379672;ENST00000340825	T;T	0.29397	1.57;1.57	5.82	5.82	0.92795	BAR (3);	0.176128	0.51477	D	0.000091	T	0.25680	0.0625	N	0.21373	0.66	0.43122	D	0.994846	P;B	0.43578	0.811;0.045	P;B	0.45660	0.489;0.098	T	0.01692	-1.1294	10	0.06099	T	0.92	.	17.5831	0.87973	0.0:0.0:1.0:0.0	.	178;178	A6NCP5;Q17R89	.;RHG44_HUMAN	T	178	ENSP00000368994:A178T;ENSP00000342566:A178T	ENSP00000342566:A178T	A	+	1	0	ARHGAP44	12773038	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.083000	0.50136	2.761000	0.94854	0.655000	0.94253	GCC		0.542	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
DPH1	1801	broad.mit.edu	37	17	1943065	1943065	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:1943065C>A	ENST00000263083.6	+	7	757	c.712C>A	c.(712-714)Cgc>Agc	p.R238S	DPH1_ENST00000570477.1_Missense_Mutation_p.R158S|OVCA2_ENST00000572195.1_5'Flank	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	238					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R238S(1)		endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						TGGAGATGGCCGCTTCCATCT	0.602																																					p.R238S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C712A	17						.						141.0	145.0	144.0					17																	1943065		2004	4157	6161	1889815	SO:0001583	missense	1801	exon7			S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.712C>A	17.37:g.1943065C>A	ENSP00000263083:p.Arg238Ser	Somatic		Capture	Illumina HiSeq	Phase_I	1889815	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.486300	0.84854	.	.	ENSG00000108963	ENST00000263083	T	0.46819	0.86	4.66	4.66	0.58398	.	0.220504	0.46145	D	0.000309	T	0.59891	0.2227	M	0.79693	2.465	0.58432	D	0.999999	B;B;B	0.30511	0.147;0.282;0.176	B;B;B	0.40066	0.145;0.318;0.157	T	0.66508	-0.5906	10	0.87932	D	0	-8.5515	16.7631	0.85517	0.0:1.0:0.0:0.0	.	248;248;238	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	S	238	ENSP00000263083:R238S	ENSP00000263083:R238S	R	+	1	0	DPH1	1889815	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.012000	0.57131	2.425000	0.82216	0.449000	0.29647	CGC		0.602	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
MYO15A	51168	broad.mit.edu	37	17	18025430	18025430	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:18025430C>T	ENST00000205890.5	+	2	3654	c.3316C>T	c.(3316-3318)Cgg>Tgg	p.R1106W		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	1106					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.R1106W(1)		breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GGGGGGTGAACGGCGCCAGGC	0.672																																					p.R1106W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3316T	17						.						40.0	46.0	44.0					17																	18025430		1976	4148	6124	17966155	SO:0001583	missense	51168	exon2			AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.3316C>T	17.37:g.18025430C>T	ENSP00000205890:p.Arg1106Trp	Somatic		Capture	Illumina HiSeq	Phase_I	17966155	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	c	9.815	1.184092	0.21870	.	.	ENSG00000091536	ENST00000205890	D	0.88509	-2.39	4.95	-3.5	0.04710	.	.	.	.	.	T	0.79540	0.4463	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.66160	-0.5993	9	0.87932	D	0	.	8.2602	0.31779	0.6634:0.2524:0.0:0.0842	.	1106	Q9UKN7	MYO15_HUMAN	W	1106	ENSP00000205890:R1106W	ENSP00000205890:R1106W	R	+	1	2	MYO15A	17966155	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-1.681000	0.01937	-0.488000	0.06726	-0.521000	0.04368	CGG		0.672	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
TSR1	55720	broad.mit.edu	37	17	2232665	2232665	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:2232665G>A	ENST00000301364.5	-	11	2954	c.1875C>T	c.(1873-1875)gcC>gcT	p.A625A	SNORD91B_ENST00000391250.1_RNA|SNORD91A_ENST00000390861.1_RNA	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	625					ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.A625A(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						ATAAAGGTGAGGCTCGGAAGC	0.507																																					p.A625A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1875T	17						.						95.0	88.0	90.0					17																	2232665		2203	4300	6503	2179415	SO:0001819	synonymous_variant	55720	exon11			AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.1875C>T	17.37:g.2232665G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2179415	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Silent	SNP	ENST00000301364.5	37	CCDS32525.1																																																																																				0.507	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
MAPK7	5598	broad.mit.edu	37	17	19285573	19285573	+	Missense_Mutation	SNP	G	G	A	rs144078337	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:19285573G>A	ENST00000308406.5	+	5	2343	c.1957G>A	c.(1957-1959)Gcg>Acg	p.A653T	MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000299612.7_Missense_Mutation_p.A514T|MAPK7_ENST00000395602.4_Missense_Mutation_p.A653T|MAPK7_ENST00000395604.3_Missense_Mutation_p.A653T|MFAP4_ENST00000574313.2_5'Flank	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	653	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)	p.A653T(1)		autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					CCCTGTCCCCGCGCCACCCCA	0.697													G|||	3	0.000599042	0.0	0.0	5008	,	,		10497	0.0		0.0	False		,,,				2504	0.0031				p.A653T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1957A	17						.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4380		0,0,2190	24.0	28.0	27.0		1957,1957,1540,1957	1.8	0.1	17	dbSNP_134	27	1,8553		0,1,4276	no	missense,missense,missense,missense	MAPK7	NM_139034.2,NM_139033.2,NM_139032.2,NM_002749.3	58,58,58,58	0,1,6466	AA,AG,GG		0.0117,0.0,0.0077	benign,benign,benign,benign	653/817,653/817,514/678,653/817	19285573	1,12933	2190	4277	6467	19226166	SO:0001583	missense	5598	exon5			U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1957G>A	17.37:g.19285573G>A	ENSP00000311005:p.Ala653Thr	Somatic		Capture	Illumina HiSeq	Phase_I	19226166	NM_139033	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	G	4.107	0.017869	0.07959	0.0	1.17E-4	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.73258	-0.46;-0.73;-0.46;-0.46	3.78	1.77	0.24775	.	0.584295	0.16959	N	0.192586	T	0.45438	0.1342	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.31052	-0.9957	10	0.41790	T	0.15	-1.8036	6.0403	0.19730	0.2374:0.0:0.7626:0.0	.	653	Q13164	MK07_HUMAN	T	653;514;653;653	ENSP00000311005:A653T;ENSP00000299612:A514T;ENSP00000378968:A653T;ENSP00000378966:A653T	ENSP00000299612:A514T	A	+	1	0	MAPK7	19226166	0.000000	0.05858	0.057000	0.19452	0.007000	0.05969	-0.124000	0.10595	0.575000	0.29434	0.305000	0.20034	GCG		0.697	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
TNFAIP1	7126	broad.mit.edu	37	17	26669341	26669341	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:26669341G>A	ENST00000226225.2	+	6	854	c.587G>A	c.(586-588)cGc>cAc	p.R196H	TNFAIP1_ENST00000583213.1_3'UTR|TNFAIP1_ENST00000544907.2_Missense_Mutation_p.R92H	NM_021137.4	NP_066960.1	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1 (endothelial)	196					apoptotic process (GO:0006915)|cell migration (GO:0016477)|DNA replication (GO:0006260)|embryo development (GO:0009790)|immune response (GO:0006955)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleolus (GO:0005730)	GTP-Rho binding (GO:0017049)	p.R196H(1)		endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	12	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TTCAACGGCCGCGTGCTCTTC	0.547																																					p.R196H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G587A	17						.						140.0	109.0	120.0					17																	26669341		2203	4300	6503	23693468	SO:0001583	missense	7126	exon6				CCDS11227.1	17q22-q23	2013-01-09			ENSG00000109079	ENSG00000109079		"""BTB/POZ domain containing"""	11894	protein-coding gene	gene with protein product		191161		EDP1		2406243, 2233719	Standard	NM_021137		Approved	B61, B12, MGC2317, BTBD34	uc002hay.3	Q13829	OTTHUMG00000132501	ENST00000226225.2:c.587G>A	17.37:g.26669341G>A	ENSP00000226225:p.Arg196His	Somatic		Capture	Illumina HiSeq	Phase_I	23693468	NM_021137	B7Z6M4|Q5TZQ1	Missense_Mutation	SNP	ENST00000226225.2	37	CCDS11227.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988435	0.93106	.	.	ENSG00000109079	ENST00000226225;ENST00000544907	T	0.59083	0.29	5.68	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	M	0.85373	2.75	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.80367	-0.1412	10	0.51188	T	0.08	-15.1661	13.9323	0.64003	0.0729:0.0:0.9271:0.0	.	196	Q13829	BACD2_HUMAN	H	196;92	ENSP00000226225:R196H	ENSP00000226225:R196H	R	+	2	0	TNFAIP1	23693468	1.000000	0.71417	0.880000	0.34516	0.823000	0.46562	9.869000	0.99810	1.411000	0.46957	0.655000	0.94253	CGC		0.547	TNFAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255681.2	NM_021137	
VTN	7448	broad.mit.edu	37	17	26695973	26695973	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:26695973C>T	ENST00000226218.4	-	5	1364	c.746G>A	c.(745-747)gGc>gAc	p.G249D	SARM1_ENST00000457710.3_5'Flank|SARM1_ENST00000379061.4_Intron|VTN_ENST00000536498.1_5'UTR|CTB-96E2.3_ENST00000591482.1_RNA|VTN_ENST00000438614.1_5'Flank|TMEM199_ENST00000509083.1_Intron|CTB-96E2.2_ENST00000555059.2_5'Flank	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin	249					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.G249D(1)		kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GTCCGGGATGCCATCGAAGCC	0.577																																					p.G249D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G746A	17						.						97.0	95.0	96.0					17																	26695973		2203	4300	6503	23720100	SO:0001583	missense	7448	exon5			BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500	ENST00000226218.4:c.746G>A	17.37:g.26695973C>T	ENSP00000226218:p.Gly249Asp	Somatic		Capture	Illumina HiSeq	Phase_I	23720100	NM_000638	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.500845	0.26861	.	.	ENSG00000255604	ENST00000226218	T	0.04275	3.66	5.74	4.69	0.59074	Hemopexin/matrixin (2);	0.445985	0.27464	N	0.019241	T	0.13372	0.0324	M	0.86651	2.83	0.38157	D	0.938918	P	0.48834	0.916	P	0.48063	0.565	T	0.00651	-1.1626	10	0.54805	T	0.06	-33.3689	9.77	0.40585	0.0:0.8189:0.0:0.1811	.	249	P04004	VTNC_HUMAN	D	249	ENSP00000226218:G249D	ENSP00000226218:G249D	G	-	2	0	AC002094.1	23720100	0.999000	0.42202	0.991000	0.47740	0.037000	0.13140	1.786000	0.38694	2.702000	0.92279	0.655000	0.94253	GGC		0.577	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
SPAG5	10615	broad.mit.edu	37	17	26906245	26906245	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:26906245C>T	ENST00000321765.5	-	19	3363	c.3031G>A	c.(3031-3033)Gcc>Acc	p.A1011T	ALDOC_ENST00000226253.4_5'Flank|ALDOC_ENST00000395321.2_5'Flank|ALDOC_ENST00000395319.3_5'Flank	NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	1011					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)		p.A1011T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TCTTCCTGGGCCTGCAGCCTA	0.512																																					p.A1011T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3031A	17						.						124.0	105.0	111.0					17																	26906245		2203	4300	6503	23930372	SO:0001583	missense	10615	exon19			AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.3031G>A	17.37:g.26906245C>T	ENSP00000323300:p.Ala1011Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23930372	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	c	11.36	1.616336	0.28801	.	.	ENSG00000076382	ENST00000321765	T	0.32515	1.45	5.79	5.79	0.91817	.	0.103413	0.43110	D	0.000603	T	0.26629	0.0651	L	0.34521	1.04	0.35080	D	0.763342	B	0.26744	0.158	B	0.27715	0.082	T	0.21008	-1.0258	10	0.25106	T	0.35	-0.6636	16.9715	0.86301	0.0:1.0:0.0:0.0	.	1011	Q96R06	SPAG5_HUMAN	T	1011	ENSP00000323300:A1011T	ENSP00000323300:A1011T	A	-	1	0	SPAG5	23930372	1.000000	0.71417	1.000000	0.80357	0.219000	0.24729	1.315000	0.33608	2.753000	0.94483	0.645000	0.84053	GCC		0.512	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
ABHD15	116236	broad.mit.edu	37	17	27890051	27890051	+	Missense_Mutation	SNP	C	C	T	rs201536407		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:27890051C>T	ENST00000307201.4	-	2	1105	c.935G>A	c.(934-936)cGt>cAt	p.R312H	RP11-68I3.2_ENST00000581474.1_RNA	NM_198147.2	NP_937790.2	Q6UXT9	ABH15_HUMAN	abhydrolase domain containing 15	312						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)	p.R312H(1)		breast(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	10						TCGAAGGGAACGGCTCCTGAA	0.582																																					p.R312H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G935A	17						.	C	HIS/ARG	0,4406		0,0,2203	50.0	46.0	47.0		935	5.9	1.0	17		47	1,8599		0,1,4299	no	missense	ABHD15	NM_198147.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	312/469	27890051	1,13005	2203	4300	6503	24914177	SO:0001583	missense	116236	exon2			AK056717	CCDS32602.1	17q11.2	2009-11-20			ENSG00000168792	ENSG00000168792		"""Abhydrolase domain containing"""	26971	protein-coding gene	gene with protein product						12975309	Standard	NM_198147		Approved		uc002hed.2	Q6UXT9		ENST00000307201.4:c.935G>A	17.37:g.27890051C>T	ENSP00000302657:p.Arg312His	Somatic		Capture	Illumina HiSeq	Phase_I	24914177	NM_198147	Q96EC5	Missense_Mutation	SNP	ENST00000307201.4	37	CCDS32602.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.101969	0.56183	0.0	1.16E-4	ENSG00000168792	ENST00000307201	T	0.71103	-0.54	5.91	5.91	0.95273	.	0.346172	0.30620	N	0.009227	T	0.67126	0.2860	L	0.48642	1.525	0.24864	N	0.992322	B	0.26635	0.155	B	0.19391	0.025	T	0.62248	-0.6894	10	0.66056	D	0.02	-13.7509	18.8833	0.92365	0.0:1.0:0.0:0.0	.	312	Q6UXT9	ABH15_HUMAN	H	312	ENSP00000302657:R312H	ENSP00000302657:R312H	R	-	2	0	ABHD15	24914177	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.123000	0.50453	2.814000	0.96858	0.650000	0.86243	CGT		0.582	ABHD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447796.2	NM_198147	
SSH2	85464	broad.mit.edu	37	17	28011582	28011582	+	Splice_Site	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:28011582T>C	ENST00000269033.3	-	5	548	c.397A>G	c.(397-399)Agt>Ggt	p.S133G	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000324677.7_5'UTR|SSH2_ENST00000540801.1_Splice_Site_p.S160G	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	133					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.S133G(1)	SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CCACCATACCTGTCATTAGAG	0.373																																					p.S133G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A397G	17						.						209.0	174.0	186.0					17																	28011582		2203	4300	6503	25035708	SO:0001630	splice_region_variant	85464	exon5			AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.398+1A>G	17.37:g.28011582T>C		Somatic		Capture	Illumina HiSeq	Phase_I	25035708	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.896867	0.52121	.	.	ENSG00000141298	ENST00000269033;ENST00000540801;ENST00000394848;ENST00000324677	T;T	0.35789	1.29;1.29	5.16	5.16	0.70880	.	0.313087	0.39544	N	0.001321	T	0.39627	0.1085	L	0.53561	1.675	0.47621	D	0.999475	B;B;B;B;B	0.33212	0.198;0.002;0.01;0.023;0.402	B;B;B;B;B	0.36959	0.237;0.005;0.019;0.037;0.074	T	0.38542	-0.9656	10	0.72032	D	0.01	-9.6692	15.0156	0.71581	0.0:0.0:0.0:1.0	.	160;133;140;133;133	F5H527;Q76I76-3;G5E957;Q76I76-4;Q76I76	.;.;.;.;SSH2_HUMAN	G	133;160;133;140	ENSP00000269033:S133G;ENSP00000444743:S160G	ENSP00000269033:S133G	S	-	1	0	SSH2	25035708	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	3.190000	0.50973	1.941000	0.56285	0.455000	0.32223	AGT		0.373	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	Missense_Mutation
SSH2	85464	broad.mit.edu	37	17	28120938	28120938	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:28120938C>A	ENST00000269033.3	-	2	232	c.81G>T	c.(79-81)gaG>gaT	p.E27D	SSH2_ENST00000540801.1_Missense_Mutation_p.E54D	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	27					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.E27D(1)	SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						GGCATTCTTCCTCCCCACTGT	0.328																																					p.E27D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G81T	17						.						68.0	68.0	68.0					17																	28120938		2203	4300	6503	25145064	SO:0001583	missense	85464	exon2			AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.81G>T	17.37:g.28120938C>A	ENSP00000269033:p.Glu27Asp	Somatic		Capture	Illumina HiSeq	Phase_I	25145064	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	37	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.808125	0.31961	.	.	ENSG00000141298	ENST00000269033;ENST00000540801;ENST00000394848	T;T	0.10005	2.92;2.93	5.55	2.38	0.29361	.	0.726018	0.12742	N	0.442931	T	0.20129	0.0484	L	0.48642	1.525	0.80722	D	1	P;D;B;B	0.56035	0.951;0.974;0.002;0.342	P;D;B;B	0.67725	0.718;0.953;0.004;0.064	T	0.06092	-1.0846	10	0.23891	T	0.37	-13.338	7.1229	0.25454	0.0:0.7047:0.0:0.2953	.	54;27;27;27	F5H527;Q76I76-3;Q76I76-4;Q76I76	.;.;.;SSH2_HUMAN	D	27;54;27	ENSP00000269033:E27D;ENSP00000444743:E54D	ENSP00000269033:E27D	E	-	3	2	SSH2	25145064	0.998000	0.40836	1.000000	0.80357	0.988000	0.76386	0.177000	0.16801	0.256000	0.21614	-0.355000	0.07637	GAG		0.328	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
RAB11FIP4	84440	broad.mit.edu	37	17	29761063	29761063	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:29761063C>T	ENST00000325874.8	+	3	488	c.259C>T	c.(259-261)Ctg>Ttg	p.L87L		NM_032932.3	NP_116321.2	Q86YS3	RFIP4_HUMAN	RAB11 family interacting protein 4 (class II)	87	Necessary for interaction with RAB11A, subcellular location, homo- or heterooligomerization.				cytokinesis (GO:0000910)|transport (GO:0006810)|viral process (GO:0016032)	cleavage furrow (GO:0032154)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|midbody (GO:0030496)|recycling endosome membrane (GO:0055038)	ADP-ribosylation factor binding (GO:0030306)|calcium ion binding (GO:0005509)|protein homodimerization activity (GO:0042803)|Rab GTPase binding (GO:0017137)	p.L87L(1)|p.?(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(10;3.62e-13)|all_epithelial(10;0.000387)|all_lung(9;0.0132)|Breast(31;0.014)|all_hematologic(16;0.015)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0259)|Ovarian(249;0.0423)|Lung NSC(157;0.066)				GTGCGAGGAGCTGCTGAAGGA	0.652																																					p.L87L												.	.	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|autonomic_ganglia(1)	c.C259T	17						.						69.0	58.0	62.0					17																	29761063		2200	4297	6497	26785189	SO:0001819	synonymous_variant	84440	exon3			AB058724	CCDS11267.1	17q11.2	2013-01-10			ENSG00000131242	ENSG00000131242		"""EF-hand domain containing"""	30267	protein-coding gene	gene with protein product		611999				11347906, 11468690	Standard	NM_032932		Approved	RAB11-FIP4, KIAA1821, MGC11316, FLJ00131	uc002hgn.1	Q86YS3	OTTHUMG00000132787	ENST00000325874.8:c.259C>T	17.37:g.29761063C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26785189	NM_032932	Q52LI1|Q8N829|Q8NDT7|Q969D8	Silent	SNP	ENST00000325874.8	37	CCDS11267.1																																																																																				0.652	RAB11FIP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256195.2	NM_032932	
RAP1GAP2	23108	broad.mit.edu	37	17	2929731	2929731	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:2929731C>T	ENST00000254695.8	+	21	2043	c.1953C>T	c.(1951-1953)ggC>ggT	p.G651G	RAP1GAP2_ENST00000542807.1_Silent_p.G651G|RAP1GAP2_ENST00000540393.2_Silent_p.G632G|RAP1GAP2_ENST00000366401.4_Silent_p.G636G	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	651	Ser-rich.				negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)	p.G651G(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						CAGGGGAGGGCGAGGCCATGG	0.642																																					p.G651G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1953T	17						.						16.0	21.0	19.0					17																	2929731		2044	4119	6163	2876481	SO:0001819	synonymous_variant	23108	exon21			AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1953C>T	17.37:g.2929731C>T		Somatic		Capture	Illumina HiSeq	Phase_I	2876481	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																				0.642	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
CDK5R1	8851	broad.mit.edu	37	17	30814875	30814875	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:30814875G>A	ENST00000313401.3	+	2	926	c.237G>A	c.(235-237)acG>acA	p.T79T		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	79					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)	p.T79T(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			ACAACATCACGCACCTCAACA	0.607																																					p.T79T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G237A	17						.						143.0	130.0	135.0					17																	30814875		2203	4300	6503	27838988	SO:0001819	synonymous_variant	8851	exon2			X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.237G>A	17.37:g.30814875G>A		Somatic		Capture	Illumina HiSeq	Phase_I	27838988	NM_003885	E1P664|Q5U0G3	Silent	SNP	ENST00000313401.3	37	CCDS11273.1																																																																																				0.607	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885	
TMEM132E	124842	broad.mit.edu	37	17	32953233	32953233	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:32953233C>T	ENST00000321639.5	+	2	483	c.155C>T	c.(154-156)aCg>aTg	p.T52M		NM_207313.1	NP_997196.1	Q6IEE7	T132E_HUMAN	transmembrane protein 132E	52						integral component of membrane (GO:0016021)		p.T52M(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(28)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	57				BRCA - Breast invasive adenocarcinoma(366;0.231)		CTGTCGCACACGCGGCTGGCC	0.736																																					p.T52M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C155T	17						.						7.0	7.0	7.0					17																	32953233		2143	4162	6305	29977346	SO:0001583	missense	124842	exon2			BN000149	CCDS11283.1	17q12	2012-11-01			ENSG00000181291	ENSG00000181291			26991	protein-coding gene	gene with protein product							Standard	NM_207313		Approved		uc002hif.3	Q6IEE7	OTTHUMG00000132927	ENST00000321639.5:c.155C>T	17.37:g.32953233C>T	ENSP00000316532:p.Thr52Met	Somatic		Capture	Illumina HiSeq	Phase_I	29977346	NM_207313	Q8WUF4|Q8WVA5	Missense_Mutation	SNP	ENST00000321639.5	37	CCDS11283.1	.	.	.	.	.	.	.	.	.	.	C	26.8	4.776046	0.90195	.	.	ENSG00000181291	ENST00000321639	T	0.11604	2.76	5.09	5.09	0.68999	.	0.055755	0.64402	D	0.000001	T	0.29749	0.0743	L	0.56769	1.78	0.32035	N	0.598948	D	0.89917	1.0	D	0.67382	0.951	T	0.18272	-1.0342	10	0.87932	D	0	-15.5441	17.4638	0.87627	0.0:1.0:0.0:0.0	.	52	Q6IEE7	T132E_HUMAN	M	52	ENSP00000316532:T52M	ENSP00000316532:T52M	T	+	2	0	TMEM132E	29977346	1.000000	0.71417	0.936000	0.37596	0.986000	0.74619	7.498000	0.81546	2.359000	0.80004	0.478000	0.44815	ACG		0.736	TMEM132E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256440.2	NM_207313	
AP2B1	163	broad.mit.edu	37	17	33966776	33966776	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:33966776C>T	ENST00000262325.7	+	11	1987	c.1434C>T	c.(1432-1434)acC>acT	p.T478T	AP2B1_ENST00000545922.2_3'UTR|AP2B1_ENST00000312678.8_Silent_p.T478T|AP2B1_ENST00000537622.2_Silent_p.T478T|AP2B1_ENST00000592545.1_Silent_p.T440T|AP2B1_ENST00000589344.1_Silent_p.T478T|AP2B1_ENST00000538556.1_Silent_p.T421T	NM_001282.2	NP_001273.1	P63010	AP2B1_HUMAN	adaptor-related protein complex 2, beta 1 subunit	478					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	clathrin binding (GO:0030276)|protein transporter activity (GO:0008565)	p.T478T(1)		NS(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		ATGAAAGCACCCAGGTAAGTT	0.408																																					p.T478T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1434T	17						.						86.0	84.0	85.0					17																	33966776		2203	4300	6503	30990889	SO:0001819	synonymous_variant	163	exon11			M34175	CCDS32621.1, CCDS32622.1	17q11.2-q12	2010-06-18			ENSG00000006125	ENSG00000006125			563	protein-coding gene	gene with protein product		601025		ADTB2, CLAPB1		8262066, 8595912	Standard	XM_005257937		Approved		uc002hjq.3	P63010		ENST00000262325.7:c.1434C>T	17.37:g.33966776C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30990889	NM_001282	A6NJP3|P21851|Q7Z451|Q96J19	Silent	SNP	ENST00000262325.7	37	CCDS32622.1																																																																																				0.408	AP2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448969.1		
GPR179	440435	broad.mit.edu	37	17	36484691	36484691	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:36484691A>G	ENST00000342292.4	-	11	4781	c.4761T>C	c.(4759-4761)ccT>ccC	p.P1587P	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1587					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P1587P(1)		breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTGTTTTGGCAGGTGTTGCTT	0.507																																					p.P1587P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T4761C	17						.						153.0	153.0	153.0					17																	36484691		2010	4189	6199	33738217	SO:0001819	synonymous_variant	440435	exon11				CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.4761T>C	17.37:g.36484691A>G		Somatic		Capture	Illumina HiSeq	Phase_I	33738217	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																				0.507	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
PCGF2	7703	broad.mit.edu	37	17	36891758	36891758	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:36891758G>A	ENST00000580830.1	-	12	1454	c.753C>T	c.(751-753)agC>agT	p.S251S	PCGF2_ENST00000579882.1_Missense_Mutation_p.R253W|PCGF2_ENST00000578109.1_Missense_Mutation_p.R199W|PCGF2_ENST00000581345.1_Silent_p.S251S|PCGF2_ENST00000585100.1_Missense_Mutation_p.R253W|PCGF2_ENST00000360797.2_Silent_p.S251S			P35227	PCGF2_HUMAN	polycomb group ring finger 2	251	Pro/Ser-rich.				anterior/posterior pattern specification (GO:0009952)|cellular response to hydrogen peroxide (GO:0070301)|embryonic skeletal system morphogenesis (GO:0048704)|histone acetylation (GO:0016573)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S251S(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	10	Breast(7;9.07e-22)					CGGACGCCCCGCTGGTGTTGG	0.697											OREG0024367	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S251S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C753T	17						.						14.0	14.0	14.0					17																	36891758		2192	4294	6486	34145284	SO:0001819	synonymous_variant	7703	exon11			D13969	CCDS32638.1	17q12	2013-01-09	2005-01-17	2005-01-19		ENSG00000277258		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	12929	protein-coding gene	gene with protein product		600346	"""ring finger protein 110"""	ZNF144, RNF110		8325509	Standard	NM_007144		Approved	MEL-18	uc002hqp.1	P35227		ENST00000580830.1:c.753C>T	17.37:g.36891758G>A		Somatic	866	Capture	Illumina HiSeq	Phase_I	34145284	NM_007144	A6NGD8	Missense_Mutation	SNP	ENST00000580830.1	37	CCDS32638.1																																																																																				0.697	PCGF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442246.2	NM_007144	
PLXDC1	57125	broad.mit.edu	37	17	37243922	37243922	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:37243922C>T	ENST00000315392.4	-	8	1056	c.845G>A	c.(844-846)cGc>cAc	p.R282H	PLXDC1_ENST00000394316.2_Missense_Mutation_p.R282H|PLXDC1_ENST00000539608.1_Missense_Mutation_p.R209H|PLXDC1_ENST00000444911.2_Missense_Mutation_p.R242H|PLXDC1_ENST00000493200.1_5'UTR	NM_020405.4	NP_065138.2	Q8IUK5	PLDX1_HUMAN	plexin domain containing 1	282					angiogenesis (GO:0001525)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|tight junction (GO:0005923)	receptor activity (GO:0004872)	p.R282H(1)		kidney(2)|large_intestine(6)|liver(1)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						CAGCTCTATGCGGTGATATTC	0.567																																					p.R282H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G845A	17						.						88.0	67.0	74.0					17																	37243922		2203	4300	6503	34497448	SO:0001583	missense	57125	exon8			AF279144	CCDS11333.1	17q21.1	2006-04-12			ENSG00000161381	ENSG00000161381			20945	protein-coding gene	gene with protein product	"""tumor endothelial marker 7 precursor"""	606826				10947988, 11559528	Standard	NM_020405		Approved	TEM3, TEM7	uc002hrg.2	Q8IUK5	OTTHUMG00000133183	ENST00000315392.4:c.845G>A	17.37:g.37243922C>T	ENSP00000323927:p.Arg282His	Somatic		Capture	Illumina HiSeq	Phase_I	34497448	NM_020405	B2R7I8|Q5QCZ7|Q5QCZ8|Q5QCZ9|Q9HCT9	Missense_Mutation	SNP	ENST00000315392.4	37	CCDS11333.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.822943	0.50739	.	.	ENSG00000161381	ENST00000315392;ENST00000394318;ENST00000539608;ENST00000444911;ENST00000394316;ENST00000441877	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	6.04	6.04	0.98038	.	0.060535	0.64402	D	0.000004	D	0.88570	0.6472	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89196	0.3554	10	0.87932	D	0	-16.3115	16.0793	0.80989	0.0:1.0:0.0:0.0	.	282	Q8IUK5	PXDC1_HUMAN	H	282;209;209;242;282;209	ENSP00000323927:R282H;ENSP00000441881:R209H;ENSP00000409687:R242H;ENSP00000377851:R282H;ENSP00000393227:R209H	ENSP00000323927:R282H	R	-	2	0	PLXDC1	34497448	1.000000	0.71417	0.998000	0.56505	0.762000	0.43233	5.403000	0.66338	2.873000	0.98535	0.561000	0.74099	CGC		0.567	PLXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256892.2	NM_020405	
MED1	5469	broad.mit.edu	37	17	37566906	37566906	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:37566906G>T	ENST00000394287.3	-	17	1773	c.1568C>A	c.(1567-1569)cCa>cAa	p.P523Q	MED1_ENST00000300651.6_Missense_Mutation_p.P523Q			O95243	MBD4_HUMAN	mediator complex subunit 1	0					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)	p.P523Q(1)		NS(1)|breast(2)|cervix(3)|kidney(3)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(7)|urinary_tract(1)	59		Ovarian(249;1.78e-06)|Lung SC(565;0.0262)	Lung(15;0.0178)|LUAD - Lung adenocarcinoma(14;0.146)	UCEC - Uterine corpus endometrioid carcinoma (308;6.64e-05)|BRCA - Breast invasive adenocarcinoma(366;0.00136)|READ - Rectum adenocarcinoma(1115;0.0649)		GGACAGTGCTGGGGTGTCGGC	0.493										HNSCC(31;0.082)																											p.P523Q	Pancreas(21;279 768 2492 4877 24026)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1568A	17						.						95.0	89.0	91.0					17																	37566906		2203	4300	6503	34820432	SO:0001583	missense	5469	exon17			L40366	CCDS11336.1	17q12	2007-07-30	2007-07-30	2007-07-30	ENSG00000125686	ENSG00000125686			9234	protein-coding gene	gene with protein product		604311	"""PPAR binding protein"""	TRIP2, PPARGBP, PPARBP		9325263, 10485914	Standard	NM_004774		Approved	PBP, TRAP220, RB18A, DRIP230, CRSP200, CRSP1	uc002hrv.4	Q15648	OTTHUMG00000133216	ENST00000394287.3:c.1568C>A	17.37:g.37566906G>T	ENSP00000377828:p.Pro523Gln	Somatic		Capture	Illumina HiSeq	Phase_I	34820432	NM_004774	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000394287.3	37		.	.	.	.	.	.	.	.	.	.	G	17.73	3.462200	0.63513	.	.	ENSG00000125686	ENST00000394287;ENST00000300651	T;T	0.55052	0.54;0.54	5.8	5.8	0.92144	.	.	.	.	.	T	0.62122	0.2402	N	0.22421	0.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.59595	-0.7425	9	0.35671	T	0.21	-7.8266	20.0505	0.97625	0.0:0.0:1.0:0.0	.	523;523	Q15648;Q15648-3	MED1_HUMAN;.	Q	523	ENSP00000377828:P523Q;ENSP00000300651:P523Q	ENSP00000300651:P523Q	P	-	2	0	MED1	34820432	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.434000	0.97515	2.739000	0.93911	0.561000	0.74099	CCA		0.493	MED1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000256944.1	NM_004774	
ERBB2	2064	broad.mit.edu	37	17	37884185	37884185	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:37884185A>G	ENST00000269571.5	+	27	3815	c.3656A>G	c.(3655-3657)aAc>aGc	p.N1219S	ERBB2_ENST00000445658.2_Missense_Mutation_p.N943S|MIR4728_ENST00000580969.1_RNA|ERBB2_ENST00000541774.1_Missense_Mutation_p.N1204S|ERBB2_ENST00000406381.2_Missense_Mutation_p.N1189S|ERBB2_ENST00000584601.1_Missense_Mutation_p.N1189S|ERBB2_ENST00000540147.1_Missense_Mutation_p.N1189S|MIEN1_ENST00000474210.1_5'Flank|ERBB2_ENST00000584450.1_3'UTR			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	1219					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)	p.N1219S(1)		NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GCCTTCGACAACCTCTATTAC	0.642		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)																											p.N1189S			Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3566G	17						.						46.0	51.0	49.0					17																	37884185		2203	4300	6503	35137711	SO:0001583	missense	2064	exon30			X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.3656A>G	17.37:g.37884185A>G	ENSP00000269571:p.Asn1219Ser	Somatic		Capture	Illumina HiSeq	Phase_I	35137711	NM_001005862	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.291937	0.80914	.	.	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.80909	-1.39;-1.4;-1.43;-1.4;-1.39	4.96	4.96	0.65561	.	.	.	.	.	D	0.84183	0.5416	L	0.35288	1.05	0.80722	D	1	B;D;P	0.89917	0.264;1.0;0.629	B;D;B	0.83275	0.074;0.996;0.269	D	0.85433	0.1150	9	0.54805	T	0.06	.	14.3096	0.66407	1.0:0.0:0.0:0.0	.	943;1204;1219	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	S	1189;1204;943;1219;1189	ENSP00000385185:N1189S;ENSP00000446466:N1204S;ENSP00000404047:N943S;ENSP00000269571:N1219S;ENSP00000443562:N1189S	ENSP00000269571:N1219S	N	+	2	0	ERBB2	35137711	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.532000	0.73825	1.855000	0.53841	0.460000	0.39030	AAC		0.642	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
KRT10	3858	broad.mit.edu	37	17	38976896	38976896	+	Missense_Mutation	SNP	C	C	T	rs369473843		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:38976896C>T	ENST00000269576.5	-	3	743	c.734G>A	c.(733-735)cGc>cAc	p.R245H	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	245	Coil 1B.|Gly-rich.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)	p.R245H(1)		NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				CACGCTCTGGCGCAGAGCTAC	0.483													C|||	1	0.000199681	0.0	0.0	5008	,	,		19378	0.0		0.0	False		,,,				2504	0.001				p.R245H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G734A	17						.	C	HIS/ARG,,,	0,4406		0,0,2203	84.0	81.0	82.0		734,,,	3.9	1.0	17		82	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron,intron,intron	KRT10,TMEM99	NM_000421.3,NM_001195386.1,NM_001195387.1,NM_145274.3	29,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,,,	245/585,,,	38976896	1,13005	2203	4300	6503	36230422	SO:0001583	missense	3858	exon3			J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.734G>A	17.37:g.38976896C>T	ENSP00000269576:p.Arg245His	Somatic		Capture	Illumina HiSeq	Phase_I	36230422	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.179877	0.57800	0.0	1.16E-4	ENSG00000186395	ENST00000269576	D	0.91945	-2.94	5.84	3.86	0.44501	Filament (1);	0.000000	0.36482	N	0.002567	D	0.89364	0.6694	L	0.41356	1.27	0.80722	D	1	B	0.31611	0.331	B	0.38683	0.279	D	0.86127	0.1572	10	0.42905	T	0.14	.	12.7557	0.57335	0.0:0.8669:0.0:0.1331	.	245	P13645	K1C10_HUMAN	H	245	ENSP00000269576:R245H	ENSP00000269576:R245H	R	-	2	0	KRT10	36230422	0.998000	0.40836	1.000000	0.80357	0.999000	0.98932	2.720000	0.47252	0.817000	0.34445	0.655000	0.94253	CGC		0.483	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
KRT10	3858	broad.mit.edu	37	17	38978257	38978257	+	Missense_Mutation	SNP	C	C	T	rs373319671		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:38978257C>T	ENST00000269576.5	-	1	590	c.581G>A	c.(580-582)cGt>cAt	p.R194H	TMEM99_ENST00000301665.3_Intron|TMEM99_ENST00000496847.1_Intron	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	194	Gly-rich.|Linker 1.|Rod.				cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)	p.R194H(1)		NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				GCTGTAGTCACGAGGCTCCCC	0.413																																					p.R194H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581A	17						.	C	HIS/ARG,,,	0,4406		0,0,2203	207.0	187.0	194.0		581,,,	4.0	1.0	17		194	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron,intron,intron	KRT10,TMEM99	NM_000421.3,NM_001195386.1,NM_001195387.1,NM_145274.3	29,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,,,	194/585,,,	38978257	1,13005	2203	4300	6503	36231783	SO:0001583	missense	3858	exon1			J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.581G>A	17.37:g.38978257C>T	ENSP00000269576:p.Arg194His	Somatic		Capture	Illumina HiSeq	Phase_I	36231783	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	37	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.334074	0.41297	0.0	1.16E-4	ENSG00000186395	ENST00000269576	D	0.89552	-2.53	4.96	3.98	0.46160	Filament (1);	0.000000	0.35870	N	0.002922	D	0.82549	0.5061	L	0.28504	0.86	0.80722	D	1	B	0.29037	0.231	B	0.34452	0.183	T	0.77327	-0.2629	10	0.30078	T	0.28	.	10.4293	0.44398	0.1458:0.6987:0.1555:0.0	.	194	P13645	K1C10_HUMAN	H	194	ENSP00000269576:R194H	ENSP00000269576:R194H	R	-	2	0	KRT10	36231783	0.001000	0.12720	0.977000	0.42913	0.610000	0.37248	0.252000	0.18278	1.196000	0.43129	0.603000	0.83216	CGT		0.413	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
KRT12	3859	broad.mit.edu	37	17	39019451	39019451	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39019451G>A	ENST00000251643.4	-	6	1263	c.1240C>T	c.(1240-1242)Cgg>Tgg	p.R414W	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	414	Coil 2.|Rod.				visual perception (GO:0007601)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R414W(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|upper_aerodigestive_tract(2)	15		Breast(137;0.000301)			Griseofulvin(DB00400)	TTCAGCAGCCGCTGGTGGTCC	0.662																																					p.R414W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1240T	17						.						27.0	26.0	27.0					17																	39019451		2198	4287	6485	36272977	SO:0001583	missense	3859	exon6				CCDS11378.1	17q21.2	2013-06-20	2008-08-01		ENSG00000187242	ENSG00000187242		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6414	protein-coding gene	gene with protein product	"""Meesmann corneal dystrophy"""	601687				9171831, 16831889	Standard	NM_000223		Approved	K12	uc002hvk.2	Q99456	OTTHUMG00000133369	ENST00000251643.4:c.1240C>T	17.37:g.39019451G>A	ENSP00000251643:p.Arg414Trp	Somatic		Capture	Illumina HiSeq	Phase_I	36272977	NM_000223	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.328705	0.41197	.	.	ENSG00000187242	ENST00000251643	D	0.89196	-2.48	5.04	4.05	0.47172	Filament (1);	0.152719	0.31051	N	0.008357	D	0.86997	0.6068	L	0.43152	1.355	0.29734	N	0.837656	D	0.71674	0.998	P	0.51229	0.663	T	0.82598	-0.0378	10	0.38643	T	0.18	.	9.6325	0.39787	0.0:0.245:0.5519:0.2032	.	414	Q99456	K1C12_HUMAN	W	414	ENSP00000251643:R414W	ENSP00000251643:R414W	R	-	1	2	KRT12	36272977	0.001000	0.12720	0.968000	0.41197	0.195000	0.23768	0.542000	0.23222	1.321000	0.45227	0.561000	0.74099	CGG		0.662	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223	
KRT23	25984	broad.mit.edu	37	17	39092540	39092540	+	Nonsense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39092540T>A	ENST00000209718.3	-	2	740	c.316A>T	c.(316-318)Aaa>Taa	p.K106*	KRT23_ENST00000582283.1_5'Flank|AC004231.2_ENST00000418393.1_RNA|KRT23_ENST00000436344.3_Intron	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	106	Coil 1A.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000301)|Ovarian(249;0.15)				TGGTGCCATTTCAGGATGCGG	0.547																																					p.K106X												.	.	0			c.A316T	17						.						91.0	93.0	92.0					17																	39092540		2203	4300	6503	36346066	SO:0001587	stop_gained	25984	exon2			AF102848	CCDS11380.1, CCDS62182.1	17q21.2	2013-01-16			ENSG00000108244	ENSG00000108244		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6438	protein-coding gene	gene with protein product		606194				11135429, 16831889	Standard	NM_015515		Approved	K23, DKFZP434G032, HAIK1, CK23, MGC26158	uc002hvm.1	Q9C075	OTTHUMG00000133376	ENST00000209718.3:c.316A>T	17.37:g.39092540T>A	ENSP00000209718:p.Lys106*	None		Capture	Illumina HiSeq	Phase_I	36346066	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Nonsense_Mutation	SNP	ENST00000209718.3	37	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	T	37	6.389015	0.97529	.	.	ENSG00000108244	ENST00000209718	.	.	.	5.73	-4.46	0.03536	.	0.779065	0.11182	N	0.590819	.	.	.	.	.	.	0.42882	D	0.994173	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	6.9516	0.24548	0.0:0.4104:0.2008:0.3888	.	.	.	.	X	106	.	ENSP00000209718:K106X	K	-	1	0	KRT23	36346066	0.065000	0.20965	0.003000	0.11579	0.854000	0.48673	0.394000	0.20834	-0.543000	0.06240	-0.472000	0.04984	AAA		0.547	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1		
KRT39	390792	broad.mit.edu	37	17	39115110	39115110	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39115110G>A	ENST00000355612.2	-	7	1254	c.1219C>T	c.(1219-1221)Cgt>Tgt	p.R407C	AC004231.2_ENST00000418393.1_RNA	NM_213656.3	NP_998821.3	Q6A163	K1C39_HUMAN	keratin 39	407	Tail.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R407C(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	17		Breast(137;0.00043)|Ovarian(249;0.15)				TAACAGGGACGCCTAAGGAAA	0.468																																					p.R407C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1219T	17						.						80.0	86.0	84.0					17																	39115110		2203	4296	6499	36368636	SO:0001630	splice_region_variant	390792	exon7			AJ786657	CCDS11382.1	17q21.2	2013-01-16			ENSG00000196859	ENSG00000196859		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	32971	protein-coding gene	gene with protein product						16831889	Standard	NM_213656		Approved	KA35	uc002hvo.1	Q6A163	OTTHUMG00000133424	ENST00000355612.2:c.1218-1C>T	17.37:g.39115110G>A		Somatic		Capture	Illumina HiSeq	Phase_I	36368636	NM_213656	B2RXK6|Q6IFU6	Missense_Mutation	SNP	ENST00000355612.2	37	CCDS11382.1	.	.	.	.	.	.	.	.	.	.	G	8.788	0.929768	0.18131	.	.	ENSG00000196859	ENST00000355612	D	0.82893	-1.66	5.43	2.36	0.29203	.	0.692491	0.11954	N	0.513447	T	0.60560	0.2278	N	0.08118	0	0.35961	D	0.834615	P	0.40398	0.716	B	0.25884	0.064	T	0.61466	-0.7057	10	0.72032	D	0.01	.	7.8993	0.29725	0.2623:0.0:0.7377:0.0	.	407	Q6A163	K1C39_HUMAN	C	407	ENSP00000347823:R407C	ENSP00000347823:R407C	R	-	1	0	KRT39	36368636	0.994000	0.37717	0.992000	0.48379	0.014000	0.08584	0.298000	0.19120	0.270000	0.21984	-0.126000	0.14955	CGT		0.468	KRT39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257287.1	NM_213656	Missense_Mutation
KRTAP4-3	85290	broad.mit.edu	37	17	39323973	39323973	+	Missense_Mutation	SNP	C	C	T	rs368282974		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39323973C>T	ENST00000391356.2	-	1	451	c.452G>A	c.(451-453)cGc>cAc	p.R151H		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	151	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R151H(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCAAGCCGGGCGGCAGCAGGA	0.632																																					p.R151H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G452A	17						.	C	HIS/ARG	1,4223		0,1,2111	17.0	20.0	19.0		452	-2.3	0.0	17		19	0,8500		0,0,4250	no	missense	KRTAP4-3	NM_033187.1	29	0,1,6361	TT,TC,CC		0.0,0.0237,0.0079	benign	151/196	39323973	1,12723	2112	4250	6362	36577499	SO:0001583	missense	85290	exon1			AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.452G>A	17.37:g.39323973C>T	ENSP00000375151:p.Arg151His	Somatic		Capture	Illumina HiSeq	Phase_I	36577499	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	11.87	1.769158	0.31320	2.37E-4	0.0	ENSG00000196156	ENST00000391356	T	0.01505	4.82	3.9	-2.29	0.06805	.	0.000000	0.28236	U	0.016081	T	0.02888	0.0086	M	0.85710	2.77	0.09310	N	1	B	0.18461	0.028	B	0.18561	0.022	T	0.31998	-0.9923	10	0.66056	D	0.02	.	4.8704	0.13629	0.1467:0.3447:0.0:0.5086	.	151	Q9BYR4	KRA43_HUMAN	H	151	ENSP00000375151:R151H	ENSP00000375151:R151H	R	-	2	0	KRTAP4-3	36577499	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.435000	0.00472	-0.565000	0.06061	-0.459000	0.05422	CGC		0.632	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
KRTAP9-2	83899	broad.mit.edu	37	17	39383041	39383041	+	Silent	SNP	C	C	T	rs71371479		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39383041C>T	ENST00000377721.3	+	1	142	c.135C>T	c.(133-135)tcC>tcT	p.S45S	KRTAP9-2_ENST00000455970.2_Silent_p.S45S	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	45	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)		p.S45S(1)		large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGTGTGTCCAGCTGCTGCC	0.647																																					p.S45S												.	.	1	Substitution - coding silent(1)	prostate(1)	c.C135T	17						.						62.0	56.0	58.0					17																	39383041		2203	4299	6502	36636567	SO:0001819	synonymous_variant	83899	exon1			AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.135C>T	17.37:g.39383041C>T		Germline		Capture	Illumina HiSeq	Phase_I	36636567	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Silent	SNP	ENST00000377721.3	37	CCDS32651.1																																																																																				0.647	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
KRT13	3860	broad.mit.edu	37	17	39661609	39661610	+	Missense_Mutation	DNP	TA	TA	AG			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	TA	TA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:39661609_39661610TA>AG	ENST00000246635.3	-	1	239_240	c.193_194TA>CT	c.(193-195)TAt>CTt	p.Y65L	KRT13_ENST00000587544.1_Missense_Mutation_p.Y65L|KRT13_ENST00000336861.3_Missense_Mutation_p.Y65L|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000587118.1_5'Flank	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	65	Gly-rich.|Head.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.Y65>?(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				gccacctccatagccacctcca	0.599																																					.												.	.	1	Complex(1)	large_intestine(1)	c.193_194CT	17						.																																			36915136	SO:0001583	missense	3860	exon1				CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.193_194delinsAG	17.37:g.39661609_39661610delinsAG	ENSP00000246635:p.Tyr65Leu	Somatic		Capture	Illumina HiSeq	Phase_I	36915135	NM_153490	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	DNP	ENST00000246635.3	37	CCDS11396.1																																																																																				0.599	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490	
WNK4	65266	broad.mit.edu	37	17	40934874	40934874	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:40934874G>A	ENST00000246914.5	+	2	738	c.717G>A	c.(715-717)tcG>tcA	p.S239S		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	239	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)	p.S227S(1)|p.S239S(1)		NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		TCTATGATTCGTGGAAGTCGG	0.597																																					p.S239S	Esophageal Squamous(6;201 374 4964 23855 42828)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G717A	17						.						103.0	90.0	95.0					17																	40934874		2203	4300	6503	38188400	SO:0001819	synonymous_variant	65266	exon2			AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.717G>A	17.37:g.40934874G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38188400	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Silent	SNP	ENST00000246914.5	37	CCDS11439.1																																																																																				0.597	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
NBR1	4077	broad.mit.edu	37	17	41338374	41338374	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:41338374G>T	ENST00000422280.1	+	6	774	c.315G>T	c.(313-315)agG>agT	p.R105S	NBR1_ENST00000542611.1_Missense_Mutation_p.R84S|NBR1_ENST00000389312.4_Missense_Mutation_p.R105S|NBR1_ENST00000589872.1_Missense_Mutation_p.R105S|NBR1_ENST00000590996.1_Missense_Mutation_p.R105S|NBR1_ENST00000341165.6_Missense_Mutation_p.R105S	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	105					macroautophagy (GO:0016236)|negative regulation of osteoblast differentiation (GO:0045668)|protein oligomerization (GO:0051259)|regulation of bone mineralization (GO:0030500)|regulation of stress-activated MAPK cascade (GO:0032872)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	mitogen-activated protein kinase binding (GO:0051019)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)	p.R105S(1)		NS(1)|breast(1)|cervix(1)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	24		Breast(137;0.00086)		BRCA - Breast invasive adenocarcinoma(366;0.0934)		TAGCTGCCAGGGCAGGGAAGA	0.522																																					p.R105S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G315T	17						.						55.0	58.0	57.0					17																	41338374		1953	4146	6099	38591900	SO:0001583	missense	4077	exon6			X76952	CCDS45694.1	17q21.31	2008-02-01	2005-02-15	2005-02-16		ENSG00000188554			6746	protein-coding gene	gene with protein product		166945	"""membrane component, chromosome 17, surface marker 2 (ovarian carcinoma antigen CA125)"""	M17S2		8069304	Standard	XM_006721903		Approved	CA125, KIAA0049, 1A1-3B	uc010whv.2	Q14596		ENST00000422280.1:c.315G>T	17.37:g.41338374G>T	ENSP00000411250:p.Arg105Ser	Somatic		Capture	Illumina HiSeq	Phase_I	38591900	NM_005899	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Missense_Mutation	SNP	ENST00000422280.1	37	CCDS45694.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.968900	0.34754	.	.	ENSG00000188554	ENST00000422280;ENST00000542611;ENST00000341165;ENST00000389312;ENST00000389311	T;T;T;T	0.44881	1.54;0.91;1.54;1.52	5.52	2.23	0.28157	.	0.254734	0.42053	D	0.000770	T	0.33498	0.0865	L	0.60455	1.87	0.09310	N	1	B;B;B	0.14012	0.001;0.009;0.0	B;B;B	0.11329	0.002;0.006;0.002	T	0.24621	-1.0155	10	0.45353	T	0.12	-6.0676	4.7335	0.12977	0.3012:0.0:0.5545:0.1443	.	84;105;105	B7Z5R6;Q14596-2;Q14596	.;.;NBR1_HUMAN	S	105;84;105;105;105	ENSP00000411250:R105S;ENSP00000437545:R84S;ENSP00000343479:R105S;ENSP00000373963:R105S	ENSP00000343479:R105S	R	+	3	2	NBR1	38591900	0.262000	0.24073	0.036000	0.18154	0.967000	0.64934	0.573000	0.23699	0.688000	0.31529	0.511000	0.50034	AGG		0.522	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899	
DUSP3	1845	broad.mit.edu	37	17	41847025	41847025	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:41847025G>T	ENST00000226004.3	-	3	573	c.510C>A	c.(508-510)ctC>ctA	p.L170L	DUSP3_ENST00000397937.2_Silent_p.L129L	NM_004090.3	NP_004081.1	P51452	DUS3_HUMAN	dual specificity phosphatase 3	170					in utero embryonic development (GO:0001701)|inactivation of MAPK activity (GO:0000188)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of JNK cascade (GO:0046329)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of T cell activation (GO:0050868)|negative regulation of T cell receptor signaling pathway (GO:0050860)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of mitotic cell cycle (GO:0045931)|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)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L170L(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	7		Breast(137;0.00725)		BRCA - Breast invasive adenocarcinoma(366;0.116)		TGAGCTGGCAGAGCTGGGCCA	0.612																																					p.L170L	Esophageal Squamous(114;1511 1593 4801 6912 51717)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C510A	17						.						86.0	68.0	74.0					17																	41847025		2203	4300	6503	39202551	SO:0001819	synonymous_variant	1845	exon3			BC035701	CCDS11469.1	17q21	2011-06-09	2008-02-04			ENSG00000108861		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	3069	protein-coding gene	gene with protein product		600183	"""vaccinia virus phosphatase VH1-related"""	VHR		7829094	Standard	NM_004090		Approved		uc002ied.4	P51452		ENST00000226004.3:c.510C>A	17.37:g.41847025G>T		Somatic		Capture	Illumina HiSeq	Phase_I	39202551	NM_004090	D3DX45|Q5U0J1|Q8IYJ9	Silent	SNP	ENST00000226004.3	37	CCDS11469.1																																																																																				0.612	DUSP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453503.1	NM_004090	
C17orf53	78995	broad.mit.edu	37	17	42231987	42231987	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:42231987A>G	ENST00000319977.4	+	6	1753	c.1516A>G	c.(1516-1518)Act>Gct	p.T506A	C17orf53_ENST00000245382.6_Missense_Mutation_p.T430A|C17orf53_ENST00000585683.1_Missense_Mutation_p.T505A	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	506								p.T506A(1)		NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		CAAGTCCCTGACTCGGAGCAC	0.552																																					p.T505A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1513G	17						.						136.0	115.0	122.0					17																	42231987		2203	4300	6503	39587513	SO:0001583	missense	78995	exon6			AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.1516A>G	17.37:g.42231987A>G	ENSP00000313500:p.Thr506Ala	Somatic		Capture	Illumina HiSeq	Phase_I	39587513	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	.	.	.	.	.	.	.	.	.	.	A	16.91	3.251549	0.59212	.	.	ENSG00000125319	ENST00000319977;ENST00000245382	T;T	0.49139	0.79;0.89	6.04	6.04	0.98038	.	0.225469	0.46442	D	0.000297	T	0.49081	0.1536	M	0.68952	2.095	0.33808	D	0.627456	P;B;P	0.34615	0.459;0.428;0.459	B;B;B	0.33254	0.16;0.154;0.16	T	0.65467	-0.6161	10	0.59425	D	0.04	-12.6857	15.5589	0.76223	1.0:0.0:0.0:0.0	.	505;430;506	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	A	506;430	ENSP00000313500:T506A;ENSP00000245382:T430A	ENSP00000245382:T430A	T	+	1	0	C17orf53	39587513	0.996000	0.38824	1.000000	0.80357	0.960000	0.62799	2.893000	0.48633	2.317000	0.78254	0.459000	0.35465	ACT		0.552	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
SLC4A1	6521	broad.mit.edu	37	17	42337865	42337865	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:42337865A>G	ENST00000262418.6	-	6	547	c.392T>C	c.(391-393)gTg>gCg	p.V131A	SLC4A1_ENST00000471005.1_5'UTR|AC003043.1_ENST00000597382.1_Intron	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	131	Globular.				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.V131A(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TTGGTTGGCCACTCCAGCCAG	0.597																																					p.V131A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T392C	17						.						60.0	56.0	57.0					17																	42337865		2203	4300	6503	39693391	SO:0001583	missense	6521	exon6				CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.392T>C	17.37:g.42337865A>G	ENSP00000262418:p.Val131Ala	Somatic		Capture	Illumina HiSeq	Phase_I	39693391	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	a	25.8	4.676009	0.88445	.	.	ENSG00000004939	ENST00000262418	T	0.73258	-0.73	5.38	5.38	0.77491	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.065462	0.56097	D	0.000025	D	0.83436	0.5254	M	0.84082	2.675	0.43114	D	0.994828	D;P	0.58970	0.984;0.92	P;P	0.62435	0.902;0.793	D	0.86556	0.1838	10	0.87932	D	0	.	14.3726	0.66852	1.0:0.0:0.0:0.0	.	131;131	E2RVJ0;P02730	.;B3AT_HUMAN	A	131	ENSP00000262418:V131A	ENSP00000262418:V131A	V	-	2	0	SLC4A1	39693391	1.000000	0.71417	0.947000	0.38551	0.759000	0.43091	9.339000	0.96797	2.043000	0.60533	0.379000	0.24179	GTG		0.597	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
ITGA2B	3674	broad.mit.edu	37	17	42461276	42461276	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:42461276G>A	ENST00000262407.5	-	11	1015	c.984C>T	c.(982-984)gaC>gaT	p.D328D	ITGA2B_ENST00000353281.4_Silent_p.D328D|ITGA2B_ENST00000377068.3_Silent_p.D13D	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	328					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)	p.D328D(1)		biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CCCCGTTGACGTCAGTGACAG	0.557																																					p.D328D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C984T	17						.						71.0	66.0	68.0					17																	42461276		2203	4300	6503	39816802	SO:0001819	synonymous_variant	3674	exon11				CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.984C>T	17.37:g.42461276G>A		Somatic		Capture	Illumina HiSeq	Phase_I	39816802	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																				0.557	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
GPATCH8	23131	broad.mit.edu	37	17	42541864	42541864	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:42541864G>A	ENST00000591680.1	-	3	199	c.169C>T	c.(169-171)Cag>Tag	p.Q57*	GPATCH8_ENST00000434000.1_5'UTR	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	57	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q57*(1)		breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		CCCAATCCCTGGCCCAGCTTC	0.383																																					p.Q57X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C169T	17						.						187.0	194.0	192.0					17																	42541864		2203	4300	6503	39897390	SO:0001587	stop_gained	23131	exon3			AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.169C>T	17.37:g.42541864G>A	ENSP00000467556:p.Gln57*	Somatic		Capture	Illumina HiSeq	Phase_I	39897390	NM_001002909	B9EGP9|O60300|Q8TB99	Nonsense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.570817	0.86542	.	.	ENSG00000186566	ENST00000335500	.	.	.	5.47	5.47	0.80525	.	0.000000	0.56097	D	0.000026	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-15.8888	19.3249	0.94258	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000335486:Q57X	Q	-	1	0	GPATCH8	39897390	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.861000	0.87004	2.556000	0.86216	0.467000	0.42956	CAG		0.383	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
HIGD1B	51751	broad.mit.edu	37	17	42926663	42926663	+	Missense_Mutation	SNP	C	C	T	rs370827709		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:42926663C>T	ENST00000253410.2	+	2	393	c.142C>T	c.(142-144)Cgg>Tgg	p.R48W	HIGD1B_ENST00000587021.1_Intron|HIGD1B_ENST00000591513.1_Missense_Mutation_p.R48W	NM_016438.2	NP_057522.1	Q9P298	HIG1B_HUMAN	HIG1 hypoxia inducible domain family, member 1B	48	HIG1. {ECO:0000255|PROSITE- ProRule:PRU00836}.					integral component of membrane (GO:0016021)		p.R48W(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(1)	5		Prostate(33;0.109)				CAGGATTTACCGGCTGAGGTC	0.577																																					p.R48W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C142T	17						.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	131.0	112.0	119.0		142	4.3	1.0	17		119	0,8600		0,0,4300	no	missense	HIGD1B	NM_016438.2	101	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	48/100	42926663	1,13005	2203	4300	6503	40282189	SO:0001583	missense	51751	exon2			AB038021	CCDS11488.1	17q21.31	2009-03-17	2009-03-17			ENSG00000131097			24318	protein-coding gene	gene with protein product			"""HIG1 domain family, member 1B"""			12477932	Standard	NM_016438		Approved	CLST11240, CLST11240-15	uc031rau.1	Q9P298		ENST00000253410.2:c.142C>T	17.37:g.42926663C>T	ENSP00000253410:p.Arg48Trp	Somatic		Capture	Illumina HiSeq	Phase_I	40282189	NM_016438	D3DX57|Q9P297	Missense_Mutation	SNP	ENST00000253410.2	37	CCDS11488.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.427315	0.43122	2.27E-4	0.0	ENSG00000131097	ENST00000253410	T	0.34275	1.37	5.25	4.28	0.50868	Hypoxia induced protein, domain (2);	0.125811	0.52532	D	0.000077	T	0.32346	0.0826	.	.	.	0.80722	D	1	B	0.19073	0.033	B	0.17979	0.02	T	0.15723	-1.0427	9	0.66056	D	0.02	-22.3963	13.113	0.59285	0.0:0.9215:0.0:0.0785	.	48	Q9P298	HIG1B_HUMAN	W	48	ENSP00000253410:R48W	ENSP00000253410:R48W	R	+	1	2	HIGD1B	40282189	1.000000	0.71417	1.000000	0.80357	0.697000	0.40408	0.620000	0.24403	1.462000	0.47948	-0.254000	0.11334	CGG		0.577	HIGD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448669.1	NM_016438	
DCAKD	79877	broad.mit.edu	37	17	43101979	43101979	+	Missense_Mutation	SNP	C	C	T	rs201376374		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:43101979C>T	ENST00000452796.2	-	4	773	c.518G>A	c.(517-519)cGc>cAc	p.R173H	DCAKD_ENST00000342350.5_Missense_Mutation_p.R173H|DCAKD_ENST00000588499.1_Missense_Mutation_p.R173H			Q8WVC6	DCAKD_HUMAN	dephospho-CoA kinase domain containing	173	DPCK.				coenzyme A biosynthetic process (GO:0015937)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)	p.R173H(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(2)|skin(1)	6		Prostate(33;0.155)				TAGGACATGGCGGGCCATGCG	0.647																																					p.R173H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G518A	17						.						69.0	63.0	65.0					17																	43101979		2203	4300	6503	40457505	SO:0001583	missense	79877	exon5			BC006546	CCDS11493.1	17q21.31	2005-12-20				ENSG00000172992			26238	protein-coding gene	gene with protein product							Standard	XM_005257688		Approved	FLJ22955	uc010daa.1	Q8WVC6		ENST00000452796.2:c.518G>A	17.37:g.43101979C>T	ENSP00000413483:p.Arg173His	Somatic		Capture	Illumina HiSeq	Phase_I	40457505	NM_024819	A8K3Z0|D3DX60|D3DX62|Q9BR71|Q9H5W1	Missense_Mutation	SNP	ENST00000452796.2	37	CCDS11493.1	.	.	.	.	.	.	.	.	.	.	C	10.67	1.415957	0.25552	.	.	ENSG00000172992	ENST00000342350;ENST00000452796	T;T	0.41065	1.01;1.01	4.86	-2.19	0.07015	.	0.666589	0.16246	N	0.222902	T	0.13670	0.0331	N	0.01168	-0.975	0.40900	D	0.984143	B	0.09022	0.002	B	0.04013	0.001	T	0.05869	-1.0859	10	0.39692	T	0.17	-7.4621	8.7676	0.34713	0.0:0.239:0.1268:0.6342	.	173	Q8WVC6	DCAKD_HUMAN	H	173	ENSP00000341504:R173H;ENSP00000413483:R173H	ENSP00000341504:R173H	R	-	2	0	DCAKD	40457505	0.001000	0.12720	0.903000	0.35520	0.990000	0.78478	-0.215000	0.09279	-0.248000	0.09583	0.542000	0.68232	CGC		0.647	DCAKD-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449066.1	NM_024819	
PLCD3	113026	broad.mit.edu	37	17	43197777	43197777	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:43197777C>T	ENST00000322765.5	-	4	712	c.599G>A	c.(598-600)aGc>aAc	p.S200N	PLCD3_ENST00000540511.1_5'UTR	NM_133373.3	NP_588614.1	Q8N3E9	PLCD3_HUMAN	phospholipase C, delta 3	200	EF-hand 1.				angiogenesis (GO:0001525)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|labyrinthine layer blood vessel development (GO:0060716)|lipid catabolic process (GO:0016042)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)	p.S200N(2)		breast(2)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	17						GCTCATCTTGCTGTCCTGGTT	0.567																																					p.S200N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G599A	17						.						135.0	147.0	143.0					17																	43197777		2193	4297	6490	40553303	SO:0001583	missense	113026	exon4			AC002117	CCDS74077.1	17q21	2012-04-20			ENSG00000161714	ENSG00000161714	3.1.4.11		9061	protein-coding gene	gene with protein product		608795				10702670, 9056492	Standard	NM_133373		Approved		uc002iib.3	Q8N3E9	OTTHUMG00000168029	ENST00000322765.5:c.599G>A	17.37:g.43197777C>T	ENSP00000313731:p.Ser200Asn	Somatic		Capture	Illumina HiSeq	Phase_I	40553303	NM_133373	Q8TEC1|Q8TF37|Q96FL6	Missense_Mutation	SNP	ENST00000322765.5	37		.	.	.	.	.	.	.	.	.	.	C	5.241	0.229907	0.09969	.	.	ENSG00000161714	ENST00000322765	T	0.40225	1.04	4.05	4.05	0.47172	.	0.351454	0.33346	N	0.005006	T	0.26085	0.0636	.	.	.	0.29285	N	0.869758	B	0.13145	0.007	B	0.12156	0.007	T	0.06409	-1.0828	9	0.33940	T	0.23	.	6.3011	0.21113	0.0:0.7943:0.0:0.2057	.	200	Q8N3E9	PLCD3_HUMAN	N	200	ENSP00000313731:S200N	ENSP00000313731:S200N	S	-	2	0	PLCD3	40553303	0.985000	0.35326	0.996000	0.52242	0.988000	0.76386	2.360000	0.44151	2.257000	0.74773	0.455000	0.32223	AGC		0.567	PLCD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_133373	
SPNS3	201305	broad.mit.edu	37	17	4381918	4381918	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:4381918G>A	ENST00000355530.2	+	9	1445	c.1165G>A	c.(1165-1167)Gcc>Acc	p.A389T	SPNS3_ENST00000333476.2_Missense_Mutation_p.A262T	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	389					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)		p.A389T(1)		NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						GGCAGTGGTTGCCGACATCCT	0.647																																					p.A389T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1165A	17						.						61.0	48.0	52.0					17																	4381918		2203	4300	6503	4328667	SO:0001583	missense	201305	exon9				CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.1165G>A	17.37:g.4381918G>A	ENSP00000347721:p.Ala389Thr	Somatic		Capture	Illumina HiSeq	Phase_I	4328667	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	.	.	.	.	.	.	.	.	.	.	G	14.10	2.435165	0.43224	.	.	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.58358	0.34;0.34	4.97	1.77	0.24775	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.246769	0.41194	N	0.000931	T	0.38719	0.1051	L	0.35414	1.06	0.41263	D	0.986799	B;B	0.23854	0.092;0.04	B;B	0.30716	0.113;0.119	T	0.13980	-1.0489	10	0.34782	T	0.22	-5.703	7.3008	0.26420	0.3141:0.0:0.6859:0.0	.	262;389	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	T	389;262	ENSP00000347721:A389T;ENSP00000333207:A262T	ENSP00000333207:A262T	A	+	1	0	SPNS3	4328667	0.962000	0.33011	0.879000	0.34478	0.830000	0.47004	1.925000	0.40074	0.568000	0.29311	0.655000	0.94253	GCC		0.647	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
FMNL1	752	broad.mit.edu	37	17	43323295	43323295	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:43323295G>T	ENST00000331495.3	+	24	3381	c.3045G>T	c.(3043-3045)gaG>gaT	p.E1015D	MAP3K14-AS1_ENST00000590100.1_RNA|MAP3K14-AS1_ENST00000588504.1_RNA|CTD-2020K17.4_ENST00000420431.2_RNA|MAP3K14-AS1_ENST00000592422.1_RNA|FMNL1_ENST00000587489.1_Missense_Mutation_p.E593D|CTD-2020K17.4_ENST00000591361.1_RNA|MAP3K14-AS1_ENST00000588698.1_RNA|FMNL1_ENST00000328118.3_Missense_Mutation_p.E1015D|CTD-2020K17.4_ENST00000589518.1_RNA|MAP3K14-AS1_ENST00000585346.1_RNA|MAP3K14-AS1_ENST00000591263.1_RNA	NM_005892.3	NP_005883	O95466	FMNL_HUMAN	formin-like 1	1015	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament severing (GO:0051014)|cortical actin cytoskeleton organization (GO:0030866)|regulation of cell shape (GO:0008360)|substrate-dependent cell migration (GO:0006929)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|GTPase activating protein binding (GO:0032794)|Rac GTPase binding (GO:0048365)	p.E1015D(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(12)|pancreas(1)|skin(1)|urinary_tract(2)	33						CTGCCCAGGAGGCAGGCGCTG	0.622																																					p.E1015D	GBM(164;1247 1997 8702 11086 51972)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3045T	17						.						21.0	24.0	23.0					17																	43323295		2202	4299	6501	40679078	SO:0001583	missense	752	exon24			AJ008112	CCDS11497.1	17q21.31	2008-05-14	2003-12-02	2003-12-03		ENSG00000184922			1212	protein-coding gene	gene with protein product		604656	"""formin-like"""	C17orf1B, FMNL		9799091	Standard	NM_005892		Approved	C17orf1	uc002iin.3	O95466		ENST00000331495.3:c.3045G>T	17.37:g.43323295G>T	ENSP00000329219:p.Glu1015Asp	Somatic		Capture	Illumina HiSeq	Phase_I	40679078	NM_005892	D2DGW2|Q6DKG5|Q6IBP3|Q86UH1|Q8N671|Q8TDH1|Q96H10	Missense_Mutation	SNP	ENST00000331495.3	37	CCDS11497.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652789	0.67472	.	.	ENSG00000184922	ENST00000328118;ENST00000331495	T;T	0.65549	-0.16;-0.16	4.31	4.31	0.51392	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (2);	0.475392	0.20632	U	0.088572	T	0.73814	0.3635	M	0.80422	2.495	0.45621	D	0.998555	P	0.45768	0.866	P	0.52031	0.688	T	0.76465	-0.2949	10	0.44086	T	0.13	.	15.5112	0.75782	0.0:0.0:1.0:0.0	.	1015	O95466	FMNL_HUMAN	D	1015	ENSP00000327442:E1015D;ENSP00000329219:E1015D	ENSP00000327442:E1015D	E	+	3	2	FMNL1	40679078	1.000000	0.71417	1.000000	0.80357	0.586000	0.36452	4.792000	0.62467	2.232000	0.73038	0.462000	0.41574	GAG		0.622	FMNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450198.1	NM_005892	
HOXB5	3215	broad.mit.edu	37	17	46670858	46670858	+	Missense_Mutation	SNP	A	A	G	rs199973674		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:46670858A>G	ENST00000239151.5	-	1	465	c.187T>C	c.(187-189)Tcc>Ccc	p.S63P	HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000481995.1_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000466037.2_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000477144.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000474324.1_RNA|HOXB-AS3_ENST00000460041.1_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	63					anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell differentiation (GO:0045446)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			large_intestine(1)|lung(2)	3						AAGTGGCTGGAGGAGGCCGAG	0.667																																					p.S63P												.	.	0			c.T187C	17						.						15.0	16.0	16.0					17																	46670858		2136	4162	6298	44025857	SO:0001583	missense	3215	exon1				CCDS11530.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120075	ENSG00000120075		"""Homeoboxes / ANTP class : HOXL subclass"""	5116	protein-coding gene	gene with protein product		142960	"""homeo box B5"""	HOX2, HOX2A		1973146, 1358459	Standard	NM_002147		Approved		uc002inr.3	P09067	OTTHUMG00000159913	ENST00000239151.5:c.187T>C	17.37:g.46670858A>G	ENSP00000239151:p.Ser63Pro	None		Capture	Illumina HiSeq	Phase_I	44025857	NM_002147	B2RC69|P09069|Q17RP4	Missense_Mutation	SNP	ENST00000239151.5	37	CCDS11530.1	.	.	.	.	.	.	.	.	.	.	A	11.41	1.630328	0.28978	.	.	ENSG00000120075	ENST00000239151	D	0.92545	-3.06	5.44	4.37	0.52481	.	0.346876	0.30556	N	0.009362	D	0.85932	0.5812	L	0.42008	1.315	0.45704	D	0.998614	B	0.02656	0.0	B	0.04013	0.001	T	0.79579	-0.1745	10	0.27785	T	0.31	.	6.082	0.19946	0.7793:0.0:0.0761:0.1446	.	63	P09067	HXB5_HUMAN	P	63	ENSP00000239151:S63P	ENSP00000239151:S63P	S	-	1	0	HOXB5	44025857	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.492000	0.35594	2.062000	0.61559	0.454000	0.30748	TCC		0.667	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2		
DLX4	1748	broad.mit.edu	37	17	48046988	48046988	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:48046988C>T	ENST00000240306.3	+	1	451	c.156C>T	c.(154-156)ggC>ggT	p.G52G	DLX4_ENST00000503410.1_3'UTR|DLX4_ENST00000505318.2_Silent_p.G52G	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	52				MTSLPCPLPGRDASKAVFPDLAPVPSVAAAYPLGLSPTTAA SPNLSYSRPYGHLLSYPYTEPANPGDSYLSCQQPAALSQPL CGPAEHPQELEA -> GGSLSLPPEPLCARCPTKEGAAPRR PGFWGSLETQAATVWRGRHGHFSCRVRLSRGAARYSRRGQG KPGVTISAARLVFKVLSAGPLTHPAGRSRRLPRGHRLKPLS IALSLCLQCPSSVISRPRLSPGPSLSAPPYPKLAPPPVAEL RPPTAGAAVPWLWPSARFLPRVTGPIRVGAPLGAELRLVSP GAVNVGVETLHAE (in Ref. 9). {ECO:0000305}.	multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G52G(1)		central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						GGCCGTATGGCCACCTCCTGT	0.662																																					p.G52G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C156T	17						.						96.0	97.0	97.0					17																	48046988		2203	4300	6503	45401987	SO:0001819	synonymous_variant	1748	exon1				CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"""Homeoboxes / ANTP class : NKL subclass"""	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.156C>T	17.37:g.48046988C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45401987	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Silent	SNP	ENST00000240306.3	37	CCDS11555.1																																																																																				0.662	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1		
PPP1R9B	84687	broad.mit.edu	37	17	48226517	48226517	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:48226517C>T	ENST00000316878.6	-	3	1358	c.1356G>A	c.(1354-1356)gcG>gcA	p.A452A	PPP1R9B_ENST00000501501.2_5'UTR|AC002401.1_ENST00000451776.1_RNA	NM_032595.3	NP_115984.3	Q96SB3	NEB2_HUMAN	protein phosphatase 1, regulatory subunit 9B	452	Interacts with protein phosphatase 1. {ECO:0000250}.				actin filament organization (GO:0007015)|calcium-mediated signaling (GO:0019722)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to morphine (GO:0071315)|dendrite development (GO:0016358)|filopodium assembly (GO:0046847)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|regulation of cell growth by extracellular stimulus (GO:0001560)|regulation of cell proliferation (GO:0042127)|regulation of exit from mitosis (GO:0007096)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of protein phosphorylation (GO:0001932)|RNA splicing (GO:0008380)	cell junction (GO:0030054)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|protein phosphatase type 1 complex (GO:0000164)|ruffle membrane (GO:0032587)|synapse (GO:0045202)	protein phosphatase 1 binding (GO:0008157)|protein phosphatase inhibitor activity (GO:0004864)	p.A451A(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8						CTTGGATGGGCGCCGTGCTGA	0.746																																					p.R453H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1358A	17						.						6.0	7.0	7.0					17																	48226517		1806	4027	5833	45581516	SO:0001819	synonymous_variant	84687	exon1			AJ401189	CCDS74102.1	17q21.33	2013-01-31	2011-10-04	2001-07-02	ENSG00000108819	ENSG00000108819		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9298	protein-coding gene	gene with protein product	"""spinophilin"", ""Neurabin-2"""	603325	"""protein phosphatase 1, regulatory subunit 9B, spinophilin"", ""protein phosphatase 1, regulatory (inhibitor) subunit 9B"""	PPP1R6, PPP1R9		9275233	Standard	NM_032595		Approved	Spn, SPINO	uc002iqh.4	Q96SB3	OTTHUMG00000162008	ENST00000316878.6:c.1356G>A	17.37:g.48226517C>T		Somatic		Capture	Illumina HiSeq	Phase_I	45581516	NM_032595	Q8TCR9	Silent	SNP	ENST00000316878.6	37																																																																																					0.746	PPP1R9B-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032595	
MYCBPAP	84073	broad.mit.edu	37	17	48594671	48594671	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:48594671T>C	ENST00000323776.5	+	3	513	c.351T>C	c.(349-351)ctT>ctC	p.L117L	MYCBPAP_ENST00000436259.2_Silent_p.L80L	NM_032133.4	NP_115509.4			MYCBP associated protein									p.L80L(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TTCCTCGCCTTACTGAAAAGG	0.453																																					p.L117L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T351C	17						.						116.0	115.0	115.0					17																	48594671		2203	4300	6503	45949670	SO:0001819	synonymous_variant	84073	exon3			BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.351T>C	17.37:g.48594671T>C		Somatic		Capture	Illumina HiSeq	Phase_I	45949670	NM_032133		Silent	SNP	ENST00000323776.5	37	CCDS32680.2																																																																																				0.453	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
TM4SF5	9032	broad.mit.edu	37	17	4685827	4685827	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:4685827C>T	ENST00000270560.3	+	3	319	c.288C>T	c.(286-288)ttC>ttT	p.F96F		NM_003963.2	NP_003954.2	O14894	T4S5_HUMAN	transmembrane 4 L six family member 5	96						integral component of plasma membrane (GO:0005887)		p.F96F(1)		large_intestine(2)|lung(3)|ovary(1)	6						CCTCGGCGTTCGGGGTGCTTG	0.617																																					p.F96F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C288T	17						.						129.0	114.0	119.0					17																	4685827		2203	4300	6503	4632574	SO:0001819	synonymous_variant	9032	exon3			AF027204	CCDS11054.1	17p13.3	2007-01-06	2005-03-21		ENSG00000142484	ENSG00000142484			11857	protein-coding gene	gene with protein product		604657	"""transmembrane 4 superfamily member 5"""			9479038	Standard	NM_003963		Approved		uc002fyw.1	O14894	OTTHUMG00000090776	ENST00000270560.3:c.288C>T	17.37:g.4685827C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4632574	NM_003963	Q17RW9|Q6IB79	Silent	SNP	ENST00000270560.3	37	CCDS11054.1																																																																																				0.617	TM4SF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207558.2		
GP1BA	2811	broad.mit.edu	37	17	4837780	4837780	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:4837780G>A	ENST00000329125.5	+	2	1956	c.1881G>A	c.(1879-1881)agG>agA	p.R627R		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	627					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)	p.R627R(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						CAGGAAGGAGGCCCTCAGCTC	0.612											OREG0024109	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R614R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1842A	17						.						43.0	48.0	46.0					17																	4837780		1979	4154	6133	4778521	SO:0001819	synonymous_variant	2811	exon2				CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1881G>A	17.37:g.4837780G>A		Somatic	621	Capture	Illumina HiSeq	Phase_I	4778521	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Silent	SNP	ENST00000329125.5	37	CCDS54068.1																																																																																				0.612	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
CACNA1G	8913	broad.mit.edu	37	17	48668981	48668981	+	Splice_Site	SNP	G	G	T	rs33999699		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:48668981G>T	ENST00000359106.5	+	11	2639	c.2639G>T	c.(2638-2640)aGc>aTc	p.S880I	CACNA1G_ENST00000429973.2_Splice_Site_p.S880I|CACNA1G_ENST00000515411.1_Splice_Site_p.S880I|CACNA1G_ENST00000502264.1_Splice_Site_p.S880I|CACNA1G_ENST00000510366.1_Splice_Site_p.S880I|CACNA1G_ENST00000442258.2_Splice_Site_p.S880I|CACNA1G_ENST00000513689.2_Splice_Site_p.S880I|CACNA1G_ENST00000360761.4_Splice_Site_p.S880I|CACNA1G_ENST00000358244.5_Splice_Site_p.S880I|CACNA1G_ENST00000505165.1_Splice_Site_p.S880I|CACNA1G_ENST00000507896.1_Splice_Site_p.S880I|CACNA1G_ENST00000352832.5_Splice_Site_p.S880I|CACNA1G_ENST00000507510.2_Splice_Site_p.S880I|CACNA1G_ENST00000515765.1_Splice_Site_p.S880I|CACNA1G_ENST00000512389.1_Splice_Site_p.S880I|CACNA1G_ENST00000514079.1_Splice_Site_p.S880I|CACNA1G_ENST00000503485.1_Splice_Site_p.S880I|CACNA1G_ENST00000515165.1_Splice_Site_p.S880I|CACNA1G_ENST00000354983.4_Splice_Site_p.S880I|CACNA1G_ENST00000513964.1_Splice_Site_p.S880I|CACNA1G_ENST00000510115.1_Splice_Site_p.S880I|CACNA1G_ENST00000507336.1_Splice_Site_p.S880I|CACNA1G_ENST00000416767.4_Splice_Site_p.S880I|CACNA1G_ENST00000514717.1_Splice_Site_p.S880I|CACNA1G_ENST00000514181.1_Splice_Site_p.S880I|CACNA1G_ENST00000507609.1_Splice_Site_p.S880I	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	880					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	TTCATCTTCAGGTGAGGGCGG	0.627																																					p.S880I												.	.	0			c.G2639T	17						.						40.0	42.0	41.0					17																	48668981		2155	4256	6411	46023980	SO:0001630	splice_region_variant	8913	exon11			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2639+1G>T	17.37:g.48668981G>T		None		Capture	Illumina HiSeq	Phase_I	46023980	NM_198382	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	g	23.7	4.444990	0.83993	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97811	-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55;-4.55	5.39	4.41	0.53225	Ion transport (1);	0.137426	0.64402	D	0.000001	D	0.98912	0.9631	M	0.93062	3.375	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.998;1.0;0.999;0.999;0.999;0.999;0.999;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.995;0.999;0.987;0.998;0.996;0.999;0.997;0.995;0.997;0.995;0.993;0.998;0.999;0.998;0.997;0.999;0.998;0.999;0.998;0.998;0.993;0.999;0.993;0.999;0.977;0.996	D	0.99525	1.0959	10	0.87932	D	0	.	13.8113	0.63266	0.074:0.0:0.926:0.0	.	880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880;880	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	I	880	ENSP00000353990:S880I;ENSP00000339302:S880I;ENSP00000392390:S880I;ENSP00000347078:S880I;ENSP00000409759:S880I;ENSP00000425522:S880I;ENSP00000426261:S880I;ENSP00000425451:S880I;ENSP00000422407:S880I;ENSP00000426814:S880I;ENSP00000427238:S880I;ENSP00000423112:S880I;ENSP00000420918:S880I;ENSP00000426172:S880I;ENSP00000423045:S880I;ENSP00000427173:S880I;ENSP00000426098:S880I;ENSP00000425698:S880I;ENSP00000426232:S880I;ENSP00000423317:S880I;ENSP00000350979:S880I;ENSP00000352011:S880I;ENSP00000414388:S880I;ENSP00000423155:S880I;ENSP00000422268:S880I;ENSP00000421518:S880I	ENSP00000339302:S880I	S	+	2	0	CACNA1G	46023980	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	9.832000	0.99423	1.278000	0.44430	0.462000	0.41574	AGC		0.627	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	Missense_Mutation
KIF2B	84643	broad.mit.edu	37	17	51902011	51902011	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:51902011A>G	ENST00000268919.4	+	1	1773	c.1617A>G	c.(1615-1617)agA>agG	p.R539R		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	539	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of chromosome segregation (GO:0051983)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R539R(1)		NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(15)|lung(58)|ovary(5)|prostate(4)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						ATGCAAACAGAGTAAAAAAAT	0.428																																					p.R539R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1617G	17						.						68.0	66.0	67.0					17																	51902011		2203	4300	6503	49257010	SO:0001819	synonymous_variant	84643	exon1			AF333335	CCDS32685.1	17q22	2014-08-12			ENSG00000141200	ENSG00000141200		"""Kinesins"""	29443	protein-coding gene	gene with protein product		615142				11416179	Standard	NM_032559		Approved		uc002iua.2	Q8N4N8	OTTHUMG00000177756	ENST00000268919.4:c.1617A>G	17.37:g.51902011A>G		Somatic		Capture	Illumina HiSeq	Phase_I	49257010	NM_032559	Q96MA2|Q9BXG6	Silent	SNP	ENST00000268919.4	37	CCDS32685.1																																																																																				0.428	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559	
DERL2	51009	broad.mit.edu	37	17	5389431	5389431	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:5389431G>A	ENST00000158771.4	-	1	106	c.51C>T	c.(49-51)agC>agT	p.S17S	DERL2_ENST00000570848.1_Silent_p.S17S|DERL2_ENST00000571968.1_Intron|DERL2_ENST00000572834.1_Silent_p.S17S|MIS12_ENST00000381165.3_5'Flank|MIS12_ENST00000573759.1_5'Flank	NM_016041.3	NP_057125.2	Q9GZP9	DERL2_HUMAN	derlin 2	17					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|retrograde protein transport, ER to cytosol (GO:0030970)|suckling behavior (GO:0001967)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|late endosome (GO:0005770)|membrane (GO:0016020)		p.S17S(1)		large_intestine(3)	3						TGTAGGCGCGGCTGACCGGTG	0.647																																					p.S17S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C51T	17						.						44.0	39.0	41.0					17																	5389431		2198	4293	6491	5330155	SO:0001819	synonymous_variant	51009	exon1			BC010890	CCDS11073.1	17p13.2	2012-02-01	2012-02-01		ENSG00000072849	ENSG00000072849			17943	protein-coding gene	gene with protein product		610304	"""Der1-like domain family, member 2"""			10810093, 11500051	Standard	NM_016041		Approved	F-LAN-1, FLANa, F-LANa, CGI-101, derlin-2	uc002gcc.1	Q9GZP9	OTTHUMG00000102040	ENST00000158771.4:c.51C>T	17.37:g.5389431G>A		Somatic		Capture	Illumina HiSeq	Phase_I	5330155	NM_016041	Q9Y3A7	Silent	SNP	ENST00000158771.4	37	CCDS11073.1																																																																																				0.647	DERL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219825.1	NM_016041	
TRIM25	7706	broad.mit.edu	37	17	54976525	54976525	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:54976525A>G	ENST00000316881.4	-	5	1153	c.1104T>C	c.(1102-1104)caT>caC	p.H368H	TRIM25_ENST00000537230.1_Silent_p.H368H	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	368	Interaction with influenza A virus NS1.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein ubiquitination (GO:0016567)|regulation of viral entry into host cell (GO:0046596)|regulation of viral release from host cell (GO:1902186)|response to estrogen (GO:0043627)|response to vitamin D (GO:0033280)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.H368H(1)		breast(2)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Breast(9;6.15e-08)					ACGCTGGGTCATGCTCTCCAG	0.607																																					p.H368H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1104C	17						.						299.0	226.0	251.0					17																	54976525		2203	4300	6503	52331524	SO:0001819	synonymous_variant	7706	exon5			D21205	CCDS11591.1	17q23.1	2013-01-09	2011-01-25	2004-03-30				"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12932	protein-coding gene	gene with protein product		600453	"""zinc finger protein 147 (estrogen-responsive finger protein)"", ""tripartite motif-containing 25"""	ZNF147		7789997	Standard	NM_005082		Approved	EFP, RNF147	uc002iut.3	Q14258		ENST00000316881.4:c.1104T>C	17.37:g.54976525A>G		Somatic		Capture	Illumina HiSeq	Phase_I	52331524	NM_005082		Silent	SNP	ENST00000316881.4	37	CCDS11591.1																																																																																				0.607	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082	
BZRAP1	9256	broad.mit.edu	37	17	56396603	56396603	+	Missense_Mutation	SNP	C	C	T	rs11652447		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:56396603C>T	ENST00000343736.4	-	13	1710	c.1547G>A	c.(1546-1548)aGc>aAc	p.S516N	BZRAP1_ENST00000355701.3_Missense_Mutation_p.S516N|BZRAP1_ENST00000268893.6_Missense_Mutation_p.S456N			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	516						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)	p.S516N(2)		cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGCCAGGAGGCTGAACTGCTC	0.647																																					p.S516N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1547A	17						.						48.0	41.0	43.0					17																	56396603		2199	4296	6495	53751602	SO:0001583	missense	9256	exon13			AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.1547G>A	17.37:g.56396603C>T	ENSP00000345824:p.Ser516Asn	Somatic		Capture	Illumina HiSeq	Phase_I	53751602	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021146	0.54576	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04454	3.62;3.62;3.62	4.38	4.38	0.52667	.	0.049443	0.85682	D	0.000000	T	0.08537	0.0212	N	0.13235	0.315	0.27448	N	0.953526	P;D;P	0.69078	0.473;0.997;0.546	B;D;B	0.64144	0.056;0.922;0.298	T	0.40664	-0.9551	10	0.21014	T	0.42	.	16.4509	0.83990	0.0:1.0:0.0:0.0	rs11652447	516;456;516	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	N	516;516;456	ENSP00000347929:S516N;ENSP00000345824:S516N;ENSP00000268893:S456N	ENSP00000268893:S456N	S	-	2	0	BZRAP1	53751602	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.174000	0.31932	2.420000	0.82092	0.561000	0.74099	AGC		0.647	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
TRIM37	4591	broad.mit.edu	37	17	57106034	57106034	+	Nonsense_Mutation	SNP	G	G	A	rs312262702		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:57106034G>A	ENST00000262294.7	-	19	2258	c.1999C>T	c.(1999-2001)Cga>Tga	p.R667*	TRIM37_ENST00000393065.2_Nonsense_Mutation_p.R633*|TRIM37_ENST00000393066.3_Nonsense_Mutation_p.R667*|TRIM37_ENST00000376149.3_Nonsense_Mutation_p.R545*	NM_015294.3	NP_056109.1	O94972	TRI37_HUMAN	tripartite motif containing 37	667					aggresome assembly (GO:0070842)|negative regulation of centriole replication (GO:0046600)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autoubiquitination (GO:0051865)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisome (GO:0005777)	chromatin binding (GO:0003682)|ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R667*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(13)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					GAGGGCACTCGCCACATTGCC	0.338									Mulibrey Nanism																												p.R667X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1999T	17						.						104.0	102.0	103.0					17																	57106034		2203	4300	6503	54460816	SO:0001587	stop_gained	4591	exon19	Familial Cancer Database	Perheentupa syndrome	AB020705	CCDS32694.1, CCDS45746.1	17q	2014-02-17	2011-01-25	2001-11-30		ENSG00000108395		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	7523	protein-coding gene	gene with protein product	"""RING-B-box-coiled-coil protein"""	605073	"""tripartite motif-containing 37"""	MUL		9106536, 10888877	Standard	NM_015294		Approved	KIAA0898, POB1, TEF3	uc002iwy.4	O94972		ENST00000262294.7:c.1999C>T	17.37:g.57106034G>A	ENSP00000262294:p.Arg667*	Somatic		Capture	Illumina HiSeq	Phase_I	54460816	NM_001005207	Q7Z3E6|Q8IYF7|Q8WYF7	Nonsense_Mutation	SNP	ENST00000262294.7	37	CCDS32694.1	.	.	.	.	.	.	.	.	.	.	G	39	7.789635	0.98492	.	.	ENSG00000108395	ENST00000393066;ENST00000262294;ENST00000376149;ENST00000393065	.	.	.	5.57	-1.12	0.09808	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9103	18.428	0.90615	0.0:0.0:0.4173:0.5827	.	.	.	.	X	667;667;545;633	.	ENSP00000262294:R667X	R	-	1	2	TRIM37	54460816	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	2.026000	0.41069	0.007000	0.14760	-1.350000	0.01237	CGA		0.338	TRIM37-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445930.1	NM_015294	
BRIP1	83990	broad.mit.edu	37	17	59763475	59763475	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:59763475C>T	ENST00000259008.2	-	19	2894	c.2627G>A	c.(2626-2628)aGt>aAt	p.S876N	BRIP1_ENST00000577598.1_Missense_Mutation_p.S876N	NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	876					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S876N(1)		NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						TTCCAGTGCACTTTCAAAGGT	0.363			"""F, N, Mis"""			"""AML, leukemia, breast"""		Involved in tolerance or repair of DNA crosslinks																													p.S876N		yes	Rec		"""Fanconi anaemia J, breast cancer susceptiblity"""	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"""L, E"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2627A	17						.						85.0	94.0	91.0					17																	59763475		2203	4300	6503	57118257	SO:0001583	missense	83990	exon19			AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"""Fanconi anemia, complementation groups"""	20473	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-associated helicase 1"""	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.2627G>A	17.37:g.59763475C>T	ENSP00000259008:p.Ser876Asn	Somatic		Capture	Illumina HiSeq	Phase_I	57118257	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.347615	0.41599	.	.	ENSG00000136492	ENST00000259008	T	0.74421	-0.84	5.81	4.79	0.61399	.	0.098845	0.64402	D	0.000001	T	0.76227	0.3958	L	0.50333	1.59	0.35468	D	0.797085	B;D	0.59767	0.031;0.986	B;P	0.53266	0.006;0.722	T	0.80360	-0.1415	9	.	.	.	-20.3182	13.4556	0.61197	0.0:0.843:0.157:0.0	.	876;876	C9JGZ0;Q9BX63	.;FANCJ_HUMAN	N	876	ENSP00000259008:S876N	.	S	-	2	0	BRIP1	57118257	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.815000	0.27253	2.746000	0.94184	0.655000	0.94253	AGT		0.363	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043	
MRC2	9902	broad.mit.edu	37	17	60759623	60759623	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:60759623C>T	ENST00000303375.5	+	20	3233	c.2831C>T	c.(2830-2832)aCa>aTa	p.T944I	RNU6-446P_ENST00000362827.1_RNA|MRC2_ENST00000446119.2_5'UTR	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	944	C-type lectin 5. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)	p.T944I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						AGGTGCCTGACAGCCTTGCCC	0.657																																					p.T944I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2831T	17						.						31.0	26.0	27.0					17																	60759623		2200	4296	6496	58113355	SO:0001583	missense	9902	exon20			AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.2831C>T	17.37:g.60759623C>T	ENSP00000307513:p.Thr944Ile	Somatic		Capture	Illumina HiSeq	Phase_I	58113355	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917156	0.52546	.	.	ENSG00000011028	ENST00000303375	T	0.19532	2.14	5.84	5.84	0.93424	C-type lectin fold (1);C-type lectin, conserved site (1);C-type lectin-like (1);C-type lectin (3);	0.056479	0.64402	D	0.000001	T	0.35335	0.0928	L	0.46670	1.46	0.80722	D	1	D	0.54964	0.969	P	0.55455	0.776	T	0.00441	-1.1737	10	0.26408	T	0.33	-8.0229	20.1386	0.98045	0.0:1.0:0.0:0.0	.	944	Q9UBG0	MRC2_HUMAN	I	944	ENSP00000307513:T944I	ENSP00000307513:T944I	T	+	2	0	MRC2	58113355	0.998000	0.40836	0.968000	0.41197	0.981000	0.71138	4.272000	0.58908	2.767000	0.95098	0.561000	0.74099	ACA		0.657	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
DCAF7	10238	broad.mit.edu	37	17	61655938	61655938	+	Silent	SNP	C	C	T	rs143007748	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:61655938C>T	ENST00000310827.4	+	2	463	c.246C>T	c.(244-246)ggC>ggT	p.G82G	DCAF7_ENST00000577702.1_3'UTR|DCAF7_ENST00000431926.1_Silent_p.G82G|DCAF7_ENST00000415273.2_Intron	NM_005828.3	NP_005819.3	P61962	DCAF7_HUMAN	DDB1 and CUL4 associated factor 7	82					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|protein complex (GO:0043234)		p.G82G(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	18						ACACAAAAGGCGTCTATCCAG	0.493													C|||	47	0.00938498	0.0	0.049	5008	,	,		21340	0.0129		0.0	False		,,,				2504	0.0				p.G82G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C246T	17						.	C		1,3959		0,1,1979	195.0	189.0	191.0		246	-1.7	1.0	17	dbSNP_134	191	5,8349		0,5,4172	no	coding-synonymous	DCAF7	NM_005828.3		0,6,6151	TT,TC,CC		0.0599,0.0253,0.0487		82/343	61655938	6,12308	1980	4177	6157	59009670	SO:0001819	synonymous_variant	10238	exon2			U94747	CCDS74127.1	17q23.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000136485		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	30915	protein-coding gene	gene with protein product	"""seven-WD-repeat protein of the AN11 family-1"", ""human anthocyanin"""	605973	"""WD repeat domain 68"""	WDR68		9192870, 20940704	Standard	NM_005828		Approved	HAN11, SWAN-1	uc002jbc.4	P61962		ENST00000310827.4:c.246C>T	17.37:g.61655938C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59009670	NM_005828	B4E039|D3DU14|O15491|Q9DAE4	Silent	SNP	ENST00000310827.4	37																																																																																					0.493	DCAF7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005828	
PSMC5	5705	broad.mit.edu	37	17	61901581	61901581	+	5'Flank	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:61901581T>A	ENST00000310144.6	+	0	0				FTSJ3_ENST00000580295.1_5'Flank|FTSJ3_ENST00000427159.2_Missense_Mutation_p.E339D	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)	p.E339D(1)		endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						CACCTTCATCTTCCTCTCCAG	0.547																																					p.E339D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1017T	17						.						145.0	146.0	146.0					17																	61901581		2203	4300	6503	59255313	SO:0001631	upstream_gene_variant	117246	exon12			L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61901581T>A	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	59255313	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Missense_Mutation	SNP	ENST00000310144.6	37	CCDS11645.1	.	.	.	.	.	.	.	.	.	.	T	11.16	1.556230	0.27827	.	.	ENSG00000108592	ENST00000427159	T	0.35421	1.31	5.38	-0.663	0.11410	Ribosomal RNA methyltransferase Spb1, domain of unknown function DUF3381 (1);	0.352815	0.30269	N	0.010005	T	0.24353	0.0590	N	0.05124	-0.11	0.27929	N	0.937959	D	0.56746	0.977	P	0.57152	0.814	T	0.31024	-0.9958	10	0.19590	T	0.45	-26.0819	8.6519	0.34040	0.0:0.4946:0.0:0.5054	.	339	Q8IY81	RRMJ3_HUMAN	D	339	ENSP00000396673:E339D	ENSP00000396673:E339D	E	-	3	2	FTSJ3	59255313	0.079000	0.21365	0.966000	0.40874	0.725000	0.41563	-0.934000	0.03955	-0.056000	0.13221	-0.263000	0.10527	GAA		0.547	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
WSCD1	23302	broad.mit.edu	37	17	6023917	6023917	+	Missense_Mutation	SNP	C	C	T	rs555182532		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:6023917C>T	ENST00000574946.1	+	9	2054	c.1664C>T	c.(1663-1665)aCg>aTg	p.T555M	WSCD1_ENST00000573634.1_Missense_Mutation_p.T439M|WSCD1_ENST00000574232.1_Missense_Mutation_p.T555M|WSCD1_ENST00000317744.5_Missense_Mutation_p.T555M|WSCD1_ENST00000539421.1_Missense_Mutation_p.T555M			Q658N2	WSCD1_HUMAN	WSC domain containing 1	555						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)	p.T555M(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TACATCCGGACGGTGGACCAA	0.662													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16306	0.0		0.0	False		,,,				2504	0.0				p.T555M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1664T	17						.						52.0	59.0	57.0					17																	6023917		2203	4300	6503	5964641	SO:0001583	missense	23302	exon9				CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.1664C>T	17.37:g.6023917C>T	ENSP00000460825:p.Thr555Met	Somatic		Capture	Illumina HiSeq	Phase_I	5964641	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774966	0.49786	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	T;T	0.32988	1.43;1.43	5.44	5.44	0.79542	.	0.048967	0.85682	D	0.000000	T	0.48519	0.1504	L	0.52126	1.63	0.52099	D	0.999942	D	0.89917	1.0	D	0.68621	0.959	T	0.22906	-1.0203	10	0.30078	T	0.28	-14.4041	16.7537	0.85493	0.0:1.0:0.0:0.0	.	555	Q658N2	WSCD1_HUMAN	M	555	ENSP00000323087:T555M;ENSP00000446032:T555M	ENSP00000323087:T555M	T	+	2	0	WSCD1	5964641	1.000000	0.71417	0.986000	0.45419	0.773000	0.43773	4.497000	0.60367	2.549000	0.85964	0.655000	0.94253	ACG		0.662	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
SCN4A	6329	broad.mit.edu	37	17	62018939	62018939	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:62018939C>T	ENST00000435607.1	-	24	4779	c.4703G>A	c.(4702-4704)tGc>tAc	p.C1568Y	SCN4A_ENST00000578147.1_Missense_Mutation_p.C1568Y	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1568					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.C1568Y(1)		breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGGGTTGCCGCAGTCACCCTT	0.592																																					p.C1568Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4703A	17						.						43.0	48.0	47.0					17																	62018939		2135	4251	6386	59372671	SO:0001583	missense	6329	exon24			U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4703G>A	17.37:g.62018939C>T	ENSP00000396320:p.Cys1568Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	59372671	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	c	17.05	3.290064	0.59976	.	.	ENSG00000007314	ENST00000435607	D	0.98455	-4.94	3.9	3.9	0.45041	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99453	0.9806	H	0.99582	4.64	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.97692	1.0179	10	0.87932	D	0	.	15.4266	0.75055	0.0:1.0:0.0:0.0	.	1568	P35499	SCN4A_HUMAN	Y	1568	ENSP00000396320:C1568Y	ENSP00000396320:C1568Y	C	-	2	0	SCN4A	59372671	1.000000	0.71417	0.995000	0.50966	0.657000	0.38888	7.609000	0.82925	2.177000	0.69029	0.556000	0.70494	TGC		0.592	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
LRRC37A3	374819	broad.mit.edu	37	17	62856713	62856713	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:62856713C>A	ENST00000584306.1	-	11	4081	c.3551G>T	c.(3550-3552)aGg>aTg	p.R1184M	LRRC37A3_ENST00000334962.5_Missense_Mutation_p.R161M|LRRC37A3_ENST00000339474.5_Missense_Mutation_p.R302M|LRRC37A3_ENST00000400877.3_Missense_Mutation_p.R222M|LRRC37A3_ENST00000319651.5_Missense_Mutation_p.R1184M	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1184						integral component of membrane (GO:0016021)		p.R1184M(1)		NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|liver(1)|lung(10)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GATGCTCTGCCTTCCTACCTC	0.532																																					p.R1184M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3551T	17						.						91.0	96.0	94.0					17																	62856713		2203	4297	6500	60287175	SO:0001583	missense	374819	exon11			AB011135	CCDS32708.1	17q24.1	2008-10-22			ENSG00000176809	ENSG00000176809			32427	protein-coding gene	gene with protein product							Standard	NM_199340		Approved	FLJ34306, KIAA0563	uc031rbi.1	O60309	OTTHUMG00000132307	ENST00000584306.1:c.3551G>T	17.37:g.62856713C>A	ENSP00000464535:p.Arg1184Met	Somatic		Capture	Illumina HiSeq	Phase_I	60287175	NM_199340	Q49A01|Q49A80|Q8NB33	Missense_Mutation	SNP	ENST00000584306.1	37	CCDS32708.1	.	.	.	.	.	.	.	.	.	.	.	8.573	0.880614	0.17467	.	.	ENSG00000176809	ENST00000339474;ENST00000400877;ENST00000334962;ENST00000319651	T;T;T	0.61158	1.36;1.36;0.13	2.46	-4.92	0.03075	.	.	.	.	.	T	0.40694	0.1127	N	0.19112	0.55	0.09310	N	1	D;P	0.54601	0.967;0.94	B;P	0.47075	0.423;0.536	T	0.49808	-0.8900	9	0.87932	D	0	.	5.1346	0.14928	0.5365:0.3111:0.0:0.1525	.	302;1184	B4DG20;O60309	.;L37A3_HUMAN	M	265;222;161;1184	ENSP00000383674:R222M;ENSP00000335617:R161M;ENSP00000325713:R1184M	ENSP00000325713:R1184M	R	-	2	0	LRRC37A3	60287175	0.000000	0.05858	0.000000	0.03702	0.081000	0.17604	-2.152000	0.01288	-2.979000	0.00283	-0.856000	0.03024	AGG		0.532	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340	
CACNG5	27091	broad.mit.edu	37	17	64873500	64873500	+	Missense_Mutation	SNP	C	C	T	rs147124881		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:64873500C>T	ENST00000533854.1	+	2	287	c.50C>T	c.(49-51)gCt>gTt	p.A17V	CACNG5_ENST00000169565.3_Missense_Mutation_p.A17V|CACNG5_ENST00000307139.3_Missense_Mutation_p.A17V			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	17					regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)	p.A17V(1)		NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			AGTGTCTTTGCTGTCTGTGGC	0.617																																					p.A17V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C50T	17						.	C	VAL/ALA	0,4406		0,0,2203	178.0	128.0	145.0		50	3.8	1.0	17	dbSNP_134	145	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CACNG5	NM_145811.2	64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	17/276	64873500	1,13005	2203	4300	6503	62303962	SO:0001583	missense	27091	exon1			AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"""Calcium channel subunits"""	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.50C>T	17.37:g.64873500C>T	ENSP00000436836:p.Ala17Val	Somatic		Capture	Illumina HiSeq	Phase_I	62303962	NM_014404	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Missense_Mutation	SNP	ENST00000533854.1	37	CCDS11665.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.098031	0.76870	0.0	1.16E-4	ENSG00000075429	ENST00000533854;ENST00000307139;ENST00000169565	D;D;D	0.89415	-2.51;-2.51;-2.51	4.86	3.82	0.43975	.	0.000000	0.85682	D	0.000000	D	0.93334	0.7875	M	0.79926	2.475	0.52501	D	0.999956	D	0.69078	0.997	D	0.80764	0.994	D	0.93078	0.6489	10	0.87932	D	0	-35.2136	10.1525	0.42803	0.1496:0.7051:0.1453:0.0	.	17	Q9UF02	CCG5_HUMAN	V	17	ENSP00000436836:A17V;ENSP00000303092:A17V;ENSP00000169565:A17V	ENSP00000169565:A17V	A	+	2	0	CACNG5	62303962	0.997000	0.39634	0.986000	0.45419	0.685000	0.39939	3.513000	0.53414	2.676000	0.91093	0.655000	0.94253	GCT		0.617	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811	
FAM64A	54478	broad.mit.edu	37	17	6348464	6348464	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:6348464G>A	ENST00000250056.8	+	2	117	c.34G>A	c.(34-36)Gtg>Atg	p.V12M	FAM64A_ENST00000572595.2_Missense_Mutation_p.V12M|FAM64A_ENST00000570337.2_Missense_Mutation_p.V12M|FAM64A_ENST00000576056.1_Missense_Mutation_p.V12M|FAM64A_ENST00000572447.1_Missense_Mutation_p.V12M|FAM64A_ENST00000571373.1_Missense_Mutation_p.V12M	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	12					mitotic nuclear division (GO:0007067)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.V12M(1)		breast(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				COAD - Colon adenocarcinoma(228;0.141)		GGGGACCTCCGTGCGCCGGAG	0.627																																					p.V12M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G34A	17						.						26.0	29.0	28.0					17																	6348464		2203	4300	6503	6289188	SO:0001583	missense	54478	exon2				CCDS32541.1, CCDS56016.1	17p13.2	2013-10-11			ENSG00000129195	ENSG00000129195			25483	protein-coding gene	gene with protein product	"""CALM interacting protein expressed in thymus and spleen"""					19383357, 16491119	Standard	NM_019013		Approved	FLJ10156, FLJ10491, CATS	uc002gcw.2	Q9BSJ6	OTTHUMG00000177832	ENST00000250056.8:c.34G>A	17.37:g.6348464G>A	ENSP00000250056:p.Val12Met	Somatic		Capture	Illumina HiSeq	Phase_I	6289188	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Missense_Mutation	SNP	ENST00000250056.8	37	CCDS56016.1	.	.	.	.	.	.	.	.	.	.	G	7.685	0.689915	0.15039	.	.	ENSG00000129195	ENST00000250056;ENST00000308855	T	0.57273	0.41	4.33	-8.66	0.00866	.	2.066750	0.02622	N	0.103327	T	0.30759	0.0775	L	0.27053	0.805	0.09310	N	1	B;B	0.29766	0.256;0.036	B;B	0.19148	0.024;0.01	T	0.07908	-1.0748	10	0.26408	T	0.33	0.3946	6.6775	0.23102	0.2881:0.3347:0.3772:0.0	.	12;12	Q9BSJ6;Q9BSJ6-2	FA64A_HUMAN;.	M	12	ENSP00000250056:V12M	ENSP00000250056:V12M	V	+	1	0	FAM64A	6289188	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.657000	0.05335	-1.751000	0.01326	-0.136000	0.14681	GTG		0.627	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013	
PITPNM3	83394	broad.mit.edu	37	17	6364730	6364730	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:6364730C>A	ENST00000262483.8	-	18	2540	c.2453G>T	c.(2452-2454)cGg>cTg	p.R818L	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Missense_Mutation_p.R782L	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	818					phosphatidylinositol metabolic process (GO:0046488)|phospholipid transport (GO:0015914)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)|receptor tyrosine kinase binding (GO:0030971)	p.R818L(1)		autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(3)|skin(2)	36				Colorectal(2;0.000372)|READ - Rectum adenocarcinoma(2;0.0276)|LUAD - Lung adenocarcinoma(2;0.0836)|COAD - Colon adenocarcinoma(228;0.185)		GGCCTTCTGCCGCAGCGGGTC	0.632																																					p.R818L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2453T	17						.						113.0	101.0	105.0					17																	6364730		2203	4300	6503	6305454	SO:0001583	missense	83394	exon18			AF334586	CCDS11076.1, CCDS54080.1	17p13	2013-07-18	2013-07-18	2013-07-18	ENSG00000091622	ENSG00000091622		"""GPCR / Class A : Chemokine receptors : Atypical"""	21043	protein-coding gene	gene with protein product	"""atypical chemokine receptor 6"""	608921	"""cone rod dystrophy 5"""	CORD5		10022914	Standard	NM_031220		Approved	NIR1, RDGBA3, ACKR6	uc002gdd.4	Q9BZ71	OTTHUMG00000102039	ENST00000262483.8:c.2453G>T	17.37:g.6364730C>A	ENSP00000262483:p.Arg818Leu	Somatic		Capture	Illumina HiSeq	Phase_I	6305454	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Missense_Mutation	SNP	ENST00000262483.8	37	CCDS11076.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.938166	0.92526	.	.	ENSG00000091622	ENST00000262483;ENST00000421306	T;T	0.75704	-0.96;-0.96	4.94	4.94	0.65067	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.85682	D	0.000000	D	0.82486	0.5047	M	0.61703	1.905	0.52099	D	0.999943	P;D	0.60160	0.756;0.987	B;P	0.61477	0.38;0.889	D	0.83829	0.0251	10	0.54805	T	0.06	.	15.6383	0.76973	0.0:1.0:0.0:0.0	.	782;818	F8WEW5;Q9BZ71	.;PITM3_HUMAN	L	818;782	ENSP00000262483:R818L;ENSP00000407882:R782L	ENSP00000262483:R818L	R	-	2	0	PITPNM3	6305454	0.986000	0.35501	1.000000	0.80357	0.991000	0.79684	7.722000	0.84778	2.293000	0.77203	0.462000	0.41574	CGG		0.632	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220	
KIAA0753	9851	broad.mit.edu	37	17	6483074	6483074	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:6483074G>A	ENST00000361413.3	-	19	3255	c.2897C>T	c.(2896-2898)gCt>gTt	p.A966V	KIAA0753_ENST00000572370.1_Missense_Mutation_p.A667V|KIAA0753_ENST00000589033.1_Missense_Mutation_p.A422V|KIAA0753_ENST00000542606.1_Missense_Mutation_p.A667V	NM_014804.2	NP_055619.2	Q2KHM9	K0753_HUMAN	KIAA0753	966						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.A966V(1)		endometrium(4)|large_intestine(11)|lung(5)|prostate(4)	24				COAD - Colon adenocarcinoma(228;0.157)		CCTTTATGTAGCAGCCTCTAA	0.498																																					p.A966V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2897T	17						.						112.0	111.0	112.0					17																	6483074		1968	4156	6124	6423798	SO:0001583	missense	9851	exon19				CCDS42247.1	17p13.1	2014-04-04			ENSG00000198920	ENSG00000198920			29110	protein-coding gene	gene with protein product						24613305	Standard	NM_014804		Approved		uc002gde.4	Q2KHM9	OTTHUMG00000177928	ENST00000361413.3:c.2897C>T	17.37:g.6483074G>A	ENSP00000355250:p.Ala966Val	Somatic		Capture	Illumina HiSeq	Phase_I	6423798	NM_014804	A8KA11|B7Z479|O94853|Q05D97|Q2KHN0|Q9UG45	Missense_Mutation	SNP	ENST00000361413.3	37	CCDS42247.1	.	.	.	.	.	.	.	.	.	.	G	36	5.793733	0.96952	.	.	ENSG00000198920	ENST00000361413;ENST00000542606;ENST00000542826	T;T	0.49139	0.79;0.79	5.5	5.5	0.81552	.	0.202192	0.45606	D	0.000360	T	0.56455	0.1986	N	0.24115	0.695	0.42178	D	0.991677	D	0.89917	1.0	D	0.74674	0.984	T	0.60915	-0.7168	10	0.87932	D	0	-14.6879	17.2767	0.87118	0.0:0.0:1.0:0.0	.	966	Q2KHM9	K0753_HUMAN	V	966;667;422	ENSP00000355250:A966V;ENSP00000444634:A667V	ENSP00000355250:A966V	A	-	2	0	KIAA0753	6423798	0.372000	0.25064	0.924000	0.36721	0.694000	0.40290	3.569000	0.53827	2.755000	0.94549	0.557000	0.71058	GCT		0.498	KIAA0753-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439769.3	NM_014804	
CACNG4	27092	broad.mit.edu	37	17	65026733	65026733	+	Silent	SNP	C	C	T	rs142496896	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:65026733C>T	ENST00000262138.3	+	4	599	c.597C>T	c.(595-597)ggC>ggT	p.G199G	RP11-74H8.1_ENST00000579138.1_RNA|AC005544.1_ENST00000375684.1_5'Flank	NM_014405.3	NP_055220.1	Q9UBN1	CCG4_HUMAN	calcium channel, voltage-dependent, gamma subunit 4	199					membrane depolarization (GO:0051899)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.G199G(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(3)	19	all_cancers(12;9.86e-11)		BRCA - Breast invasive adenocarcinoma(6;1.35e-07)			AGACCGTGGGCGTCCTGGCTG	0.453													C|||	4	0.000798722	0.0015	0.0	5008	,	,		17340	0.0		0.0	False		,,,				2504	0.002				p.G199G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C597T	17						.	C		1,4405	4.2+/-10.8	0,1,2202	92.0	87.0	89.0		597	1.7	1.0	17	dbSNP_134	89	0,8600		0,0,4300	no	coding-synonymous	CACNG4	NM_014405.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		199/328	65026733	1,13005	2203	4300	6503	62457195	SO:0001819	synonymous_variant	27092	exon4			AH008289	CCDS11667.1	17q24	2006-01-23				ENSG00000075461		"""Calcium channel subunits"""	1408	protein-coding gene	gene with protein product		606404				10613843	Standard	NM_014405		Approved	MGC11138, MGC24983	uc002jft.2	Q9UBN1		ENST00000262138.3:c.597C>T	17.37:g.65026733C>T		Somatic		Capture	Illumina HiSeq	Phase_I	62457195	NM_014405	B2RCK0	Silent	SNP	ENST00000262138.3	37	CCDS11667.1																																																																																				0.453	CACNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447036.1	NM_014405	
FBXO39	162517	broad.mit.edu	37	17	6683787	6683787	+	Silent	SNP	C	C	T	rs371283331		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:6683787C>T	ENST00000321535.4	+	2	730	c.600C>T	c.(598-600)atC>atT	p.I200I		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	200								p.I200I(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	26						AGCTCAACATCGAGGACTATT	0.493																																					p.I200I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C600T	17						.	C		1,4405	2.1+/-5.4	0,1,2202	79.0	74.0	76.0		600	-3.2	1.0	17		76	0,8600		0,0,4300	no	coding-synonymous	FBXO39	NM_153230.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		200/443	6683787	1,13005	2203	4300	6503	6624511	SO:0001819	synonymous_variant	162517	exon2			BC034782	CCDS11082.1	17p13.2	2014-01-21			ENSG00000177294	ENSG00000177294		"""F-boxes /  ""other"""""	28565	protein-coding gene	gene with protein product		609106				12477932	Standard	NM_153230		Approved	MGC35179, Fbx39, CT144	uc010vtg.2	Q8N4B4	OTTHUMG00000102062	ENST00000321535.4:c.600C>T	17.37:g.6683787C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6624511	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																				0.493	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230	
YBX2	51087	broad.mit.edu	37	17	7193799	7193799	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7193799C>T	ENST00000007699.5	-	5	578	c.515G>A	c.(514-516)cGt>cAt	p.R172H	YBX2_ENST00000570627.1_5'UTR	NM_015982.3	NP_057066.2	Q9Y2T7	YBOX2_HUMAN	Y box binding protein 2	172					mRNA stabilization (GO:0048255)|negative regulation of binding (GO:0051100)|negative regulation of translation (GO:0017148)|oocyte development (GO:0048599)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|translational attenuation (GO:0009386)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|polysome (GO:0005844)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lipid binding (GO:0008289)|mRNA 3'-UTR binding (GO:0003730)|ribonucleoprotein complex binding (GO:0043021)|translation regulator activity (GO:0045182)	p.R172H(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|skin(3)	12						GGGGGCATAACGGCTGCCCTT	0.627																																					p.R172H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G515A	17						.						30.0	34.0	32.0					17																	7193799		2198	4295	6493	7134523	SO:0001583	missense	51087	exon5			AF096834	CCDS11098.1	17p13.1	2013-12-20			ENSG00000006047	ENSG00000006047			17948	protein-coding gene	gene with protein product		611447				10100484, 9780336	Standard	NM_015982		Approved	MSY2, CSDA3	uc002gfq.2	Q9Y2T7	OTTHUMG00000177992	ENST00000007699.5:c.515G>A	17.37:g.7193799C>T	ENSP00000007699:p.Arg172His	Somatic		Capture	Illumina HiSeq	Phase_I	7134523	NM_015982	D3DTP1|Q8N4P0	Missense_Mutation	SNP	ENST00000007699.5	37	CCDS11098.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.990150	0.93106	.	.	ENSG00000006047	ENST00000007699	T	0.26518	1.73	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	M	0.77103	2.36	0.58432	D	0.999992	D	0.76494	0.999	P	0.57101	0.813	T	0.47548	-0.9109	10	0.51188	T	0.08	-11.429	15.478	0.75501	0.0:1.0:0.0:0.0	.	172	Q9Y2T7	YBOX2_HUMAN	H	172	ENSP00000007699:R172H	ENSP00000007699:R172H	R	-	2	0	YBX2	7134523	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.534000	0.53568	2.613000	0.88420	0.561000	0.74099	CGT		0.627	YBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440172.2	NM_015982	
ABCA10	10349	broad.mit.edu	37	17	67183905	67183905	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:67183905T>C	ENST00000269081.4	-	20	3156	c.2247A>G	c.(2245-2247)gcA>gcG	p.A749A	ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	749					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.A749A(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(34)|ovary(2)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	81	Breast(10;6.95e-12)					TCCAGAGAGCTGCACTACTGA	0.408																																					p.A749A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2247G	17						.						168.0	156.0	160.0					17																	67183905		2203	4300	6503	64695500	SO:0001819	synonymous_variant	10349	exon20			AY247065	CCDS11684.1	17q24	2012-03-14			ENSG00000154263	ENSG00000154263		"""ATP binding cassette transporters / subfamily A"""	30	protein-coding gene	gene with protein product		612508				12821155, 11435397	Standard	NM_080282		Approved	EST698739	uc010dfa.1	Q8WWZ4	OTTHUMG00000164716	ENST00000269081.4:c.2247A>G	17.37:g.67183905T>C		Somatic		Capture	Illumina HiSeq	Phase_I	64695500	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Silent	SNP	ENST00000269081.4	37	CCDS11684.1																																																																																				0.408	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282	
FBF1	85302	broad.mit.edu	37	17	73933672	73933672	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:73933672T>C	ENST00000586717.1	-	3	279	c.6A>G	c.(4-6)gcA>gcG	p.A2A	FBF1_ENST00000588478.1_5'Flank|FBF1_ENST00000319129.5_Silent_p.A2A|FBF1_ENST00000389570.4_Silent_p.A2A			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	2					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.A2A(1)		large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TGGTTTTTGGTGCCTAAAATG	0.383																																					p.A2A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A6G	17						.						152.0	137.0	142.0					17																	73933672		1886	4108	5994	71445267	SO:0001819	synonymous_variant	85302	exon3			AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.6A>G	17.37:g.73933672T>C		Somatic		Capture	Illumina HiSeq	Phase_I	71445267	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																					0.383	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
NEURL4	84461	broad.mit.edu	37	17	7221645	7221645	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7221645C>T	ENST00000399464.2	-	24	3910	c.3895G>A	c.(3895-3897)Gcc>Acc	p.A1299T	RP11-542C16.2_ENST00000575474.1_Silent_p.L112L|GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000570460.1_Missense_Mutation_p.A1275T|GPS2_ENST00000380728.2_5'Flank|NEURL4_ENST00000315614.7_Missense_Mutation_p.A1297T|GPS2_ENST00000391950.3_5'Flank|NEURL4_ENST00000574120.1_5'UTR	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1299						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A1299T(1)|p.A1297T(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TTCCCACTGGCAGCCCCTGGC	0.622																																					p.A1299T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3895A	17						.						122.0	135.0	131.0					17																	7221645		2018	4181	6199	7162369	SO:0001583	missense	84461	exon24				CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.3895G>A	17.37:g.7221645C>T	ENSP00000382390:p.Ala1299Thr	Somatic		Capture	Illumina HiSeq	Phase_I	7162369	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	C	14.17	2.455455	0.43634	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.30448	1.53;1.53	5.7	2.59	0.31030	.	0.266482	0.36200	N	0.002735	T	0.20941	0.0504	L	0.36672	1.1	0.27483	N	0.952515	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17410	-1.0370	10	0.25106	T	0.35	-7.7706	8.5183	0.33259	0.0:0.6918:0.0:0.3081	.	1297;1299	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	T	1297;1299	ENSP00000319826:A1297T;ENSP00000382390:A1299T	ENSP00000319826:A1297T	A	-	1	0	NEURL4	7162369	0.961000	0.32948	0.998000	0.56505	0.912000	0.54170	0.647000	0.24812	0.330000	0.23485	0.462000	0.41574	GCC		0.622	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
EVPL	2125	broad.mit.edu	37	17	74004103	74004103	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:74004103G>T	ENST00000301607.3	-	22	5436	c.5183C>A	c.(5182-5184)aCc>aAc	p.T1728N	EVPL_ENST00000586740.1_Missense_Mutation_p.T1750N|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1728	Globular 2.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.T1728N(1)		breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						GGGCCCCGAGGTGGTGACCTC	0.637																																					p.T1728N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5183A	17						.						61.0	60.0	60.0					17																	74004103		2203	4300	6503	71515698	SO:0001583	missense	2125	exon22			U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.5183C>A	17.37:g.74004103G>T	ENSP00000301607:p.Thr1728Asn	Somatic		Capture	Illumina HiSeq	Phase_I	71515698	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.878851	0.72294	.	.	ENSG00000167880	ENST00000301607	T	0.67865	-0.29	4.94	4.94	0.65067	.	0.061167	0.64402	D	0.000006	T	0.76779	0.4035	L	0.48642	1.525	0.53688	D	0.999971	D;D	0.76494	0.999;0.999	D;D	0.66084	0.922;0.941	T	0.79242	-0.1884	10	0.66056	D	0.02	-50.3814	18.1623	0.89712	0.0:0.0:1.0:0.0	.	1750;1728	B7ZLH8;Q92817	.;EVPL_HUMAN	N	1728	ENSP00000301607:T1728N	ENSP00000301607:T1728N	T	-	2	0	EVPL	71515698	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.990000	0.88215	2.289000	0.77006	0.561000	0.74099	ACC		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
CHRNB1	1140	broad.mit.edu	37	17	7358653	7358653	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7358653C>T	ENST00000306071.2	+	9	1162	c.1095C>T	c.(1093-1095)ccC>ccT	p.P365P	CHRNB1_ENST00000575379.1_5'Flank|CHRNB1_ENST00000576360.1_Silent_p.P244P|CHRNB1_ENST00000536404.2_Silent_p.P293P	NM_000747.2	NP_000738.2	P11230	ACHB_HUMAN	cholinergic receptor, nicotinic, beta 1 (muscle)	365					behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|neurological system process (GO:0050877)|neuromuscular synaptic transmission (GO:0007274)|postsynaptic membrane organization (GO:0001941)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	acetylcholine binding (GO:0042166)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)|ligand-gated ion channel activity (GO:0015276)	p.P365P(1)		NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(3)	23		Prostate(122;0.157)			Galantamine(DB00674)	GGCCCAAACCCGAGAGAGACC	0.527																																					p.P365P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1095T	17						.						104.0	108.0	107.0					17																	7358653		2203	4300	6503	7299377	SO:0001819	synonymous_variant	1140	exon9			X14830	CCDS11106.1	17p13.1	2012-02-11	2006-02-01		ENSG00000170175	ENSG00000170175		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1961	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 1 (muscle)"""	100710	"""cholinergic receptor, nicotinic, beta polypeptide 1 (muscle)"""	CHRNB			Standard	NM_000747		Approved		uc002ghb.3	P11230	OTTHUMG00000108139	ENST00000306071.2:c.1095C>T	17.37:g.7358653C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7299377	NM_000747	B7Z5H1|Q8IZ46|Q96FB8	Silent	SNP	ENST00000306071.2	37	CCDS11106.1																																																																																				0.527	CHRNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226942.3		
ZBTB4	57659	broad.mit.edu	37	17	7366387	7366387	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7366387C>A	ENST00000311403.4	-	4	2253	c.1914G>T	c.(1912-1914)gaG>gaT	p.E638D	ZBTB4_ENST00000380599.4_Missense_Mutation_p.E638D	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	638	Glu-rich.				cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)	p.E638D(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		cctcttcgtcctcctcactct	0.607																																					p.E638D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1914T	17						.						59.0	40.0	46.0					17																	7366387		2203	4300	6503	7307111	SO:0001583	missense	57659	exon4			AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1914G>T	17.37:g.7366387C>A	ENSP00000307858:p.Glu638Asp	Somatic		Capture	Illumina HiSeq	Phase_I	7307111	NM_020899	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	C	0.022	-1.407695	0.01155	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.36340	1.26;1.26	5.08	-5.86	0.02304	.	0.390462	0.22892	N	0.054372	T	0.20780	0.0500	L	0.49126	1.545	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.09292	-1.0681	10	0.44086	T	0.13	-2.5986	1.7483	0.02967	0.2503:0.2439:0.3337:0.1722	.	638	Q9P1Z0	ZBTB4_HUMAN	D	638	ENSP00000307858:E638D;ENSP00000369973:E638D	ENSP00000307858:E638D	E	-	3	2	ZBTB4	7307111	0.004000	0.15560	0.273000	0.24645	0.001000	0.01503	-1.206000	0.03011	-1.102000	0.03023	-2.780000	0.00118	GAG		0.607	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
ZBTB4	57659	broad.mit.edu	37	17	7367147	7367147	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7367147C>T	ENST00000311403.4	-	4	1493	c.1154G>A	c.(1153-1155)cGa>cAa	p.R385Q	ZBTB4_ENST00000380599.4_Missense_Mutation_p.R385Q	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	385					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)	p.R385Q(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GTGGAAGGCTCGCTGGTGGGT	0.557																																					p.R385Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1154A	17						.						107.0	113.0	111.0					17																	7367147		2203	4300	6503	7307871	SO:0001583	missense	57659	exon4			AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.1154G>A	17.37:g.7367147C>T	ENSP00000307858:p.Arg385Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7307871	NM_020899	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Missense_Mutation	SNP	ENST00000311403.4	37	CCDS11107.1	.	.	.	.	.	.	.	.	.	.	C	18.12	3.552623	0.65425	.	.	ENSG00000174282	ENST00000311403;ENST00000380599	T;T	0.06849	3.25;3.25	4.92	4.92	0.64577	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.304893	0.25875	N	0.027730	T	0.10035	0.0246	N	0.14661	0.345	0.32477	N	0.541973	D	0.67145	0.996	P	0.56563	0.801	T	0.03630	-1.1018	10	0.66056	D	0.02	-6.759	9.1722	0.37089	0.0:0.9033:0.0:0.0967	.	385	Q9P1Z0	ZBTB4_HUMAN	Q	385	ENSP00000307858:R385Q;ENSP00000369973:R385Q	ENSP00000307858:R385Q	R	-	2	0	ZBTB4	7307871	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.202000	0.65169	2.578000	0.87016	0.456000	0.33151	CGA		0.557	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
TNFSF12	8742	broad.mit.edu	37	17	7460624	7460624	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7460624C>T	ENST00000293825.6	+	7	970	c.707C>T	c.(706-708)gCt>gTt	p.A236V	TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000338784.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000380535.4_5'Flank|TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000349228.4_5'Flank|TNFSF13_ENST00000396545.4_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	236					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)	p.A236V(1)		central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CATCTCAAGGCTGCCCCCTTC	0.692																																					p.A236V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C707T	17						.						42.0	40.0	41.0					17																	7460624		2203	4299	6502	7401348	SO:0001583	missense	8742	exon7			AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.707C>T	17.37:g.7460624C>T	ENSP00000293825:p.Ala236Val	Somatic		Capture	Illumina HiSeq	Phase_I	7401348	NM_003809	Q8IZK7|Q8WUZ7	Missense_Mutation	SNP	ENST00000293825.6	37	CCDS11109.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.138899	0.77775	.	.	ENSG00000239697	ENST00000293825	T	0.29142	1.58	4.24	3.25	0.37280	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	.	.	.	.	T	0.20901	0.0503	L	0.29908	0.895	0.80722	D	1	B	0.24963	0.115	B	0.25987	0.065	T	0.05971	-1.0853	9	0.48119	T	0.1	.	6.7433	0.23449	0.1783:0.7292:0.0:0.0925	.	236	O43508	TNF12_HUMAN	V	236	ENSP00000293825:A236V	ENSP00000293825:A236V	A	+	2	0	TNFSF12	7401348	0.980000	0.34600	0.999000	0.59377	0.995000	0.86356	1.289000	0.33307	1.129000	0.42072	0.561000	0.74099	GCT		0.692	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
FXR2	9513	broad.mit.edu	37	17	7495879	7495879	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7495879G>T	ENST00000250113.7	-	15	2102	c.1768C>A	c.(1768-1770)Cgc>Agc	p.R590S	SOX15_ENST00000250055.2_5'Flank|SOX15_ENST00000570788.1_5'Flank|SOX15_ENST00000538513.2_5'Flank|MPDU1_ENST00000423172.2_3'UTR|FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	590	Poly-Arg.					cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R590S(1)		NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		TTACGGCGGCGGCGGCTGCGA	0.547																																					p.R590S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1768A	17						.						134.0	140.0	138.0					17																	7495879		2024	4164	6188	7436604	SO:0001583	missense	9513	exon15			U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1768C>A	17.37:g.7495879G>T	ENSP00000250113:p.Arg590Ser	Somatic		Capture	Illumina HiSeq	Phase_I	7436604	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Missense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.813855	0.70912	.	.	ENSG00000129245	ENST00000250113	T	0.57436	0.4	4.89	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	L	0.39898	1.24	0.50171	D	0.999851	D	0.63880	0.993	D	0.71184	0.972	T	0.57289	-0.7837	10	0.49607	T	0.09	0.1383	9.9408	0.41578	0.0:0.0:0.7976:0.2024	.	590	P51116	FXR2_HUMAN	S	590	ENSP00000250113:R590S	ENSP00000250113:R590S	R	-	1	0	FXR2	7436604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.712000	0.68407	2.709000	0.92574	0.655000	0.94253	CGC		0.547	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
DNAH2	146754	broad.mit.edu	37	17	7640486	7640486	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7640486G>A	ENST00000572933.1	+	8	2540	c.1080G>A	c.(1078-1080)aaG>aaA	p.K360K	DNAH2_ENST00000082259.3_Silent_p.K360K|DNAH2_ENST00000570791.1_Silent_p.K360K|DNAH2_ENST00000389173.2_Silent_p.K360K			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	360	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.K360K(1)		NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCTCTAGCAAGCTCCCTAAGC	0.502																																					p.K360K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1080A	17						.						129.0	112.0	117.0					17																	7640486		2203	4300	6503	7581211	SO:0001819	synonymous_variant	146754	exon7			U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.1080G>A	17.37:g.7640486G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7581211	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																				0.502	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
PRPSAP1	5635	broad.mit.edu	37	17	74328397	74328397	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:74328397C>A	ENST00000446526.3	-	4	855	c.410G>T	c.(409-411)aGg>aTg	p.R137M	PRPSAP1_ENST00000324684.4_Missense_Mutation_p.R34M	NM_002766.2	NP_002757.2	Q14558	KPRA_HUMAN	phosphoribosyl pyrophosphate synthetase-associated protein 1	108					negative regulation of kinase activity (GO:0033673)|nucleobase-containing compound metabolic process (GO:0006139)|nucleotide biosynthetic process (GO:0009165)	ribose phosphate diphosphokinase complex (GO:0002189)	enzyme inhibitor activity (GO:0004857)|magnesium ion binding (GO:0000287)|ribose phosphate diphosphokinase activity (GO:0004749)	p.R108M(1)		cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	17						ACCCCTCTTCCTCATCTTGCT	0.557																																					p.R137M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G410T	17						.						204.0	183.0	190.0					17																	74328397		2203	4300	6503	71839992	SO:0001583	missense	5635	exon4			D61391	CCDS11743.2	17q24-q25	2008-07-18			ENSG00000161542	ENSG00000161542			9466	protein-coding gene	gene with protein product		601249				8660991	Standard	NM_002766		Approved	PAP39	uc010wta.1	Q14558	OTTHUMG00000155969	ENST00000446526.3:c.410G>T	17.37:g.74328397C>A	ENSP00000414624:p.Arg137Met	Somatic		Capture	Illumina HiSeq	Phase_I	71839992	NM_002766	B2R6M4|Q96H06	Missense_Mutation	SNP	ENST00000446526.3	37	CCDS11743.2	.	.	.	.	.	.	.	.	.	.	C	33	5.212352	0.95069	.	.	ENSG00000161542	ENST00000446526;ENST00000324684;ENST00000435555;ENST00000436498;ENST00000423915;ENST00000442767	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89;-2.89	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	D	0.94804	0.8322	L	0.47016	1.485	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.974	D	0.95015	0.8155	10	0.62326	D	0.03	.	19.1228	0.93371	0.0:1.0:0.0:0.0	.	108;137	Q14558;Q14558-2	KPRA_HUMAN;.	M	137;34;34;34;34;95	ENSP00000414624:R137M;ENSP00000314973:R34M;ENSP00000392838:R34M;ENSP00000387494:R34M;ENSP00000409190:R34M;ENSP00000402126:R95M	ENSP00000314973:R34M	R	-	2	0	PRPSAP1	71839992	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.783000	0.85696	2.519000	0.84933	0.655000	0.94253	AGG		0.557	PRPSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342480.2	NM_002766	
GP1BA	2811	broad.mit.edu	37	17	4837373	4837373	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:4837373delA	ENST00000329125.5	+	2	1549	c.1474delA	c.(1474-1476)aaafs	p.K493fs		NM_000173.5	NP_000164.5	P07359	GP1BA_HUMAN	glycoprotein Ib (platelet), alpha polypeptide	493					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|fibrinolysis (GO:0042730)|platelet activation (GO:0030168)|regulation of blood coagulation (GO:0030193)|thrombin receptor signaling pathway (GO:0070493)	anchored component of external side of plasma membrane (GO:0031362)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)	p.T494fs*59(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(5)|stomach(1)|urinary_tract(1)	20						AGAATCCACCAAAAAAACCAT	0.502																																					p.K479fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1435delA	17						.						73.0	77.0	76.0					17																	4837373		1915	4113	6028	4778114	SO:0001589	frameshift_variant	2811	exon2				CCDS54068.1	17p13.2	2014-09-17			ENSG00000185245	ENSG00000185245		"""CD molecules"""	4439	protein-coding gene	gene with protein product		606672		GP1B		3353370	Standard	NM_000173		Approved	CD42b	uc021tnz.1	P07359	OTTHUMG00000177946	ENST00000329125.5:c.1474delA	17.37:g.4837373delA	ENSP00000329380:p.Lys493fs	Somatic		Capture	Illumina HiSeq	Phase_I	4778114	NM_000173	E7ES66|Q14441|Q16469|Q8N1F3|Q8NG39|Q9HDC7|Q9UEK1|Q9UQS4	Frame_Shift_Del	DEL	ENST00000329125.5	37	CCDS54068.1																																																																																				0.502	GP1BA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439889.1		
DVL2	1856	broad.mit.edu	37	17	7129594	7129594	+	Frame_Shift_Del	DEL	C	C	-	rs370880170		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:7129594delC	ENST00000005340.5	-	15	2083	c.1801delG	c.(1801-1803)gcafs	p.A601fs	DVL2_ENST00000574642.1_5'Flank|DVL2_ENST00000575458.1_Frame_Shift_Del_p.A595fs|MIR324_ENST00000362183.1_RNA	NM_004422.2	NP_004413.1	O14641	DVL2_HUMAN	dishevelled segment polarity protein 2	601					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in regulation of cell proliferation (GO:0044340)|cell migration in hindbrain (GO:0021535)|cellular protein localization (GO:0034613)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hippo signaling (GO:0035329)|neural tube closure (GO:0001843)|non-canonical Wnt signaling pathway (GO:0035567)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|segment specification (GO:0007379)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|clathrin-coated endocytic vesicle (GO:0045334)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|identical protein binding (GO:0042802)	p.A601fs*80(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(7)|skin(1)	25						GTGCGCCCTGCCCCCCCATCA	0.726																																					p.A601fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1801delG	17						.						19.0	24.0	22.0					17																	7129594		2192	4258	6450	7070318	SO:0001589	frameshift_variant	1856	exon15			BC014844	CCDS11091.1	17p13.1	2013-05-22	2013-05-22		ENSG00000004975	ENSG00000004975		"""Dishevelled homologs"""	3086	protein-coding gene	gene with protein product		602151	"""dishevelled 2 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 2 (Drosophila)"""			8662242	Standard	NM_004422		Approved		uc002gez.1	O14641	OTTHUMG00000102155	ENST00000005340.5:c.1801delG	17.37:g.7129594delC	ENSP00000005340:p.Ala601fs	Somatic		Capture	Illumina HiSeq	Phase_I	7070318	NM_004422	D3DTN3|Q53XM0	Frame_Shift_Del	DEL	ENST00000005340.5	37	CCDS11091.1																																																																																				0.726	DVL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219999.2	NM_004422	
RCVRN	5957	broad.mit.edu	37	17	9808162	9808162	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:9808162G>A	ENST00000226193.5	-	1	776	c.336C>T	c.(334-336)gaC>gaT	p.D112D		NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	112	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.D112D(2)		endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						TCCCGTTACCGTCCACGTCGT	0.627																																					p.D112D												.	.	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)	c.C336T	17						.						167.0	132.0	144.0					17																	9808162		2203	4300	6503	9748887	SO:0001819	synonymous_variant	5957	exon1			BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.336C>T	17.37:g.9808162G>A		Somatic		Capture	Illumina HiSeq	Phase_I	9748887	NM_002903	Q53XL0	Silent	SNP	ENST00000226193.5	37	CCDS11151.1																																																																																				0.627	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903	
DNAH9	1770	broad.mit.edu	37	17	11556168	11556168	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:11556168delA	ENST00000262442.4	+	14	2512	c.2444delA	c.(2443-2445)caafs	p.Q815fs	DNAH9_ENST00000454412.2_Frame_Shift_Del_p.Q815fs	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	815	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.N816fs*3(1)		NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAAGAGATCCAAAACATCATG	0.373																																					p.Q815fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2444delA	17						.						125.0	121.0	122.0					17																	11556168		2203	4300	6503	11496893	SO:0001589	frameshift_variant	1770	exon14			U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.2444delA	17.37:g.11556168delA	ENSP00000262442:p.Gln815fs	Somatic		Capture	Illumina HiSeq	Phase_I	11496893	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Frame_Shift_Del	DEL	ENST00000262442.4	37	CCDS11160.1																																																																																				0.373	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ZNF624	57547	broad.mit.edu	37	17	16526202	16526202	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:16526202delT	ENST00000311331.7	-	6	2089	c.1998delA	c.(1996-1998)aaafs	p.K666fs		NM_020787.3	NP_065838.2	Q9P2J8	ZN624_HUMAN	zinc finger protein 624	666					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K666fs*130(1)		breast(4)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	26				UCEC - Uterine corpus endometrioid carcinoma (92;0.0837)		ATTTATATGGTTTTTCTCCAG	0.388																																					p.K666fs	NSCLC(186;1023 2134 13330 38202 39800)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1998delA	17						.						116.0	117.0	117.0					17																	16526202		2203	4300	6503	16466927	SO:0001589	frameshift_variant	57547	exon6			AB037770	CCDS11180.1	17p11.2	2013-01-08			ENSG00000197566	ENSG00000197566		"""Zinc fingers, C2H2-type"", ""-"""	29254	protein-coding gene	gene with protein product						10718198	Standard	NM_020787		Approved	KIAA1349	uc010cpi.2	Q9P2J8	OTTHUMG00000058996	ENST00000311331.7:c.1998delA	17.37:g.16526202delT	ENSP00000310472:p.Lys666fs	Somatic		Capture	Illumina HiSeq	Phase_I	16466927	NM_020787	Q3SY62|Q3SY63|Q6ZN27	Frame_Shift_Del	DEL	ENST00000311331.7	37	CCDS11180.1																																																																																				0.388	ZNF624-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130512.3	XM_047617	
SDF2	6388	broad.mit.edu	37	17	26988863	26988863	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:26988863delC	ENST00000247020.4	-	1	330	c.32delG	c.(31-33)ggtfs	p.G11fs	SDF2_ENST00000592250.1_Intron|SUPT6H_ENST00000314616.6_5'Flank|SUPT6H_ENST00000347486.4_5'Flank	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	11					protein glycosylation (GO:0006486)|protein O-linked mannosylation (GO:0035269)	extracellular space (GO:0005615)|membrane (GO:0016020)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)	p.G11fs*20(1)		endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Lung NSC(42;0.00431)					GCTCCACAAACCCCCCAACAA	0.582																																					p.G11fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.32delG	17						.						152.0	135.0	140.0					17																	26988863		2203	4300	6503	24012990	SO:0001589	frameshift_variant	6388	exon1			BC001406	CCDS11238.1	17q11.2	2004-02-16			ENSG00000132581	ENSG00000132581			10675	protein-coding gene	gene with protein product		602934				8918255	Standard	NR_045585		Approved		uc002hbw.3	Q99470	OTTHUMG00000132681	ENST00000247020.4:c.32delG	17.37:g.26988863delC	ENSP00000247020:p.Gly11fs	Somatic		Capture	Illumina HiSeq	Phase_I	24012990	NM_006923	Q9BQ79	Frame_Shift_Del	DEL	ENST00000247020.4	37	CCDS11238.1																																																																																				0.582	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
ATAD5	79915	broad.mit.edu	37	17	29185289	29185289	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:29185289delA	ENST00000321990.4	+	9	3282	c.2904delA	c.(2902-2904)ctafs	p.L968fs	CTD-2349P21.11_ENST00000580873.1_RNA	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	968					cellular response to DNA damage stimulus (GO:0006974)	nucleus (GO:0005634)	ATP binding (GO:0005524)	p.K970fs*32(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(18)|lung(13)|ovary(3)|pancreas(1)	51		all_hematologic(16;0.0202)|Acute lymphoblastic leukemia(14;0.0238)|Myeloproliferative disorder(56;0.0393)				CCTTACTCCTAAAAAAACAAA	0.308																																					p.L968fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2904delA	17						.						46.0	46.0	46.0					17																	29185289		2203	4298	6501	26209415	SO:0001589	frameshift_variant	79915	exon9				CCDS11260.1	17q11.2	2010-04-21	2007-02-08	2007-02-08	ENSG00000176208	ENSG00000176208		"""ATPases / AAA-type"""	25752	protein-coding gene	gene with protein product	"""enhanced level of genomic instability 1 homolog (S. cerevisiae)"""	609534	"""chromosome 17 open reading frame 41"""	C17orf41		15983387, 11468690, 19755857	Standard	NM_024857		Approved	FLJ12735, FRAG1, ELG1	uc002hfs.1	Q96QE3	OTTHUMG00000132794	ENST00000321990.4:c.2904delA	17.37:g.29185289delA	ENSP00000313171:p.Leu968fs	Somatic		Capture	Illumina HiSeq	Phase_I	26209415	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Frame_Shift_Del	DEL	ENST00000321990.4	37	CCDS11260.1																																																																																				0.308	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857	
TMEM92	162461	broad.mit.edu	37	17	48356337	48356337	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:48356337delC	ENST00000300433.3	+	5	456	c.346delC	c.(346-348)cccfs	p.P119fs	RP11-893F2.9_ENST00000508851.1_RNA|TMEM92_ENST00000507382.1_Frame_Shift_Del_p.P119fs|TMEM92_ENST00000511882.1_3'UTR	NM_001168215.1	NP_001161687.1	Q6UXU6	TMM92_HUMAN	transmembrane protein 92	119	Pro-rich.					integral component of membrane (GO:0016021)		p.P117fs*7(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(1)|lung(1)	7						CCTTTCTGCGCCCCCACCCCC	0.657																																					p.P116fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.346delC	17						.						34.0	40.0	38.0					17																	48356337		2203	4300	6503	45711336	SO:0001589	frameshift_variant	162461	exon5				CCDS11562.1	17q21.33	2005-12-13							26579	protein-coding gene	gene with protein product						12975309	Standard	NM_153229		Approved	FLJ33318	uc002iqn.2	Q6UXU6		ENST00000300433.3:c.346delC	17.37:g.48356337delC	ENSP00000300433:p.Pro119fs	Somatic		Capture	Illumina HiSeq	Phase_I	45711336	NM_001168215	Q8NBF0	Frame_Shift_Del	DEL	ENST00000300433.3	37	CCDS11562.1																																																																																				0.657	TMEM92-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367053.2	NM_153229	
PRR11	55771	broad.mit.edu	37	17	57247171	57247171	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:57247171delA	ENST00000262293.4	+	2	370	c.58delA	c.(58-60)aaafs	p.K22fs		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	22						cytoplasm (GO:0005737)|membrane (GO:0016020)		p.E23fs*9(3)|p.E23fs*46(1)		breast(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|pancreas(1)	16	Medulloblastoma(34;0.0922)|all_neural(34;0.101)					AAGATTATTCAAAAAAAAAGA	0.363																																					p.K20fs												.	.	4	Deletion - Frameshift(3)|Insertion - Frameshift(1)	large_intestine(2)|ovary(1)|lung(1)	c.58delA	17						.						79.0	79.0	79.0					17																	57247171		2203	4300	6503	54601953	SO:0001589	frameshift_variant	55771	exon2				CCDS11614.1	17q23.2	2005-12-13				ENSG00000068489			25619	protein-coding gene	gene with protein product		615920				11799066	Standard	NM_018304		Approved	FLJ11029	uc002ixf.2	Q96HE9		ENST00000262293.4:c.58delA	17.37:g.57247171delA	ENSP00000262293:p.Lys22fs	Somatic		Capture	Illumina HiSeq	Phase_I	54601953	NM_018304	Q9NUZ7|Q9NXE9	Frame_Shift_Del	DEL	ENST00000262293.4	37	CCDS11614.1																																																																																				0.363	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304	
ABCA9	10350	broad.mit.edu	37	17	67004285	67004285	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:67004285delA	ENST00000340001.4	-	24	3450	c.3239delT	c.(3238-3240)ttgfs	p.L1080fs	ABCA9-AS1_ENST00000458677.1_RNA|ABCA9_ENST00000370732.2_Frame_Shift_Del_p.L1080fs|ABCA9_ENST00000453985.2_Frame_Shift_Del_p.L1080fs	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	1080					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.L1080fs*1(1)		NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					CAGGAGGATCAAAAAGTACAG	0.383																																					p.L1080X												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3239delT	17						.						80.0	89.0	86.0					17																	67004285		2203	4300	6503	64515880	SO:0001589	frameshift_variant	10350	exon24			AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.3239delT	17.37:g.67004285delA	ENSP00000342216:p.Leu1080fs	Somatic		Capture	Illumina HiSeq	Phase_I	64515880	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Frame_Shift_Del	DEL	ENST00000340001.4	37	CCDS11681.1																																																																																				0.383	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
CBX8	57332	broad.mit.edu	37	17	77768449	77768449	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:77768449delA	ENST00000269385.4	-	5	1272	c.1155delT	c.(1153-1155)tttfs	p.F385fs	CBX8_ENST00000485449.1_5'Flank	NM_020649.2	NP_065700.1	Q9HC52	CBX8_HUMAN	chromobox homolog 8	385					histone ubiquitination (GO:0016574)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	heterochromatin (GO:0000792)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	methylated histone binding (GO:0035064)|single-stranded RNA binding (GO:0003727)|ubiquitin-protein transferase activity (GO:0004842)	p.D381fs*>5(1)|p.F385fs*>5(1)		breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)	14			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			TTTTCTCTTTAAAAAAGCCTT	0.502																																					p.F385fs												.	.	2	Deletion - Frameshift(2)	large_intestine(1)|stomach(1)	c.1155delT	17						.						157.0	173.0	168.0					17																	77768449		2203	4300	6503	75383044	SO:0001589	frameshift_variant	57332	exon5			AF174482	CCDS11765.1	17q25.3	2010-07-06	2010-06-24		ENSG00000141570	ENSG00000141570			15962	protein-coding gene	gene with protein product	"""polycomb 3"", ""Pc class 3 homolog (Drosophila)"""		"""chromobox homolog 8 (Drosophila Pc class)"""			10825164	Standard	NM_020649		Approved	RC1, HPC3, PC3	uc002jxd.2	Q9HC52	OTTHUMG00000150416	ENST00000269385.4:c.1155delT	17.37:g.77768449delA	ENSP00000269385:p.Phe385fs	Somatic		Capture	Illumina HiSeq	Phase_I	75383044	NM_020649	Q96H39|Q9NR07	Frame_Shift_Del	DEL	ENST00000269385.4	37	CCDS11765.1																																																																																				0.502	CBX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318011.1	NM_020649	
TMEM105	284186	broad.mit.edu	37	17	79287547	79287547	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:79287547delC	ENST00000332900.1	-	3	843	c.294delG	c.(292-294)gggfs	p.G98fs		NM_178520.3	NP_848615.1	Q8N8V8	TM105_HUMAN	transmembrane protein 105	98						integral component of membrane (GO:0016021)		p.L99fs*16(2)		NS(1)|large_intestine(3)|lung(1)|ovary(2)	7	all_neural(118;0.0804)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0272)|OV - Ovarian serous cystadenocarcinoma(97;0.0892)			CCAGGTGCAGCCCCCCTGCAA	0.647																																					p.G98fs												.	.	2	Deletion - Frameshift(2)	ovary(1)|large_intestine(1)	c.294delG	17						.						62.0	70.0	67.0					17																	79287547		2203	4300	6503	76902142	SO:0001589	frameshift_variant	284186	exon3			AK096111	CCDS11781.1	17q25.3	2008-04-21	2008-04-21	2008-04-21		ENSG00000185332			26794	protein-coding gene	gene with protein product							Standard	NM_178520		Approved	FLJ38792	uc002kad.2	Q8N8V8		ENST00000332900.1:c.294delG	17.37:g.79287547delC	ENSP00000329795:p.Gly98fs	Somatic		Capture	Illumina HiSeq	Phase_I	76902142	NM_178520		Frame_Shift_Del	DEL	ENST00000332900.1	37	CCDS11781.1																																																																																				0.647	TMEM105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439607.1	NM_178520	
FN3KRP	79672	broad.mit.edu	37	17	80684727	80684727	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr17:80684727T>C	ENST00000269373.6	+	6	683	c.610T>C	c.(610-612)Ttc>Ctc	p.F204L	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Missense_Mutation_p.F154L	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	204							kinase activity (GO:0016301)	p.F204L(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)			CCCTGACCTGTTCCGTGACCT	0.592																																					p.F204L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T610C	17						.						73.0	80.0	78.0					17																	80684727		2203	4300	6503	78278016	SO:0001583	missense	79672	exon6			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.610T>C	17.37:g.80684727T>C	ENSP00000269373:p.Phe204Leu	Somatic		Capture	Illumina HiSeq	Phase_I	78278016	NM_024619	Q969F4|Q9H0U7	Missense_Mutation	SNP	ENST00000269373.6	37	CCDS11817.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.759327	0.89932	.	.	ENSG00000141560	ENST00000269373;ENST00000535965	T;T	0.42513	0.97;0.97	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	L	0.31371	0.925	0.80722	D	1	D	0.71674	0.998	D	0.67382	0.951	T	0.32798	-0.9893	10	0.02654	T	1	-32.2329	15.8343	0.78787	0.0:0.0:0.0:1.0	.	204	Q9HA64	KT3K_HUMAN	L	204;154	ENSP00000269373:F204L;ENSP00000444994:F154L	ENSP00000269373:F204L	F	+	1	0	FN3KRP	78278016	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	7.843000	0.86859	2.228000	0.72767	0.533000	0.62120	TTC		0.592	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
CEP192	55125	broad.mit.edu	37	18	13100360	13100360	+	Silent	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:13100360T>G	ENST00000325971.8	+	36	6525	c.4932T>G	c.(4930-4932)cgT>cgG	p.R1644R	CEP192_ENST00000430049.2_Silent_p.R1765R|CEP192_ENST00000540847.2_3'UTR|CEP192_ENST00000506447.1_Silent_p.R2240R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	1644					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTTTAACTCGTTTGACCTCCA	0.368																																					p.R2240R												.	.	0			c.T6720G	18						.						76.0	74.0	75.0					18																	13100360		2203	4300	6503	13090360	SO:0001819	synonymous_variant	55125	exon38			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.4932T>G	18.37:g.13100360T>G		None		Capture	Illumina HiSeq	Phase_I	13090360	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																					0.368	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
NDC80	10403	broad.mit.edu	37	18	2578016	2578016	+	Nonsense_Mutation	SNP	C	C	T	rs542320666		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:2578016C>T	ENST00000261597.4	+	5	534	c.352C>T	c.(352-354)Caa>Taa	p.Q118*		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	118	Interaction with the N-terminus of CDCA1.|Nuclear localization.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)		p.Q118*(1)		NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GAAATCTCTACAAGCTCCCTC	0.363													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18558	0.0		0.0	False		,,,				2504	0.0				p.Q118X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C352T	18						.						152.0	138.0	143.0					18																	2578016		2203	4300	6503	2568016	SO:0001587	stop_gained	10403	exon5			AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.352C>T	18.37:g.2578016C>T	ENSP00000261597:p.Gln118*	Somatic		Capture	Illumina HiSeq	Phase_I	2568016	NM_006101	Q6PJX2	Nonsense_Mutation	SNP	ENST00000261597.4	37	CCDS11827.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.814650	0.90790	.	.	ENSG00000080986	ENST00000261597;ENST00000543946	.	.	.	5.95	5.07	0.68467	.	0.100012	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.956	16.5069	0.84274	0.132:0.868:0.0:0.0	.	.	.	.	X	118	.	ENSP00000261597:Q118X	Q	+	1	0	NDC80	2568016	1.000000	0.71417	0.978000	0.43139	0.991000	0.79684	6.670000	0.74467	1.501000	0.48654	0.655000	0.94253	CAA		0.363	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
CTAGE1	64693	broad.mit.edu	37	18	19996814	19996814	+	5'Flank	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:19996814T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Missense_Mutation_p.T321A			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)		p.T321A(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					ATATGCTCTGTAAGCTCTTCC	0.323																																					p.T321A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A961G	18						.						35.0	40.0	38.0					18																	19996814		2130	4265	6395	18250812	SO:0001631	upstream_gene_variant	64693	exon1			AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996814T>C	Exception_encountered	Somatic		Capture	Illumina HiSeq	Phase_I	18250812	NM_172241	B0YIZ3	Missense_Mutation	SNP	ENST00000525417.1	37		.	.	.	.	.	.	.	.	.	.	T	2.596	-0.294195	0.05568	.	.	ENSG00000212710	ENST00000391403	T	0.39229	1.09	0.87	0.87	0.19102	.	.	.	.	.	T	0.39937	0.1097	M	0.80847	2.515	0.20307	N	0.999917	B	0.17038	0.02	B	0.17979	0.02	T	0.37731	-0.9693	8	.	.	.	.	4.019	0.09657	0.0:0.0:0.0:1.0	.	321	Q96RT6	CTGE2_HUMAN	A	321	ENSP00000375220:T321A	.	T	-	1	0	CTAGE1	18250812	1.000000	0.71417	0.379000	0.26080	0.264000	0.26372	1.085000	0.30840	0.631000	0.30412	0.449000	0.29647	ACA		0.323	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
DSC1	1823	broad.mit.edu	37	18	28714037	28714037	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:28714037G>A	ENST00000257198.5	-	13	2194	c.1933C>T	c.(1933-1935)Cct>Tct	p.P645S	RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_Missense_Mutation_p.P645S|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	645	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P645S(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			ATTTGAATAGGCACAGAATAA	0.348																																					p.P645S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1933T	18						.						121.0	120.0	121.0					18																	28714037		2203	4299	6502	26968035	SO:0001583	missense	1823	exon13			AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1933C>T	18.37:g.28714037G>A	ENSP00000257198:p.Pro645Ser	Somatic		Capture	Illumina HiSeq	Phase_I	26968035	NM_004948	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.523993	0.44866	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	T;T	0.60797	0.16;0.16	5.73	4.85	0.62838	Cadherin (2);Cadherin-like (1);	0.260033	0.27393	N	0.019572	T	0.79505	0.4457	M	0.87682	2.9	0.52099	D	0.999942	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.83619	0.0138	10	0.66056	D	0.02	.	16.3177	0.82934	0.0:0.1328:0.8672:0.0	.	645;645	Q08554;Q9HB00	DSC1_HUMAN;.	S	645	ENSP00000257197:P645S;ENSP00000257198:P645S	ENSP00000257197:P645S	P	-	1	0	DSC1	26968035	0.997000	0.39634	0.984000	0.44739	0.048000	0.14542	2.961000	0.49168	1.400000	0.46741	-0.291000	0.09656	CCT		0.348	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
FHOD3	80206	broad.mit.edu	37	18	34174816	34174816	+	Missense_Mutation	SNP	G	G	A	rs144223411		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:34174816G>A	ENST00000359247.4	+	7	673	c.673G>A	c.(673-675)Gca>Aca	p.A225T	FHOD3_ENST00000591635.1_5'UTR|FHOD3_ENST00000445677.1_Missense_Mutation_p.A225T|FHOD3_ENST00000257209.4_Missense_Mutation_p.A225T|FHOD3_ENST00000590592.1_Missense_Mutation_p.A225T	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	225	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.A225T(2)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GGAGTCCAACGCACCTCTCCT	0.517													G|||	1	0.000199681	0.0	0.0	5008	,	,		20901	0.0		0.001	False		,,,				2504	0.0				p.A225T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G673A	18						.	G	THR/ALA	0,4406		0,0,2203	151.0	117.0	128.0		673	5.3	0.4	18	dbSNP_134	128	8,8592	6.4+/-24.3	0,8,4292	yes	missense	FHOD3	NM_025135.2	58	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	probably-damaging	225/1440	34174816	8,12998	2203	4300	6503	32428814	SO:0001583	missense	80206	exon7			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.673G>A	18.37:g.34174816G>A	ENSP00000352186:p.Ala225Thr	Somatic		Capture	Illumina HiSeq	Phase_I	32428814	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	16.89	3.248499	0.59103	0.0	9.3E-4	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.78481	-1.18;-1.18;-1.18	5.3	5.3	0.74995	GTPase-binding/formin homology 3 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.051376	0.85682	D	0.000000	D	0.84370	0.5457	M	0.70595	2.14	0.47037	D	0.999296	D;D;D	0.89917	0.999;1.0;0.998	P;P;P	0.60173	0.87;0.837;0.846	D	0.85804	0.1375	10	0.87932	D	0	.	11.8602	0.52461	0.0:0.0:0.8253:0.1746	.	225;225;225	Q2V2M9;Q2V2M9-3;E5F5Q0	FHOD3_HUMAN;.;.	T	225	ENSP00000257209:A225T;ENSP00000352186:A225T;ENSP00000411430:A225T	ENSP00000257209:A225T	A	+	1	0	FHOD3	32428814	1.000000	0.71417	0.407000	0.26434	0.001000	0.01503	7.500000	0.81588	2.625000	0.88918	0.655000	0.94253	GCA		0.517	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
FHOD3	80206	broad.mit.edu	37	18	34335237	34335237	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:34335237G>C	ENST00000359247.4	+	21	3812	c.3812G>C	c.(3811-3813)aGa>aCa	p.R1271T	FHOD3_ENST00000591635.1_Missense_Mutation_p.R484T|FHOD3_ENST00000445677.1_Missense_Mutation_p.R1250T|FHOD3_ENST00000257209.4_Missense_Mutation_p.R1288T|FHOD3_ENST00000590592.1_Missense_Mutation_p.R1463T|FHOD3_ENST00000592128.1_Missense_Mutation_p.R267T	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1271	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)		p.R1288T(3)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GCCAACCACAGAGAGAGAAAT	0.413																																					p.R1288T												.	.	3	Substitution - Missense(3)	endometrium(2)|large_intestine(1)	c.G3863C	18						.						90.0	67.0	75.0					18																	34335237		2203	4300	6503	32589235	SO:0001583	missense	80206	exon22			AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.3812G>C	18.37:g.34335237G>C	ENSP00000352186:p.Arg1271Thr	Somatic		Capture	Illumina HiSeq	Phase_I	32589235	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	22.5	4.300015	0.81136	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.63913	-0.07;-0.07;-0.07	6.17	5.3	0.74995	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (2);	0.042087	0.85682	D	0.000000	T	0.77412	0.4126	M	0.81112	2.525	0.80722	D	1	D;D;D;D	0.67145	0.996;0.977;0.961;0.989	P;P;P;D	0.68943	0.889;0.787;0.617;0.961	T	0.80246	-0.1462	10	0.87932	D	0	.	10.265	0.43449	0.1493:0.0:0.8507:0.0	.	492;1250;1271;1288	E7ETX5;Q2V2M9-2;Q2V2M9;Q2V2M9-3	.;.;FHOD3_HUMAN;.	T	1288;1271;1250	ENSP00000257209:R1288T;ENSP00000352186:R1271T;ENSP00000411430:R1250T	ENSP00000257209:R1288T	R	+	2	0	FHOD3	32589235	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.061000	0.89467	1.630000	0.50440	0.655000	0.94253	AGA		0.413	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
TCEB3B	51224	broad.mit.edu	37	18	44561531	44561531	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:44561531G>A	ENST00000332567.4	-	1	457	c.105C>T	c.(103-105)tcC>tcT	p.S35S	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	35	TFIIS N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00649}.				regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S35S(1)		breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TGGGCAAGGCGGAGAGTTTCT	0.582																																					p.S35S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C105T	18						.						45.0	42.0	43.0					18																	44561531		2197	4285	6482	42815529	SO:0001819	synonymous_variant	51224	exon1			BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.105C>T	18.37:g.44561531G>A		Somatic		Capture	Illumina HiSeq	Phase_I	42815529	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																				0.582	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
KATNAL2	83473	broad.mit.edu	37	18	44603829	44603829	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:44603829C>T	ENST00000592005.1	+	5	924	c.251C>T	c.(250-252)cCg>cTg	p.P84L	KATNAL2_ENST00000356157.7_Missense_Mutation_p.P403L|RP11-49K24.4_ENST00000592747.1_RNA|KATNAL2_ENST00000245121.5_Missense_Mutation_p.P331L					katanin p60 subunit A-like 2									p.P331L(1)		central_nervous_system(2)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	27						TCTAACCTGCCGTGGTAAGAG	0.428																																					p.P331L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C992T	18						.						114.0	102.0	106.0					18																	44603829		2203	4300	6503	42857827	SO:0001583	missense	83473	exon12			BC034999	CCDS32828.1	18q21.1	2010-04-21			ENSG00000167216	ENSG00000167216		"""ATPases / AAA-type"""	25387	protein-coding gene	gene with protein product		614697				12477932	Standard	NM_031303		Approved	MGC33211, DKFZP667C165	uc002lco.3	Q8IYT4		ENST00000592005.1:c.251C>T	18.37:g.44603829C>T	ENSP00000467610:p.Pro84Leu	Somatic		Capture	Illumina HiSeq	Phase_I	42857827	NM_031303		Missense_Mutation	SNP	ENST00000592005.1	37		.	.	.	.	.	.	.	.	.	.	C	21.1	4.105710	0.77096	.	.	ENSG00000167216	ENST00000356157;ENST00000245121;ENST00000454462	D;D	0.95035	-3.59;-3.59	5.83	5.83	0.93111	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.97256	0.9103	M	0.76574	2.34	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97357	0.9967	10	0.87932	D	0	-2.0E-4	20.1208	0.97960	0.0:1.0:0.0:0.0	.	171;403	F8WBL0;Q8IYT4	.;KATL2_HUMAN	L	403;331;171	ENSP00000348478:P403L;ENSP00000245121:P331L	ENSP00000245121:P331L	P	+	2	0	KATNAL2	42857827	1.000000	0.71417	0.989000	0.46669	0.262000	0.26303	7.431000	0.80335	2.758000	0.94735	0.655000	0.94253	CCG		0.428	KATNAL2-008	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000446324.2	NM_031303	
DCC	1630	broad.mit.edu	37	18	50848502	50848502	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:50848502A>G	ENST00000442544.2	+	14	2755	c.2139A>G	c.(2137-2139)gcA>gcG	p.A713A	DCC_ENST00000581580.1_Silent_p.A368A|DCC_ENST00000412726.1_Silent_p.A561A	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	713	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.A713A(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GGTATACTGCAGAGACTCCAG	0.403																																					p.A713A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A2139G	18						.						115.0	100.0	105.0					18																	50848502		2203	4300	6503	49102500	SO:0001819	synonymous_variant	1630	exon14			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.2139A>G	18.37:g.50848502A>G		Somatic		Capture	Illumina HiSeq	Phase_I	49102500	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																				0.403	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
CETN1	1068	broad.mit.edu	37	18	580586	580586	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:580586C>A	ENST00000327228.3	+	1	220	c.178C>A	c.(178-180)Ctg>Atg	p.L60M		NM_004066.1	NP_004057.1	Q12798	CETN1_HUMAN	centrin, EF-hand protein, 1	60	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cellular response to heat (GO:0034605)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|photoreceptor connecting cilium (GO:0032391)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|calcium ion binding (GO:0005509)|nucleic acid binding (GO:0003676)	p.L60M(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(2)	25						CATGAGAGCGCTGGGCTTCGA	0.547																																					p.L60M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C178A	18						.						82.0	62.0	69.0					18																	580586		2203	4300	6503	570586	SO:0001583	missense	1068	exon1			U03270	CCDS11820.1	18p11.32	2013-01-10			ENSG00000177143	ENSG00000177143		"""EF-hand domain containing"""	1866	protein-coding gene	gene with protein product		603187		CETN		8175926	Standard	NM_004066		Approved	CEN1	uc002kko.1	Q12798	OTTHUMG00000131471	ENST00000327228.3:c.178C>A	18.37:g.580586C>A	ENSP00000319052:p.Leu60Met	Somatic		Capture	Illumina HiSeq	Phase_I	570586	NM_004066	B2R536	Missense_Mutation	SNP	ENST00000327228.3	37	CCDS11820.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.040904	0.35989	.	.	ENSG00000177143	ENST00000327228	T	0.44482	0.92	5.2	2.48	0.30137	EF-hand-like domain (1);	0.000000	0.64402	D	0.000007	T	0.51483	0.1677	L	0.46885	1.475	0.58432	D	0.999997	D	0.71674	0.998	D	0.77557	0.99	T	0.48906	-0.8993	10	0.87932	D	0	.	7.1625	0.25672	0.0:0.654:0.0:0.346	.	60	Q12798	CETN1_HUMAN	M	60	ENSP00000319052:L60M	ENSP00000319052:L60M	L	+	1	2	CETN1	570586	0.557000	0.26546	0.472000	0.27241	0.114000	0.19823	1.208000	0.32345	0.465000	0.27167	0.655000	0.94253	CTG		0.547	CETN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254314.2	NM_004066	
POLI	11201	broad.mit.edu	37	18	51807102	51807102	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:51807102C>T	ENST00000579534.1	+	5	768	c.625C>T	c.(625-627)Cgg>Tgg	p.R209W	POLI_ENST00000579434.1_Missense_Mutation_p.R106W|POLI_ENST00000406285.3_Intron|POLI_ENST00000217800.5_Missense_Mutation_p.R83W	NM_007195.2	NP_009126.2	Q9UNA4	POLI_HUMAN	polymerase (DNA directed) iota	209	UmuC. {ECO:0000255|PROSITE- ProRule:PRU00216}.				DNA repair (GO:0006281)|DNA-dependent DNA replication (GO:0006261)	intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)	p.R184W(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(5)|ovary(3)|urinary_tract(1)	26				Colorectal(16;0.0234)|READ - Rectum adenocarcinoma(59;0.197)		AGCAGAGATGCGGGAAGCCAT	0.413								DNA polymerases (catalytic subunits)																													p.R209W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C625T	18						.						175.0	173.0	174.0					18																	51807102		2203	4300	6503	50061100	SO:0001583	missense	11201	exon5				CCDS11954.2	18q21.1	2012-05-18			ENSG00000101751	ENSG00000101751		"""DNA polymerases"""	9182	protein-coding gene	gene with protein product		605252		RAD3OB, RAD30B		17609217	Standard	NM_007195		Approved		uc002lfj.4	Q9UNA4	OTTHUMG00000132704	ENST00000579534.1:c.625C>T	18.37:g.51807102C>T	ENSP00000462664:p.Arg209Trp	Somatic		Capture	Illumina HiSeq	Phase_I	50061100	NM_007195	Q8N590|Q9H0S1|Q9NYH6	Missense_Mutation	SNP	ENST00000579534.1	37	CCDS11954.2	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256370	0.39896	.	.	ENSG00000101751	ENST00000217800	.	.	.	5.72	3.66	0.41972	DNA-repair protein, UmuC-like, N-terminal (1);DNA-repair protein, UmuC-like (1);	0.000000	0.85682	D	0.000000	D	0.86293	0.5898	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89414	0.3705	9	0.87932	D	0	-12.2842	11.161	0.48516	0.4562:0.5438:0.0:0.0	.	209	Q9UNA4	POLI_HUMAN	W	209	.	ENSP00000217800:R209W	R	+	1	2	POLI	50061100	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.595000	0.54016	1.542000	0.49330	0.650000	0.86243	CGG		0.413	POLI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256002.3	NM_007195	
TNFRSF11A	8792	broad.mit.edu	37	18	60052048	60052048	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:60052048C>T	ENST00000586569.1	+	10	1670	c.1632C>T	c.(1630-1632)ggC>ggT	p.G544G	TNFRSF11A_ENST00000269485.7_Silent_p.G227G	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	544					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				ACTTCAAGGGCGACATCATCG	0.652																																					p.G544G												.	.	0			c.C1632T	18						.						44.0	35.0	38.0					18																	60052048		2203	4300	6503	58203028	SO:0001819	synonymous_variant	8792	exon10			AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.1632C>T	18.37:g.60052048C>T		None		Capture	Illumina HiSeq	Phase_I	58203028	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	37	CCDS11980.1																																																																																				0.652	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
SERPINB3	6317	broad.mit.edu	37	18	61328349	61328349	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:61328349G>A	ENST00000283752.5	-	2	245	c.102C>T	c.(100-102)atC>atT	p.I34I	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Silent_p.I34I	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	34					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)	p.I34I(2)		breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATGCTGATGTGATGCTGATAG	0.418																																					p.I34I												.	.	2	Substitution - coding silent(2)	large_intestine(1)|endometrium(1)	c.C102T	18						.						226.0	195.0	206.0					18																	61328349		2203	4297	6500	59479329	SO:0001819	synonymous_variant	6318	exon2			U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.102C>T	18.37:g.61328349G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59479329	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Silent	SNP	ENST00000283752.5	37	CCDS11987.1																																																																																				0.418	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
SERPINB11	89778	broad.mit.edu	37	18	61388133	61388133	+	RNA	SNP	G	G	A	rs367834202		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:61388133G>A	ENST00000382749.5	+	0	932				SERPINB11_ENST00000536691.1_RNA|SERPINB11_ENST00000489748.1_RNA|SERPINB11_ENST00000538847.1_RNA|SERPINB11_ENST00000544088.1_RNA			Q96P15	SPB11_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 11 (gene/pseudogene)						negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P229P(1)		breast(1)|cervix(1)|kidney(1)|lung(3)	6		Esophageal squamous(42;0.129)				TAAAGGAGCCGCAGATGCAAG	0.343																																					p.P229P	Ovarian(27;496 784 5942 8975 23930)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G687A	18						.	G		0,3744		0,0,1872	59.0	59.0	59.0		687	-11.5	0.0	18		59	1,8229		0,1,4114	no	coding-synonymous	SERPINB11	NM_080475.2		0,1,5986	AA,AG,GG		0.0122,0.0,0.0084		229/393	61388133	1,11973	1872	4115	5987	59539113			89778	exon7					18q21.33	2014-02-18	2009-01-22		ENSG00000206072	ENSG00000206072		"""Serine (or cysteine) peptidase inhibitors"""	14221	protein-coding gene	gene with protein product		615682	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 11"", ""serpin peptidase inhibitor, clade B (ovalbumin), member 11"""			17562709, 24172014	Standard	XM_006722569		Approved	EPIPIN	uc002ljk.4	Q96P15	OTTHUMG00000060404		18.37:g.61388133G>A		Somatic		Capture	Illumina HiSeq	Phase_I	59539113	NM_080475	A8K9R0|Q5Q120|Q5Q121|Q5Q122|Q5Q123|Q6ISD3|Q96P13|Q96P14	Silent	SNP	ENST00000382749.5	37																																																																																					0.343	SERPINB11-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000207392.3	NM_080475	
SERPINB8	5271	broad.mit.edu	37	18	61654230	61654230	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:61654230T>C	ENST00000397985.2	+	7	1099	c.843T>C	c.(841-843)ccT>ccC	p.P281P	SERPINB8_ENST00000493661.1_Intron|SERPINB8_ENST00000353706.2_Silent_p.P281P|SERPINB8_ENST00000542677.1_Silent_p.P99P	NM_001276490.1	NP_001263419.1	P50452	SPB8_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 8	281					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.P281P(1)		breast(2)|kidney(1)|large_intestine(4)|lung(9)|skin(1)	17		Esophageal squamous(42;0.129)				ACTTGGAGCCTTTCCTTCGAA	0.423																																					p.P281P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T843C	18						.						111.0	106.0	108.0					18																	61654230		2203	4300	6503	59805210	SO:0001819	synonymous_variant	5271	exon7			L40377	CCDS11991.1, CCDS42442.1, CCDS62460.1	18q22.1	2014-02-18	2005-08-18		ENSG00000166401	ENSG00000166401		"""Serine (or cysteine) peptidase inhibitors"""	8952	protein-coding gene	gene with protein product	"""cytoplasmic antiproteinase 2"""	601697	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 8"""	PI8		8530382, 9268635, 24172014	Standard	NM_198833		Approved	CAP2	uc002lju.3	P50452	OTTHUMG00000060596	ENST00000397985.2:c.843T>C	18.37:g.61654230T>C		Somatic		Capture	Illumina HiSeq	Phase_I	59805210	NM_002640	B4DTW2|Q7Z2V6|Q8N178	Silent	SNP	ENST00000397985.2	37	CCDS11991.1																																																																																				0.423	SERPINB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134014.1	NM_001031848	
CDH7	1005	broad.mit.edu	37	18	63430217	63430217	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:63430217C>T	ENST00000397968.2	+	2	565	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	CDH7_ENST00000536984.2_Missense_Mutation_p.R47C|CDH7_ENST00000323011.3_Missense_Mutation_p.R47C	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	47					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R47C(1)		NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				CCGGACCAAGCGCAGCTGGGT	0.478																																					p.R47C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C139T	18						.						97.0	91.0	93.0					18																	63430217		2203	4300	6503	61581197	SO:0001583	missense	1005	exon2			AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.139C>T	18.37:g.63430217C>T	ENSP00000381058:p.Arg47Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61581197	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.067204	0.76301	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.00587	6.38;6.38;6.38	5.56	5.56	0.83823	.	0.117851	0.64402	D	0.000014	T	0.02727	0.0082	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.99	T	0.56733	-0.7930	10	0.87932	D	0	.	19.5386	0.95266	0.0:1.0:0.0:0.0	.	47;47	F5H5X9;Q9ULB5	.;CADH7_HUMAN	C	47	ENSP00000319166:R47C;ENSP00000443030:R47C;ENSP00000381058:R47C	ENSP00000319166:R47C	R	+	1	0	CDH7	61581197	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.142000	0.58044	2.610000	0.88304	0.650000	0.86243	CGC		0.478	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
CDH19	28513	broad.mit.edu	37	18	64202230	64202230	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:64202230T>A	ENST00000540086.1	-	8	1575	c.1329A>T	c.(1327-1329)acA>acT	p.T443T	CDH19_ENST00000262150.2_Silent_p.T443T	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	551	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.T443T(1)		NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TACATTTTTCTGTGGCTGTAA	0.333																																					p.T443T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1329T	18						.						137.0	130.0	132.0					18																	64202230		2202	4296	6498	62353210	SO:0001819	synonymous_variant	28513	exon8			AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.1329A>T	18.37:g.64202230T>A		Somatic		Capture	Illumina HiSeq	Phase_I	62353210	NM_021153	O15098	Silent	SNP	ENST00000540086.1	37	CCDS59325.1																																																																																				0.333	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153	
DSEL	92126	broad.mit.edu	37	18	65180529	65180529	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:65180529C>A	ENST00000310045.7	-	2	2820	c.1347G>T	c.(1345-1347)aaG>aaT	p.K449N	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	439					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)	p.K449N(1)		NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				GTCCCCCCAGCTTCCCAGATT	0.463																																					p.K449N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1347T	18						.						68.0	68.0	68.0					18																	65180529		2203	4300	6503	63331509	SO:0001583	missense	92126	exon2			AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.1347G>T	18.37:g.65180529C>A	ENSP00000310565:p.Lys449Asn	Somatic		Capture	Illumina HiSeq	Phase_I	63331509	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	10.94	1.494082	0.26774	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.19938	2.11	5.46	1.1	0.20463	.	0.064007	0.64402	U	0.000013	T	0.35799	0.0944	M	0.74258	2.255	0.37158	D	0.902474	D	0.71674	0.998	P	0.57425	0.82	T	0.38200	-0.9672	10	0.40728	T	0.16	-15.9043	10.9486	0.47315	0.0:0.6083:0.0:0.3917	.	439	Q8IZU8	DSEL_HUMAN	N	449;439	ENSP00000310565:K449N	ENSP00000310565:K449N	K	-	3	2	DSEL	63331509	0.994000	0.37717	0.989000	0.46669	0.242000	0.25591	0.399000	0.20916	0.281000	0.22233	-0.253000	0.11424	AAG		0.463	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
ARHGAP28	79822	broad.mit.edu	37	18	6882152	6882152	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:6882152T>G	ENST00000383472.4	+	11	1411	c.1307T>G	c.(1306-1308)cTt>cGt	p.L436R	ARHGAP28_ENST00000419673.2_Missense_Mutation_p.L277R|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.L272R|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.L277R|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.L436R|ARHGAP28_ENST00000532996.1_Missense_Mutation_p.L259R|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.L277R|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.L384R			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	436	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)	p.L436P(1)|p.L277P(1)|p.L436R(1)|p.L277R(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				CGTGAAGAACTTGATGCCAAG	0.378																																					p.L277R												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.T830G	18						.						151.0	146.0	148.0					18																	6882152		2203	4300	6503	6872152	SO:0001583	missense	79822	exon10			BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.1307T>G	18.37:g.6882152T>G	ENSP00000372964:p.Leu436Arg	Somatic		Capture	Illumina HiSeq	Phase_I	6872152	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	T	21.3	4.127366	0.77549	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87;1.87	5.68	5.68	0.88126	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.151215	0.44285	D	0.000463	T	0.60702	0.2289	M	0.91612	3.225	0.58432	D	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.997;0.999;0.998;0.997	T	0.70718	-0.4795	10	0.87932	D	0	.	15.9369	0.79717	0.0:0.0:0.0:1.0	.	436;268;277;384	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	R	436;384;277;272;277;277;268;259	ENSP00000382963:L436R;ENSP00000262227:L384R;ENSP00000392660:L277R;ENSP00000437262:L272R;ENSP00000313506:L277R;ENSP00000406907:L277R	ENSP00000262227:L384R	L	+	2	0	ARHGAP28	6872152	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.655000	0.74392	2.172000	0.68678	0.533000	0.62120	CTT		0.378	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
LAMA1	284217	broad.mit.edu	37	18	6950835	6950835	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:6950835T>G	ENST00000389658.3	-	58	8436	c.8343A>C	c.(8341-8343)aaA>aaC	p.K2781N		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2781	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)	p.K2781N(1)		NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTGTTCTGCCTTTGCCAAGGT	0.562																																					p.K2781N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A8343C	18						.						125.0	106.0	112.0					18																	6950835		2203	4300	6503	6940835	SO:0001583	missense	284217	exon58			X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.8343A>C	18.37:g.6950835T>G	ENSP00000374309:p.Lys2781Asn	Somatic		Capture	Illumina HiSeq	Phase_I	6940835	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.113159	0.56398	.	.	ENSG00000101680	ENST00000389658	T	0.75821	-0.97	5.5	0.26	0.15588	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.110120	0.64402	D	0.000014	T	0.75496	0.3857	M	0.65498	2.005	0.44006	D	0.996711	D;P	0.55605	0.972;0.457	P;B	0.54629	0.757;0.173	T	0.70357	-0.4894	10	0.22706	T	0.39	.	9.1614	0.37025	0.0:0.3098:0.0:0.6902	.	2781;111	P25391;B3KSD8	LAMA1_HUMAN;.	N	2781	ENSP00000374309:K2781N	ENSP00000374309:K2781N	K	-	3	2	LAMA1	6940835	1.000000	0.71417	0.942000	0.38095	0.501000	0.33797	0.769000	0.26604	0.056000	0.16144	0.459000	0.35465	AAA		0.562	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CD226	10666	broad.mit.edu	37	18	67563231	67563231	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:67563231C>A	ENST00000280200.4	-	4	701	c.433G>T	c.(433-435)Gga>Tga	p.G145*	CD226_ENST00000581982.1_5'UTR|CD226_ENST00000577287.1_5'UTR|CD226_ENST00000582621.1_Nonsense_Mutation_p.G145*	NM_006566.2	NP_006557.2	Q15762	CD226_HUMAN	CD226 molecule	145	Ig-like C2-type 2.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)|cytokine production (GO:0001816)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)	p.G145*(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(14)|prostate(1)|urinary_tract(1)	24		Esophageal squamous(42;0.129)				ACATTCTTTCCAGGTTCCGAA	0.458																																					p.G145X	NSCLC(184;838 2130 8673 21498 50749)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G433T	18						.						98.0	81.0	86.0					18																	67563231		2203	4300	6503	65714211	SO:0001587	stop_gained	10666	exon4			U56102	CCDS11997.1	18q22.3	2013-01-11	2006-03-28		ENSG00000150637	ENSG00000150637		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	16961	protein-coding gene	gene with protein product		605397	"""CD226 antigen"""			8673704	Standard	NM_006566		Approved	DNAM-1, DNAM1, PTA1, TLiSA1	uc002lkm.4	Q15762	OTTHUMG00000132809	ENST00000280200.4:c.433G>T	18.37:g.67563231C>A	ENSP00000280200:p.Gly145*	Somatic		Capture	Illumina HiSeq	Phase_I	65714211	NM_006566	B2R818	Nonsense_Mutation	SNP	ENST00000280200.4	37	CCDS11997.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374615	0.82573	.	.	ENSG00000150637	ENST00000280200	.	.	.	5.09	5.09	0.68999	.	0.357805	0.32301	N	0.006297	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.1723	0.65517	0.0:1.0:0.0:0.0	.	.	.	.	X	145	.	ENSP00000280200:G145X	G	-	1	0	CD226	65714211	0.995000	0.38212	0.573000	0.28510	0.013000	0.08279	3.447000	0.52936	2.804000	0.96469	0.650000	0.86243	GGA		0.458	CD226-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256226.3	NM_006566	
FAM69C	125704	broad.mit.edu	37	18	72103739	72103739	+	Missense_Mutation	SNP	C	C	A	rs76187278		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:72103739C>A	ENST00000343998.6	-	4	1265	c.1257G>T	c.(1255-1257)aaG>aaT	p.K419N	FAM69C_ENST00000400291.2_Missense_Mutation_p.K120N	NM_001044369.2	NP_001037834.2	Q0P6D2	FA69C_HUMAN	family with sequence similarity 69, member C	419						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring phosphorus-containing groups (GO:0016772)	p.K120N(2)		breast(1)|large_intestine(2)|ovary(2)	5						AGAGTGGCTACTTCTCTGCCT	0.547																																					p.K419N												.	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G1257T	18						.						28.0	32.0	31.0					18																	72103739		1943	4141	6084	70254719	SO:0001583	missense	125704	exon4			BC019628	CCDS42445.2	18q22.3	2012-08-03	2009-07-23	2009-07-23	ENSG00000187773	ENSG00000187773			31729	protein-coding gene	gene with protein product		614544	"""chromosome 18 open reading frame 51"""	C18orf51		21334309	Standard	NM_001044369		Approved		uc002llk.3	Q0P6D2	OTTHUMG00000156984	ENST00000343998.6:c.1257G>T	18.37:g.72103739C>A	ENSP00000344331:p.Lys419Asn	Somatic		Capture	Illumina HiSeq	Phase_I	70254719	NM_001044369		Missense_Mutation	SNP	ENST00000343998.6	37	CCDS42445.2	.	.	.	.	.	.	.	.	.	.	C	12.19	1.862932	0.32884	.	.	ENSG00000187773	ENST00000400291;ENST00000343998	.	.	.	4.95	0.704	0.18121	.	1.137480	0.06325	N	0.705187	T	0.42494	0.1205	L	0.57536	1.79	0.09310	N	1	B	0.15141	0.012	B	0.09377	0.004	T	0.39482	-0.9612	9	0.51188	T	0.08	.	5.4945	0.16795	0.1275:0.5409:0.2498:0.0817	.	419	Q0P6D2	FA69C_HUMAN	N	120;419	.	ENSP00000344331:K419N	K	-	3	2	FAM69C	70254719	0.106000	0.21978	0.002000	0.10522	0.049000	0.14656	0.316000	0.19469	0.573000	0.29400	0.558000	0.71614	AAG		0.547	FAM69C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346971.2	XM_058931	
TSHZ1	10194	broad.mit.edu	37	18	73000344	73000344	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:73000344C>T	ENST00000580243.1	+	2	3330	c.2982C>T	c.(2980-2982)ggC>ggT	p.G994G	TSHZ1_ENST00000322038.5_Silent_p.G949G			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	994					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G949G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		CACACTTGGGCTTCAGCCTGA	0.478																																					p.G949G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2847T	18						.						94.0	87.0	89.0					18																	73000344		2203	4300	6503	71129332	SO:0001819	synonymous_variant	10194	exon2			AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2982C>T	18.37:g.73000344C>T		Somatic		Capture	Illumina HiSeq	Phase_I	71129332	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																					0.478	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
ATP9B	374868	broad.mit.edu	37	18	77063609	77063609	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:77063609C>A	ENST00000426216.2	+	14	1434	c.1417C>A	c.(1417-1419)Ctc>Atc	p.L473I	ATP9B_ENST00000307671.7_Missense_Mutation_p.L473I	NM_198531.3	NP_940933.3	O43861	ATP9B_HUMAN	ATPase, class II, type 9B	473					establishment of protein localization to Golgi (GO:0072600)|phospholipid translocation (GO:0045332)	integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(3)|prostate(1)|skin(2)|stomach(1)	38		Esophageal squamous(42;0.018)|Melanoma(33;0.0964)|Prostate(75;0.171)		OV - Ovarian serous cystadenocarcinoma(15;1.44e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0405)		CCTAGGAACCCTCACCCAGAA	0.537																																					p.L473I												.	.	0			c.C1417A	18						.						76.0	70.0	72.0					18																	77063609		2203	4300	6503	75164597	SO:0001583	missense	374868	exon14			R51412	CCDS12014.1	18q23	2010-04-20	2007-09-19		ENSG00000166377	ENSG00000166377		"""ATPases / P-type"""	13541	protein-coding gene	gene with protein product		614446	"""ATPase, Class II, type 9B"""			9548971, 11015572	Standard	NM_198531		Approved	ATPIIB	uc002lmx.3	O43861	OTTHUMG00000132898	ENST00000426216.2:c.1417C>A	18.37:g.77063609C>A	ENSP00000398076:p.Leu473Ile	None		Capture	Illumina HiSeq	Phase_I	75164597	NM_198531	O60872|Q08AD8|Q08AD9	Missense_Mutation	SNP	ENST00000426216.2	37	CCDS12014.1	.	.	.	.	.	.	.	.	.	.	C	17.92	3.506299	0.64410	.	.	ENSG00000166377	ENST00000426216;ENST00000307671	D;D	0.87256	-2.23;-2.23	4.92	4.92	0.64577	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068994	0.64402	D	0.000013	D	0.95840	0.8646	H	0.97158	3.95	0.80722	D	1	D;D	0.64830	0.994;0.993	D;D	0.68765	0.96;0.933	D	0.97421	1.0009	10	0.87932	D	0	.	18.5172	0.90939	0.0:1.0:0.0:0.0	.	473;473	O43861;O43861-2	ATP9B_HUMAN;.	I	473	ENSP00000398076:L473I;ENSP00000304500:L473I	ENSP00000304500:L473I	L	+	1	0	ATP9B	75164597	1.000000	0.71417	0.996000	0.52242	0.079000	0.17450	5.441000	0.66569	2.432000	0.82394	0.655000	0.94253	CTC		0.537	ATP9B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256402.3	NM_198531	
CTDP1	9150	broad.mit.edu	37	18	77474531	77474531	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:77474531G>A	ENST00000299543.7	+	8	1218	c.1071G>A	c.(1069-1071)ccG>ccA	p.P357P	CTDP1_ENST00000075430.7_Silent_p.P357P	NM_001202504.1|NM_004715.4	NP_001189433.1|NP_004706.3	Q9Y5B0	CTDP1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) phosphatase, subunit 1	357					exit from mitosis (GO:0010458)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|protein dephosphorylation (GO:0006470)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	CTD phosphatase activity (GO:0008420)|DNA-directed RNA polymerase activity (GO:0003899)	p.P357P(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(2)|urinary_tract(1)	35		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;5.2e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0277)		AGCCATCTCCGCCCGTGAGAG	0.532																																					p.P357P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1071A	18						.						35.0	42.0	40.0					18																	77474531		2202	4296	6498	75575519	SO:0001819	synonymous_variant	9150	exon8			AF081287	CCDS12017.1, CCDS12018.1, CCDS74239.1	18q23	2014-09-17			ENSG00000060069	ENSG00000060069		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	2498	protein-coding gene	gene with protein product		604927				9405607, 9765293	Standard	NM_004715		Approved	FCP1	uc002lnh.2	Q9Y5B0	OTTHUMG00000132920	ENST00000299543.7:c.1071G>A	18.37:g.77474531G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75575519	NM_048368	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Silent	SNP	ENST00000299543.7	37	CCDS12017.1																																																																																				0.532	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715	
THOC1	9984	broad.mit.edu	37	18	265499	265499	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:265499delT	ENST00000261600.6	-	2	93	c.86delA	c.(85-87)aacfs	p.N29fs	RP11-705O1.8_ENST00000581677.1_lincRNA|THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	29					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)	p.N29fs*6(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				TGGCTTGATGTTTTTGTTGTT	0.333																																					p.N29fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.86delA	18						.						77.0	71.0	73.0					18																	265499		1826	4078	5904	255499	SO:0001589	frameshift_variant	9984	exon2			AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"""THO complex subunits"""	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.86delA	18.37:g.265499delT	ENSP00000261600:p.Asn29fs	Somatic		Capture	Illumina HiSeq	Phase_I	255499	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Frame_Shift_Del	DEL	ENST00000261600.6	37	CCDS45820.1																																																																																				0.333	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131	
PTPRM	5797	broad.mit.edu	37	18	8394504	8394504	+	Silent	SNP	C	C	T	rs377577785		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:8394504C>T	ENST00000332175.8	+	30	5237	c.4200C>T	c.(4198-4200)tgC>tgT	p.C1400C	PTPRM_ENST00000580170.1_Silent_p.C1413C|PTPRM_ENST00000400053.4_Silent_p.C1338C|PTPRM_ENST00000400060.4_Silent_p.C1414C|PTPRM_ENST00000444013.1_Silent_p.C1187C	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	1400	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.C1400C(1)		breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GGACGTTCTGCGCCATCAGCA	0.537																																					p.C1400C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4200T	18						.	C	,	0,4406		0,0,2203	77.0	57.0	64.0		4239,4200	-4.8	0.9	18		64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRM	NM_001105244.1,NM_002845.3	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	1413/1466,1400/1453	8394504	1,13005	2203	4300	6503	8384504	SO:0001819	synonymous_variant	5797	exon30			X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.4200C>T	18.37:g.8394504C>T		Somatic		Capture	Illumina HiSeq	Phase_I	8384504	NM_002845	A7MBN1|D3DUH8|J3QL11	Silent	SNP	ENST00000332175.8	37	CCDS11840.1																																																																																				0.537	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
MTCL1	23255	broad.mit.edu	37	18	8784753	8784753	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:8784753A>G	ENST00000306329.11	+	5	2723	c.2723A>G	c.(2722-2724)gAg>gGg	p.E908G	SOGA2_ENST00000359865.3_Missense_Mutation_p.E548G|SOGA2_ENST00000400050.3_Missense_Mutation_p.E548G|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000517570.1_Missense_Mutation_p.E548G														p.E548G(1)									CACCTCACAGAGTCCTCTAGC	0.602																																					p.E548G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1643G	18						.						89.0	89.0	89.0					18																	8784753		2203	4300	6503	8774753	SO:0001583	missense	23255	exon6																														ENST00000306329.11:c.2723A>G	18.37:g.8784753A>G	ENSP00000305027:p.Glu908Gly	Somatic		Capture	Illumina HiSeq	Phase_I	8774753	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	A	12.72	2.022157	0.35701	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050	T;T;T	0.54071	0.59;0.59;0.59	5.35	5.35	0.76521	.	0.000000	0.47455	D	0.000240	T	0.70037	0.3178	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.73347	-0.4011	10	0.72032	D	0.01	-30.8104	15.3364	0.74260	1.0:0.0:0.0:0.0	.	569;548	A8MQ54;Q9Y4B5-3	.;.	G	569;548;548;548	ENSP00000429556:E548G;ENSP00000352927:E548G;ENSP00000382924:E548G	ENSP00000305027:E569G	E	+	2	0	CCDC165	8774753	1.000000	0.71417	0.866000	0.34008	0.989000	0.77384	8.962000	0.93254	2.021000	0.59480	0.533000	0.62120	GAG		0.602	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1		
MTCL1	23255	broad.mit.edu	37	18	8793058	8793058	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:8793058C>T	ENST00000359865.3	+	8	2092	c.1950C>T	c.(1948-1950)ctC>ctT	p.L650L	SOGA2_ENST00000400050.3_Intron|SOGA2_ENST00000518815.1_Intron|SOGA2_ENST00000306285.7_5'UTR|SOGA2_ENST00000306329.11_Intron|SOGA2_ENST00000517570.1_Intron	NM_015210.3	NP_056025.2												p.L650L(1)									AGGGTCAGCTCGTGCAGGCGG	0.498																																					p.L650L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1950T	18						.						100.0	111.0	107.0					18																	8793058		2203	4300	6503	8783058	SO:0001819	synonymous_variant	23255	exon8																														ENST00000359865.3:c.1950C>T	18.37:g.8793058C>T		Somatic		Capture	Illumina HiSeq	Phase_I	8783058	NM_015210		Silent	SNP	ENST00000359865.3	37	CCDS11841.1																																																																																				0.498	SOGA2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254476.1		
CEP192	55125	broad.mit.edu	37	18	13049146	13049146	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:13049146delA	ENST00000325971.8	+	14	2161	c.568delA	c.(568-570)aaafs	p.K191fs	CEP192_ENST00000430049.2_Frame_Shift_Del_p.K312fs|CEP192_ENST00000506447.1_Frame_Shift_Del_p.K787fs			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	191					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)	p.T192fs*40(1)|p.T788fs*40(1)		NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GAAATACCTTAAAAAAACAGA	0.333																																					p.K786fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2356delA	18						.						59.0	58.0	58.0					18																	13049146		2203	4299	6502	13039146	SO:0001589	frameshift_variant	55125	exon16			AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.568delA	18.37:g.13049146delA	ENSP00000317156:p.Lys191fs	Somatic		Capture	Illumina HiSeq	Phase_I	13039146	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Frame_Shift_Del	DEL	ENST00000325971.8	37																																																																																					0.333	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
ESCO1	114799	broad.mit.edu	37	18	19154506	19154506	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:19154506delT	ENST00000269214.5	-	4	1236	c.299delA	c.(298-300)aagfs	p.K101fs		NM_052911.2	NP_443143.2	Q5FWF5	ESCO1_HUMAN	establishment of sister chromatid cohesion N-acetyltransferase 1	101					mitotic cell cycle (GO:0000278)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)|sister chromatid cohesion (GO:0007062)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|transferase activity, transferring acyl groups (GO:0016746)	p.K100fs*8(1)		breast(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(10)|prostate(3)|upper_aerodigestive_tract(1)	35						AGATAATTTCTTTTTTGTAGA	0.338																																					p.K100fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.299delA	18						.						143.0	148.0	146.0					18																	19154506		2203	4300	6503	17408504	SO:0001589	frameshift_variant	114799	exon4			AL832041	CCDS32800.1	18q11.2	2013-05-02	2013-05-02		ENSG00000141446	ENSG00000141446			24645	protein-coding gene	gene with protein product		609674	"""establishment of cohesion 1 homolog 1 (S. cerevisiae)"""			11572484, 14576321, 15958495	Standard	NM_052911		Approved	ESO1, EFO1, KIAA1911	uc002kth.1	Q5FWF5		ENST00000269214.5:c.299delA	18.37:g.19154506delT	ENSP00000269214:p.Lys101fs	Somatic		Capture	Illumina HiSeq	Phase_I	17408504	NM_052911	B0YJ11|B0YJ12|Q69YG4|Q69YS3|Q6IMD7|Q8N3Z5|Q8NBG2|Q96PX7	Frame_Shift_Del	DEL	ENST00000269214.5	37	CCDS32800.1																																																																																				0.338	ESCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443942.1	NM_052911	
ZNF271	10778	broad.mit.edu	37	18	32887117	32887117	+	RNA	SNP	G	G	A	rs76452317	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:32887117G>A	ENST00000399070.3	+	0	1511					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A177T(1)		large_intestine(3)|lung(9)	12						AGCTTTAGTCGCCGTTCAGAT	0.393													G|||	11	0.00219649	0.0008	0.0	5008	,	,		21955	0.0099		0.0	False		,,,				2504	0.0				.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	18						.	G		0,4406		0,0,2203	96.0	99.0	98.0			0.5	0.8	18	dbSNP_131	98	1,8599	1.2+/-3.3	0,1,4299	no	intergenic				0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			32887117	1,13005	2203	4300	6503	31141115			10778	.			X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32887117G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31141115	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	Missense_Mutation	SNP	ENST00000399070.3	37																																																																																					0.393	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
PARD6G	84552	broad.mit.edu	37	18	77918086	77918086	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr18:77918086C>T	ENST00000353265.3	-	3	896	c.699G>A	c.(697-699)acG>acA	p.T233T	AC139100.2_ENST00000585422.1_Intron|AC139100.2_ENST00000586421.1_Intron|AC139100.2_ENST00000587254.1_Intron|AC139100.2_ENST00000589574.1_Intron	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	233	Interaction with PARD3 and CDC42. {ECO:0000250}.|PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)		p.T233T(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		TCATCATGTCCGTGACCTGGT	0.672																																					p.T233T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G699A	18						.						99.0	69.0	79.0					18																	77918086		2203	4300	6503	76019077	SO:0001819	synonymous_variant	84552	exon3				CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"""par-6 (partitioning defective 6, C.elegans) homolog gamma"", ""par-6 partitioning defective 6 homolog gamma (C. elegans)"""			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.699G>A	18.37:g.77918086C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76019077	NM_032510	A8QM57	Silent	SNP	ENST00000353265.3	37	CCDS12022.1																																																																																				0.672	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510	
HAPLN4	404037	broad.mit.edu	37	19	19371885	19371886	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:19371885_19371886insC	ENST00000291481.7	-	3	283_284	c.220_221insG	c.(220-222)gcafs	p.A74fs	AC138430.4_ENST00000586064.2_RNA	NM_023002.2	NP_075378.1	Q86UW8	HPLN4_HUMAN	hyaluronan and proteoglycan link protein 4	74	Ig-like C2-type.				cell adhesion (GO:0007155)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)	p.A74fs*44(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(1)	16			Epithelial(12;0.00575)		Hyaluronan(DB08818)	GTGGGCGGCTGCCTCATAGTGG	0.663																																					p.A74fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.221_222insG	19						.																																			19232886	SO:0001589	frameshift_variant	404037	exon3			AB107883	CCDS12398.1	19p13.1	2013-01-11						"""Immunoglobulin superfamily / V-set domain containing"""	31357	protein-coding gene	gene with protein product	"""brain link protein 2"""					12663660	Standard	NM_023002		Approved	BRAL2, KIAA1926	uc002nmb.3	Q86UW8		ENST00000291481.7:c.221dupG	19.37:g.19371887_19371887dupC	ENSP00000291481:p.Ala74fs	Somatic		Capture	Illumina HiSeq	Phase_I	19232885	NM_023002	A5PKW5|Q96PW2	Frame_Shift_Ins	INS	ENST00000291481.7	37	CCDS12398.1																																																																																				0.663	HAPLN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460117.2	NM_023002	
DMKN	93099	broad.mit.edu	37	19	36004319	36004320	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:36004319_36004320insC	ENST00000339686.3	-	1	234_235	c.58_59insG	c.(58-60)gagfs	p.E20fs	DMKN_ENST00000419602.1_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000451297.2_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000424570.2_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000429837.1_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000418261.1_Frame_Shift_Ins_p.E20fs|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000440396.1_Frame_Shift_Ins_p.E20fs	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	20	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.E20fs*47(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGGGCCAGCCTCCCCACTGCCC	0.658																																					p.E20fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.59_60insG	19						.																																			40696160	SO:0001589	frameshift_variant	93099	exon1			BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.59dupG	19.37:g.36004323_36004323dupC	ENSP00000342012:p.Glu20fs	Somatic		Capture	Illumina HiSeq	Phase_I	40696159	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Frame_Shift_Ins	INS	ENST00000339686.3	37	CCDS12463.1																																																																																				0.658	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
ARHGAP35	2909	broad.mit.edu	37	19	47424840	47424841	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:47424840_47424841insC	ENST00000404338.3	+	1	2908_2909	c.2908_2909insC	c.(2908-2910)tccfs	p.S970fs		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	970					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)	p.R972fs*40(1)									GGTGTTTAACTCCCCCCGGGCA	0.47																																					p.S970fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2908_2909insC	19						.																																			52116681	SO:0001589	frameshift_variant	2909	exon1			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.2914dupC	19.37:g.47424846_47424846dupC	ENSP00000385720:p.Ser970fs	Somatic		Capture	Illumina HiSeq	Phase_I	52116680	NM_004491	A7E2A4|Q14452|Q9C0E1	Frame_Shift_Ins	INS	ENST00000404338.3	37	CCDS46127.1																																																																																				0.470	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
TPRX1	284355	broad.mit.edu	37	19	48305112	48305113	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:48305112_48305113insT	ENST00000322175.3	-	2	1310_1311	c.1155_1156insA	c.(1153-1158)aaacacfs	p.H386fs	TPRX1_ENST00000543508.1_Frame_Shift_Ins_p.H376fs|TPRX1_ENST00000535759.1_Frame_Shift_Ins_p.H483fs	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	386						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.H386fs*15(1)		endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		GACCCTGAGTGTTTTTTGCCCA	0.53																																					p.H386fs	Esophageal Squamous(123;175 2281 3051 32395)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1156_1157insA	19						.																																			52996925	SO:0001589	frameshift_variant	284355	exon2				CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.1156dupA	19.37:g.48305118_48305118dupT	ENSP00000323455:p.His386fs	Somatic		Capture	Illumina HiSeq	Phase_I	52996924	NM_198479	A5D8Y3|B2RPL5	Frame_Shift_Ins	INS	ENST00000322175.3	37	CCDS33066.1																																																																																				0.530	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
ZNF677	342926	broad.mit.edu	37	19	53740289	53740290	+	Frame_Shift_Ins	INS	-	-	T	rs143950468		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:53740289_53740290insT	ENST00000598513.1	-	5	1840_1841	c.1690_1691insA	c.(1690-1692)agtfs	p.S564fs	ZNF677_ENST00000333952.4_Frame_Shift_Ins_p.S564fs	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	564					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S564fs*3(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(13)|lung(6)|ovary(1)|pancreas(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(134;0.00352)		TCTATTATAACTTTTTTGATGA	0.297																																					p.S564fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1691_1692insA	19						.																																			58432102	SO:0001589	frameshift_variant	342926	exon5			BC050038	CCDS12861.1	19q13.42	2013-01-08				ENSG00000197928		"""Zinc fingers, C2H2-type"", ""-"""	28730	protein-coding gene	gene with protein product	"""hypothetical protein MGC48625"""					12477932	Standard	NM_182609		Approved	MGC48625	uc002qbg.1	Q86XU0		ENST00000598513.1:c.1691dupA	19.37:g.53740295_53740295dupT	ENSP00000469391:p.Ser564fs	Somatic		Capture	Illumina HiSeq	Phase_I	58432101	NM_182609		Frame_Shift_Ins	INS	ENST00000598513.1	37	CCDS12861.1																																																																																				0.297	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609	
RAVER1	125950	broad.mit.edu	37	19	10439472	10439472	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:10439472C>T	ENST00000293677.6	-	3	734	c.653G>A	c.(652-654)cGc>cAc	p.R218H		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	201						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.R201H(1)		breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	18			OV - Ovarian serous cystadenocarcinoma(20;1.81e-09)|Epithelial(33;3.65e-06)|all cancers(31;8.35e-06)			GTAGAGGGTGCGTGGTCCCAG	0.637																																					p.R218H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G653A	19						.						28.0	35.0	32.0					19																	10439472		2173	4254	6427	10300472	SO:0001583	missense	125950	exon3				CCDS45960.1	19p13.2	2013-02-12				ENSG00000161847		"""RNA binding motif (RRM) containing"""	30296	protein-coding gene	gene with protein product		609950				11853319, 11724819	Standard	NM_133452		Approved	KIAA1978	uc002moa.3	Q8IY67		ENST00000293677.6:c.653G>A	19.37:g.10439472C>T	ENSP00000293677:p.Arg218His	Somatic		Capture	Illumina HiSeq	Phase_I	10300472	NM_133452	A6NMU4|Q8IY60|Q8TF24	Missense_Mutation	SNP	ENST00000293677.6	37	CCDS45960.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.441782	0.83993	.	.	ENSG00000161847	ENST00000293677;ENST00000331131	T	0.20069	2.1	5.07	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.48714	0.1515	M	0.86805	2.84	0.50039	D	0.999845	D	0.89917	1.0	D	0.77557	0.99	T	0.53837	-0.8382	10	0.52906	T	0.07	-32.2627	11.9902	0.53171	0.1737:0.8263:0.0:0.0	.	218	E9PAU2	.	H	218;201	ENSP00000293677:R218H	ENSP00000293677:R218H	R	-	2	0	RAVER1	10300472	1.000000	0.71417	0.998000	0.56505	0.977000	0.68977	3.019000	0.49635	2.357000	0.79964	0.650000	0.86243	CGC		0.637	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452	
SLC44A2	57153	broad.mit.edu	37	19	10736932	10736932	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:10736932C>T	ENST00000335757.5	+	2	417	c.41C>T	c.(40-42)aCg>aTg	p.T14M	SLC44A2_ENST00000407327.4_Missense_Mutation_p.T12M|SLC44A2_ENST00000586078.1_Missense_Mutation_p.T14M			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	14					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)	p.T14M(1)		NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	CTTTCAGGAACGCCACAGAAG	0.512																																					p.T14M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C41T	19						.						107.0	108.0	108.0					19																	10736932		2203	4300	6503	10597932	SO:0001583	missense	57153	exon2			AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000335757.5:c.41C>T	19.37:g.10736932C>T	ENSP00000336888:p.Thr14Met	Somatic		Capture	Illumina HiSeq	Phase_I	10597932	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	37	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	C	18.91	3.723080	0.68959	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.17054	2.3;2.3	4.09	4.09	0.47781	.	0.129020	0.52532	D	0.000080	T	0.27629	0.0679	L	0.54323	1.7	0.31304	N	0.687957	B;D	0.60160	0.274;0.987	B;P	0.55667	0.043;0.781	T	0.15867	-1.0422	10	0.59425	D	0.04	.	10.6041	0.45384	0.1927:0.8073:0.0:0.0	.	14;12	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	M	12;14;14	ENSP00000385135:T12M;ENSP00000336888:T14M	ENSP00000336888:T14M	T	+	2	0	SLC44A2	10597932	1.000000	0.71417	0.742000	0.31022	0.732000	0.41865	5.318000	0.65829	2.132000	0.65825	0.462000	0.41574	ACG		0.512	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1		
ZNF799	90576	broad.mit.edu	37	19	12502429	12502429	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:12502429G>T	ENST00000430385.3	-	4	983	c.783C>A	c.(781-783)gcC>gcA	p.A261A	ZNF799_ENST00000419318.1_Silent_p.A229A|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	261					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A48A(1)|p.A261A(1)		breast(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(2)|prostate(2)|skin(2)	19						AATCAGGGAAGGCTTTAGAAC	0.383																																					p.A261A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C783A	19						.						99.0	105.0	103.0					19																	12502429		2203	4299	6502	12363429	SO:0001819	synonymous_variant	90576	exon4			BC009517	CCDS45989.1	19p13.2	2013-01-08			ENSG00000196466	ENSG00000196466		"""Zinc fingers, C2H2-type"", ""-"""	28071	protein-coding gene	gene with protein product			"""zinc finger protein 842"""	ZNF842			Standard	NM_001080821		Approved	HIT-40, MGC71805	uc002mts.4	Q96GE5	OTTHUMG00000156408	ENST00000430385.3:c.783C>A	19.37:g.12502429G>T		Somatic		Capture	Illumina HiSeq	Phase_I	12363429	NM_001080821		Silent	SNP	ENST00000430385.3	37	CCDS45989.1																																																																																				0.383	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
CACNA1A	773	broad.mit.edu	37	19	13445249	13445249	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:13445249G>A	ENST00000360228.5	-	8	1140	c.1141C>T	c.(1141-1143)Cgg>Tgg	p.R381W	CACNA1A_ENST00000573710.2_Missense_Mutation_p.R381W	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	381					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)	p.R381W(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTTGTTGCCGCCTCAGCTTC	0.527																																					p.R381W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1141T	19						.						103.0	100.0	101.0					19																	13445249		1893	4114	6007	13306249	SO:0001583	missense	773	exon8			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.1141C>T	19.37:g.13445249G>A	ENSP00000353362:p.Arg381Trp	Somatic		Capture	Illumina HiSeq	Phase_I	13306249	NM_001174080	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	.	.	.	.	.	.	.	.	.	.	G	15.10	2.732106	0.48939	.	.	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.93366	-3.21	5.13	2.91	0.33838	.	0.153352	0.41823	D	0.000804	D	0.96962	0.9008	M	0.91459	3.21	0.45183	D	0.998192	D;D	0.89917	1.0;1.0	D;D	0.87578	0.993;0.998	D	0.96887	0.9650	10	0.87932	D	0	.	12.5032	0.55968	0.0:0.0:0.423:0.5769	.	381;381	O00555;Q9NS88	CAC1A_HUMAN;.	W	381	ENSP00000353362:R381W	ENSP00000317661:R381W	R	-	1	2	CACNA1A	13306249	0.416000	0.25424	1.000000	0.80357	0.995000	0.86356	0.395000	0.20850	0.596000	0.29794	0.655000	0.94253	CGG		0.527	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
ZSWIM4	65249	broad.mit.edu	37	19	13930237	13930237	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:13930237G>A	ENST00000254323.2	+	9	1829	c.1640G>A	c.(1639-1641)cGc>cAc	p.R547H	ZSWIM4_ENST00000440752.2_Missense_Mutation_p.R381H	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	547							zinc ion binding (GO:0008270)	p.R547H(1)		central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			ACCTGTGCCCGCTACCTGTTC	0.642																																					p.R547H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1640A	19						.						64.0	40.0	48.0					19																	13930237		2203	4300	6503	13791237	SO:0001583	missense	65249	exon9			AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.1640G>A	19.37:g.13930237G>A	ENSP00000254323:p.Arg547His	Somatic		Capture	Illumina HiSeq	Phase_I	13791237	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.764574	0.69878	.	.	ENSG00000132003	ENST00000254323;ENST00000440752	T;T	0.49139	0.79;0.8	3.65	2.61	0.31194	.	0.409242	0.19587	N	0.110712	T	0.46054	0.1373	L	0.43152	1.355	0.29026	N	0.88603	D;P	0.64830	0.994;0.881	P;P	0.51582	0.674;0.576	T	0.37686	-0.9695	10	0.44086	T	0.13	-10.3787	8.6661	0.34121	0.1164:0.0:0.8836:0.0	.	381;547	E7ERX2;Q9H7M6	.;ZSWM4_HUMAN	H	547;381	ENSP00000254323:R547H;ENSP00000405278:R381H	ENSP00000254323:R547H	R	+	2	0	ZSWIM4	13791237	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.554000	0.53720	0.771000	0.33359	0.485000	0.47835	CGC		0.642	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
OR10H2	26538	broad.mit.edu	37	19	15838993	15838993	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:15838993C>T	ENST00000305899.3	+	1	160	c.140C>T	c.(139-141)gCc>gTc	p.A47V		NM_013939.2	NP_039227.1	O60403	O10H2_HUMAN	olfactory receptor, family 10, subfamily H, member 2	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A47V(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|skin(3)|stomach(1)	27	all_hematologic(1;0.0517)|Acute lymphoblastic leukemia(2;0.074)					CTCATCATGGCCACCGTCTGG	0.612																																					p.A47V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C140T	19						.						198.0	163.0	175.0					19																	15838993		2203	4296	6499	15699993	SO:0001583	missense	26538	exon1			AC004597	CCDS12333.1	19p13.1	2012-08-09				ENSG00000171942		"""GPCR / Class A : Olfactory receptors"""	8173	protein-coding gene	gene with protein product							Standard	NM_013939		Approved		uc002nbm.2	O60403		ENST00000305899.3:c.140C>T	19.37:g.15838993C>T	ENSP00000306095:p.Ala47Val	Somatic		Capture	Illumina HiSeq	Phase_I	15699993	NM_013939	Q6IFQ1|Q96R58	Missense_Mutation	SNP	ENST00000305899.3	37	CCDS12333.1	.	.	.	.	.	.	.	.	.	.	.	9.647	1.140608	0.21205	.	.	ENSG00000171942	ENST00000305899	T	0.01025	5.43	2.88	1.72	0.24424	GPCR, rhodopsin-like superfamily (1);	0.529356	0.16060	N	0.231538	T	0.00580	0.0019	N	0.20357	0.565	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.49588	-0.8924	10	0.05721	T	0.95	.	3.6238	0.08105	0.0:0.6392:0.0:0.3608	.	47	O60403	O10H2_HUMAN	V	47	ENSP00000306095:A47V	ENSP00000306095:A47V	A	+	2	0	OR10H2	15699993	0.000000	0.05858	0.991000	0.47740	0.735000	0.41995	-0.135000	0.10420	1.446000	0.47643	0.537000	0.68136	GCC		0.612	OR10H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460917.1		
SLC35E1	79939	broad.mit.edu	37	19	16677437	16677437	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:16677437C>A	ENST00000595753.1	-	4	679	c.662G>T	c.(661-663)cGg>cTg	p.R221L	CTD-3222D19.10_ENST00000597851.1_RNA|SLC35E1_ENST00000431408.1_Missense_Mutation_p.R65L|CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.G415C	NM_024881.4	NP_079157.3	Q96K37	S35E1_HUMAN	solute carrier family 35, member E1	221					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.R77L(1)		central_nervous_system(1)|endometrium(3)|large_intestine(7)|liver(1)|lung(2)|ovary(1)	15						GTTGAGCAGCCGGAGATGGTG	0.537																																					p.R221L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G662T	19						.						92.0	90.0	90.0					19																	16677437		2203	4300	6503	16538437	SO:0001583	missense	79939	exon4			AK024313	CCDS12346.2	19p13.11	2013-05-22			ENSG00000127526	ENSG00000127526		"""Solute carriers"""	20803	protein-coding gene	gene with protein product							Standard	NM_024881		Approved	FLJ14251	uc010xph.2	Q96K37	OTTHUMG00000152575	ENST00000595753.1:c.662G>T	19.37:g.16677437C>A	ENSP00000470652:p.Arg221Leu	Somatic		Capture	Illumina HiSeq	Phase_I	16538437	NM_024881	Q8NBQ2|Q96JV7	Missense_Mutation	SNP	ENST00000595753.1	37	CCDS12346.2	.	.	.	.	.	.	.	.	.	.	C	21.6	4.175859	0.78564	.	.	ENSG00000127526	ENST00000409648;ENST00000436553;ENST00000431408	T;T	0.63580	-0.05;-0.05	5.4	5.4	0.78164	Domain of unknown function DUF250 (1);	0.055438	0.64402	D	0.000001	T	0.74543	0.3730	M	0.76574	2.34	0.80722	D	1	P;P	0.52577	0.954;0.889	P;P	0.53809	0.735;0.591	T	0.77624	-0.2518	10	0.62326	D	0.03	-38.5899	18.1728	0.89752	0.0:1.0:0.0:0.0	.	221;77	Q96K37;Q9H7U6	S35E1_HUMAN;.	L	221;155;65	ENSP00000400435:R155L;ENSP00000397670:R65L	ENSP00000387152:R221L	R	-	2	0	SLC35E1	16538437	1.000000	0.71417	0.983000	0.44433	0.657000	0.38888	5.551000	0.67274	2.527000	0.85204	0.655000	0.94253	CGG		0.537	SLC35E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326809.2	NM_024881	
USHBP1	83878	broad.mit.edu	37	19	17367291	17367291	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:17367291C>T	ENST00000252597.3	-	9	1632	c.1459G>A	c.(1459-1461)Gtg>Atg	p.V487M	USHBP1_ENST00000431146.2_Missense_Mutation_p.V423M|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1									p.V487M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						CTTGCGGCCACCAGGTCCTGC	0.577																																					p.V487M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1459A	19						.						80.0	83.0	82.0					19																	17367291		2203	4300	6503	17228291	SO:0001583	missense	83878	exon9			AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1459G>A	19.37:g.17367291C>T	ENSP00000252597:p.Val487Met	Somatic		Capture	Illumina HiSeq	Phase_I	17228291	NM_031941		Missense_Mutation	SNP	ENST00000252597.3	37	CCDS12353.1	.	.	.	.	.	.	.	.	.	.	C	1.084	-0.666174	0.03428	.	.	ENSG00000130307	ENST00000252597;ENST00000431146	T;T	0.15487	2.42;2.42	5.01	0.183	0.15082	.	0.913052	0.09342	N	0.815393	T	0.07818	0.0196	N	0.08118	0	0.09310	N	0.999999	B;B	0.29716	0.003;0.255	B;B	0.31290	0.01;0.127	T	0.36040	-0.9764	10	0.41790	T	0.15	-1.1408	3.0292	0.06101	0.3193:0.4372:0.155:0.0886	.	423;487	B4DUE8;Q8N6Y0	.;USBP1_HUMAN	M	487;423	ENSP00000252597:V487M;ENSP00000407902:V423M	ENSP00000252597:V487M	V	-	1	0	USHBP1	17228291	0.192000	0.23301	0.018000	0.16275	0.057000	0.15508	0.417000	0.21214	-0.099000	0.12263	-0.152000	0.13540	GTG		0.577	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
BABAM1	29086	broad.mit.edu	37	19	17387698	17387698	+	Missense_Mutation	SNP	G	G	A	rs199960321		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:17387698G>A	ENST00000359435.4	+	8	959	c.766G>A	c.(766-768)Gag>Aag	p.E256K	BABAM1_ENST00000447614.2_Missense_Mutation_p.E256K|BABAM1_ENST00000595632.1_Missense_Mutation_p.E181K|BABAM1_ENST00000601043.1_Missense_Mutation_p.E256K|CTD-2278I10.6_ENST00000596542.1_Missense_Mutation_p.E178K|BABAM1_ENST00000598188.1_Missense_Mutation_p.E256K	NM_001033549.1	NP_001028721.1	Q9NWV8	BABA1_HUMAN	BRISC and BRCA1 A complex member 1	256	VWFA-like.				chromatin modification (GO:0016568)|double-strand break repair (GO:0006302)|G2 DNA damage checkpoint (GO:0031572)|positive regulation of DNA repair (GO:0045739)|protein K63-linked deubiquitination (GO:0070536)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRISC complex (GO:0070552)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.E256K(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5						TGAGGAGAAGGAGGAGGAGAT	0.532																																					p.E256K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G766A	19						.	G	LYS/GLU,LYS/GLU	0,4132		0,0,2066	64.0	60.0	61.0		766,766	4.4	1.0	19		61	1,8417		0,1,4208	no	missense,missense	BABAM1	NM_001033549.1,NM_014173.2	56,56	0,1,6274	AA,AG,GG		0.0119,0.0,0.0080	benign,benign	256/330,256/330	17387698	1,12549	2066	4209	6275	17248698	SO:0001583	missense	29086	exon8			AK000578	CCDS46012.1, CCDS74310.1	19p13.11	2011-02-21	2011-02-21	2011-01-31	ENSG00000105393	ENSG00000105393			25008	protein-coding gene	gene with protein product	"""Mediator of Rap80 Interactions and Targeting 40 kD"", ""new component of the BRCA1 A complex"""	612766	"""chromosome 19 open reading frame 62"""	C19orf62		11042152	Standard	NM_001288756		Approved	FLJ20571, HSPC142, NBA1, MERIT40	uc002nfv.3	Q9NWV8		ENST00000359435.4:c.766G>A	19.37:g.17387698G>A	ENSP00000352408:p.Glu256Lys	Somatic		Capture	Illumina HiSeq	Phase_I	17248698	NM_001033549	A8MQT0|B4DRY9|B4DVR1|Q6FIA0|Q9P018	Missense_Mutation	SNP	ENST00000359435.4	37	CCDS46012.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475479	0.26511	0.0	1.19E-4	ENSG00000105393	ENST00000359435;ENST00000447614;ENST00000300965	.	.	.	5.4	4.36	0.52297	.	0.148800	0.45126	D	0.000387	T	0.48696	0.1514	L	0.36672	1.1	0.80722	D	1	B	0.28291	0.206	B	0.28011	0.085	T	0.49062	-0.8978	9	0.52906	T	0.07	-25.3098	13.8865	0.63712	0.0:0.1541:0.8459:0.0	.	256	Q9NWV8	BABA1_HUMAN	K	256;256;178	.	ENSP00000300965:E178K	E	+	1	0	BABAM1	17248698	1.000000	0.71417	0.998000	0.56505	0.309000	0.27889	4.621000	0.61233	1.268000	0.44264	-0.189000	0.12847	GAG		0.532	BABAM1-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463471.1	NM_014173	
JAK3	3718	broad.mit.edu	37	19	17947972	17947972	+	Silent	SNP	G	G	A	rs200582253		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:17947972G>A	ENST00000527670.1	-	12	1781	c.1752C>T	c.(1750-1752)ctC>ctT	p.L584L	JAK3_ENST00000526008.1_5'Flank|JAK3_ENST00000534444.1_Silent_p.L584L|JAK3_ENST00000458235.1_Silent_p.L584L			P52333	JAK3_HUMAN	Janus kinase 3	584	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.L584L(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGAGCAGCACGAGATGCCGGT	0.607		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""								G|||	1	0.000199681	0.0	0.0	5008	,	,		8706	0.0		0.001	False		,,,				2504	0.0				p.L584L			Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1752T	19						.																																			17808972	SO:0001819	synonymous_variant	3718	exon13			U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.1752C>T	19.37:g.17947972G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17808972	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Silent	SNP	ENST00000527670.1	37	CCDS12366.1																																																																																				0.607	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
BTBD2	55643	broad.mit.edu	37	19	1990031	1990031	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:1990031C>T	ENST00000255608.4	-	5	976	c.960G>A	c.(958-960)ccG>ccA	p.P320P	AC005306.3_ENST00000587498.1_RNA|AC005306.3_ENST00000588480.1_RNA	NM_017797.3	NP_060267.2	Q9BX70	BTBD2_HUMAN	BTB (POZ) domain containing 2	320						cytoplasmic mRNA processing body (GO:0000932)		p.P320P(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)	12		Ovarian(11;2.11e-07)|Hepatocellular(1079;0.137)		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)		TGGTCATGAGCGGGAAGCGAA	0.647																																					p.P320P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G960A	19						.						52.0	48.0	49.0					19																	1990031		2203	4300	6503	1941031	SO:0001819	synonymous_variant	55643	exon5			AF355797	CCDS12078.1	19p13.3	2013-10-02			ENSG00000133243	ENSG00000133243		"""BTB/POZ domain containing"""	15504	protein-coding gene	gene with protein product		608531				11179693	Standard	XM_005259593		Approved		uc002lup.1	Q9BX70	OTTHUMG00000180017	ENST00000255608.4:c.960G>A	19.37:g.1990031C>T		Somatic		Capture	Illumina HiSeq	Phase_I	1941031	NM_017797	O60418|O75248|Q4VBZ1|Q6IAC5|Q7Z5W0|Q96SX8|Q9NPS1|Q9NX81	Silent	SNP	ENST00000255608.4	37	CCDS12078.1																																																																																				0.647	BTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449300.2		
FKBP8	23770	broad.mit.edu	37	19	18649032	18649032	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:18649032C>T	ENST00000596558.2	-	5	872	c.763G>A	c.(763-765)Gcc>Acc	p.A255T	FKBP8_ENST00000608443.1_Missense_Mutation_p.A256T|FKBP8_ENST00000610101.1_Intron|FKBP8_ENST00000597960.3_Missense_Mutation_p.A256T|AC005387.2_ENST00000596596.1_RNA|FKBP8_ENST00000453489.2_Missense_Mutation_p.A284T|FKBP8_ENST00000222308.4_Missense_Mutation_p.A255T			Q14318	FKBP8_HUMAN	FK506 binding protein 8, 38kDa	255					apoptotic process (GO:0006915)|camera-type eye development (GO:0043010)|cell fate specification (GO:0001708)|chaperone-mediated protein folding (GO:0061077)|dorsal/ventral neural tube patterning (GO:0021904)|intracellular signal transduction (GO:0035556)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|positive regulation of BMP signaling pathway (GO:0030513)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of gene expression (GO:0010468)|smoothened signaling pathway (GO:0007224)|viral process (GO:0016032)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	FK506 binding (GO:0005528)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.A256T(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	15						TCACCTTTGGCGCTGGAGGTG	0.622																																					p.A256T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G766A	19						.						69.0	64.0	65.0					19																	18649032		2203	4300	6503	18510032	SO:0001583	missense	23770	exon5			L37033	CCDS32961.1	19p12	2013-01-10	2002-08-29		ENSG00000105701	ENSG00000105701		"""Tetratricopeptide (TTC) repeat domain containing"""	3724	protein-coding gene	gene with protein product	"""FK506-binding protein 8 (38kD)"""	604840	"""FK506-binding protein 8 (38kD)"""			7543869	Standard	NM_012181		Approved	FKBP38, FKBPr38	uc002njj.1	Q14318		ENST00000596558.2:c.763G>A	19.37:g.18649032C>T	ENSP00000472302:p.Ala255Thr	Somatic		Capture	Illumina HiSeq	Phase_I	18510032	NM_012181	C8C9T5|Q53GU3|Q7Z349|Q86YK6	Missense_Mutation	SNP	ENST00000596558.2	37		.	.	.	.	.	.	.	.	.	.	C	11.83	1.756637	0.31137	.	.	ENSG00000105701	ENST00000222308;ENST00000453489	T;T	0.74209	-0.82;-0.82	3.9	1.49	0.22878	Elongated TPR repeat-containing domain (1);	0.121632	0.56097	N	0.000022	T	0.42675	0.1213	N	0.14661	0.345	0.80722	D	1	P;B;B;P	0.43633	0.813;0.207;0.16;0.632	B;B;B;B	0.31101	0.124;0.031;0.026;0.104	T	0.34900	-0.9810	10	0.12103	T	0.63	-8.8339	5.0181	0.14347	0.3625:0.5205:0.0:0.117	.	284;199;255;256	B7Z6M0;B2R8G6;Q14318;Q14318-2	.;.;FKBP8_HUMAN;.	T	256;284	ENSP00000222308:A256T;ENSP00000388891:A284T	ENSP00000222308:A256T	A	-	1	0	FKBP8	18510032	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.579000	0.46059	0.824000	0.34613	0.561000	0.74099	GCC		0.622	FKBP8-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000466374.3	NM_012181	
ZNF506	440515	broad.mit.edu	37	19	19905931	19905931	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:19905931T>G	ENST00000540806.2	-	4	853	c.765A>C	c.(763-765)aaA>aaC	p.K255N	ZNF506_ENST00000443905.2_Missense_Mutation_p.K255N|ZNF506_ENST00000587461.1_Intron|ZNF506_ENST00000450683.2_Missense_Mutation_p.K223N|CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	255					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K255N(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						ATCTGTAGGGTTTCTCTCCAG	0.383																																					p.K223N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A669C	19						.						48.0	53.0	51.0					19																	19905931		2177	4287	6464	19766931	SO:0001583	missense	440515	exon3			AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"""Zinc fingers, C2H2-type"", ""-"""	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.765A>C	19.37:g.19905931T>G	ENSP00000440625:p.Lys255Asn	Somatic		Capture	Illumina HiSeq	Phase_I	19766931	NM_001145404	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	.	.	.	.	.	.	.	.	.	.	t	15.18	2.755990	0.49362	.	.	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.26067	1.76;1.76;1.76	0.974	0.974	0.19715	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38453	0.1041	M	0.79614	2.46	0.32624	N	0.52288	P;D	0.62365	0.549;0.991	B;P	0.54759	0.363;0.76	T	0.51872	-0.8650	9	0.87932	D	0	.	5.7771	0.18285	0.0:0.0:0.0:1.0	.	255;223	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	N	255;255;223	ENSP00000393835:K255N;ENSP00000440625:K255N;ENSP00000408892:K223N	ENSP00000393835:K255N	K	-	3	2	ZNF506	19766931	0.118000	0.22208	0.468000	0.27192	0.427000	0.31564	-0.099000	0.11007	0.358000	0.24211	0.347000	0.21830	AAA		0.383	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218	
ZNF431	170959	broad.mit.edu	37	19	21365584	21365584	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:21365584G>T	ENST00000311048.7	+	5	622	c.478G>T	c.(478-480)Ggt>Tgt	p.G160C	ZNF431_ENST00000594425.1_Intron|ZNF431_ENST00000600692.1_3'UTR	NM_133473.2	NP_597730.2	Q8TF32	ZN431_HUMAN	zinc finger protein 431	160					cell differentiation (GO:0030154)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)	p.G160C(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23						GCACAAAGAAGGTTATAATGA	0.328																																					p.G160C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G478T	19						.						87.0	87.0	87.0					19																	21365584		2203	4300	6503	21157424	SO:0001583	missense	170959	exon5			AB075849	CCDS32979.1	19p12	2013-01-08				ENSG00000196705		"""Zinc fingers, C2H2-type"", ""-"""	20809	protein-coding gene	gene with protein product						11853319	Standard	NM_133473		Approved	KIAA1969	uc002npp.2	Q8TF32		ENST00000311048.7:c.478G>T	19.37:g.21365584G>T	ENSP00000308578:p.Gly160Cys	Somatic		Capture	Illumina HiSeq	Phase_I	21157424	NM_133473	A8KAK7|Q8IWC4	Missense_Mutation	SNP	ENST00000311048.7	37	CCDS32979.1	.	.	.	.	.	.	.	.	.	.	.	0.035	-1.311663	0.01342	.	.	ENSG00000196705	ENST00000311048	T	0.06768	3.26	0.381	-0.761	0.11038	.	.	.	.	.	T	0.07908	0.0198	L	0.60845	1.875	0.09310	N	1	B	0.23937	0.094	B	0.25614	0.062	T	0.39722	-0.9600	9	0.35671	T	0.21	.	2.0361	0.03540	0.4729:0.0:0.2676:0.2595	.	160	Q8TF32	ZN431_HUMAN	C	160	ENSP00000308578:G160C	ENSP00000308578:G160C	G	+	1	0	ZNF431	21157424	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-1.217000	0.02979	-1.631000	0.01543	-1.685000	0.00733	GGT		0.328	ZNF431-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463943.1	XM_086098	
ZNF43	7594	broad.mit.edu	37	19	21992052	21992052	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:21992052A>G	ENST00000354959.4	-	4	956	c.787T>C	c.(787-789)Tgt>Cgt	p.C263R	ZNF43_ENST00000595461.1_Missense_Mutation_p.C257R|ZNF43_ENST00000598381.1_Missense_Mutation_p.C257R|ZNF43_ENST00000594012.1_Missense_Mutation_p.C257R	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C263R(1)		autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		GCTTTGCCACATTCTTCACAT	0.343																																					p.C263R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T787C	19						.						50.0	54.0	53.0					19																	21992052		2199	4297	6496	21783892	SO:0001583	missense	7594	exon4			X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.787T>C	19.37:g.21992052A>G	ENSP00000347045:p.Cys263Arg	Somatic		Capture	Illumina HiSeq	Phase_I	21783892	NM_003423	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368648	0.42003	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.59224	0.28	1.68	1.68	0.24146	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.77143	0.4087	H	0.95645	3.7	0.58432	D	0.999991	D	0.57257	0.979	P	0.60286	0.872	T	0.79245	-0.1883	9	0.87932	D	0	.	8.1342	0.31046	1.0:0.0:0.0:0.0	.	263	P17038	ZNF43_HUMAN	R	262;263	ENSP00000347045:C263R	ENSP00000347045:C263R	C	-	1	0	ZNF43	21783892	1.000000	0.71417	0.015000	0.15790	0.038000	0.13279	6.263000	0.72521	0.760000	0.33108	0.332000	0.21555	TGT		0.343	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
THEG	51298	broad.mit.edu	37	19	362260	362260	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:362260C>G	ENST00000342640.4	-	8	1122	c.1080G>C	c.(1078-1080)atG>atC	p.M360I	THEG_ENST00000346878.2_Missense_Mutation_p.M336I	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	360					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)		p.M360I(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)		GTGGCAAGCTCATAGAGGCGA	0.607																																					p.M336I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1008C	19						.						170.0	170.0	170.0					19																	362260		2203	4300	6503	313260	SO:0001583	missense	51298	exon7			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.1080G>C	19.37:g.362260C>G	ENSP00000340088:p.Met360Ile	Somatic		Capture	Illumina HiSeq	Phase_I	313260	NM_199202	A6NMJ8	Missense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.69|12.69	2.014413|2.014413	0.35511|0.35511	.|.	.|.	ENSG00000105549|ENSG00000105549	ENST00000342640;ENST00000346878|ENST00000530711	T;T|.	0.17691|.	2.26;2.29|.	4.05|4.05	4.05|4.05	0.47172|0.47172	.|.	1.390360|.	0.04399|.	N|.	0.363908|.	T|.	0.21427|.	0.0516|.	N|N	0.08118|0.08118	0|0	0.24770|0.24770	N|N	0.992871|0.992871	B;B|.	0.32160|.	0.358;0.358|.	B;B|.	0.27608|.	0.081;0.081|.	T|.	0.14420|.	-1.0473|.	10|.	0.59425|.	D|.	0.04|.	-14.2884|-14.2884	11.6076|11.6076	0.51041|0.51041	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	336;360|.	Q9P2T0-2;Q9P2T0|.	.;THEG_HUMAN|.	I|S	360;336|138	ENSP00000340088:M360I;ENSP00000264820:M336I|.	ENSP00000340088:M360I|.	M|X	-|-	3|2	0|2	THEG|THEG	313260|313260	0.969000|0.969000	0.33509|0.33509	0.540000|0.540000	0.28089|0.28089	0.654000|0.654000	0.38779|0.38779	2.907000|2.907000	0.48743|0.48743	2.088000|2.088000	0.63022|0.63022	0.650000|0.650000	0.86243|0.86243	ATG|TGA		0.607	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		
ZNF554	115196	broad.mit.edu	37	19	2834045	2834045	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:2834045G>T	ENST00000317243.5	+	5	1010	c.812G>T	c.(811-813)aGa>aTa	p.R271I	ZNF554_ENST00000591265.1_3'UTR	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	271					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R271I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		Hepatocellular(1079;0.137)		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)		GCAGATCGGAGACCTTGTGAA	0.453																																					p.R271I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G812T	19						.						85.0	87.0	87.0					19																	2834045		1956	4142	6098	2785045	SO:0001583	missense	115196	exon5			AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.812G>T	19.37:g.2834045G>T	ENSP00000321132:p.Arg271Ile	Somatic		Capture	Illumina HiSeq	Phase_I	2785045	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510675	0.27036	.	.	ENSG00000172006	ENST00000317243	T	0.07021	3.23	2.77	0.533	0.17121	.	.	.	.	.	T	0.05593	0.0147	L	0.34521	1.04	0.25123	N	0.990627	B	0.26935	0.164	B	0.21151	0.033	T	0.38779	-0.9645	9	0.87932	D	0	.	1.9615	0.03387	0.2719:0.0:0.4459:0.2822	.	271	Q86TJ5	ZN554_HUMAN	I	271	ENSP00000321132:R271I	ENSP00000321132:R271I	R	+	2	0	ZNF554	2785045	0.000000	0.05858	0.006000	0.13384	0.005000	0.04900	0.511000	0.22739	0.477000	0.27464	-0.313000	0.08912	AGA		0.453	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
NFIC	4782	broad.mit.edu	37	19	3449072	3449072	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:3449072C>T	ENST00000443272.2	+	7	1070	c.1019C>T	c.(1018-1020)cCc>cTc	p.P340L	NFIC_ENST00000586919.1_Missense_Mutation_p.P307L|NFIC_ENST00000589123.1_Missense_Mutation_p.P331L|NFIC_ENST00000346156.5_Missense_Mutation_p.P307L|NFIC_ENST00000395111.3_Missense_Mutation_p.P331L|NFIC_ENST00000590282.1_Missense_Mutation_p.P340L|NFIC_ENST00000341919.3_Missense_Mutation_p.P340L	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	340					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P331L(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		AGCCCGTCCCCCCAGGACTCT	0.672																																					p.P340L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1019T	19						.						97.0	68.0	78.0					19																	3449072		2203	4300	6503	3400072	SO:0001583	missense	4782	exon7			X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1019C>T	19.37:g.3449072C>T	ENSP00000396843:p.Pro340Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3400072	NM_005597	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	37	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.290271	0.80914	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.49139	0.79;0.79;0.79	3.96	3.96	0.45880	.	0.197075	0.44285	D	0.000467	T	0.62122	0.2402	M	0.66939	2.045	0.58432	D	0.999999	D;D;P;D;P	0.58268	0.968;0.982;0.557;0.96;0.763	P;P;B;P;B	0.59825	0.773;0.864;0.299;0.59;0.387	T	0.66610	-0.5880	10	0.54805	T	0.06	.	14.6163	0.68552	0.0:1.0:0.0:0.0	.	340;340;331;340;331	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	L	331;331;307;340;340;340	ENSP00000378543:P331L;ENSP00000301935:P307L;ENSP00000342194:P340L	ENSP00000269778:P340L	P	+	2	0	NFIC	3400072	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.082000	0.76851	1.764000	0.52075	0.561000	0.74099	CCC		0.672	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597	
ZNF492	57615	broad.mit.edu	37	19	22846697	22846697	+	Missense_Mutation	SNP	T	T	C	rs62118831	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:22846697T>C	ENST00000456783.2	+	4	470	c.226T>C	c.(226-228)Tgt>Cgt	p.C76R	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	76					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AAAATGTGGATGTGAAAATTT	0.348																																					p.C76R												.	.	0			c.T226C	19						.						42.0	51.0	48.0					19																	22846697		1869	4136	6005	22638537	SO:0001583	missense	57615	exon4			AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.226T>C	19.37:g.22846697T>C	ENSP00000413660:p.Cys76Arg	Germline		Capture	Illumina HiSeq	Phase_I	22638537	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	142	0.06501831501831502	55	0.11178861788617886	18	0.049723756906077346	31	0.05419580419580419	38	0.05013192612137203	.	1.077	-0.668120	0.03428	.	.	ENSG00000229676	ENST00000456783	T	0.07444	3.19	0.769	-0.852	0.10713	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40515	-0.9559	8	0.56958	D	0.05	.	4.6246	0.12472	0.0:0.2798:0.0:0.7202	rs62118831	76	Q9P255	ZN492_HUMAN	R	76	ENSP00000413660:C76R	ENSP00000413660:C76R	C	+	1	0	ZNF492	22638537	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.635000	0.02018	-1.043000	0.03258	-1.309000	0.01313	TGT		0.348	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
TSHZ3	57616	broad.mit.edu	37	19	31767961	31767961	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:31767961C>T	ENST00000240587.4	-	2	3065	c.2738G>A	c.(2737-2739)aGc>aAc	p.S913N		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	913					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S913N(1)|p.S730N(1)		breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTGCCGGAGGCTGGCGGCAAA	0.627																																					p.S913N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2738A	19						.						38.0	39.0	39.0					19																	31767961		2203	4300	6503	36459801	SO:0001583	missense	57616	exon2			AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2738G>A	19.37:g.31767961C>T	ENSP00000240587:p.Ser913Asn	Somatic		Capture	Illumina HiSeq	Phase_I	36459801	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	22.8	4.331470	0.81690	.	.	ENSG00000121297	ENST00000240587	D	0.90900	-2.75	5.39	5.39	0.77823	Homeobox (2);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.92570	0.7640	L	0.58810	1.83	0.80722	D	1	D	0.58268	0.982	P	0.52554	0.702	D	0.93302	0.6677	10	0.87932	D	0	-23.0443	19.1608	0.93531	0.0:1.0:0.0:0.0	.	913	Q63HK5	TSH3_HUMAN	N	913	ENSP00000240587:S913N	ENSP00000240587:S913N	S	-	2	0	TSHZ3	36459801	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.713000	0.68415	2.509000	0.84616	0.591000	0.81541	AGC		0.627	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
ANKRD27	84079	broad.mit.edu	37	19	33117695	33117695	+	Missense_Mutation	SNP	C	C	T	rs143385599	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:33117695C>T	ENST00000306065.4	-	16	1617	c.1459G>A	c.(1459-1461)Gcc>Acc	p.A487T		NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	487					early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.A487T(1)		breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TTTACCATGGCGCCCTTGGAA	0.597													C|||	3	0.000599042	0.0	0.0	5008	,	,		17874	0.0		0.0	False		,,,				2504	0.0031				p.A487T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1459A	19						.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	94.0	74.0	81.0		1459	5.4	1.0	19	dbSNP_134	81	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ANKRD27	NM_032139.2	58	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	487/1051	33117695	6,13000	2203	4300	6503	37809535	SO:0001583	missense	84079	exon16			AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.1459G>A	19.37:g.33117695C>T	ENSP00000304292:p.Ala487Thr	Somatic		Capture	Illumina HiSeq	Phase_I	37809535	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Missense_Mutation	SNP	ENST00000306065.4	37	CCDS32986.1	.	.	.	.	.	.	.	.	.	.	C	18.43	3.621442	0.66787	2.27E-4	5.81E-4	ENSG00000105186	ENST00000306065	T	0.70869	-0.52	5.36	5.36	0.76844	Ankyrin repeat-containing domain (4);	0.000000	0.52532	D	0.000067	D	0.82917	0.5141	L	0.61036	1.89	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.83578	0.0116	10	0.56958	D	0.05	-22.2648	19.0728	0.93147	0.0:1.0:0.0:0.0	.	487	Q96NW4	ANR27_HUMAN	T	487	ENSP00000304292:A487T	ENSP00000304292:A487T	A	-	1	0	ANKRD27	37809535	1.000000	0.71417	0.977000	0.42913	0.036000	0.12997	6.940000	0.75917	2.507000	0.84556	0.603000	0.83216	GCC		0.597	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
WDR88	126248	broad.mit.edu	37	19	33639752	33639752	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:33639752C>T	ENST00000355868.3	+	5	691	c.615C>T	c.(613-615)ttC>ttT	p.F205F	WDR88_ENST00000361680.2_Silent_p.F205F	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	205								p.F205F(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					TCTCAGGCTTCGACGTGGATC	0.493																																					p.F205F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C615T	19						.						245.0	189.0	208.0					19																	33639752		2203	4300	6503	38331592	SO:0001819	synonymous_variant	126248	exon5			BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.615C>T	19.37:g.33639752C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38331592	NM_173479	Q8NEF8	Silent	SNP	ENST00000355868.3	37	CCDS12429.1																																																																																				0.493	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
LRP3	4037	broad.mit.edu	37	19	33695661	33695661	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:33695661T>C	ENST00000253193.7	+	4	580	c.378T>C	c.(376-378)ccT>ccC	p.P126P	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	126	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)		p.P126P(1)		breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CCATCCCACCTGCCTTCATCT	0.662																																					p.P126P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T378C	19						.						71.0	68.0	69.0					19																	33695661		2203	4300	6503	38387501	SO:0001819	synonymous_variant	4037	exon4			AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.378T>C	19.37:g.33695661T>C		Somatic		Capture	Illumina HiSeq	Phase_I	38387501	NM_002333	B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	CCDS12430.1																																																																																				0.662	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
SLC7A10	56301	broad.mit.edu	37	19	33702139	33702139	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:33702139G>T	ENST00000253188.4	-	7	1154	c.1008C>A	c.(1006-1008)acC>acA	p.T336T		NM_019849.2	NP_062823.1	Q9NS82	AAA1_HUMAN	solute carrier family 7 (neutral amino acid transporter light chain, asc system), member 10	336					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|D-alanine transport (GO:0042941)|D-serine transport (GO:0042942)|ion transport (GO:0006811)|L-serine transport (GO:0015825)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)	p.T336T(1)		central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|stomach(1)	18	Esophageal squamous(110;0.137)					ACCTGGAGTAGGTGAACAGGT	0.607																																					p.T336T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1008A	19						.						87.0	69.0	75.0					19																	33702139		2203	4300	6503	38393979	SO:0001819	synonymous_variant	56301	exon7			AB037670	CCDS12431.1	19q13.11	2013-05-28	2011-07-12		ENSG00000130876	ENSG00000130876		"""Solute carriers"""	11058	protein-coding gene	gene with protein product		607959				10734121, 10863037	Standard	NM_019849		Approved	asc-1	uc002num.2	Q9NS82	OTTHUMG00000180344	ENST00000253188.4:c.1008C>A	19.37:g.33702139G>T		Somatic		Capture	Illumina HiSeq	Phase_I	38393979	NM_019849	B2RE84	Missense_Mutation	SNP	ENST00000253188.4	37	CCDS12431.1																																																																																				0.607	SLC7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450846.2	NM_019849	
ZNF599	148103	broad.mit.edu	37	19	35250681	35250681	+	Missense_Mutation	SNP	C	C	T	rs557904206		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:35250681C>T	ENST00000329285.8	-	4	1398	c.1025G>A	c.(1024-1026)gGt>gAt	p.G342D		NM_001007248.2	NP_001007249.1	Q96NL3	ZN599_HUMAN	zinc finger protein 599	342					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G342D(1)		endometrium(3)|large_intestine(10)|lung(8)|ovary(1)|pancreas(1)|skin(1)	24	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			TCCACATTCACCGCACTCATA	0.408													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22137	0.0		0.0	False		,,,				2504	0.0				p.G342D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1025A	19						.						54.0	52.0	53.0					19																	35250681		2203	4300	6503	39942521	SO:0001583	missense	148103	exon4			AK055225	CCDS32991.1	19q13.13	2013-01-08				ENSG00000153896		"""Zinc fingers, C2H2-type"", ""-"""	26408	protein-coding gene	gene with protein product							Standard	NM_001007248		Approved	FLJ30663	uc010edn.1	Q96NL3		ENST00000329285.8:c.1025G>A	19.37:g.35250681C>T	ENSP00000333802:p.Gly342Asp	Somatic		Capture	Illumina HiSeq	Phase_I	39942521	NM_001007248	Q569K0|Q5PRG1	Missense_Mutation	SNP	ENST00000329285.8	37	CCDS32991.1	.	.	.	.	.	.	.	.	.	.	C	0.690	-0.794945	0.02862	.	.	ENSG00000153896	ENST00000392231;ENST00000329285;ENST00000392229	T	0.07216	3.21	2.75	-1.36	0.09085	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03053	0.0090	N	0.02697	-0.525	0.20307	N	0.999917	B	0.19935	0.04	B	0.25614	0.062	T	0.44436	-0.9328	9	0.34782	T	0.22	.	3.7459	0.08548	0.0:0.305:0.2023:0.4927	.	342	Q96NL3	ZN599_HUMAN	D	341;342;116	ENSP00000333802:G342D	ENSP00000333802:G342D	G	-	2	0	ZNF599	39942521	0.000000	0.05858	0.067000	0.19924	0.394000	0.30568	-5.020000	0.00159	-0.197000	0.10350	0.491000	0.48974	GGT		0.408	ZNF599-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460648.2	XM_086046	
LSR	51599	broad.mit.edu	37	19	35757339	35757339	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:35757339G>A	ENST00000361790.3	+	6	1159	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T	LSR_ENST00000602122.1_Missense_Mutation_p.A315T|USF2_ENST00000222305.3_5'Flank|USF2_ENST00000343550.5_5'Flank|USF2_ENST00000595068.1_5'Flank|USF2_ENST00000379134.3_5'Flank|LSR_ENST00000347609.4_Missense_Mutation_p.A297T|USF2_ENST00000594064.1_5'Flank|LSR_ENST00000354900.3_Missense_Mutation_p.A315T|LSR_ENST00000360798.3_Missense_Mutation_p.A266T|LSR_ENST00000427250.1_Missense_Mutation_p.A178T|AD000684.2_ENST00000602262.1_RNA	NM_205834.3	NP_991403.1	Q86X29	LSR_HUMAN	lipolysis stimulated lipoprotein receptor	334					embryo development (GO:0009790)|liver development (GO:0001889)	chylomicron (GO:0042627)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)		p.A334T(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	13	all_lung(56;3.91e-09)|Lung NSC(56;5.64e-09)|Esophageal squamous(110;0.162)		Epithelial(14;1.33e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.29e-18)|all cancers(14;7.11e-17)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCTGTCTCCCGCCAAGACCCC	0.592																																					p.A315T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G943A	19						.						69.0	66.0	67.0					19																	35757339		2203	4300	6503	40449179	SO:0001583	missense	51599	exon5			AF130366	CCDS12449.1, CCDS12450.1, CCDS12451.1, CCDS59376.1	19q13.12	2013-01-11			ENSG00000105699	ENSG00000105699		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29572	protein-coding gene	gene with protein product	"""lipolysis-stimulated remnant"", ""immunoglobulin-like domain containing receptor 3"""					10224102	Standard	NM_015925		Approved	LISCH7, ILDR3	uc002nyl.3	Q86X29		ENST00000361790.3:c.1000G>A	19.37:g.35757339G>A	ENSP00000354575:p.Ala334Thr	Somatic		Capture	Illumina HiSeq	Phase_I	40449179	NM_015925	A6NDW3|B4DKL4|E9PHD4|O00112|O00426|Q6ZT80|Q8NBM0|Q9BT33|Q9UQL3	Missense_Mutation	SNP	ENST00000361790.3	37	CCDS12450.1	.	.	.	.	.	.	.	.	.	.	G	8.760	0.923316	0.18056	.	.	ENSG00000105699	ENST00000361790;ENST00000354900;ENST00000360798;ENST00000347609;ENST00000427250	T;T;T;T;T	0.68479	0.38;0.52;0.19;0.25;-0.33	3.75	2.68	0.31781	.	0.400832	0.24960	N	0.034224	T	0.49218	0.1544	L	0.47716	1.5	0.34591	D	0.715522	B;P;B;P;B;B	0.38455	0.148;0.454;0.196;0.632;0.123;0.089	B;B;B;B;B;B	0.28849	0.011;0.049;0.017;0.095;0.005;0.011	T	0.57717	-0.7763	10	0.48119	T	0.1	-16.1368	4.747	0.13042	0.1148:0.0:0.6751:0.2101	.	272;297;315;266;315;334	Q9BT33;Q86X29-2;Q86X29-3;A6NDW3;E9PHD4;Q86X29	.;.;.;.;.;LSR_HUMAN	T	334;315;266;297;178	ENSP00000354575:A334T;ENSP00000346976:A315T;ENSP00000354034:A266T;ENSP00000262627:A297T;ENSP00000394479:A178T	ENSP00000262627:A297T	A	+	1	0	LSR	40449179	0.930000	0.31532	0.998000	0.56505	0.075000	0.17131	0.456000	0.21859	0.751000	0.32900	0.462000	0.41574	GCC		0.592	LSR-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465513.2	NM_015925	
MAG	4099	broad.mit.edu	37	19	35801523	35801523	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:35801523C>T	ENST00000392213.3	+	9	1752	c.1593C>T	c.(1591-1593)tgC>tgT	p.C531C	MAG_ENST00000593348.1_3'UTR|MAG_ENST00000537831.2_Silent_p.C506C|MAG_ENST00000361922.4_Silent_p.C531C	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	531					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)	p.C531C(2)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CCATCGTCTGCTACATTACCC	0.607																																					p.C506C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1518T	19						.						88.0	77.0	81.0					19																	35801523		2203	4300	6503	40493363	SO:0001819	synonymous_variant	4099	exon9			M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6783	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 4A"""	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.1593C>T	19.37:g.35801523C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40493363	NM_001199216	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																				0.607	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600	
HSPB6	126393	broad.mit.edu	37	19	36245368	36245368	+	IGR	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:36245368G>A	ENST00000592984.1	-	0	1634				AC002398.9_ENST00000591613.2_3'UTR|AC002398.11_ENST00000591091.1_RNA|AC002398.12_ENST00000587767.1_RNA|LIN37_ENST00000301159.9_Missense_Mutation_p.R245Q			O14558	HSPB6_HUMAN	heat shock protein, alpha-crystallin-related, B6						regulation of muscle contraction (GO:0006937)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)|structural constituent of eye lens (GO:0005212)	p.R245Q(1)		lung(1)	1	all_lung(56;3.33e-07)|Lung NSC(56;5.02e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ATGTACGAACGACAGTGATGT	0.577																																					p.R245Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G734A	19						.						55.0	57.0	56.0					19																	36245368		2031	4175	6206	40937208	SO:0001628	intergenic_variant	55957	exon9			AJ278121	CCDS12475.1	19q13.13	2014-06-12			ENSG00000004776	ENSG00000004776		"""Heat shock proteins / HSPB"""	26511	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 91"""	610695				12820654, 14717697	Standard	NM_144617		Approved	FLJ32389, Hsp20, PPP1R91	uc002obn.2	O14558	OTTHUMG00000048122		19.37:g.36245368G>A		Somatic		Capture	Illumina HiSeq	Phase_I	40937208	NM_019104	O14551|Q6NVI3|Q96MG9	Missense_Mutation	SNP	ENST00000592984.1	37	CCDS12475.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655209	0.67472	.	.	ENSG00000188223	ENST00000301159	T	0.18016	2.24	5.81	4.77	0.60923	.	0.067469	0.64402	D	0.000015	T	0.13586	0.0329	L	0.47716	1.5	0.45733	D	0.998635	P	0.42161	0.772	B	0.29176	0.099	T	0.03306	-1.1050	10	0.72032	D	0.01	-20.3857	12.2218	0.54437	0.08:0.0:0.92:0.0	.	245	Q96GY3	LIN37_HUMAN	Q	245	ENSP00000301159:R245Q	ENSP00000301159:R245Q	R	+	2	0	LIN37	40937208	1.000000	0.71417	0.977000	0.42913	0.224000	0.24922	7.049000	0.76613	1.470000	0.48102	0.655000	0.94253	CGA		0.577	HSPB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109498.3	NM_144617	
KIRREL2	84063	broad.mit.edu	37	19	36357406	36357406	+	3'UTR	SNP	T	T	C	rs148345309	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:36357406T>C	ENST00000360202.5	+	0	2337				KIRREL2_ENST00000347900.6_Missense_Mutation_p.W574R|APLP1_ENST00000221891.4_5'Flank|NPHS1_ENST00000591817.1_5'UTR|KIRREL2_ENST00000262625.7_Missense_Mutation_p.W624R|APLP1_ENST00000586861.1_5'Flank|APLP1_ENST00000537454.2_5'Flank	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)						cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)		p.W624R(1)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			ATCTTTCCAATGGAAGAGTCC	0.557																																					p.W624R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1870C	19						.	T	ARG/TRP,ARG/TRP,	3,4403	6.2+/-15.9	0,3,2200	105.0	108.0	107.0		1870,1720,	-8.6	0.0	19	dbSNP_134	107	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,utr-3	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	101,101,	0,9,6494	CC,CT,TT		0.0698,0.0681,0.0692	,,	624/634,574/584,	36357406	9,12997	2203	4300	6503	41049246	SO:0001624	3_prime_UTR_variant	84063	exon16			AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.*12T>C	19.37:g.36357406T>C		Somatic		Capture	Illumina HiSeq	Phase_I	41049246	NM_032123	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	.	.	.	.	.	.	.	.	.	.	T	3.810	-0.039950	0.07497	6.81E-4	6.98E-4	ENSG00000126259	ENST00000262625;ENST00000347900	T;T	0.64085	-0.08;0.14	4.31	-8.61	0.00885	.	.	.	.	.	T	0.35913	0.0948	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.21999	-1.0229	8	0.45353	T	0.12	.	0.0134	0.00001	0.3078:0.2088:0.2037:0.2797	.	574;624	Q6UWL6-3;Q6UWL6-2	.;.	R	624;574	ENSP00000262625:W624R;ENSP00000345067:W574R	ENSP00000262625:W624R	W	+	1	0	KIRREL2	41049246	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.078000	0.01370	-1.972000	0.01001	-0.379000	0.06801	TGG		0.557	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
WDR62	284403	broad.mit.edu	37	19	36574080	36574080	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:36574080G>A	ENST00000270301.7	+	11	1487	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	WDR62_ENST00000401500.2_Missense_Mutation_p.R496Q			O43379	WDR62_HUMAN	WD repeat domain 62	496					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.R496Q(1)		cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GCCGGGGTGCGGGTCATGCAG	0.602																																					p.R496Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1487A	19						.						53.0	49.0	50.0					19																	36574080		2203	4300	6503	41265920	SO:0001583	missense	284403	exon11			BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.1487G>A	19.37:g.36574080G>A	ENSP00000270301:p.Arg496Gln	Somatic		Capture	Illumina HiSeq	Phase_I	41265920	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	.	.	.	.	.	.	.	.	.	.	G	36	5.848865	0.97023	.	.	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.63580	0.97;-0.05	5.71	5.71	0.89125	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.78811	0.4342	M	0.72894	2.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.996	T	0.78775	-0.2072	10	0.52906	T	0.07	-12.0685	17.3615	0.87351	0.0:0.0:1.0:0.0	.	496;496	O43379-4;O43379	.;WDR62_HUMAN	Q	496	ENSP00000384792:R496Q;ENSP00000270301:R496Q	ENSP00000270301:R496Q	R	+	2	0	WDR62	41265920	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	6.208000	0.72165	2.709000	0.92574	0.655000	0.94253	CGG		0.602	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
SH3GL1	6455	broad.mit.edu	37	19	4365618	4365618	+	Silent	SNP	C	C	T	rs572316012	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:4365618C>T	ENST00000269886.3	-	4	370	c.192G>A	c.(190-192)tcG>tcA	p.S64S	SH3GL1_ENST00000417295.2_Intron|AC007292.6_ENST00000594444.1_RNA|SH3GL1_ENST00000598564.1_Silent_p.S64S	NM_003025.3	NP_003016.1	Q99961	SH3G1_HUMAN	SH3-domain GRB2-like 1	64	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Required for dimerization upon membrane association. {ECO:0000250}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|endosome (GO:0005768)|membrane (GO:0016020)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.S64S(1)		NS(1)|endometrium(2)|kidney(16)|large_intestine(3)|lung(2)|ovary(2)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0152)|STAD - Stomach adenocarcinoma(1328;0.182)		GCTTAGCCCGCGAGGCTGGGA	0.652			T	MLL	AL								c|||	2	0.000399361	0.0015	0.0	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.S64S	NSCLC(94;1152 2133 30346 33362)		Dom	yes		19	19p13.3	6455	SH3-domain GRB2-like 1 (EEN)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G192A	19						.						74.0	77.0	76.0					19																	4365618		2203	4300	6503	4316618	SO:0001819	synonymous_variant	6455	exon4				CCDS32874.1, CCDS56076.1, CCDS59335.1	19p13.3	2008-07-22							10830	protein-coding gene	gene with protein product	"""extra 11-19 leukemia fusion"", ""fusion partner of MLL"", ""SH3-containing Grb-2-like 1 protein"", ""SH3-containing protein EEN"", ""SH3 domain GRB2-like 1"""	601768				9169142	Standard	NM_003025		Approved	SH3P8, SH3D2B, CNSA1, EEN, MGC111371	uc002maj.3	Q99961		ENST00000269886.3:c.192G>A	19.37:g.4365618C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4316618	NM_003025	B4DRA1|E7EVZ4|M0QZV5|Q99668	Silent	SNP	ENST00000269886.3	37	CCDS32874.1																																																																																				0.652	SH3GL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458302.1	NM_003025	
ZNF607	84775	broad.mit.edu	37	19	38189332	38189332	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:38189332C>T	ENST00000355202.4	-	5	2295	c.1700G>A	c.(1699-1701)gGc>gAc	p.G567D	CTD-2528L19.4_ENST00000586606.2_Intron|ZNF607_ENST00000395835.3_Missense_Mutation_p.G566D	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	567					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G567D(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|lung(8)|urinary_tract(1)	27			UCEC - Uterine corpus endometrioid carcinoma (49;0.0775)			AAAGGCCTTGCCACATTCCTT	0.413																																					p.G567D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1700A	19						.						43.0	41.0	42.0					19																	38189332		2203	4300	6503	42881172	SO:0001583	missense	84775	exon5			AK127464	CCDS33006.1, CCDS54259.1	19q13.1	2013-01-08				ENSG00000198182		"""Zinc fingers, C2H2-type"", ""-"""	28192	protein-coding gene	gene with protein product						14702039	Standard	NM_032689		Approved	MGC13071, FLJ14802	uc002ohc.2	Q96SK3		ENST00000355202.4:c.1700G>A	19.37:g.38189332C>T	ENSP00000347338:p.Gly567Asp	Somatic		Capture	Illumina HiSeq	Phase_I	42881172	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530586	0.85706	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.58358	0.34;0.34	1.96	1.96	0.26148	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.61565	0.2357	L	0.41356	1.27	0.26817	N	0.968877	P;D	0.89917	0.77;1.0	B;D	0.78314	0.416;0.991	T	0.52185	-0.8609	9	0.72032	D	0.01	.	10.9085	0.47094	0.0:1.0:0.0:0.0	.	567;566	Q96SK3;F5H141	ZN607_HUMAN;.	D	567;566	ENSP00000347338:G567D;ENSP00000438015:G566D	ENSP00000347338:G567D	G	-	2	0	ZNF607	42881172	0.130000	0.22417	0.484000	0.27391	0.980000	0.70556	1.073000	0.30691	1.076000	0.40961	0.462000	0.41574	GGC		0.413	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689	
UBXN6	80700	broad.mit.edu	37	19	4457678	4457678	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:4457678T>C	ENST00000301281.6	-	1	141	c.17A>G	c.(16-18)cAg>cGg	p.Q6R	UBXN6_ENST00000394765.3_5'Flank|CTB-50L17.16_ENST00000591414.1_lincRNA|CTB-50L17.9_ENST00000592034.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	6						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.Q6R(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						CTTGAACTCCTGAAAGAATTT	0.706																																					p.Q6R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A17G	19						.						26.0	23.0	24.0					19																	4457678		2200	4297	6497	4408678	SO:0001583	missense	80700	exon1			AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.17A>G	19.37:g.4457678T>C	ENSP00000301281:p.Gln6Arg	Somatic		Capture	Illumina HiSeq	Phase_I	4408678	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	.	.	.	.	.	.	.	.	.	.	T	18.14	3.557589	0.65425	.	.	ENSG00000167671	ENST00000301281	T	0.45276	0.9	4.29	4.29	0.51040	.	0.282051	0.33792	N	0.004546	T	0.40094	0.1103	M	0.65975	2.015	0.80722	D	1	P	0.48764	0.915	B	0.41764	0.366	T	0.42241	-0.9463	10	0.66056	D	0.02	-26.7378	7.99	0.30235	0.1823:0.0:0.0:0.8177	.	6	Q9BZV1	UBXN6_HUMAN	R	6	ENSP00000301281:Q6R	ENSP00000301281:Q6R	Q	-	2	0	UBXN6	4408678	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.487000	0.53222	1.567000	0.49668	0.477000	0.44152	CAG		0.706	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
LGALS4	3960	broad.mit.edu	37	19	39292967	39292967	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:39292967G>A	ENST00000307751.4	-	8	1125	c.648C>T	c.(646-648)ccC>ccT	p.P216P		NM_006149.3	NP_006140.1	P56470	LEG4_HUMAN	lectin, galactoside-binding, soluble, 4	216	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				cell adhesion (GO:0007155)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.P216P(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17	all_cancers(60;1.02e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			TCTTGCCTGTGGGAGGCACAT	0.567																																					p.P216P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C648T	19						.						227.0	197.0	207.0					19																	39292967		2203	4300	6503	43984807	SO:0001819	synonymous_variant	3960	exon8				CCDS12521.1	19q13.2	2014-03-19	2008-07-25		ENSG00000171747	ENSG00000171747		"""Lectins, galactoside-binding"""	6565	protein-coding gene	gene with protein product	"""galectin 4"""	602518				8063692	Standard	NM_006149		Approved	GAL4	uc002ojg.3	P56470	OTTHUMG00000182608	ENST00000307751.4:c.648C>T	19.37:g.39292967G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43984807	NM_006149		Silent	SNP	ENST00000307751.4	37	CCDS12521.1																																																																																				0.567	LGALS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462641.1	NM_006149	
PLIN4	729359	broad.mit.edu	37	19	4512763	4512763	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:4512763C>T	ENST00000301286.3	-	3	1166	c.1167G>A	c.(1165-1167)atG>atA	p.M389I		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	389	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)		p.M317I(1)		NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GCCCAGTGGACATCGTGTCTT	0.572																																					p.M389I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1167A	19						.						64.0	85.0	79.0					19																	4512763		1492	4137	5629	4463763	SO:0001583	missense	729359	exon3			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1167G>A	19.37:g.4512763C>T	ENSP00000301286:p.Met389Ile	Somatic		Capture	Illumina HiSeq	Phase_I	4463763	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	c	11.37	1.619695	0.28801	.	.	ENSG00000167676	ENST00000301286	T	0.04454	3.62	4.51	3.43	0.39272	.	0.175253	0.27354	N	0.019750	T	0.02418	0.0074	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44003	-0.9356	10	0.22109	T	0.4	-7.9954	2.5083	0.04650	0.1615:0.4817:0.2444:0.1124	.	389	Q96Q06	PLIN4_HUMAN	I	389	ENSP00000301286:M389I	ENSP00000301286:M389I	M	-	3	0	PLIN4	4463763	0.000000	0.05858	0.026000	0.17262	0.139000	0.21198	-0.249000	0.08842	2.097000	0.63578	0.442000	0.29010	ATG		0.572	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
LRFN1	57622	broad.mit.edu	37	19	39805746	39805746	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:39805746G>A	ENST00000248668.4	-	1	230	c.231C>T	c.(229-231)atC>atT	p.I77I	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	77						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)		p.I29I(1)		central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GCACGGCGGCGATGAAGTTGT	0.677																																					p.I77I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C231T	19						.						11.0	14.0	13.0					19																	39805746		2163	4254	6417	44497586	SO:0001819	synonymous_variant	57622	exon1			BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.231C>T	19.37:g.39805746G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44497586	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	37	CCDS46071.1																																																																																				0.677	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
SUPT5H	6829	broad.mit.edu	37	19	39963513	39963513	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:39963513G>A	ENST00000599117.1	+	23	2466	c.2099G>A	c.(2098-2100)cGg>cAg	p.R700Q	SUPT5H_ENST00000598725.1_Missense_Mutation_p.R700Q|SUPT5H_ENST00000359191.6_Missense_Mutation_p.R696Q|SUPT5H_ENST00000432763.2_Missense_Mutation_p.R700Q|SUPT5H_ENST00000402194.2_Missense_Mutation_p.R696Q			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	700					7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)	p.R700Q(1)		breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			GGCCGGGGCCGGAGGGACAAC	0.677																																					p.R700Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2099A	19						.						49.0	49.0	49.0					19																	39963513		2203	4300	6503	44655353	SO:0001583	missense	6829	exon21			U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2099G>A	19.37:g.39963513G>A	ENSP00000470252:p.Arg700Gln	Somatic		Capture	Illumina HiSeq	Phase_I	44655353	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.005262	0.74932	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.9	4.9	0.64082	.	0.082161	0.64402	D	0.000015	T	0.27765	0.0683	N	0.08118	0	0.80722	D	1	P;P;P;P	0.44006	0.824;0.809;0.608;0.474	B;B;B;B	0.37304	0.246;0.08;0.115;0.087	T	0.10567	-1.0624	8	.	.	.	-16.8098	16.8478	0.85985	0.0:0.0:1.0:0.0	.	678;492;696;700	B4DZJ7;B4DJK4;O00267-2;O00267	.;.;.;SPT5H_HUMAN	Q	700;696;678;700	.	.	R	+	2	0	SUPT5H	44655353	1.000000	0.71417	0.928000	0.36995	0.960000	0.62799	7.415000	0.80131	2.263000	0.75096	0.557000	0.71058	CGG		0.677	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
DLL3	10683	broad.mit.edu	37	19	39994770	39994770	+	Nonsense_Mutation	SNP	C	C	T	rs104894675		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:39994770C>T	ENST00000205143.4	+	5	719	c.712C>T	c.(712-714)Cga>Tga	p.R238*	DLL3_ENST00000356433.5_Nonsense_Mutation_p.R238*	NM_016941.3	NP_058637.1	Q9NYJ7	DLL3_HUMAN	delta-like 3 (Drosophila)	238	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				compartment pattern specification (GO:0007386)|negative regulation of neurogenesis (GO:0050768)|Notch signaling pathway (GO:0007219)|paraxial mesoderm development (GO:0048339)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)	integral component of membrane (GO:0016021)	Notch binding (GO:0005112)	p.R238*(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)	19	all_cancers(60;4.04e-06)|all_lung(34;1.77e-07)|Lung NSC(34;2.09e-07)|all_epithelial(25;1.13e-05)|Ovarian(47;0.159)		Epithelial(26;5.89e-26)|all cancers(26;1.96e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CGGTGAATGCCGATGCCTAGA	0.642																																					p.R238X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C712T	19	GRCh37	CM031159	DLL3	M	rs104894675	.	C	stop/ARG,stop/ARG	0,4406		0,0,2203	73.0	70.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	712,712	4.9	0.8	19	dbSNP_132	71	2,8598	2.2+/-6.3	0,2,4298	no	stop-gained,stop-gained	DLL3	NM_016941.3,NM_203486.2	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	238/619,238/588	39994770	2,13004	2203	4300	6503	44686610	SO:0001587	stop_gained	10683	exon5			AF241373	CCDS12537.1, CCDS12538.1	19q13.2	2008-05-14	2001-12-03			ENSG00000090932			2909	protein-coding gene	gene with protein product		602768	"""delta (Drosophila)-like 3"""			10364530, 10742114	Standard	NM_203486		Approved	SCDO1	uc002olx.2	Q9NYJ7		ENST00000205143.4:c.712C>T	19.37:g.39994770C>T	ENSP00000205143:p.Arg238*	Somatic		Capture	Illumina HiSeq	Phase_I	44686610	NM_203486	E9PFG2|Q8NBS4	Nonsense_Mutation	SNP	ENST00000205143.4	37	CCDS12538.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.041309	0.93685	0.0	2.33E-4	ENSG00000090932	ENST00000356433;ENST00000205143	.	.	.	4.87	4.87	0.63330	.	0.762154	0.11247	N	0.584049	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8645	0.46847	0.291:0.709:0.0:0.0	.	.	.	.	X	238	.	.	R	+	1	2	DLL3	44686610	0.011000	0.17503	0.760000	0.31359	0.621000	0.37620	-0.150000	0.10189	2.698000	0.92095	0.561000	0.74099	CGA		0.642	DLL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464958.1		
FCGBP	8857	broad.mit.edu	37	19	40392496	40392496	+	Missense_Mutation	SNP	C	C	T	rs143680639	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40392496C>T	ENST00000221347.6	-	16	8015	c.8008G>A	c.(8008-8010)Ggg>Agg	p.G2670R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2670	VWFD 6. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.G2670R(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGTGGCCCTGTGGGGCTG	0.597																																					p.G2670R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G8008A	19						.						36.0	38.0	37.0					19																	40392496		2171	4287	6458	45084336	SO:0001583	missense	8857	exon16			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.8008G>A	19.37:g.40392496C>T	ENSP00000221347:p.Gly2670Arg	Germline		Capture	Illumina HiSeq	Phase_I	45084336	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.401441	0.42613	.	.	ENSG00000090920	ENST00000221347	T	0.24908	1.83	2.66	2.66	0.31614	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.85682	D	0.000000	T	0.57533	0.2060	M	0.92784	3.345	0.42617	D	0.993336	D	0.89917	1.0	D	0.97110	1.0	T	0.70223	-0.4931	10	0.87932	D	0	.	12.5273	0.56093	0.0:1.0:0.0:0.0	.	2670	Q9Y6R7	FCGBP_HUMAN	R	2670	ENSP00000221347:G2670R	ENSP00000221347:G2670R	G	-	1	0	FCGBP	45084336	1.000000	0.71417	0.382000	0.26119	0.147000	0.21601	5.593000	0.67550	1.495000	0.48549	0.298000	0.19748	GGG		0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
FCGBP	8857	broad.mit.edu	37	19	40430341	40430341	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40430341G>A	ENST00000221347.6	-	3	1609	c.1602C>T	c.(1600-1602)cgC>cgT	p.R534R		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	534	VWFD 1. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)		p.R534R(1)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCTGTAGGCGCGCACAGTGA	0.662																																					p.R534R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1602T	19						.						49.0	41.0	44.0					19																	40430341		2203	4300	6503	45122181	SO:0001819	synonymous_variant	8857	exon3			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1602C>T	19.37:g.40430341G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45122181	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
FCGBP	8857	broad.mit.edu	37	19	40433201	40433201	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40433201G>A	ENST00000221347.6	-	2	1075	c.1068C>T	c.(1066-1068)ggC>ggT	p.G356G		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	356	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)		p.G356G(2)		NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CCAGGGCCACGCCCTCACAGC	0.597																																					p.G356G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1068T	19						.						86.0	66.0	73.0					19																	40433201		2203	4300	6503	45125041	SO:0001819	synonymous_variant	8857	exon2			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.1068C>T	19.37:g.40433201G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45125041	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																				0.597	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ZNF780B	163131	broad.mit.edu	37	19	40540533	40540533	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40540533T>A	ENST00000434248.1	-	5	2298	c.2233A>T	c.(2233-2235)Atc>Ttc	p.I745F	ZNF780B_ENST00000221355.6_Missense_Mutation_p.I597F	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	745					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I745F(1)		endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					GTATGAATGATCTGATGTTGA	0.423																																					p.I745F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2233T	19						.						69.0	74.0	73.0					19																	40540533		2200	4296	6496	45232373	SO:0001583	missense	163131	exon5			AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.2233A>T	19.37:g.40540533T>A	ENSP00000391641:p.Ile745Phe	Somatic		Capture	Illumina HiSeq	Phase_I	45232373	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	.	.	.	.	.	.	.	.	.	.	t	11.61	1.689613	0.29962	.	.	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.18502	2.21;2.21	2.55	1.48	0.22813	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10723	0.0262	L	0.31526	0.94	0.19300	N	0.99998	B	0.30686	0.29	B	0.30316	0.114	T	0.32640	-0.9899	9	0.87932	D	0	.	1.9714	0.03406	0.2677:0.1567:0.0:0.5755	.	745	Q9Y6R6	Z780B_HUMAN	F	745;597	ENSP00000391641:I745F;ENSP00000221355:I597F	ENSP00000221355:I597F	I	-	1	0	ZNF780B	45232373	0.000000	0.05858	0.063000	0.19743	0.063000	0.16089	-0.175000	0.09825	0.107000	0.17824	0.374000	0.22700	ATC		0.423	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
MAP3K10	4294	broad.mit.edu	37	19	40710396	40710396	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40710396G>A	ENST00000253055.3	+	3	1156	c.868G>A	c.(868-870)Ggg>Agg	p.G290R	MAP3K10_ENST00000593906.1_3'UTR|AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	290	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|JNK cascade (GO:0007254)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of apoptotic process (GO:0043065)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|protein autophosphorylation (GO:0046777)|signal transduction (GO:0007165)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|bHLH transcription factor binding (GO:0043425)|JUN kinase kinase kinase activity (GO:0004706)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription corepressor activity (GO:0003714)	p.G290R(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						CTGCAGCTTCGGGGTGCTGCT	0.657																																					p.G290R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G868A	19						.						69.0	48.0	55.0					19																	40710396		2203	4300	6503	45402236	SO:0001583	missense	4294	exon3			X90846	CCDS12549.1	19q13.2	2014-08-12			ENSG00000130758		2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6849	protein-coding gene	gene with protein product	"""MKN28 kinase"", ""mixed lineage kinase 2"", ""MKN28 derived nonreceptor_type serine/threonine kinase"""	600137		MLK2		8536694, 7731697	Standard	NM_002446		Approved	MST, MEKK10	uc002ona.3	Q02779	OTTHUMG00000182591	ENST00000253055.3:c.868G>A	19.37:g.40710396G>A	ENSP00000253055:p.Gly290Arg	Somatic		Capture	Illumina HiSeq	Phase_I	45402236	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	32	5.171522	0.94807	.	.	ENSG00000130758	ENST00000253055	D	0.99462	-5.94	5.13	5.13	0.70059	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.112431	0.64402	D	0.000015	D	0.99711	0.9889	H	0.97214	3.96	0.80722	D	1	D	0.67145	0.996	D	0.71656	0.974	D	0.97305	0.9933	10	0.87932	D	0	.	16.4246	0.83810	0.0:0.0:1.0:0.0	.	290	Q02779	M3K10_HUMAN	R	290	ENSP00000253055:G290R	ENSP00000253055:G290R	G	+	1	0	MAP3K10	45402236	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.790000	0.99075	2.542000	0.85734	0.650000	0.86243	GGG		0.657	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446	
PLD3	23646	broad.mit.edu	37	19	40877626	40877626	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:40877626G>A	ENST00000409587.1	+	9	1122	c.725G>A	c.(724-726)cGa>cAa	p.R242Q	PLD3_ENST00000356508.5_Missense_Mutation_p.R242Q|PLD3_ENST00000409281.1_Missense_Mutation_p.R242Q|PLD3_ENST00000409419.1_Missense_Mutation_p.R242Q|PLD3_ENST00000409735.4_Missense_Mutation_p.R242Q			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	242					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)	p.R189Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			TGCCTGGCTCGAGACCTGACC	0.587																																					p.R242Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G725A	19						.						96.0	63.0	74.0					19																	40877626		2203	4300	6503	45569466	SO:0001583	missense	23646	exon9			BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.725G>A	19.37:g.40877626G>A	ENSP00000387050:p.Arg242Gln	Somatic		Capture	Illumina HiSeq	Phase_I	45569466	NM_001031696	Q92853|Q9BW87	Missense_Mutation	SNP	ENST00000409587.1	37	CCDS33027.1	.	.	.	.	.	.	.	.	.	.	G	5.940	0.357443	0.11239	.	.	ENSG00000105223	ENST00000409419;ENST00000409587;ENST00000356508;ENST00000536031;ENST00000409735;ENST00000409281	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.77	0.972	0.19704	Phospholipase D/viral envelope (1);	0.430601	0.24318	N	0.039570	T	0.16257	0.0391	N	0.05510	-0.035	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.26710	-1.0095	10	0.07482	T	0.82	-14.494	6.4956	0.22140	0.5409:0.0:0.4591:0.0	.	242	Q8IV08	PLD3_HUMAN	Q	242;242;242;223;242;242	ENSP00000386293:R242Q;ENSP00000387050:R242Q;ENSP00000348901:R242Q;ENSP00000386938:R242Q;ENSP00000387022:R242Q	ENSP00000348901:R242Q	R	+	2	0	PLD3	45569466	0.000000	0.05858	0.208000	0.23602	0.981000	0.71138	0.369000	0.20416	0.378000	0.24764	0.561000	0.74099	CGA		0.587	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
SPTBN4	57731	broad.mit.edu	37	19	41019317	41019317	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:41019317G>A	ENST00000352632.3	+	14	2707	c.2621G>A	c.(2620-2622)cGc>cAc	p.R874H	SPTBN4_ENST00000338932.3_Missense_Mutation_p.R874H|SPTBN4_ENST00000595535.1_Missense_Mutation_p.R874H|SPTBN4_ENST00000344104.3_Missense_Mutation_p.R874H|SPTBN4_ENST00000598249.1_Missense_Mutation_p.R874H			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	874					actin filament capping (GO:0051693)|adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cardiac conduction (GO:0061337)|central nervous system projection neuron axonogenesis (GO:0021952)|clustering of voltage-gated sodium channels (GO:0045162)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization to plasma membrane (GO:0090002)|fertilization (GO:0009566)|negative regulation of heart rate (GO:0010459)|positive regulation of multicellular organism growth (GO:0040018)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of sodium ion transport (GO:0002028)|sensory perception of sound (GO:0007605)|transmission of nerve impulse (GO:0019226)|vesicle-mediated transport (GO:0016192)	adherens junction (GO:0005912)|axon hillock (GO:0043203)|axon initial segment (GO:0043194)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|nuclear matrix (GO:0016363)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|PML body (GO:0016605)|spectrin (GO:0008091)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phosphatase binding (GO:0019902)|phospholipid binding (GO:0005543)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.R874H(1)		breast(4)|central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	73			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GCGCTGAGGCGCCAGTGGCTG	0.667																																					p.R874H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2621A	19						.						20.0	21.0	20.0					19																	41019317		2200	4295	6495	45711157	SO:0001583	missense	57731	exon14			AF082075	CCDS12559.1, CCDS42569.1	19q13.13	2013-01-10				ENSG00000160460		"""Pleckstrin homology (PH) domain containing"""	14896	protein-coding gene	gene with protein product		606214				11086001	Standard	NM_020971		Approved	SPTBN3, KIAA1642	uc002onz.3	Q9H254		ENST00000352632.3:c.2621G>A	19.37:g.41019317G>A	ENSP00000263373:p.Arg874His	Somatic		Capture	Illumina HiSeq	Phase_I	45711157	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	G	13.25	2.179758	0.38511	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000338932;ENST00000344104	T;T;T	0.53423	0.62;0.62;0.62	3.39	3.39	0.38822	.	0.425366	0.21347	N	0.076021	T	0.51109	0.1655	L	0.27053	0.805	0.80722	D	1	D;B	0.76494	0.999;0.266	P;B	0.61201	0.885;0.039	T	0.54241	-0.8323	10	0.49607	T	0.09	.	14.0505	0.64732	0.0:0.0:1.0:0.0	.	874;874	Q9H254;Q71S06	SPTN4_HUMAN;.	H	874	ENSP00000263373:R874H;ENSP00000340345:R874H;ENSP00000340741:R874H	ENSP00000340345:R874H	R	+	2	0	SPTBN4	45711157	0.001000	0.12720	1.000000	0.80357	0.510000	0.34073	0.974000	0.29436	1.918000	0.55548	0.313000	0.20887	CGC		0.667	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2		
EGLN2	112398	broad.mit.edu	37	19	41312470	41312470	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:41312470C>T	ENST00000593726.1	+	2	1882	c.854C>T	c.(853-855)gCg>gTg	p.A285V	EGLN2_ENST00000303961.4_Missense_Mutation_p.A285V|EGLN2_ENST00000594140.1_Missense_Mutation_p.A3V|CTC-490E21.12_ENST00000601627.1_Intron|RAB4B-EGLN2_ENST00000594136.1_3'UTR|EGLN2_ENST00000406058.2_Missense_Mutation_p.A285V			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	285	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)	p.A285V(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GCCATGGTGGCGTGTTACCCA	0.562											OREG0025478	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A285V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C854T	19						.						110.0	84.0	93.0					19																	41312470		2203	4300	6503	46004310	SO:0001583	missense	112398	exon3			AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.854C>T	19.37:g.41312470C>T	ENSP00000469686:p.Ala285Val	Somatic	900	Capture	Illumina HiSeq	Phase_I	46004310	NM_080732	A8K5S0|Q8WWY4|Q9BV14	Missense_Mutation	SNP	ENST00000593726.1	37	CCDS12567.1	.	.	.	.	.	.	.	.	.	.	C	34	5.337352	0.95758	.	.	ENSG00000171570	ENST00000303961;ENST00000406058	T;T	0.59502	0.26;0.26	5.0	5.0	0.66597	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	D	0.84252	0.5431	H	0.97131	3.945	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.89646	0.3866	10	0.87932	D	0	-16.675	17.2313	0.86984	0.0:1.0:0.0:0.0	.	285	Q96KS0	EGLN2_HUMAN	V	285	ENSP00000307080:A285V;ENSP00000385253:A285V	ENSP00000307080:A285V	A	+	2	0	EGLN2	46004310	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.301000	0.78850	2.585000	0.87301	0.655000	0.94253	GCG		0.562	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
CYP2F1	1572	broad.mit.edu	37	19	41627952	41627952	+	Missense_Mutation	SNP	G	G	A	rs370865507		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:41627952G>A	ENST00000331105.2	+	6	808	c.736G>A	c.(736-738)Gcc>Acc	p.A246T		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	246					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)	p.A246T(1)		central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						AGACCTCATCGCCCACAGCGT	0.602																																					p.A246T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G736A	19						.	G	THR/ALA	0,4404		0,0,2202	46.0	45.0	45.0		736	2.1	0.2	19		45	1,8589		0,1,4294	no	missense	CYP2F1	NM_000774.3	58	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign	246/492	41627952	1,12993	2202	4295	6497	46319792	SO:0001583	missense	1572	exon6			J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.736G>A	19.37:g.41627952G>A	ENSP00000333534:p.Ala246Thr	Somatic		Capture	Illumina HiSeq	Phase_I	46319792	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	N	5.341	0.248310	0.10130	0.0	1.16E-4	ENSG00000197446	ENST00000331105	T	0.68624	-0.34	3.21	2.12	0.27331	.	0.654924	0.14892	U	0.292363	T	0.43567	0.1253	N	0.20401	0.57	0.09310	N	1	B;B;B	0.31859	0.343;0.217;0.028	B;B;B	0.21360	0.034;0.009;0.004	T	0.15838	-1.0423	10	0.24483	T	0.36	.	7.9492	0.30003	0.0:0.0:0.5603:0.4397	.	32;246;246	B4DL83;Q32MN5;P24903	.;.;CP2F1_HUMAN	T	246	ENSP00000333534:A246T	ENSP00000333534:A246T	A	+	1	0	CYP2F1	46319792	0.000000	0.05858	0.209000	0.23619	0.071000	0.16799	-0.331000	0.07914	0.526000	0.28541	0.398000	0.26397	GCC		0.602	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
HNRNPUL1	11100	broad.mit.edu	37	19	41782067	41782067	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:41782067A>G	ENST00000392006.3	+	5	823	c.650A>G	c.(649-651)aAc>aGc	p.N217S	HNRNPUL1_ENST00000263367.3_Missense_Mutation_p.N128S|HNRNPUL1_ENST00000593587.1_Missense_Mutation_p.N117S|HNRNPUL1_ENST00000378215.4_Missense_Mutation_p.N174S|HNRNPUL1_ENST00000595018.1_Missense_Mutation_p.N117S|HNRNPUL1_ENST00000594207.1_3'UTR|HNRNPUL1_ENST00000352456.3_Missense_Mutation_p.N117S|HNRNPUL1_ENST00000602130.1_Missense_Mutation_p.N217S	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	217	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Necessary for interaction with TP53.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.N217S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						TTCACAGATAACTGCGACCTC	0.493																																					p.N117S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A350G	19						.						107.0	108.0	108.0					19																	41782067		2203	4300	6503	46473907	SO:0001583	missense	11100	exon5			AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.650A>G	19.37:g.41782067A>G	ENSP00000375863:p.Asn217Ser	Somatic		Capture	Illumina HiSeq	Phase_I	46473907	NM_144732	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Missense_Mutation	SNP	ENST00000392006.3	37	CCDS12576.1	.	.	.	.	.	.	.	.	.	.	A	28.3	4.905829	0.92107	.	.	ENSG00000105323	ENST00000352456;ENST00000392006;ENST00000378215;ENST00000263367	T;T;T;T	0.72505	-0.66;-0.66;-0.66;-0.66	5.58	5.58	0.84498	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	D	0.83788	0.5330	M	0.79475	2.455	0.48696	D	0.999697	P;P;D;D;P;P	0.67145	0.879;0.879;0.992;0.996;0.944;0.926	P;P;D;D;P;P	0.77557	0.772;0.809;0.922;0.99;0.788;0.886	D	0.85773	0.1356	10	0.66056	D	0.02	-26.9227	14.7347	0.69406	1.0:0.0:0.0:0.0	.	128;117;217;174;217;117	B7Z4B8;A8K3W4;Q9BUJ2-2;Q9BUJ2-3;Q9BUJ2;Q9BUJ2-4	.;.;.;.;HNRL1_HUMAN;.	S	117;217;174;128	ENSP00000340857:N117S;ENSP00000375863:N217S;ENSP00000367460:N174S;ENSP00000263367:N128S	ENSP00000263367:N128S	N	+	2	0	HNRNPUL1	46473907	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.588000	0.90813	2.131000	0.65755	0.533000	0.62120	AAC		0.493	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
MEGF8	1954	broad.mit.edu	37	19	42861084	42861084	+	Missense_Mutation	SNP	G	G	A	rs141153248	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:42861084G>A	ENST00000251268.6	+	27	4781	c.4781G>A	c.(4780-4782)cGt>cAt	p.R1594H	MEGF8_ENST00000334370.4_Missense_Mutation_p.R1527H	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1594					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)	p.R1527H(1)|p.R1135H(1)		breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GGCGTCACCCGTGATTTCTGG	0.652													G|||	8	0.00159744	0.0	0.0	5008	,	,		17255	0.0		0.0	False		,,,				2504	0.0082				p.R1527H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G4580A	19						.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	45.0	37.0	40.0		4580	4.3	0.9	19	dbSNP_134	40	6,8592	4.3+/-15.6	0,6,4293	yes	missense	MEGF8	NM_001410.2	29	0,7,6495	AA,AG,GG		0.0698,0.0227,0.0538	possibly-damaging	1527/2779	42861084	7,12997	2203	4299	6502	47552924	SO:0001583	missense	1954	exon26			AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.4781G>A	19.37:g.42861084G>A	ENSP00000251268:p.Arg1594His	Somatic		Capture	Illumina HiSeq	Phase_I	47552924	NM_001410	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	G	16.64	3.180640	0.57800	2.27E-4	6.98E-4	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.62498	0.02;0.02	5.32	4.29	0.51040	Galactose oxidase/kelch, beta-propeller (1);Kelch-type beta propeller (1);	0.566253	0.17082	N	0.187750	T	0.51873	0.1700	N	0.19112	0.55	0.39461	D	0.967565	D;D	0.67145	0.996;0.983	P;P	0.51582	0.582;0.674	T	0.52711	-0.8539	10	0.45353	T	0.12	-12.6576	5.8254	0.18550	0.1697:0.1602:0.6701:0.0	.	1594;1527	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	H	1527;1594	ENSP00000334219:R1527H;ENSP00000251268:R1594H	ENSP00000251268:R1594H	R	+	2	0	MEGF8	47552924	0.952000	0.32445	0.938000	0.37757	0.921000	0.55340	2.585000	0.46111	1.269000	0.44280	-0.251000	0.11542	CGT		0.652	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
LYPD3	27076	broad.mit.edu	37	19	43968551	43968551	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:43968551G>A	ENST00000244333.3	-	2	225	c.137C>T	c.(136-138)cCg>cTg	p.P46L		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	46	UPAR/Ly6 1.				cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.P46L(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CATCTTGTTCGGGGAGCATCC	0.657																																					p.P46L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C137T	19						.						65.0	52.0	56.0					19																	43968551		2203	4300	6503	48660391	SO:0001583	missense	27076	exon2			AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.137C>T	19.37:g.43968551G>A	ENSP00000244333:p.Pro46Leu	Somatic		Capture	Illumina HiSeq	Phase_I	48660391	NM_014400	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.976264	0.34848	.	.	ENSG00000124466	ENST00000244333;ENST00000377995	T	0.30981	1.51	4.62	4.62	0.57501	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	0.155094	0.28606	N	0.014759	T	0.13200	0.0320	N	0.08118	0	0.50813	D	0.999896	P;P	0.43750	0.816;0.816	B;B	0.35655	0.207;0.207	T	0.11251	-1.0595	10	0.09843	T	0.71	.	13.3831	0.60780	0.0:0.0:1.0:0.0	.	46;46	B2RBR3;O95274	.;LYPD3_HUMAN	L	46	ENSP00000244333:P46L	ENSP00000244333:P46L	P	-	2	0	LYPD3	48660391	0.843000	0.29541	0.964000	0.40570	0.183000	0.23260	2.384000	0.44362	2.286000	0.76751	0.456000	0.33151	CCG		0.657	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
ZNF223	7766	broad.mit.edu	37	19	44570490	44570490	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:44570490G>A	ENST00000434772.3	+	5	764	c.509G>A	c.(508-510)cGc>cAc	p.R170H	ZNF223_ENST00000591793.1_Missense_Mutation_p.R280H	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	170					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R170H(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				CAGCAAATACGCTCAGCAGAG	0.433																																					p.R170H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G509A	19						.						157.0	150.0	152.0					19																	44570490		2203	4300	6503	49262330	SO:0001583	missense	7766	exon5			AF187989	CCDS12635.1	19q13.2	2013-01-08				ENSG00000178386		"""Zinc fingers, C2H2-type"", ""-"""	13016	protein-coding gene	gene with protein product							Standard	XM_006723365		Approved		uc002oyf.1	Q9UK11		ENST00000434772.3:c.509G>A	19.37:g.44570490G>A	ENSP00000401947:p.Arg170His	Somatic		Capture	Illumina HiSeq	Phase_I	49262330	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Missense_Mutation	SNP	ENST00000434772.3	37	CCDS12635.1	.	.	.	.	.	.	.	.	.	.	g	0.026	-1.371729	0.01225	.	.	ENSG00000178386	ENST00000434772	T	0.17213	2.29	1.9	-0.29	0.12847	.	.	.	.	.	T	0.03477	0.0100	N	0.00729	-1.24	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.47598	-0.9105	9	0.02654	T	1	.	8.3469	0.32279	0.8733:0.0:0.1267:0.0	.	170	Q9UK11	ZN223_HUMAN	H	170	ENSP00000401947:R170H	ENSP00000401947:R170H	R	+	2	0	ZNF223	49262330	0.005000	0.15991	0.053000	0.19242	0.150000	0.21749	0.668000	0.25127	-0.160000	0.11002	-2.021000	0.00431	CGC		0.433	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2		
PVRL2	5819	broad.mit.edu	37	19	45381530	45381530	+	Intron	SNP	G	G	A	rs201037066	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:45381530G>A	ENST00000252483.5	+	5	1042				PVRL2_ENST00000252485.4_Missense_Mutation_p.V365M	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)	p.V365M(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		GTGGGGGGCCGTGGGGGGGAC	0.657													G|||	20	0.00399361	0.0	0.0014	5008	,	,		12451	0.0		0.005	False		,,,				2504	0.0143				p.V365M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1093A	19						.	G	,MET/VAL	6,3682		0,6,1838	5.0	4.0	4.0		,1093	4.6	1.0	19		4	21,7117		0,21,3548	yes	intron,missense	PVRL2	NM_001042724.1,NM_002856.2	,21	0,27,5386	AA,AG,GG		0.2942,0.1627,0.2494	,	,365/480	45381530	27,10799	1844	3569	5413	50073370	SO:0001627	intron_variant	5819	exon6			X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1042+3795G>A	19.37:g.45381530G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50073370	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.731265	0.69189	0.001627	0.002942	ENSG00000130202	ENST00000252485	T	0.70986	-0.53	5.66	4.63	0.57726	.	.	.	.	.	T	0.61413	0.2345	M	0.62723	1.935	0.80722	D	1	P	0.45569	0.861	B	0.33960	0.173	T	0.66131	-0.6000	9	0.72032	D	0.01	.	8.7778	0.34774	0.1701:0.0:0.8299:0.0	.	365	Q92692-2	.	M	365	ENSP00000252485:V365M	ENSP00000252485:V365M	V	+	1	0	PVRL2	50073370	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.099000	0.50267	1.401000	0.46761	0.655000	0.94253	GTG		0.657	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
MARK4	57787	broad.mit.edu	37	19	45797675	45797675	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:45797675G>T	ENST00000262891.4	+	14	1894	c.1563G>T	c.(1561-1563)gaG>gaT	p.E521D	MARK4_ENST00000300843.4_Missense_Mutation_p.E521D	NM_001199867.1	NP_001186796.1	Q96L34	MARK4_HUMAN	MAP/microtubule affinity-regulating kinase 4	521					microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|nervous system development (GO:0007399)|positive regulation of programmed cell death (GO:0043068)|protein phosphorylation (GO:0006468)	centrosome (GO:0005813)|microtubule cytoskeleton (GO:0015630)|microtubule organizing center (GO:0005815)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)|ubiquitin binding (GO:0043130)	p.E521D(3)		NS(1)|biliary_tract(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	31		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CGGGGGCTGAGCGCCCGTCAC	0.592																																					p.E521D												.	.	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.G1563T	19						.						53.0	46.0	48.0					19																	45797675		2203	4300	6503	50489515	SO:0001583	missense	57787	exon14			AB049127	CCDS12658.1, CCDS56097.1	19q13.32	2014-04-07	2002-06-12	2002-06-14	ENSG00000007047	ENSG00000007047	2.7.11.1		13538	protein-coding gene	gene with protein product		606495	"""MAP/microtubule affinity-regulating kinase like 1"""	MARKL1		23400999, 11326310, 9108484	Standard	NM_001199867		Approved	Nbla00650, FLJ90097, KIAA1860, PAR-1D	uc002paz.2	Q96L34	OTTHUMG00000181769	ENST00000262891.4:c.1563G>T	19.37:g.45797675G>T	ENSP00000262891:p.Glu521Asp	Somatic		Capture	Illumina HiSeq	Phase_I	50489515	NM_001199867	Q8NG37|Q96JG7|Q96SQ2|Q9BYD8	Missense_Mutation	SNP	ENST00000262891.4	37	CCDS56097.1	.	.	.	.	.	.	.	.	.	.	G	8.753	0.921704	0.17982	.	.	ENSG00000007047	ENST00000262891;ENST00000300843	T;T	0.16457	2.34;2.34	4.47	2.19	0.27852	.	0.067466	0.56097	D	0.000023	T	0.02970	0.0088	N	0.00583	-1.355	0.34637	D	0.720208	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.35822	-0.9773	10	0.02654	T	1	.	4.095	0.09986	0.1971:0.0:0.618:0.1849	.	521;521	Q96L34;Q96L34-2	MARK4_HUMAN;.	D	521	ENSP00000262891:E521D;ENSP00000300843:E521D	ENSP00000262891:E521D	E	+	3	2	MARK4	50489515	0.961000	0.32948	1.000000	0.80357	0.988000	0.76386	0.070000	0.14573	0.449000	0.26747	0.655000	0.94253	GAG		0.592	MARK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457537.1	NM_031417	
ERCC2	2068	broad.mit.edu	37	19	45860623	45860623	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:45860623A>G	ENST00000391945.4	-	15	1461	c.1384T>C	c.(1384-1386)Tcc>Ccc	p.S462P	ERCC2_ENST00000391944.3_Missense_Mutation_p.S384P	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	462	Mediates interaction with MMS19.				7-methylguanosine mRNA capping (GO:0006370)|aging (GO:0007568)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|central nervous system myelin formation (GO:0032289)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)|embryonic cleavage (GO:0040016)|erythrocyte maturation (GO:0043249)|extracellular matrix organization (GO:0030198)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|hair follicle maturation (GO:0048820)|hematopoietic stem cell differentiation (GO:0060218)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|spinal cord development (GO:0021510)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	cytoplasm (GO:0005737)|holo TFIIH complex (GO:0005675)|MMXD complex (GO:0071817)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.S462P(1)		large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|stomach(1)	9		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TCCAGCGGGGACAGTGTCTGT	0.642			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.S462P		yes	Rec		Xeroderma pigmentosum (D)	19	19q13.2-q13.3	2068	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 (xeroderma pigmentosum D)"""		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1384C	19						.						85.0	76.0	79.0					19																	45860623		2203	4300	6503	50552463	SO:0001583	missense	2068	exon15	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV		CCDS33049.1, CCDS46112.1	19q13.3	2014-09-17	2014-03-07		ENSG00000104884	ENSG00000104884	3.6.4.12	"""General transcription factor IIH complex subunits"""	3434	protein-coding gene	gene with protein product	"""excision repair cross-complementing rodent repair deficiency, complementation group 2 protein"", ""TFIIH basal transcription factor complex helicase XPB subunit"""	126340	"""xeroderma pigmentosum complementary group D"", ""excision repair cross-complementing rodent repair deficiency, complementation group 2"""	XPD		8413672, 2184031	Standard	NM_000400		Approved	MAG, EM9, MGC102762, MGC126218, MGC126219, TFIIH	uc002pbj.2	P18074	OTTHUMG00000048190	ENST00000391945.4:c.1384T>C	19.37:g.45860623A>G	ENSP00000375809:p.Ser462Pro	Somatic		Capture	Illumina HiSeq	Phase_I	50552463	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.128338	0.77549	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	D;T;T	0.82893	-1.66;-0.48;-0.48	5.42	5.42	0.78866	.	0.056203	0.64402	D	0.000001	D	0.92996	0.7771	H	0.95745	3.715	0.80722	D	1	D;D;D	0.67145	0.996;0.995;0.996	D;D;D	0.69824	0.957;0.966;0.927	D	0.94450	0.7666	10	0.87932	D	0	-45.7173	11.8517	0.52415	1.0:0.0:0.0:0.0	.	384;462;155	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	P	412;438;462;384	ENSP00000375805:S412P;ENSP00000375809:S462P;ENSP00000375808:S384P	ENSP00000375805:S412P	S	-	1	0	ERCC2	50552463	1.000000	0.71417	1.000000	0.80357	0.681000	0.39784	7.813000	0.86123	2.052000	0.61016	0.533000	0.62120	TCC		0.642	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400	
SYMPK	8189	broad.mit.edu	37	19	46357672	46357672	+	Missense_Mutation	SNP	C	C	T	rs371089842		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:46357672C>T	ENST00000245934.7	-	2	326	c.82G>A	c.(82-84)Gat>Aat	p.D28N		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	28	Interaction with HSF1.				cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.D28N(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		GTCATGCCATCGATGCCCGGC	0.617																																					p.D28N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G82A	19						.	C	ASN/ASP	1,4271		0,1,2135	59.0	63.0	62.0		82	5.0	1.0	19		62	0,8480		0,0,4240	no	missense	SYMPK	NM_004819.2	23	0,1,6375	TT,TC,CC		0.0,0.0234,0.0078	possibly-damaging	28/1275	46357672	1,12751	2136	4240	6376	51049512	SO:0001583	missense	8189	exon2			U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.82G>A	19.37:g.46357672C>T	ENSP00000245934:p.Asp28Asn	Somatic		Capture	Illumina HiSeq	Phase_I	51049512	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	37	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	C	19.99	3.927951	0.73327	2.34E-4	0.0	ENSG00000125755	ENST00000245934;ENST00000340643	T	0.35048	1.33	5.04	5.04	0.67666	Armadillo-type fold (1);	0.201202	0.42053	D	0.000765	T	0.25975	0.0633	N	0.19112	0.55	0.41549	D	0.988568	P;D	0.56521	0.94;0.976	B;B	0.40636	0.335;0.309	T	0.06625	-1.0816	10	0.48119	T	0.1	.	15.9837	0.80133	0.0:1.0:0.0:0.0	.	43;28	Q4LE61;Q92797	.;SYMPK_HUMAN	N	28;32	ENSP00000245934:D28N	ENSP00000245934:D28N	D	-	1	0	SYMPK	51049512	0.998000	0.40836	0.996000	0.52242	0.964000	0.63967	3.591000	0.53986	2.644000	0.89710	0.644000	0.83932	GAT		0.617	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
NANOS2	339345	broad.mit.edu	37	19	46417770	46417770	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:46417770G>A	ENST00000341294.2	-	1	266	c.182C>T	c.(181-183)aCc>aTc	p.T61I		NM_001029861.2	NP_001025032.1	P60321	NANO2_HUMAN	nanos homolog 2 (Drosophila)	61					germ-line stem cell maintenance (GO:0030718)|mRNA catabolic process (GO:0006402)|multicellular organismal development (GO:0007275)|negative regulation of meiosis (GO:0045835)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	mRNA binding (GO:0003729)|zinc ion binding (GO:0008270)	p.T61I(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	6		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		GTTGCACAGGGTCCCCAGGCC	0.662																																					p.T61I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C182T	19						.						57.0	54.0	55.0					19																	46417770		2203	4300	6503	51109610	SO:0001583	missense	339345	exon1			BC042883	CCDS33056.1	19q13.32	2003-12-01				ENSG00000188425			23292	protein-coding gene	gene with protein product		608228				12947200, 12690449	Standard	NM_001029861		Approved	NOS2	uc002pdu.3	P60321		ENST00000341294.2:c.182C>T	19.37:g.46417770G>A	ENSP00000341021:p.Thr61Ile	Somatic		Capture	Illumina HiSeq	Phase_I	51109610	NM_001029861	Q17R30|Q4G0P8	Missense_Mutation	SNP	ENST00000341294.2	37	CCDS33056.1	.	.	.	.	.	.	.	.	.	.	G	12.36	1.913744	0.33815	.	.	ENSG00000188425	ENST00000341294	T	0.44881	0.91	4.08	-0.634	0.11516	.	0.474752	0.19063	N	0.123704	T	0.17746	0.0426	N	0.08118	0	0.09310	N	1	B	0.20671	0.047	B	0.19946	0.027	T	0.10823	-1.0613	10	0.42905	T	0.14	-9.5197	4.1171	0.10086	0.0947:0.4541:0.2961:0.1551	.	61	P60321	NANO2_HUMAN	I	61	ENSP00000341021:T61I	ENSP00000341021:T61I	T	-	2	0	NANOS2	51109610	0.000000	0.05858	0.008000	0.14137	0.160000	0.22226	0.171000	0.16685	0.133000	0.18654	0.313000	0.20887	ACC		0.662	NANOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461685.1		
PTGIR	5739	broad.mit.edu	37	19	47126797	47126797	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:47126797C>T	ENST00000291294.2	-	2	819	c.686G>A	c.(685-687)cGc>cAc	p.R229H	PTGIR_ENST00000594275.1_5'UTR|PTGIR_ENST00000596260.1_Missense_Mutation_p.R229H|PTGIR_ENST00000597185.1_Intron|PTGIR_ENST00000598865.1_Missense_Mutation_p.R17H	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	229					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)	p.R229H(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CTCTCCGGTGCGCGGCCGTGG	0.672																																					p.R229H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G686A	19						.						16.0	17.0	16.0					19																	47126797		2190	4283	6473	51818637	SO:0001583	missense	5739	exon2				CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.686G>A	19.37:g.47126797C>T	ENSP00000291294:p.Arg229His	Somatic		Capture	Illumina HiSeq	Phase_I	51818637	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	.	.	.	.	.	.	.	.	.	.	C	5.635	0.301795	0.10678	.	.	ENSG00000160013	ENST00000291294	T	0.72725	-0.68	4.75	3.72	0.42706	GPCR, rhodopsin-like superfamily (1);	0.060491	0.64402	D	0.000004	T	0.63522	0.2518	L	0.49640	1.575	0.09310	N	1	B	0.16802	0.019	B	0.20955	0.032	T	0.56980	-0.7889	10	0.45353	T	0.12	-21.8935	10.9281	0.47201	0.0:0.9083:0.0:0.0917	.	229	P43119	PI2R_HUMAN	H	229	ENSP00000291294:R229H	ENSP00000291294:R229H	R	-	2	0	PTGIR	51818637	0.477000	0.25909	0.056000	0.19401	0.027000	0.11550	3.094000	0.50227	1.219000	0.43474	-0.244000	0.11960	CGC		0.672	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
CCDC9	26093	broad.mit.edu	37	19	47774382	47774382	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:47774382C>A	ENST00000221922.6	+	11	1351	c.1129C>A	c.(1129-1131)Cca>Aca	p.P377T		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	377	Pro-rich.						poly(A) RNA binding (GO:0044822)	p.P377T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		GGCAGCATCCCCAGCCCCTGA	0.627																																					p.P377T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1129A	19						.						38.0	40.0	39.0					19																	47774382		2202	4295	6497	52466222	SO:0001583	missense	26093	exon11			AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1129C>A	19.37:g.47774382C>A	ENSP00000221922:p.Pro377Thr	Somatic		Capture	Illumina HiSeq	Phase_I	52466222	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.728553	0.30593	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.22539	1.95	4.34	-4.29	0.03721	.	0.986437	0.08262	N	0.972852	T	0.09024	0.0223	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40040	-0.9584	10	0.09843	T	0.71	1.3768	2.6446	0.04980	0.1373:0.2319:0.4414:0.1894	.	377	Q9Y3X0	CCDC9_HUMAN	T	377;359	ENSP00000221922:P377T	ENSP00000221922:P377T	P	+	1	0	CCDC9	52466222	0.001000	0.12720	0.000000	0.03702	0.328000	0.28507	-0.116000	0.10724	-0.407000	0.07576	0.305000	0.20034	CCA		0.627	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603	
CYTH2	9266	broad.mit.edu	37	19	48976634	48976634	+	Splice_Site	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:48976634A>G	ENST00000452733.2	+	5	909	c.433A>G	c.(433-435)Agg>Ggg	p.R145G	CYTH2_ENST00000427476.1_Splice_Site_p.R145G			Q99418	CYH2_HUMAN	cytohesin 2	145	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)	p.R145G(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCAGGCCCTCAGGTGAGTGAG	0.507																																					p.R145G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A433G	19						.						82.0	71.0	74.0					19																	48976634		2203	4300	6503	53668446	SO:0001630	splice_region_variant	9266	exon5			X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.434+1A>G	19.37:g.48976634A>G		Somatic		Capture	Illumina HiSeq	Phase_I	53668446	NM_004228	A8K8P0|Q8IXY9|Q92958	Missense_Mutation	SNP	ENST00000452733.2	37	CCDS12722.1	.	.	.	.	.	.	.	.	.	.	A	17.72	3.458066	0.63401	.	.	ENSG00000105443	ENST00000452733;ENST00000427476;ENST00000325139	T;T;T	0.71698	-0.59;-0.59;-0.59	4.49	3.39	0.38822	.	0.000000	0.85682	D	0.000000	D	0.90710	0.7085	H	0.99881	4.885	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90836	0.4720	10	0.87932	D	0	.	9.3875	0.38352	0.7472:0.2527:0.0:0.0	.	145	Q99418-2	.	G	145;145;167	ENSP00000408236:R145G;ENSP00000391648:R145G;ENSP00000314566:R167G	ENSP00000314566:R167G	R	+	1	2	CYTH2	53668446	0.974000	0.33945	1.000000	0.80357	0.747000	0.42532	1.048000	0.30379	0.781000	0.33589	0.379000	0.24179	AGG		0.507	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228	Missense_Mutation
FGF21	26291	broad.mit.edu	37	19	49261338	49261338	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:49261338T>C	ENST00000593756.1	+	4	1063	c.491T>C	c.(490-492)tTc>tCc	p.F164S	FGF21_ENST00000222157.3_Missense_Mutation_p.F164S|FUT1_ENST00000310160.3_5'Flank			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	164					cell-cell signaling (GO:0007267)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		CCAGCTCGCTTCCTGCCACTA	0.687																																					p.F164S												.	.	0			c.T491C	19						.						18.0	25.0	23.0					19																	49261338		2189	4286	6475	53953150	SO:0001583	missense	26291	exon3			AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.491T>C	19.37:g.49261338T>C	ENSP00000471477:p.Phe164Ser	None		Capture	Illumina HiSeq	Phase_I	53953150	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	T	8.289	0.817202	0.16607	.	.	ENSG00000105550	ENST00000222157	D	0.90620	-2.7	4.44	3.41	0.39046	.	0.592551	0.16992	N	0.191254	D	0.83450	0.5257	N	0.24115	0.695	0.42695	D	0.993592	P	0.48162	0.906	B	0.43445	0.42	T	0.81566	-0.0874	10	0.87932	D	0	-13.0334	6.9012	0.24283	0.0:0.1062:0.0:0.8938	.	164	Q9NSA1	FGF21_HUMAN	S	164	ENSP00000222157:F164S	ENSP00000222157:F164S	F	+	2	0	FGF21	53953150	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	1.557000	0.36299	0.836000	0.34901	-0.558000	0.04189	TTC		0.687	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1		
FLT3LG	2323	broad.mit.edu	37	19	49978963	49978963	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:49978963C>T	ENST00000594009.1	+	2	128	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L	FLT3LG_ENST00000600429.1_Silent_p.L17L|FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000344019.3_Silent_p.L17L|FLT3LG_ENST00000596435.1_Silent_p.L17L|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000597551.1_Silent_p.L17L|FLT3LG_ENST00000204637.2_5'UTR|CTD-3148I10.9_ENST00000599536.1_Intron	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	17					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)	p.L17L(1)		large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		TCTCCTCCTGCTGCTGCTGCT	0.627																																					p.L17L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C49T	19						.						73.0	63.0	67.0					19																	49978963		2203	4300	6503	54670775	SO:0001819	synonymous_variant	2323	exon3			U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.49C>T	19.37:g.49978963C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54670775	NM_001459	A0AVC2|B9EGH2|Q05C96	Silent	SNP	ENST00000594009.1	37	CCDS12767.1																																																																																				0.627	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		
MED25	81857	broad.mit.edu	37	19	50332240	50332240	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:50332240C>T	ENST00000312865.6	+	5	471	c.418C>T	c.(418-420)Cgg>Tgg	p.R140W	MED25_ENST00000538643.1_Intron	NM_030973.3	NP_112235.2	Q71SY5	MED25_HUMAN	mediator complex subunit 25	140	Interaction with the Mediator complex.				cell death (GO:0008219)|gene expression (GO:0010467)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of chromatin binding (GO:0035563)|positive regulation of mediator complex assembly (GO:2001178)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|transcription factor binding (GO:0008134)	p.R140W(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	17		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00822)|GBM - Glioblastoma multiforme(134;0.0122)		CCAGACGCACCGGGTCTGCCT	0.557																																					p.R140W	GBM(51;894 1657 37868)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C418T	19						.						80.0	62.0	68.0					19																	50332240		2203	4300	6503	55024052	SO:0001583	missense	81857	exon5			AL136746	CCDS33075.1	19q13.3	2014-09-17	2007-07-30			ENSG00000104973			28845	protein-coding gene	gene with protein product		610197	"""mediator of RNA polymerase II transcription, subunit 25 homolog (S. cerevisiae)"""			9110174, 11230166	Standard	NM_030973		Approved	ARC92, ACID1, TCBAP0758, DKFZp434K0512	uc002ppw.2	Q71SY5		ENST00000312865.6:c.418C>T	19.37:g.50332240C>T	ENSP00000326767:p.Arg140Trp	Somatic		Capture	Illumina HiSeq	Phase_I	55024052	NM_030973	A8K095|B9TX30|O95783|Q6P143|Q6QMH5|Q707U4|Q8TB55|Q9H0L5|Q9HB34	Missense_Mutation	SNP	ENST00000312865.6	37	CCDS33075.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.273293	0.40194	.	.	ENSG00000104973	ENST00000355584;ENST00000377077;ENST00000312881;ENST00000312865;ENST00000456294;ENST00000542221;ENST00000544580	T	0.16897	2.31	4.54	2.37	0.29283	.	0.142708	0.46758	D	0.000266	T	0.27419	0.0673	L	0.46157	1.445	0.80722	D	1	D	0.69078	0.997	D	0.63283	0.913	T	0.01460	-1.1349	10	0.87932	D	0	.	8.013	0.30363	0.4359:0.4187:0.1454:0.0	.	140	Q71SY5	MED25_HUMAN	W	140	ENSP00000326767:R140W	ENSP00000326767:R140W	R	+	1	2	MED25	55024052	1.000000	0.71417	0.990000	0.47175	0.031000	0.12232	2.804000	0.47931	0.645000	0.30675	-0.962000	0.02626	CGG		0.557	MED25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465316.1	NM_030973	
NUP62	23636	broad.mit.edu	37	19	50412113	50412113	+	Missense_Mutation	SNP	C	C	T	rs139269985	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:50412113C>T	ENST00000596217.1	-	2	2839	c.952G>A	c.(952-954)Gca>Aca	p.A318T	NUP62_ENST00000352066.3_Missense_Mutation_p.A318T|NUP62_ENST00000422090.2_Missense_Mutation_p.A318T|NUP62_ENST00000413454.1_Missense_Mutation_p.A318T|NUP62_ENST00000597029.1_Missense_Mutation_p.A318T|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000595948.1_Intron|IL4I1_ENST00000341114.3_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	318	Ala-rich.				carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|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 MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)	p.A318T(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CCTGCAGCTGCGCCAGGGCCA	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		15206	0.0		0.0	False		,,,				2504	0.0				p.A318T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G952A	19						.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,	2,4346		0,2,2172	30.0	36.0	34.0		952,952,952,952,952,	0.4	0.0	19	dbSNP_134	34	0,8512		0,0,4256	yes	missense,missense,missense,missense,missense,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	58,58,58,58,58,	0,2,6428	TT,TC,CC		0.0,0.046,0.0156	benign,benign,benign,benign,benign,	318/523,318/523,318/523,318/523,318/523,	50412113	2,12858	2174	4256	6430	55103925	SO:0001583	missense	23636	exon2			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.952G>A	19.37:g.50412113C>T	ENSP00000471191:p.Ala318Thr	Somatic		Capture	Illumina HiSeq	Phase_I	55103925	NM_012346	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	ENST00000596217.1	37	CCDS12788.1	.	.	.	.	.	.	.	.	.	.	C	7.298	0.612541	0.14066	4.6E-4	0.0	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.38401	1.14;1.14;1.14	5.73	0.444	0.16592	Nucleoporin, NSP1-like, C-terminal (1);	0.459961	0.19795	N	0.105897	T	0.16769	0.0403	N	0.22421	0.69	0.09310	N	1	B	0.29115	0.233	B	0.17722	0.019	T	0.11817	-1.0572	9	.	.	.	-3.6436	4.2607	0.10739	0.1571:0.5177:0.0:0.3252	.	318	P37198	NUP62_HUMAN	T	318	ENSP00000305503:A318T;ENSP00000407331:A318T;ENSP00000387991:A318T	.	A	-	1	0	NUP62	55103925	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	-0.383000	0.07398	0.238000	0.21222	0.655000	0.94253	GCA		0.637	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719	
POLD1	5424	broad.mit.edu	37	19	50917108	50917108	+	Missense_Mutation	SNP	C	C	T	rs199783227		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:50917108C>T	ENST00000440232.2	+	19	2413	c.2360C>T	c.(2359-2361)cCg>cTg	p.P787L	POLD1_ENST00000599857.1_Missense_Mutation_p.P787L|POLD1_ENST00000595904.1_Missense_Mutation_p.P813L|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	787			P -> L (found in a colorectal sample; somatic mutation). {ECO:0000269|PubMed:23263490}.		base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.P787L(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		GGTCACTTCCCGTCGCCCATC	0.647								DNA polymerases (catalytic subunits)																													p.P787L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2360T	19						.						53.0	56.0	55.0					19																	50917108		2203	4300	6503	55608920	SO:0001583	missense	5424	exon19				CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2360C>T	19.37:g.50917108C>T	ENSP00000406046:p.Pro787Leu	Somatic		Capture	Illumina HiSeq	Phase_I	55608920	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	37	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	C	9.725	1.160806	0.21538	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.16897	2.31	4.75	2.57	0.30868	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.336081	0.30901	N	0.008646	T	0.14270	0.0345	L	0.52011	1.625	0.34557	D	0.711932	B;B	0.24823	0.112;0.01	B;B	0.24269	0.052;0.031	T	0.15009	-1.0452	10	0.20519	T	0.43	-22.7483	9.3205	0.37962	0.0:0.755:0.0:0.245	.	813;787	E7EVW0;P28340	.;DPOD1_HUMAN	L	787;788	ENSP00000406046:P787L	ENSP00000366129:P788L	P	+	2	0	POLD1	55608920	0.588000	0.26799	0.837000	0.33122	0.754000	0.42855	1.451000	0.35145	1.144000	0.42321	0.556000	0.70494	CCG		0.647	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
LRRC4B	94030	broad.mit.edu	37	19	51021623	51021623	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:51021623G>A	ENST00000599957.1	-	3	1544	c.1347C>T	c.(1345-1347)gcC>gcT	p.A449A	LRRC4B_ENST00000389201.3_Silent_p.A449A			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	449	Ig-like C2-type.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)		p.A449A(1)		breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		CGTTGAGCGTGGCCGAGGCGG	0.706																																					p.A449A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1347T	19						.						45.0	52.0	49.0					19																	51021623		2149	4230	6379	55713435	SO:0001819	synonymous_variant	94030	exon3			BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"""Immunoglobulin superfamily / I-set domain containing"", ""Endogenous ligands"""	25042	protein-coding gene	gene with protein product	"""netrin-G3 ligand"""		"""leucine-rich repeats and immunoglobulin-like domains 4"""	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.1347C>T	19.37:g.51021623G>A		Somatic		Capture	Illumina HiSeq	Phase_I	55713435	NM_001080457	Q3ZCQ4|Q58F20	Silent	SNP	ENST00000599957.1	37	CCDS42595.1																																																																																				0.706	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
CTU1	90353	broad.mit.edu	37	19	51602367	51602367	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:51602367C>T	ENST00000421832.2	-	3	582	c.538G>A	c.(538-540)Gtg>Atg	p.V180M		NM_145232.3	NP_660275.2			cytosolic thiouridylase subunit 1									p.V180M(1)		large_intestine(2)|lung(1)|urinary_tract(1)	4						TTCATGAGCACGGTCTCCGCC	0.776																																					p.V180M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G538A	19						.						6.0	9.0	8.0					19																	51602367		1961	3827	5788	56294179	SO:0001583	missense	90353	exon3				CCDS12824.1	19q13.41	2013-05-31	2013-05-31	2009-08-19		ENSG00000142544			29590	protein-coding gene	gene with protein product		612694	"""ATP binding domain 3"", ""cytosolic thiouridylase subunit 1 homolog (S. pombe)"""	ATPBD3		19017811	Standard	NM_145232		Approved	MGC17332, NCS6	uc010eop.3	Q7Z7A3		ENST00000421832.2:c.538G>A	19.37:g.51602367C>T	ENSP00000390011:p.Val180Met	Somatic		Capture	Illumina HiSeq	Phase_I	56294179	NM_145232		Missense_Mutation	SNP	ENST00000421832.2	37	CCDS12824.1	.	.	.	.	.	.	.	.	.	.	.	24.3	4.514640	0.85389	.	.	ENSG00000142544	ENST00000421832	T	0.47177	0.85	3.64	3.64	0.41730	Rossmann-like alpha/beta/alpha sandwich fold (1);tRNA(Ile)-lysidine/2-thiocytidine synthase (1);	0.000000	0.85682	D	0.000000	T	0.67942	0.2947	M	0.81112	2.525	0.58432	D	0.999999	D	0.89917	1.0	D	0.72075	0.976	T	0.74074	-0.3782	10	0.87932	D	0	-21.4847	13.138	0.59419	0.0:1.0:0.0:0.0	.	180	Q7Z7A3	CTU1_HUMAN	M	180	ENSP00000390011:V180M	ENSP00000390011:V180M	V	-	1	0	CTU1	56294179	1.000000	0.71417	0.982000	0.44146	0.903000	0.53119	6.310000	0.72830	1.720000	0.51447	0.400000	0.26472	GTG		0.776	CTU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464292.1	NM_145232	
CD33	945	broad.mit.edu	37	19	51738479	51738479	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:51738479C>T	ENST00000262262.4	+	5	834	c.813C>T	c.(811-813)ctC>ctT	p.L271L	CD33_ENST00000436584.2_Silent_p.L144L|CD33_ENST00000391796.3_Silent_p.L271L|CD33_ENST00000421133.2_Silent_p.L144L	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	271					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.L271L(1)		NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	CAGCCCTGCTCGCTCTTTGTC	0.517																																					p.L271L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C813T	19						.						147.0	119.0	129.0					19																	51738479		2203	4300	6503	56430291	SO:0001819	synonymous_variant	945	exon5			M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.813C>T	19.37:g.51738479C>T		Somatic		Capture	Illumina HiSeq	Phase_I	56430291	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Silent	SNP	ENST00000262262.4	37	CCDS33084.1																																																																																				0.517	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
SIGLEC6	946	broad.mit.edu	37	19	52031052	52031052	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:52031052C>A	ENST00000425629.3	-	7	1291	c.1137G>T	c.(1135-1137)caG>caT	p.Q379H	SIGLEC6_ENST00000359982.4_Intron|SIGLEC6_ENST00000436458.1_Missense_Mutation_p.Q327H|SIGLEC6_ENST00000474054.1_5'UTR|SIGLEC6_ENST00000391797.3_Intron|SIGLEC6_ENST00000346477.3_Missense_Mutation_p.Q363H|SIGLEC6_ENST00000343300.4_Intron	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	379					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)	p.Q352H(1)		endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		TTTGCACTGGCTGGGCTGCTT	0.488																																					p.Q379H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1137T	19						.						173.0	171.0	172.0					19																	52031052		1939	4156	6095	56722864	SO:0001583	missense	946	exon7			D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1137G>T	19.37:g.52031052C>A	ENSP00000401502:p.Gln379His	Somatic		Capture	Illumina HiSeq	Phase_I	56722864	NM_001245	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Missense_Mutation	SNP	ENST00000425629.3	37	CCDS12834.3	.	.	.	.	.	.	.	.	.	.	.	14.83	2.653835	0.47362	.	.	ENSG00000105492	ENST00000346477;ENST00000391797;ENST00000425629;ENST00000436458	T;T	0.49139	1.23;0.79	3.02	1.98	0.26296	.	1.765100	0.03783	N	0.261716	T	0.57681	0.2070	L	0.50333	1.59	0.09310	N	1	D;D;D	0.64830	0.968;0.994;0.984	B;P;P	0.58820	0.374;0.846;0.626	T	0.35968	-0.9767	10	0.49607	T	0.09	.	5.9377	0.19175	0.0:0.8534:0.0:0.1466	.	327;363;379	C9JBE5;O43699-3;O43699	.;.;SIGL6_HUMAN	H	352;363;379;327	ENSP00000401502:Q379H;ENSP00000410679:Q327H	ENSP00000344064:Q352H	Q	-	3	2	SIGLEC6	56722864	0.000000	0.05858	0.005000	0.12908	0.385000	0.30292	-0.849000	0.04322	0.854000	0.35336	0.411000	0.27672	CAG		0.488	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
FPR3	2359	broad.mit.edu	37	19	52327673	52327673	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:52327673C>T	ENST00000339223.4	+	2	851	c.672C>T	c.(670-672)atC>atT	p.I224I	FPR3_ENST00000595991.1_Silent_p.I224I	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	224					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)	p.I224I(1)		NS(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)	35						ATGGGATCATCGCTGCCAAAA	0.468																																					p.I224I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C672T	19						.						149.0	122.0	131.0					19																	52327673		2203	4300	6503	57019485	SO:0001819	synonymous_variant	2359	exon2				CCDS12841.1	19q13.3-q13.4	2012-08-08	2008-04-17	2008-04-17		ENSG00000187474		"""GPCR / Class A : Formyl peptide receptors"""	3828	protein-coding gene	gene with protein product		136539	"""formyl peptide receptor-like 2"""	FPRL2		1612600, 8198572	Standard	NM_002030		Approved	FPRH1, FMLPY, RMLP-R-I	uc002pxt.1	P25089		ENST00000339223.4:c.672C>T	19.37:g.52327673C>T		Somatic		Capture	Illumina HiSeq	Phase_I	57019485	NM_002030		Silent	SNP	ENST00000339223.4	37	CCDS12841.1																																																																																				0.468	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030	
ZNF350	59348	broad.mit.edu	37	19	52468332	52468332	+	Silent	SNP	G	G	A	rs542665274		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:52468332G>A	ENST00000243644.4	-	5	1601	c.1374C>T	c.(1372-1374)aaC>aaT	p.N458N	HCCAT3_ENST00000595010.1_RNA|HCCAT3_ENST00000600253.1_RNA|ZNF350_ENST00000600703.1_5'Flank	NM_021632.3	NP_067645.3	Q9GZX5	ZN350_HUMAN	zinc finger protein 350	458					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.N458N(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(7)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_neural(266;0.0505)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0179)		TAGTCGCCCCGTTAGCAGAGT	0.532													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20561	0.0		0.0	False		,,,				2504	0.0				p.N458N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1374T	19						.						88.0	76.0	80.0					19																	52468332		2203	4300	6503	57160144	SO:0001819	synonymous_variant	59348	exon5			AF295096	CCDS12845.1	19q13.41	2013-05-23			ENSG00000256683	ENSG00000256683		"""Zinc fingers, C2H2-type"", ""-"""	16656	protein-coding gene	gene with protein product		605422				11090615, 11161714	Standard	NM_021632		Approved	ZBRK1, ZFQR	uc002pyd.3	Q9GZX5	OTTHUMG00000182538	ENST00000243644.4:c.1374C>T	19.37:g.52468332G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57160144	NM_021632	Q96G73|Q9HAQ4	Silent	SNP	ENST00000243644.4	37	CCDS12845.1																																																																																				0.532	ZNF350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462278.1	NM_021632	
ZNF468	90333	broad.mit.edu	37	19	53344823	53344823	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:53344823G>A	ENST00000595646.1	-	4	844	c.724C>T	c.(724-726)Caa>Taa	p.Q242*	ZNF468_ENST00000390651.4_Nonsense_Mutation_p.Q189*|ZNF468_ENST00000243639.4_3'UTR|ZNF28_ENST00000594602.1_Intron|ZNF468_ENST00000396409.4_Nonsense_Mutation_p.Q189*			Q5VIY5	ZN468_HUMAN	zinc finger protein 468	242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q242*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(3)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(134;0.0358)		CATTTACATTGTTTCTCTTCT	0.358																																					p.Q189X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C565T	19						.						102.0	89.0	93.0					19																	53344823		2203	4300	6503	58036635	SO:0001587	stop_gained	90333	exon5			AK023558	CCDS33094.1, CCDS62781.1	19q13.41	2013-01-08				ENSG00000204604		"""Zinc fingers, C2H2-type"", ""-"""	33105	protein-coding gene	gene with protein product						16144304	Standard	NM_001277120		Approved		uc002qaf.3	Q5VIY5		ENST00000595646.1:c.724C>T	19.37:g.53344823G>A	ENSP00000470381:p.Gln242*	Somatic		Capture	Illumina HiSeq	Phase_I	58036635	NM_199132	A8MV20|Q5CZB8|Q5VIY4|Q68DI7	Nonsense_Mutation	SNP	ENST00000595646.1	37	CCDS33094.1	.	.	.	.	.	.	.	.	.	.	g	22.1	4.243950	0.79912	.	.	ENSG00000204604	ENST00000243639;ENST00000396409;ENST00000390651	.	.	.	1.83	0.697	0.18081	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	4.6376	0.12531	0.1556:0.2261:0.6183:0.0	.	.	.	.	X	242;189;189	.	ENSP00000243639:Q242X	Q	-	1	0	ZNF468	58036635	0.006000	0.16342	0.000000	0.03702	0.041000	0.13682	1.490000	0.35573	0.109000	0.17891	0.416000	0.27883	CAA		0.358	ZNF468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463098.1	NM_001008801	
PRKCG	5582	broad.mit.edu	37	19	54395012	54395012	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:54395012G>A	ENST00000263431.3	+	6	896	c.614G>A	c.(613-615)cGg>cAg	p.R205Q	PRKCG_ENST00000542049.1_Missense_Mutation_p.R92Q|PRKCG_ENST00000536044.1_Missense_Mutation_p.R205Q|PRKCG_ENST00000540413.1_Missense_Mutation_p.R205Q	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	205	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)	p.R205Q(1)		large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	CCAGACCCTCGGAACCTGACG	0.532																																					p.R205Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G614A	19						.						144.0	121.0	129.0					19																	54395012		2203	4300	6503	59086824	SO:0001583	missense	5582	exon6			M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.614G>A	19.37:g.54395012G>A	ENSP00000263431:p.Arg205Gln	Somatic		Capture	Illumina HiSeq	Phase_I	59086824	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	15.70	2.911921	0.52439	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000542049	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.25	3.08	0.35506	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.22666	0.0547	N	0.25647	0.755	0.30652	N	0.755333	P;B;B;B;B	0.39181	0.663;0.008;0.091;0.01;0.003	B;B;B;B;B	0.19391	0.025;0.003;0.014;0.006;0.003	T	0.17715	-1.0360	9	0.52906	T	0.07	.	7.8663	0.29539	0.2622:0.0:0.7378:0.0	.	92;205;205;205;205	B7Z8Q0;F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;.;KPCG_HUMAN	Q	205;205;205;92	ENSP00000440541:R205Q;ENSP00000443493:R205Q;ENSP00000263431:R205Q;ENSP00000438090:R92Q	ENSP00000263431:R205Q	R	+	2	0	PRKCG	59086824	1.000000	0.71417	0.998000	0.56505	0.949000	0.60115	5.870000	0.69620	1.364000	0.46038	-0.258000	0.10820	CGG		0.532	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
PRPF31	26121	broad.mit.edu	37	19	54627181	54627181	+	Missense_Mutation	SNP	C	C	T	rs119475043		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:54627181C>T	ENST00000321030.4	+	7	930	c.581C>T	c.(580-582)gCg>gTg	p.A194V	PRPF31_ENST00000391755.1_Missense_Mutation_p.A194V|PRPF31_ENST00000419967.1_Missense_Mutation_p.A194V|PRPF31_ENST00000498612.1_3'UTR|AC012314.8_ENST00000452097.1_RNA	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	194			A -> E (in RP11; mislocation of the protein in the cytoplasm and reduced interaction with PRPF6; the result may be a deficiency in splicing function in the retina). {ECO:0000269|PubMed:11545739}.		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.A194V(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)					TGCGACATGGCGCTGGAGCTG	0.657																																					p.A194V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C581T	19	GRCh37	CM014595	PRPF31	M	rs119475043	.						83.0	64.0	70.0					19																	54627181		2203	4300	6503	59318993	SO:0001583	missense	26121	exon7			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.581C>T	19.37:g.54627181C>T	ENSP00000324122:p.Ala194Val	Somatic		Capture	Illumina HiSeq	Phase_I	59318993	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Missense_Mutation	SNP	ENST00000321030.4	37	CCDS12879.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.125088	0.77436	.	.	ENSG00000105618	ENST00000321030;ENST00000445811;ENST00000263436;ENST00000419967;ENST00000445124;ENST00000447810;ENST00000391755	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;0.4;0.4	4.96	4.96	0.65561	Pre-mRNA processing ribonucleoprotein, snoRNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	N	0.26130	0.795	0.80722	D	1	D;D	0.56746	0.977;0.958	P;B	0.44447	0.45;0.231	T	0.28004	-1.0057	10	0.07030	T	0.85	-41.352	17.368	0.87368	0.0:1.0:0.0:0.0	.	194;194	E7ESA8;Q8WWY3	.;PRP31_HUMAN	V	194	ENSP00000324122:A194V;ENSP00000395894:A194V;ENSP00000405166:A194V;ENSP00000408980:A194V;ENSP00000395089:A194V;ENSP00000375635:A194V	ENSP00000263436:A194V	A	+	2	0	PRPF31	59318993	1.000000	0.71417	0.995000	0.50966	0.708000	0.40852	6.928000	0.75846	2.469000	0.83416	0.609000	0.83330	GCG		0.657	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
LILRB5	10990	broad.mit.edu	37	19	54760466	54760466	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:54760466C>T	ENST00000316219.5	-	3	348	c.241G>A	c.(241-243)Gcc>Acc	p.A81T	LILRB5_ENST00000450632.1_Missense_Mutation_p.A81T|LILRB5_ENST00000345866.6_Missense_Mutation_p.A81T|LILRB5_ENST00000449561.2_Missense_Mutation_p.A81T	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	81	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.A81T(2)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGGAACTTGGCCTTGGCTCCA	0.612																																					p.A81T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G241A	19						.						239.0	227.0	231.0					19																	54760466		2203	4300	6503	59452278	SO:0001583	missense	10990	exon3			AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.241G>A	19.37:g.54760466C>T	ENSP00000320390:p.Ala81Thr	Somatic		Capture	Illumina HiSeq	Phase_I	59452278	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	14.67	2.604735	0.46423	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.12879	2.64;2.64;2.64;2.64	3.29	1.1	0.20463	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.660669	0.13338	N	0.395404	T	0.27697	0.0681	M	0.67953	2.075	0.09310	N	1	P;D;D;D;D	0.71674	0.839;0.996;0.998;0.996;0.986	P;D;P;P;P	0.66847	0.552;0.947;0.905;0.9;0.807	T	0.06679	-1.0813	10	0.56958	D	0.05	.	5.1777	0.15143	0.0:0.7139:0.0:0.2861	.	81;72;81;81;81	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	T	81	ENSP00000320390:A81T;ENSP00000414225:A81T;ENSP00000406478:A81T;ENSP00000263430:A81T	ENSP00000320390:A81T	A	-	1	0	LILRB5	59452278	0.004000	0.15560	0.004000	0.12327	0.027000	0.11550	1.274000	0.33132	0.226000	0.20979	0.585000	0.79938	GCC		0.612	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
KIR3DL3	115653	broad.mit.edu	37	19	55239086	55239086	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:55239086G>T	ENST00000291860.1	+	4	383	c.365G>T	c.(364-366)aGa>aTa	p.R122I	KIR2DL4_ENST00000396284.2_Intron|CTB-61M7.1_ENST00000400864.3_RNA|KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR3DL1_ENST00000538269.1_Intron	NM_153443.3	NP_703144.2	Q8N743	KI3L3_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 3	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R122I(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(3)|prostate(1)|skin(1)	21				GBM - Glioblastoma multiforme(193;0.0192)		GGAGTCCACAGAAAACCTTCC	0.532																																					p.R122I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G365T	19						.						8.0	8.0	8.0					19																	55239086		1792	3029	4821	59930898	SO:0001583	missense	115653	exon4			AF352324	CCDS12903.1	19q13.4	2014-05-22			ENSG00000242019	ENSG00000242019		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	16312	protein-coding gene	gene with protein product		610095				11513144	Standard	NM_153443		Approved	KIRC1, KIR3DL7, KIR44, CD158z	uc002qgu.1	Q8N743	OTTHUMG00000065884	ENST00000291860.1:c.365G>T	19.37:g.55239086G>T	ENSP00000291860:p.Arg122Ile	Somatic		Capture	Illumina HiSeq	Phase_I	59930898	NM_153443	A9PL62|A9PL64|A9PL65|A9PL66|A9PL67|A9PL68|A9PZV4|A9PZV7|A9PZV8|A9Q066|A9Q0R5|A9Q242|A9Q250|A9Q251|O95056|Q1X775|Q1X777|Q1X778|Q1X779|Q1X780|Q1X781|Q1X782|Q1X783|Q7Z7N4|Q8NHI2|Q8NHI3|Q9UEI4	Missense_Mutation	SNP	ENST00000291860.1	37	CCDS12903.1	.	.	.	.	.	.	.	.	.	.	N	7.919	0.738108	0.15574	.	.	ENSG00000242019	ENST00000291860	T	0.00792	5.69	1.5	-1.57	0.08506	Immunoglobulin-like fold (1);	.	.	.	.	T	0.00815	0.0027	L	0.49350	1.555	0.09310	N	1	P	0.35745	0.518	B	0.31946	0.138	T	0.44128	-0.9348	9	0.87932	D	0	.	3.2545	0.06827	0.0:0.2936:0.4098:0.2965	.	122	Q8N743	KI3L3_HUMAN	I	122	ENSP00000291860:R122I	ENSP00000291860:R122I	R	+	2	0	KIR3DL3	59930898	0.001000	0.12720	0.001000	0.08648	0.030000	0.12068	0.007000	0.13174	-0.294000	0.08973	0.407000	0.27541	AGA		0.532	KIR3DL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141147.1	NM_153443	
KIR3DL2	3812	broad.mit.edu	37	19	55363678	55363678	+	Missense_Mutation	SNP	G	G	A	rs142612567	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:55363678G>A	ENST00000326321.3	+	3	329	c.296G>A	c.(295-297)cGc>cAc	p.R99H	KIR3DL1_ENST00000402254.2_Intron|KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R99H	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	99	Ig-like C2-type 1.				cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.R99H(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		CGGGGTTCACGCCCACACTCC	0.597																																					p.R99H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G296A	19						.	A	HIS/ARG	0,4324		0,0,2162	67.0	61.0	63.0		296	-1.0	0.0	19	dbSNP_134	63	1,8247		0,1,4123	no	missense	KIR3DL2	NM_006737.3	29	0,1,6285	AA,AG,GG		0.0121,0.0,0.0080	benign	99/456	55363678	1,12571	2162	4124	6286	60055490	SO:0001583	missense	3812	exon3			L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.296G>A	19.37:g.55363678G>A	ENSP00000325525:p.Arg99His	Somatic		Capture	Illumina HiSeq	Phase_I	60055490	NM_006737	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	a	0.007	-1.942664	0.00479	0.0	1.21E-4	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00730	5.77;5.77	1.62	-0.989	0.10242	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.044860	0.02291	U	0.070352	T	0.00271	0.0008	N	0.00210	-1.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.45425	-0.9262	10	0.02654	T	1	.	2.2486	0.04038	0.3841:0.0:0.3658:0.2502	.	99;99	Q95366;P43630	.;KI3L2_HUMAN	H	99	ENSP00000325525:R99H;ENSP00000270442:R99H	ENSP00000270442:R99H	R	+	2	0	KIR3DL2	60055490	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	0.094000	0.15107	-0.915000	0.03823	-1.451000	0.01035	CGC		0.597	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1		
NLRP2	55655	broad.mit.edu	37	19	55493791	55493791	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:55493791C>T	ENST00000543010.1	+	6	868	c.725C>T	c.(724-726)gCg>gTg	p.A242V	NLRP2_ENST00000263437.6_Missense_Mutation_p.A239V|NLRP2_ENST00000391721.4_Missense_Mutation_p.A218V|NLRP2_ENST00000537859.1_Missense_Mutation_p.A220V|NLRP2_ENST00000427260.2_Missense_Mutation_p.A219V|NLRP2_ENST00000538819.1_Missense_Mutation_p.A218V|NLRP2_ENST00000339757.7_Missense_Mutation_p.A220V|NLRP2_ENST00000448584.2_Missense_Mutation_p.A242V	NM_001174081.1	NP_001167552.1	Q9NX02	NALP2_HUMAN	NLR family, pyrin domain containing 2	242	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|Pyrin domain binding (GO:0032090)	p.A242V(3)		large_intestine(4)|liver(1)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	11			BRCA - Breast invasive adenocarcinoma(297;0.163)	GBM - Glioblastoma multiforme(193;0.028)		TTCAAATATGCGTTCTACCTC	0.552																																					p.A219V												.	.	3	Substitution - Missense(3)	large_intestine(2)|prostate(1)	c.C656T	19						.						54.0	49.0	51.0					19																	55493791		2203	4300	6503	60185603	SO:0001583	missense	55655	exon7			AK000517	CCDS12913.1, CCDS54318.1, CCDS54319.1	19q13.42	2008-02-05	2006-12-08	2006-12-08	ENSG00000022556	ENSG00000022556		"""Nucleotide-binding domain and leucine rich repeat containing"""	22948	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 2"""	609364	"""NACHT, leucine rich repeat and PYD containing 2"""	NALP2		12563287, 11270363	Standard	NM_001174081		Approved	FLJ20510, PYPAF2, NBS1, PAN1, CLR19.9	uc021vbq.1	Q9NX02	OTTHUMG00000167763	ENST00000543010.1:c.725C>T	19.37:g.55493791C>T	ENSP00000445135:p.Ala242Val	Somatic		Capture	Illumina HiSeq	Phase_I	60185603	NM_001174083	B4DZL7|I3L0G4|Q53FL5|Q59G09|Q8IXT0|Q9BVN5|Q9H6G6|Q9HAV9|Q9NWK3	Missense_Mutation	SNP	ENST00000543010.1	37	CCDS12913.1	.	.	.	.	.	.	.	.	.	.	C	9.624	1.134538	0.21123	.	.	ENSG00000022556	ENST00000543010;ENST00000391721;ENST00000339757;ENST00000448584;ENST00000537859;ENST00000427260;ENST00000538819;ENST00000263437	T;T;T;T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81;-0.81	1.41	0.267	0.15622	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.62950	0.2470	N	0.11131	0.1	0.09310	N	1	D;D;D;D;D	0.89917	1.0;0.999;0.999;0.997;0.999	D;D;D;P;D	0.75484	0.986;0.919;0.951;0.704;0.951	T	0.56547	-0.7961	9	0.02654	T	1	.	4.0691	0.09874	0.0:0.5874:0.0:0.4126	.	219;220;239;218;242	B4DZL7;Q9NX02-2;A8K9G6;Q9NX02-4;Q9NX02	.;.;.;.;NALP2_HUMAN	V	242;218;220;242;220;219;218;239	ENSP00000445135:A242V;ENSP00000375601:A218V;ENSP00000344074:A220V;ENSP00000409370:A242V;ENSP00000440601:A220V;ENSP00000402474:A219V;ENSP00000441133:A218V;ENSP00000263437:A239V	ENSP00000263437:A239V	A	+	2	0	NLRP2	60185603	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.873000	0.28052	0.148000	0.19059	0.485000	0.47835	GCG		0.552	NLRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396152.1	NM_017852	
NLRP8	126205	broad.mit.edu	37	19	56459551	56459551	+	Nonsense_Mutation	SNP	C	C	T	rs145469757	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:56459551C>T	ENST00000291971.3	+	1	354	c.283C>T	c.(283-285)Cga>Tga	p.R95*	NLRP8_ENST00000590542.1_Nonsense_Mutation_p.R95*	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	95	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.R95*(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TTTCCCTGGACGACGCGCTTG	0.512																																					p.R95X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C283T	19						.	C	stop/ARG	0,4406		0,0,2203	113.0	105.0	107.0		283	-0.3	0.0	19	dbSNP_134	107	8,8592	7.1+/-27.0	0,8,4292	yes	stop-gained	NLRP8	NM_176811.2		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		95/1049	56459551	8,12998	2203	4300	6503	61151363	SO:0001587	stop_gained	126205	exon1			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.283C>T	19.37:g.56459551C>T	ENSP00000291971:p.Arg95*	Somatic		Capture	Illumina HiSeq	Phase_I	61151363	NM_176811	Q7RTR4	Nonsense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	C	19.09	3.760673	0.69763	0.0	9.3E-4	ENSG00000179709	ENST00000291971	.	.	.	2.05	-0.29	0.12847	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	.	2.5012	0.04634	0.2888:0.5333:0.0:0.178	.	.	.	.	X	95	.	ENSP00000291971:R95X	R	+	1	2	NLRP8	61151363	0.000000	0.05858	0.002000	0.10522	0.056000	0.15407	-0.237000	0.08990	0.007000	0.14760	0.514000	0.50259	CGA		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
NLRP8	126205	broad.mit.edu	37	19	56466068	56466068	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:56466068G>T	ENST00000291971.3	+	3	715	c.644G>T	c.(643-645)gGa>gTa	p.G215V	NLRP8_ENST00000590542.1_Missense_Mutation_p.G215V	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	215	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.G215V(2)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CCTGGGATCGGAAAAACAATC	0.532																																					p.G215V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G644T	19						.						86.0	71.0	76.0					19																	56466068		2203	4300	6503	61157880	SO:0001583	missense	126205	exon3			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.644G>T	19.37:g.56466068G>T	ENSP00000291971:p.Gly215Val	Somatic		Capture	Illumina HiSeq	Phase_I	61157880	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.419302	0.42918	.	.	ENSG00000179709	ENST00000291971	D	0.90133	-2.62	2.04	2.04	0.26737	NACHT nucleoside triphosphatase (1);	.	.	.	.	D	0.94621	0.8266	M	0.87971	2.92	0.35195	D	0.773771	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94935	0.8086	9	0.87932	D	0	.	7.6199	0.28179	0.0:0.0:1.0:0.0	.	215;215	Q86W28-2;Q86W28	.;NALP8_HUMAN	V	215	ENSP00000291971:G215V	ENSP00000291971:G215V	G	+	2	0	NLRP8	61157880	1.000000	0.71417	0.003000	0.11579	0.096000	0.18686	5.793000	0.69060	1.453000	0.47775	0.514000	0.50259	GGA		0.532	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
ZIM2	23619	broad.mit.edu	37	19	57286117	57286117	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:57286117T>C	ENST00000391708.3	-	12	2065	c.1523A>G	c.(1522-1524)tAc>tGc	p.Y508C	AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000594400.1_RNA|ZIM2_ENST00000601070.1_Missense_Mutation_p.Y508C|AC006115.3_ENST00000597946.1_RNA|ZIM2_ENST00000599935.1_Missense_Mutation_p.Y508C|ZIM2_ENST00000221722.5_Missense_Mutation_p.Y508C|ZIM2_ENST00000593711.1_Missense_Mutation_p.Y508C	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	508					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.Y508C(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0314)		TTGAGTGAGGTATGAGGGTCG	0.418																																					p.Y508C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1523G	19						.						111.0	104.0	106.0					19																	57286117		2203	4300	6503	61977929	SO:0001583	missense	23619	exon12			AF166122	CCDS33123.1	19q13.4	2012-10-31				ENSG00000269699		"""Zinc fingers, C2H2-type"""	12875	protein-coding gene	gene with protein product							Standard	NM_015363		Approved	ZNF656		Q9NZV7		ENST00000391708.3:c.1523A>G	19.37:g.57286117T>C	ENSP00000375589:p.Tyr508Cys	Somatic		Capture	Illumina HiSeq	Phase_I	61977929	NM_001146326	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489104	0.26686	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.15372	2.43;2.43	4.96	-0.874	0.10631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11281	0.0275	L	0.39514	1.22	.	.	.	B	0.12630	0.006	B	0.06405	0.002	T	0.30475	-0.9977	8	0.56958	D	0.05	.	1.732	0.02934	0.1434:0.3459:0.1478:0.3629	.	508	Q9NZV7	ZIM2_HUMAN	C	508	ENSP00000375589:Y508C;ENSP00000221722:Y508C	ENSP00000221722:Y508C	Y	-	2	0	ZIM2	61977929	0.000000	0.05858	0.039000	0.18376	0.529000	0.34654	-0.226000	0.09139	-0.474000	0.06862	-0.274000	0.10170	TAC		0.418	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2		
PEG3	5178	broad.mit.edu	37	19	57326712	57326712	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:57326712C>A	ENST00000326441.9	-	10	3461	c.3098G>T	c.(3097-3099)tGt>tTt	p.C1033F	PEG3_ENST00000423103.2_Missense_Mutation_p.C1033F|PEG3_ENST00000598410.1_Missense_Mutation_p.C909F|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000593695.1_Missense_Mutation_p.C907F	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1033					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.C1033F(2)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GAAGTCCTTACATTTGTTCCG	0.468																																					p.C1033F												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3098T	19						.						105.0	94.0	98.0					19																	57326712		2203	4300	6503	62018524	SO:0001583	missense	5178	exon7			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.3098G>T	19.37:g.57326712C>A	ENSP00000326581:p.Cys1033Phe	Somatic		Capture	Illumina HiSeq	Phase_I	62018524	NM_001146186	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	0.165	-1.077016	0.01903	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02863	4.13;4.13	4.09	-5.05	0.02955	.	0.618109	0.14716	N	0.302591	T	0.01254	0.0041	N	0.12182	0.205	.	.	.	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.41538	-0.9503	9	0.41790	T	0.15	.	0.6012	0.00745	0.3089:0.3066:0.1388:0.2457	.	909;1033;968	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	F	1033	ENSP00000326581:C1033F;ENSP00000403051:C1033F	ENSP00000326581:C1033F	C	-	2	0	ZIM2	62018524	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.104000	0.15313	-1.319000	0.02286	-3.025000	0.00073	TGT		0.468	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2		
ZNF419	79744	broad.mit.edu	37	19	58002859	58002859	+	Silent	SNP	T	T	C	rs62126198	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:58002859T>C	ENST00000221735.7	+	3	279	c.93T>C	c.(91-93)gaT>gaC	p.D31D	ZNF419_ENST00000424930.2_Silent_p.D32D|ZNF419_ENST00000354197.4_Silent_p.D19D|ZNF419_ENST00000520540.1_Silent_p.D19D|ZNF419_ENST00000347466.6_Silent_p.D32D|ZNF419_ENST00000442920.2_Silent_p.D18D|ZNF419_ENST00000518999.1_Silent_p.D32D|ZNF419_ENST00000426954.2_Silent_p.D19D|AC003005.4_ENST00000601674.1_Silent_p.D18D|ZNF419_ENST00000415379.2_Silent_p.D18D			Q96HQ0	ZN419_HUMAN	zinc finger protein 419	31	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D32D(1)|p.D11D(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0252)|Lung(386;0.171)		CCTTTGAGGATGTGGCTGTCT	0.498																																					p.D32D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T96C	19						.						174.0	165.0	168.0					19																	58002859		2203	4300	6503	62694671	SO:0001819	synonymous_variant	79744	exon3			AK026886	CCDS42637.1, CCDS46211.1, CCDS54325.1, CCDS54326.1, CCDS54327.1, CCDS54328.1	19q13.43	2013-01-08	2006-12-15	2006-12-15	ENSG00000105136	ENSG00000105136		"""Zinc fingers, C2H2-type"", ""-"""	20648	protein-coding gene	gene with protein product			"""zinc finger protein 419A"""	ZNF419A			Standard	NM_001098492		Approved		uc010ety.1	Q96HQ0	OTTHUMG00000037073	ENST00000221735.7:c.93T>C	19.37:g.58002859T>C		None		Capture	Illumina HiSeq	Phase_I	62694671	NM_001098494	B4DXU7|B4E348|B7ZA41|E9PCP4|E9PED0|E9PET3|E9PFX9|Q9H5P0	Silent	SNP	ENST00000221735.7	37	CCDS54326.1																																																																																				0.498	ZNF419-006	KNOWN	NAGNAG_splice_site|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378506.1	NM_024691	
ZIK1	284307	broad.mit.edu	37	19	58101924	58101924	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:58101924C>T	ENST00000597850.1	+	4	960	c.745C>T	c.(745-747)Cgt>Tgt	p.R249C	ZIK1_ENST00000599456.1_Missense_Mutation_p.R194C|ZIK1_ENST00000536878.2_Missense_Mutation_p.R236C|ZIK1_ENST00000307468.4_3'UTR	NM_001010879.2	NP_001010879.2	Q3SY52	ZIK1_HUMAN	zinc finger protein interacting with K protein 1	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R249C(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	34		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GAAAGCCTTCCGTGGCAAGTA	0.468																																					p.R249C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C745T	19						.						53.0	54.0	54.0					19																	58101924		2203	4300	6503	62793736	SO:0001583	missense	284307	exon4			AK092538	CCDS33135.1	19q13.43	2013-01-08	2012-12-07		ENSG00000171649	ENSG00000171649		"""Zinc fingers, C2H2-type"", ""-"""	33104	protein-coding gene	gene with protein product			"""zinc finger protein interacting with K protein 1 homolog (mouse)"""				Standard	XM_005258769		Approved	ZNF762	uc002qpg.3	Q3SY52		ENST00000597850.1:c.745C>T	19.37:g.58101924C>T	ENSP00000472867:p.Arg249Cys	Somatic		Capture	Illumina HiSeq	Phase_I	62793736	NM_001010879	O43339|Q3SY51|Q3SY53	Missense_Mutation	SNP	ENST00000597850.1	37	CCDS33135.1	.	.	.	.	.	.	.	.	.	.	C	9.765	1.171089	0.21621	.	.	ENSG00000171649	ENST00000536878;ENST00000356724;ENST00000307468	T	0.15952	2.38	3.23	-0.48	0.12085	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20901	0.0503	L	0.39020	1.185	0.09310	N	1	D;B	0.76494	0.999;0.032	P;B	0.58077	0.832;0.003	T	0.13415	-1.0510	9	0.56958	D	0.05	.	5.2499	0.15517	0.6187:0.245:0.0:0.1363	.	236;249	F5H435;Q3SY52	.;ZIK1_HUMAN	C	236;230;249	ENSP00000438487:R236C	ENSP00000303820:R249C	R	+	1	0	ZIK1	62793736	0.000000	0.05858	0.000000	0.03702	0.199000	0.23934	-1.218000	0.02976	-0.194000	0.10399	-0.145000	0.13849	CGT		0.468	ZIK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466791.1	NM_001010879	
ZNF551	90233	broad.mit.edu	37	19	58196688	58196688	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:58196688A>G	ENST00000282296.5	+	2	325	c.140A>G	c.(139-141)gAt>gGt	p.D47G	AC003006.7_ENST00000599221.1_Intron|AC003006.7_ENST00000594684.1_Intron|ZNF551_ENST00000596085.1_Missense_Mutation_p.D31G|ZNF551_ENST00000599402.1_Intron|ZNF551_ENST00000356715.4_Missense_Mutation_p.D31G			Q7Z340	ZN551_HUMAN	zinc finger protein 551	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.D31G(1)		endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		GAGCTCCTTGATGAGTCTCAG	0.502																																					p.D31G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A92G	19						.						240.0	208.0	219.0					19																	58196688		2203	4300	6503	62888500	SO:0001583	missense	90233	exon2			BX538151	CCDS12959.1, CCDS12959.2	19q13.43	2013-09-20			ENSG00000204519	ENSG00000204519		"""Zinc fingers, C2H2-type"", ""-"""	25108	protein-coding gene	gene with protein product							Standard	NM_138347		Approved	DKFZp686H1038	uc002qpw.5	Q7Z340	OTTHUMG00000183470	ENST00000282296.5:c.140A>G	19.37:g.58196688A>G	ENSP00000282296:p.Asp47Gly	Somatic		Capture	Illumina HiSeq	Phase_I	62888500	NM_138347	B4DU22|P17034|Q8N246|Q9BRY1	Missense_Mutation	SNP	ENST00000282296.5	37	CCDS12959.2	.	.	.	.	.	.	.	.	.	.	A	15.74	2.923461	0.52653	.	.	ENSG00000204519	ENST00000356715;ENST00000282296;ENST00000359821	.	.	.	2.17	2.17	0.27698	Krueppel-associated box (4);	.	.	.	.	T	0.59514	0.2199	M	0.76328	2.33	0.09310	N	1	P	0.45827	0.867	P	0.55615	0.78	T	0.47522	-0.9111	8	0.56958	D	0.05	.	8.2468	0.31693	1.0:0.0:0.0:0.0	.	47	Q7Z340	ZN551_HUMAN	G	47;31;19	.	ENSP00000282296:D31G	D	+	2	0	ZNF551	62888500	0.002000	0.14202	0.007000	0.13788	0.513000	0.34164	1.063000	0.30567	1.247000	0.43917	0.379000	0.24179	GAT		0.502	ZNF551-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466803.2	NM_138347	
LPPR3	79948	broad.mit.edu	37	19	814531	814531	+	Missense_Mutation	SNP	G	G	A	rs550064116		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:814531G>A	ENST00000520876.3	-	7	812	c.734C>T	c.(733-735)gCg>gTg	p.A245V	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Missense_Mutation_p.A273V	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		245						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)	p.A273V(1)									GCATACGCCCGCGGCGATGGC	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16097	0.0		0.0	False		,,,				2504	0.0				p.A273V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C818T	19						.						50.0	52.0	52.0					19																	814531		2194	4300	6494	765531	SO:0001583	missense	79948	exon6																														ENST00000520876.3:c.734C>T	19.37:g.814531G>A	ENSP00000430297:p.Ala245Val	Somatic		Capture	Illumina HiSeq	Phase_I	765531	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	Missense_Mutation	SNP	ENST00000520876.3	37	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.220787	0.79464	.	.	ENSG00000129951	ENST00000300947;ENST00000359894;ENST00000520876	D;D	0.82711	-1.64;-1.64	4.66	4.66	0.58398	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92176	0.7519	M	0.90483	3.12	0.58432	D	0.999999	D;D;D	0.71674	0.997;0.998;0.994	D;D;P	0.67382	0.918;0.951;0.768	D	0.94037	0.7306	10	0.87932	D	0	-14.8067	16.5199	0.84311	0.0:0.0:1.0:0.0	.	246;245;273	Q6T4P5-2;Q6T4P5;Q6T4P5-3	.;LPPR3_HUMAN;.	V	246;273;245	ENSP00000352962:A273V;ENSP00000430297:A245V	ENSP00000300947:A246V	A	-	2	0	AC006273.1	765531	1.000000	0.71417	0.063000	0.19743	0.136000	0.21042	5.003000	0.63959	2.137000	0.66172	0.555000	0.69702	GCG		0.637	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
LPPR3	79948	broad.mit.edu	37	19	814912	814912	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:814912G>A	ENST00000520876.3	-	5	651	c.573C>T	c.(571-573)caC>caT	p.H191H	MIR3187_ENST00000583431.1_RNA|LPPR3_ENST00000359894.2_Silent_p.H191H	NM_001270366.1	NP_001257295.1	Q6T4P5	LPPR3_HUMAN		191						integral component of membrane (GO:0016021)	phosphatidate phosphatase activity (GO:0008195)	p.H191H(1)									CGTGGATGTCGTGGCCGGAGC	0.622																																					p.H191H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C573T	19						.						132.0	107.0	115.0					19																	814912		2200	4299	6499	765912	SO:0001819	synonymous_variant	79948	exon5																														ENST00000520876.3:c.573C>T	19.37:g.814912G>A		Somatic		Capture	Illumina HiSeq	Phase_I	765912	NM_024888	Q86XQ4|Q96EH1|Q9BQF9|Q9HAJ4	De_novo_Start_OutOfFrame	SNP	ENST00000520876.3	37	CCDS58636.1	.	.	.	.	.	.	.	.	.	.	G	35	5.436287	0.96168	.	.	ENSG00000129951	ENST00000521445	.	.	.	4.73	-5.53	0.02552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.0414	6.9278	0.24424	0.3777:0.2485:0.3739:0.0	.	.	.	.	X	141	.	ENSP00000428769:R141X	R	-	1	2	AC006273.1	765912	0.000000	0.05858	0.841000	0.33234	0.938000	0.57974	-2.681000	0.00837	-0.489000	0.06716	-0.274000	0.10170	CGA		0.622	LPPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379096.3		
VAV1	7409	broad.mit.edu	37	19	6828446	6828446	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:6828446C>T	ENST00000602142.1	+	11	1122	c.1040C>T	c.(1039-1041)aCg>aTg	p.T347M	VAV1_ENST00000596764.1_Missense_Mutation_p.T315M|VAV1_ENST00000599806.1_Missense_Mutation_p.T292M|VAV1_ENST00000304076.2_Missense_Mutation_p.T347M|VAV1_ENST00000539284.1_Missense_Mutation_p.T250M	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	347	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T347M(1)		biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						GTGAAACACACGCAGGAGGCG	0.622																																					p.T347M												VAV1,kidney,NS,Substitution - coding silent,-1 	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1040T	19						.						65.0	66.0	65.0					19																	6828446		2203	4300	6503	6779446	SO:0001583	missense	7409	exon11				CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1040C>T	19.37:g.6828446C>T	ENSP00000472929:p.Thr347Met	Somatic		Capture	Illumina HiSeq	Phase_I	6779446	NM_005428	B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.273812	0.80580	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T;T	0.72394	-0.65;-0.65	4.7	4.7	0.59300	Guanine-nucleotide dissociation stimulator, CDC24, conserved site (1);Dbl homology (DH) domain (5);	0.000000	0.85682	D	0.000000	D	0.86843	0.6030	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	P;D;D;D	0.78314	0.847;0.957;0.985;0.991	D	0.89867	0.4020	10	0.72032	D	0.01	.	15.4995	0.75684	0.0:1.0:0.0:0.0	.	250;347;292;347	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	M	347;250	ENSP00000302269:T347M;ENSP00000443242:T250M	ENSP00000302269:T347M	T	+	2	0	VAV1	6779446	1.000000	0.71417	1.000000	0.80357	0.596000	0.36781	5.090000	0.64498	2.337000	0.79520	0.467000	0.42956	ACG		0.622	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
EMR1	2015	broad.mit.edu	37	19	6904182	6904182	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:6904182T>C	ENST00000312053.4	+	8	975	c.938T>C	c.(937-939)tTc>tCc	p.F313S	EMR1_ENST00000450315.3_Intron|EMR1_ENST00000250572.8_Missense_Mutation_p.F313S|EMR1_ENST00000381407.5_Missense_Mutation_p.F172S|EMR1_ENST00000381404.4_Missense_Mutation_p.F261S	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	313	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.F313S(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(8)	62	all_hematologic(4;0.166)					GATGGCAACTTCAGCTGCCAA	0.473																																					p.F313S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T938C	19						.						82.0	79.0	80.0					19																	6904182		2203	4300	6503	6855182	SO:0001583	missense	2015	exon8			X81479	CCDS12175.1, CCDS58643.1, CCDS58644.1, CCDS58645.1, CCDS58646.1	19p13.3	2014-08-08	2003-11-26					"""-"", ""GPCR / Class B : Orphans"""	3336	protein-coding gene	gene with protein product		600493	"""egf-like module containing, mucin-like, hormone receptor-like sequence 1"""	TM7LN3		7601460, 9500513	Standard	NM_001974		Approved		uc002mfw.4	Q14246		ENST00000312053.4:c.938T>C	19.37:g.6904182T>C	ENSP00000311545:p.Phe313Ser	Somatic		Capture	Illumina HiSeq	Phase_I	6855182	NM_001974	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Missense_Mutation	SNP	ENST00000312053.4	37	CCDS12175.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.187012	0.57909	.	.	ENSG00000174837	ENST00000543519;ENST00000312053;ENST00000381404;ENST00000250572;ENST00000381407	T;T;T;T	0.78126	-1.06;-1.15;-1.12;0.01	3.57	2.48	0.30137	EGF-like calcium-binding (1);	.	.	.	.	T	0.82084	0.4960	L	0.58669	1.825	0.25539	N	0.98719	P;D;D;D	0.89917	0.879;1.0;0.998;1.0	B;D;D;D	0.91635	0.319;0.997;0.978;0.999	T	0.68439	-0.5408	9	0.21014	T	0.42	.	7.014	0.24877	0.0:0.0:0.2335:0.7665	.	172;313;261;313	B7Z486;Q14246-2;E9PD45;Q14246	.;.;.;EMR1_HUMAN	S	313;313;261;313;172	ENSP00000311545:F313S;ENSP00000370811:F261S;ENSP00000250572:F313S;ENSP00000370814:F172S	ENSP00000250572:F313S	F	+	2	0	EMR1	6855182	1.000000	0.71417	0.035000	0.18076	0.697000	0.40408	1.992000	0.40737	0.469000	0.27268	0.529000	0.55759	TTC		0.473	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1		
MCOLN1	57192	broad.mit.edu	37	19	7591778	7591778	+	Silent	SNP	C	C	T	rs376002658		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:7591778C>T	ENST00000264079.6	+	4	662	c.537C>T	c.(535-537)aaC>aaT	p.N179N		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	179				ALCQRYYHRGHVDPANDTFDIDPMVVTD -> LSASGTTTE ATWTRPTTHLTLIRWWLLVN (in Ref. 3; AAG42242). {ECO:0000305}.	calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)	p.N179N(1)		breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ACCCGGCCAACGACACATTTG	0.577																																					p.N179N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C537T	19						.	C		1,4405	2.1+/-5.4	0,1,2202	127.0	100.0	109.0		537	-10.8	0.4	19		109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MCOLN1	NM_020533.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		179/581	7591778	2,13004	2203	4300	6503	7497778	SO:0001819	synonymous_variant	57192	exon4			AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.537C>T	19.37:g.7591778C>T		Somatic		Capture	Illumina HiSeq	Phase_I	7497778	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512519	0.44660	2.27E-4	1.16E-4	ENSG00000090674	ENST00000394321	.	.	.	5.39	-10.8	0.00216	.	.	.	.	.	T	0.35480	0.0933	.	.	.	0.19575	N	0.999964	B	0.13145	0.007	B	0.11329	0.006	T	0.41662	-0.9496	7	0.87932	D	0	.	17.0481	0.86510	0.0:0.3087:0.0:0.6913	.	66	Q9GZU1-2	.	M	66	.	ENSP00000377856:T66M	T	+	2	0	MCOLN1	7497778	0.000000	0.05858	0.414000	0.26521	0.719000	0.41307	-1.904000	0.01593	-2.240000	0.00710	-1.090000	0.02178	ACG		0.577	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533	
LRRC8E	80131	broad.mit.edu	37	19	7964763	7964763	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:7964763delC	ENST00000306708.6	+	3	1457	c.1356delC	c.(1354-1356)ttcfs	p.F452fs	AC010336.1_ENST00000539278.1_Frame_Shift_Del_p.G168fs|RN7SL115P_ENST00000392196.5_RNA	NM_001268284.1|NM_001268285.1|NM_025061.4	NP_001255213.1|NP_001255214.1|NP_079337.2	Q6NSJ5	LRC8E_HUMAN	leucine rich repeat containing 8 family, member E	452					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P454fs*33(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(10)	35						ATATCACCTTCCCCCCGGGGC	0.642																																					p.F452fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1356delC	19						.						40.0	30.0	34.0					19																	7964763		2202	4299	6501	7870763	SO:0001589	frameshift_variant	80131	exon3				CCDS12189.1	19p13.2	2008-02-05				ENSG00000171017			26272	protein-coding gene	gene with protein product		612891				12477932	Standard	NM_025061		Approved	FLJ23420	uc002mir.3	Q6NSJ5		ENST00000306708.6:c.1356delC	19.37:g.7964763delC	ENSP00000306524:p.Phe452fs	Somatic		Capture	Illumina HiSeq	Phase_I	7870763	NM_025061	B3KR78|Q2YDY3|Q7L236|Q8N3B0|Q9H5H8	Frame_Shift_Del	DEL	ENST00000306708.6	37	CCDS12189.1																																																																																				0.642	LRRC8E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461354.1	NM_025061	
CD320	51293	broad.mit.edu	37	19	8367483	8367483	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:8367483A>C	ENST00000301458.5	-	5	777	c.713T>G	c.(712-714)cTc>cGc	p.L238R	CD320_ENST00000537716.2_Missense_Mutation_p.L196R	NM_016579.3	NP_057663.1	Q9NPF0	CD320_HUMAN	CD320 molecule	238					cobalamin metabolic process (GO:0009235)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)	p.L238R(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)	6						GCTTGCACTGAGCACCGCTGT	0.627																																					p.L238R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T713G	19						.						47.0	44.0	45.0					19																	8367483		2203	4300	6503	8273483	SO:0001583	missense	51293	exon5			AF161254	CCDS12198.1, CCDS54210.1	19p13.3-p13.2	2008-02-05	2006-03-28			ENSG00000167775		"""CD molecules"""	16692	protein-coding gene	gene with protein product	"""8D6 antigen"""	606475	"""CD320 antigen"""			10727470	Standard	NM_016579		Approved	8D6, 8D6A	uc002mjj.2	Q9NPF0		ENST00000301458.5:c.713T>G	19.37:g.8367483A>C	ENSP00000301458:p.Leu238Arg	Somatic		Capture	Illumina HiSeq	Phase_I	8273483	NM_016579	B2RDS5|D6W668|F5H6D3|Q53HF7	Missense_Mutation	SNP	ENST00000301458.5	37	CCDS12198.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.856140	0.51376	.	.	ENSG00000167775	ENST00000301458;ENST00000537716	D;D	0.98419	-3.81;-4.92	4.04	4.04	0.47022	.	0.000000	0.37136	N	0.002221	D	0.97714	0.9250	L	0.36672	1.1	0.09310	N	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.92832	0.6281	10	0.87932	D	0	-17.1189	9.6938	0.40145	1.0:0.0:0.0:0.0	.	196;238	F5H6D3;Q9NPF0	.;CD320_HUMAN	R	238;196	ENSP00000301458:L238R;ENSP00000437697:L196R	ENSP00000301458:L238R	L	-	2	0	CD320	8273483	0.854000	0.29725	0.094000	0.20943	0.003000	0.03518	2.332000	0.43903	2.061000	0.61500	0.533000	0.62120	CTC		0.627	CD320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461366.1	NM_016579	
MYO1F	4542	broad.mit.edu	37	19	8592319	8592319	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:8592319C>A	ENST00000338257.8	-	22	2644	c.2377G>T	c.(2377-2379)Ggg>Tgg	p.G793W		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	793	Myosin tail. {ECO:0000255}.				defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)	p.G793W(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						TTCTCTCGCCCAATCACATAC	0.572																																					p.G793W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2377T	19						.						82.0	81.0	82.0					19																	8592319		2005	4184	6189	8498319	SO:0001583	missense	4542	exon22			X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.2377G>T	19.37:g.8592319C>A	ENSP00000344871:p.Gly793Trp	Somatic		Capture	Illumina HiSeq	Phase_I	8498319	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664711	0.88251	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	T	0.37915	1.17	5.16	5.16	0.70880	Myosin tail 2 (1);	0.000000	0.85682	D	0.000000	T	0.68952	0.3057	M	0.91717	3.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76642	-0.2884	10	0.62326	D	0.03	.	17.7053	0.88308	0.0:1.0:0.0:0.0	.	793	O00160	MYO1F_HUMAN	W	838;793	ENSP00000344871:G793W	ENSP00000304899:G838W	G	-	1	0	MYO1F	8498319	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.681000	0.84073	2.430000	0.82344	0.456000	0.33151	GGG		0.572	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
ADAMTS10	81794	broad.mit.edu	37	19	8660728	8660728	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:8660728G>T	ENST00000597188.1	-	12	1667	c.1397C>A	c.(1396-1398)aCa>aAa	p.T466K	ADAMTS10_ENST00000270328.4_Missense_Mutation_p.T466K|ADAMTS10_ENST00000596709.1_5'Flank	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	466	Disintegrin.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.T466K(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						CGGTGCCACTGTCGGGTACAC	0.577																																					p.T466K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1397A	19						.						131.0	130.0	130.0					19																	8660728		2203	4300	6503	8566728	SO:0001583	missense	81794	exon12			AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.1397C>A	19.37:g.8660728G>T	ENSP00000471851:p.Thr466Lys	Somatic		Capture	Illumina HiSeq	Phase_I	8566728	NM_030957	M0QZE4	Missense_Mutation	SNP	ENST00000597188.1	37	CCDS12206.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466596	0.84425	.	.	ENSG00000142303	ENST00000270328;ENST00000393912	T	0.06768	3.26	4.4	4.4	0.53042	Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.16685	0.0401	L	0.42008	1.315	0.80722	D	1	P;D	0.58970	0.714;0.984	B;P	0.61477	0.191;0.889	T	0.08126	-1.0737	10	0.10111	T	0.7	.	16.1437	0.81548	0.0:0.0:1.0:0.0	.	220;466	Q59FE5;Q9H324	.;ATS10_HUMAN	K	466;220	ENSP00000270328:T466K	ENSP00000270328:T466K	T	-	2	0	ADAMTS10	8566728	1.000000	0.71417	0.828000	0.32881	0.804000	0.45430	9.235000	0.95353	2.277000	0.76020	0.313000	0.20887	ACA		0.577	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
MBD3L1	85509	broad.mit.edu	37	19	8953859	8953859	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:8953859G>A	ENST00000595891.1	+	3	736	c.505G>A	c.(505-507)Gca>Aca	p.A169T	MBD3L1_ENST00000305625.2_Missense_Mutation_p.A169T			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	169					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.A169T(1)		NS(1)|cervix(1)|large_intestine(5)|liver(1)|lung(2)|skin(2)	12						AGAGAGACTCGCAATAGCACT	0.473																																					p.A169T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G505A	19						.						44.0	41.0	42.0					19																	8953859		2203	4297	6500	8814859	SO:0001583	missense	85509	exon1			AY038022	CCDS12209.1	19p13.2	2011-01-31	2003-03-19	2003-03-21	ENSG00000170948	ENSG00000170948			15774	protein-coding gene	gene with protein product		607963	"""methyl-CpG binding domain protein 3-like"""	MBD3L		12504854	Standard	NM_145208		Approved		uc002mko.2	Q8WWY6		ENST00000595891.1:c.505G>A	19.37:g.8953859G>A	ENSP00000471575:p.Ala169Thr	Somatic		Capture	Illumina HiSeq	Phase_I	8814859	NM_145208	B5BUM6|Q2M291	Missense_Mutation	SNP	ENST00000595891.1	37	CCDS12209.1	.	.	.	.	.	.	.	.	.	.	G	8.182	0.793989	0.16327	.	.	ENSG00000170948	ENST00000305625	T	0.49432	0.78	3.92	0.577	0.17385	.	0.646825	0.12885	N	0.431113	T	0.38506	0.1043	M	0.72894	2.215	0.09310	N	1	B	0.33612	0.419	B	0.28385	0.089	T	0.22661	-1.0210	10	0.34782	T	0.22	-14.2204	4.3308	0.11062	0.2079:0.1861:0.606:0.0	.	169	Q8WWY6	MB3L1_HUMAN	T	169	ENSP00000304198:A169T	ENSP00000304198:A169T	A	+	1	0	MBD3L1	8814859	0.329000	0.24696	0.137000	0.22149	0.007000	0.05969	1.118000	0.31246	0.230000	0.21059	-0.165000	0.13383	GCA		0.473	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208	
MUC16	94025	broad.mit.edu	37	19	9066842	9066842	+	Silent	SNP	C	C	T	rs549236989		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:9066842C>T	ENST00000397910.4	-	3	20807	c.20604G>A	c.(20602-20604)ctG>ctA	p.L6868L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6870	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.L6868L(2)|p.L2501L(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CATCTGTTGTCAGTATCTCAT	0.488																																					p.L6868L												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.G20604A	19						.						187.0	175.0	179.0					19																	9066842		2077	4223	6300	8927842	SO:0001819	synonymous_variant	94025	exon3			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.20604G>A	19.37:g.9066842C>T		Somatic		Capture	Illumina HiSeq	Phase_I	8927842	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MUC16	94025	broad.mit.edu	37	19	9067610	9067610	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:9067610G>T	ENST00000397910.4	-	3	20039	c.19836C>A	c.(19834-19836)gcC>gcA	p.A6612A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6614	Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)		p.A6612A(2)|p.A2245A(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTTCTGAGTAGGCTGGGACAG	0.438																																					p.A6612A												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.C19836A	19						.						214.0	195.0	201.0					19																	9067610		1940	4141	6081	8928610	SO:0001819	synonymous_variant	94025	exon3			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.19836C>A	19.37:g.9067610G>T		Somatic		Capture	Illumina HiSeq	Phase_I	8928610	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																				0.438	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF426	79088	broad.mit.edu	37	19	9639526	9639526	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:9639526T>C	ENST00000535489.1	-	6	1531	c.1195A>G	c.(1195-1197)Aaa>Gaa	p.K399E	ZNF426_ENST00000593003.1_Missense_Mutation_p.K361E|ZNF426_ENST00000253115.2_Missense_Mutation_p.K399E			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	399					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K399E(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						GCAAAGGCTTTCCCACATTCA	0.413																																					p.K399E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1195G	19						.						77.0	74.0	75.0					19																	9639526		2203	4300	6503	9500526	SO:0001583	missense	79088	exon8			AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.1195A>G	19.37:g.9639526T>C	ENSP00000439017:p.Lys399Glu	Somatic		Capture	Illumina HiSeq	Phase_I	9500526	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	T	15.61	2.884478	0.51908	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.27104	1.69;1.69	1.38	1.38	0.22167	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43523	0.1251	M	0.72624	2.21	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.37079	-0.9721	9	0.72032	D	0.01	.	6.8191	0.23847	0.0:0.0:0.0:1.0	.	386;399	Q59EH4;Q9BUY5	.;ZN426_HUMAN	E	386;399;399	ENSP00000253115:K399E;ENSP00000439017:K399E	ENSP00000253115:K399E	K	-	1	0	ZNF426	9500526	0.434000	0.25570	0.008000	0.14137	0.010000	0.07245	1.555000	0.36277	0.873000	0.35799	0.379000	0.24179	AAA		0.413	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
ZNF791	163049	broad.mit.edu	37	19	12739502	12739502	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:12739502delA	ENST00000343325.4	+	4	1321	c.1159delA	c.(1159-1161)aaafs	p.K388fs	ZNF791_ENST00000540038.1_Frame_Shift_Del_p.K279fs|ZNF791_ENST00000458122.3_Frame_Shift_Del_p.K356fs|ZNF490_ENST00000465656.1_Intron|ZNF791_ENST00000446165.1_3'UTR|AC010422.1_ENST00000408416.1_RNA	NM_153358.2	NP_699189.2	Q3KP31	ZN791_HUMAN	zinc finger protein 791	388					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K388fs*10(1)		endometrium(3)|large_intestine(5)|lung(6)|ovary(2)|prostate(3)	19						CTACGAATGTAAAAAATGTGG	0.363																																					p.K387fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1159delA	19						.						61.0	69.0	66.0					19																	12739502		2203	4299	6502	12600502	SO:0001589	frameshift_variant	163049	exon4			AK074877	CCDS12273.1	19p13.2-p13.13	2013-01-08			ENSG00000173875	ENSG00000173875		"""Zinc fingers, C2H2-type"", ""-"""	26895	protein-coding gene	gene with protein product							Standard	NM_153358		Approved	FLJ90396	uc002mua.2	Q3KP31	OTTHUMG00000156426	ENST00000343325.4:c.1159delA	19.37:g.12739502delA	ENSP00000342974:p.Lys388fs	Somatic		Capture	Illumina HiSeq	Phase_I	12600502	NM_153358	B7Z586|Q8NC99	Frame_Shift_Del	DEL	ENST00000343325.4	37	CCDS12273.1																																																																																				0.363	ZNF791-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344140.1	NM_153358	
CRTC1	23373	broad.mit.edu	37	19	18887993	18887993	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:18887993delC	ENST00000321949.8	+	14	1732	c.1706delC	c.(1705-1707)tccfs	p.S569fs	CRTC1_ENST00000594658.1_Frame_Shift_Del_p.S528fs|CRTC1_ENST00000601916.1_Frame_Shift_Del_p.S327fs|CRTC1_ENST00000338797.6_Frame_Shift_Del_p.S585fs	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1									p.S572fs*6(2)	CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						ACAGGAGAGTCCCCCCCCAGC	0.637																																					p.S569fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1706delC	19						.		,	36,4218		5,26,2096	32.0	37.0	35.0		,	3.8	1.0	19		34	39,8205		5,29,4088	no	frameshift,frameshift	CRTC1	NM_015321.2,NM_001098482.1	,	10,55,6184	A1A1,A1R,RR		0.4731,0.8463,0.6001	,	,	18887993	75,12423	2201	4298	6499	18748993	SO:0001589	frameshift_variant	23373	exon14			AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.1706delC	19.37:g.18887993delC	ENSP00000323332:p.Ser569fs	Somatic		Capture	Illumina HiSeq	Phase_I	18748993	NM_015321		Frame_Shift_Del	DEL	ENST00000321949.8	37	CCDS32963.1																																																																																				0.637	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
CD79A	973	broad.mit.edu	37	19	42383610	42383610	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:42383610delC	ENST00000221972.3	+	3	570	c.385delC	c.(385-387)cccfs	p.P130fs	CD79A_ENST00000444740.2_Frame_Shift_Del_p.P92fs	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	130					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)	B cell receptor complex (GO:0019815)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)	p.R131fs*61(1)		large_intestine(3)|lung(3)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	11						TGCAGAGCCGCCCCCCAGGCC	0.677			"""O, S"""		DLBCL																																p.P129fs			Dom	yes		19	19q13.2	973	"""CD79a molecule, immunoglobulin-associated alpha"""		L	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.385delC	19						.						32.0	20.0	24.0					19																	42383610		2199	4296	6495	47075450	SO:0001589	frameshift_variant	973	exon3			M80462	CCDS12589.1, CCDS46088.1	19q13.2	2014-09-17	2006-03-28					"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1698	protein-coding gene	gene with protein product		112205	"""CD79A antigen (immunoglobulin-associated alpha)"""	IGA		1538135	Standard	NM_001783		Approved	MB-1	uc002orv.3	P11912		ENST00000221972.3:c.385delC	19.37:g.42383610delC	ENSP00000221972:p.Pro130fs	Somatic		Capture	Illumina HiSeq	Phase_I	47075450	NM_001783	A0N775|Q53FB8	Frame_Shift_Del	DEL	ENST00000221972.3	37	CCDS12589.1																																																																																				0.677	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1		
VASP	7408	broad.mit.edu	37	19	46025612	46025612	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:46025612delC	ENST00000245932.6	+	6	849	c.493delC	c.(493-495)cccfs	p.P166fs		NM_003370.3	NP_003361.1	P50552	VASP_HUMAN	vasodilator-stimulated phosphoprotein	166	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|neural tube closure (GO:0001843)|positive regulation of actin filament polymerization (GO:0030838)|protein homotetramerization (GO:0051289)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	profilin binding (GO:0005522)	p.A167fs*88(1)|p.A167fs*101(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|skin(2)	18		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0145)|GBM - Glioblastoma multiforme(486;0.154)		CCCACCTGCTCCCCCCGCTGG	0.667																																					p.P165fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.493delC	19						.						8.0	7.0	7.0					19																	46025612		2179	4270	6449	50717452	SO:0001589	frameshift_variant	7408	exon6				CCDS33051.1	19q13.32	2012-02-22			ENSG00000125753	ENSG00000125753			12652	protein-coding gene	gene with protein product		601703				8812448	Standard	XM_005259199		Approved		uc002pcg.3	P50552		ENST00000245932.6:c.493delC	19.37:g.46025612delC	ENSP00000245932:p.Pro166fs	Somatic		Capture	Illumina HiSeq	Phase_I	50717452	NM_003370	B2RBT9|Q6PIZ1|Q93035	Frame_Shift_Del	DEL	ENST00000245932.6	37	CCDS33051.1																																																																																				0.667	VASP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459589.1		
SIX5	147912	broad.mit.edu	37	19	46268844	46268844	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:46268844delC	ENST00000317578.6	-	3	2516	c.2135delG	c.(2134-2136)ggtfs	p.G712fs	AC074212.5_ENST00000592217.2_RNA|AC074212.6_ENST00000590076.1_RNA|SIX5_ENST00000560168.1_3'UTR|AC074212.5_ENST00000559756.1_RNA	NM_175875.4	NP_787071	Q8N196	SIX5_HUMAN	SIX homeobox 5	712					lens development in camera-type eye (GO:0002088)|negative regulation of cell proliferation (GO:0008285)|regulation of transcription, DNA-templated (GO:0006355)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G712fs*14(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8		Ovarian(192;0.0308)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00783)|GBM - Glioblastoma multiforme(486;0.0802)|Epithelial(262;0.235)		GTCAACCTCACCCCCTGCGGT	0.682																																					p.G712fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2135delG	19						.						64.0	67.0	66.0					19																	46268844		2203	4300	6503	50960684	SO:0001589	frameshift_variant	147912	exon3			L08835	CCDS12673.1	19q13.32	2011-06-20	2007-07-13			ENSG00000177045		"""Homeoboxes / SINE class"""	10891	protein-coding gene	gene with protein product		600963	"""sine oculis homeobox (Drosophila) homolog 5"", ""sine oculis homeobox homolog 5 (Drosophila)"""	DMAHP		8595416	Standard	NM_175875		Approved		uc002pdb.3	Q8N196		ENST00000317578.6:c.2135delG	19.37:g.46268844delC	ENSP00000316842:p.Gly712fs	Somatic		Capture	Illumina HiSeq	Phase_I	50960684	NM_175875		Frame_Shift_Del	DEL	ENST00000317578.6	37	CCDS12673.1																																																																																				0.682	SIX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417341.3	NM_175875	
SYMPK	8189	broad.mit.edu	37	19	46321257	46321257	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:46321257delC	ENST00000245934.7	-	23	3285	c.3041delG	c.(3040-3042)ggcfs	p.G1014fs	RSPH6A_ENST00000597055.1_5'Flank|RSPH6A_ENST00000221538.3_5'Flank|SYMPK_ENST00000598155.1_5'UTR	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1014					cell adhesion (GO:0007155)|mRNA polyadenylation (GO:0006378)|positive regulation of protein dephosphorylation (GO:0035307)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)		p.G1014fs*4(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(25)|ovary(1)|urinary_tract(1)	45		all_neural(266;0.0299)|Ovarian(192;0.0308)		OV - Ovarian serous cystadenocarcinoma(262;0.00509)|GBM - Glioblastoma multiforme(486;0.0593)		CATGACGAAGCCCCCCAGGCG	0.637																																					p.G1014fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3041delG	19						.						36.0	32.0	33.0					19																	46321257		2195	4295	6490	51013097	SO:0001589	frameshift_variant	8189	exon23			U49240	CCDS12676.2	19q13.3	2008-02-05			ENSG00000125755	ENSG00000125755			22935	protein-coding gene	gene with protein product		602388				9330635	Standard	NM_004819		Approved	SYM, SPK	uc002pdn.3	Q92797	OTTHUMG00000150151	ENST00000245934.7:c.3041delG	19.37:g.46321257delC	ENSP00000245934:p.Gly1014fs	Somatic		Capture	Illumina HiSeq	Phase_I	51013097	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Frame_Shift_Del	DEL	ENST00000245934.7	37	CCDS12676.2																																																																																				0.637	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819	
C19orf73	55150	broad.mit.edu	37	19	49622137	49622137	+	Frame_Shift_Del	DEL	G	G	-	rs201923438		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:49622137delG	ENST00000408991.2	-	1	260	c.143delC	c.(142-144)ccafs	p.P49fs	PPFIA3_ENST00000334186.4_5'Flank	NM_018111.2	NP_060581.2	Q9NVV2	CS073_HUMAN	chromosome 19 open reading frame 73	49								p.P48fs*9(1)		large_intestine(1)|lung(2)	3						AGTCGCGGGTGGGGGTGCCGC	0.701																																					p.P48fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.143delC	19						.						16.0	20.0	19.0					19																	49622137		1931	4119	6050	54313949	SO:0001589	frameshift_variant	55150	exon1			AK001352	CCDS42589.1	19q13.33	2013-06-17			ENSG00000221916	ENSG00000221916			25534	protein-coding gene	gene with protein product						12477932	Standard	NM_018111		Approved	FLJ10490	uc002pmq.4	Q9NVV2	OTTHUMG00000183345	ENST00000408991.2:c.143delC	19.37:g.49622137delG	ENSP00000386230:p.Pro49fs	Somatic		Capture	Illumina HiSeq	Phase_I	54313949	NM_018111	Q6NSX4	Frame_Shift_Del	DEL	ENST00000408991.2	37	CCDS42589.1																																																																																				0.701	C19orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466275.1	NM_018111	
PTOV1	53635	broad.mit.edu	37	19	50363527	50363527	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:50363527delG	ENST00000601675.1	+	12	1346	c.1242delG	c.(1240-1242)atgfs	p.M414fs	AC018766.5_ENST00000593654.1_RNA|AC018766.5_ENST00000599259.1_RNA|PTOV1_ENST00000601638.1_Frame_Shift_Del_p.M382fs|PTOV1_ENST00000391842.1_Frame_Shift_Del_p.M414fs|PTOV1_ENST00000221557.9_Frame_Shift_Del_p.W359fs|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000600603.1_Frame_Shift_Del_p.W359fs|PTOV1_ENST00000599732.1_Frame_Shift_Del_p.M414fs|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000598325.1_3'UTR			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	414	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.*417fs?(1)		endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		CGCCGTAGATGGGGGGGTAGT	0.657																																					p.M414fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1242delG	19						.						24.0	26.0	25.0					19																	50363527		2203	4300	6503	55055339	SO:0001589	frameshift_variant	53635	exon12			AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.1242delG	19.37:g.50363527delG	ENSP00000472816:p.Met414fs	Somatic		Capture	Illumina HiSeq	Phase_I	55055339	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Frame_Shift_Del	DEL	ENST00000601675.1	37	CCDS12782.1																																																																																				0.657	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
KIR3DX1	90011	broad.mit.edu	37	19	55045144	55045144	+	Silent	SNP	C	C	T	rs371369615		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:55045144C>T	ENST00000335056.3	+	3	302	c.264C>T	c.(262-264)caC>caT	p.H88H				Q9H7L2	KI3X1_HUMAN	killer cell immunoglobulin-like receptor, three domains, X1	88	Ig-like C2-type 1.					extracellular region (GO:0005576)		p.H88H(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|skin(1)	24				GBM - Glioblastoma multiforme(193;0.099)		CCCCAGAACACGCAGGGACCT	0.502																																					.	Colon(183;529 2002 28270 32358 35845)|Esophageal Squamous(50;443 1006 2278 10294 37938)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	.	19						.	C		0,4198		0,0,2099	78.0	81.0	80.0			-5.6	0.0	19		80	2,8504		0,2,4251	no	intergenic				0,2,6350	TT,TC,CC		0.0235,0.0,0.0157			55045144	2,12702	2099	4253	6352	59736956	SO:0001819	synonymous_variant	90011	.			BC033195		19q13.42	2013-03-26	2006-09-12	2006-09-12	ENSG00000104970	ENSG00000104970		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	25043	other	unknown			"""leukocyte receptor cluster (LRC) member 12"""	LENG12		11441184	Standard	NR_026716		Approved	FLJ00060	uc010erm.2	Q9H7L2	OTTHUMG00000065696	ENST00000335056.3:c.264C>T	19.37:g.55045144C>T		Somatic		Capture	Illumina HiSeq	Phase_I	59736956	.	B7WNL0|Q8N0S4	Silent	SNP	ENST00000335056.3	37																																																																																					0.502	KIR3DX1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000140800.2	NR_026716	
FIZ1	84922	broad.mit.edu	37	19	56109175	56109175	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:56109175delG	ENST00000221665.3	-	2	146	c.57delC	c.(55-57)cccfs	p.P19fs	FIZ1_ENST00000592585.1_Frame_Shift_Del_p.P19fs|ZNF524_ENST00000301073.3_5'Flank	NM_032836.2	NP_116225.2	Q96SL8	FIZ1_HUMAN	FLT3-interacting zinc finger 1	19					positive regulation of protein phosphorylation (GO:0001934)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|receptor tyrosine kinase binding (GO:0030971)	p.R20fs*47(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)	11			BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		ACGGGACCCTGGGGGCGGCAG	0.662																																					p.P19fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.57delC	19						.						19.0	20.0	19.0					19																	56109175		2200	4299	6499	60800987	SO:0001589	frameshift_variant	84922	exon2			AK027674	CCDS12928.1	19q13.42	2013-01-08				ENSG00000179943		"""Zinc fingers, C2H2-type"""	25917	protein-coding gene	gene with protein product		609133				12566383	Standard	NM_032836		Approved	FLJ14768, ZNF798	uc002qli.4	Q96SL8		ENST00000221665.3:c.57delC	19.37:g.56109175delG	ENSP00000221665:p.Pro19fs	Somatic		Capture	Illumina HiSeq	Phase_I	60800987	NM_032836	A2RU72|Q6ZMJ7	Frame_Shift_Del	DEL	ENST00000221665.3	37	CCDS12928.1																																																																																				0.662	FIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453350.1	NM_032836	
ZNF606	80095	broad.mit.edu	37	19	58512097	58512097	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr19:58512097C>T	ENST00000341164.4	-	3	662	c.42G>A	c.(40-42)acG>acA	p.T14T	CTD-2368P22.1_ENST00000550135.1_5'Flank|ZNF606_ENST00000552579.1_5'UTR|ZNF606_ENST00000547121.1_Silent_p.T14T|ZNF606_ENST00000536132.1_5'UTR|ZNF606_ENST00000547828.1_Silent_p.T14T|ZNF606_ENST00000546715.1_Silent_p.T14T	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T14T(2)		NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		AAGATTGGTCCGTAAGGGCAC	0.547																																					p.T14T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G42A	19						.						97.0	93.0	95.0					19																	58512097		2203	4300	6503	63203909	SO:0001819	synonymous_variant	80095	exon3			AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.42G>A	19.37:g.58512097C>T		Somatic		Capture	Illumina HiSeq	Phase_I	63203909	NM_025027	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																				0.547	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
KCNA10	3744	broad.mit.edu	37	1	111060107	111060108	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:111060107_111060108insC	ENST00000369771.2	-	1	1689_1690	c.1302_1303insG	c.(1300-1305)gggaagfs	p.K435fs		NM_005549.2	NP_005540.1	Q16322	KCA10_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 10	435					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|intracellular cyclic nucleotide activated cation channel activity (GO:0005221)	p.K435fs*35(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(3)|skin(1)|urinary_tract(1)	35		all_cancers(81;4.57e-06)|all_epithelial(167;1.52e-05)|all_lung(203;0.000152)|Lung NSC(277;0.000301)		Lung(183;0.0238)|all cancers(265;0.0874)|Colorectal(144;0.103)|Epithelial(280;0.116)|LUSC - Lung squamous cell carcinoma(189;0.134)	Dalfampridine(DB06637)	CCCACAATCTTCCCCCCTGGGG	0.559																																					p.K435fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1303_1304insG	1						.																																			110861631	SO:0001589	frameshift_variant	3744	exon1			U96110	CCDS826.1	1p13.1	2012-07-05			ENSG00000143105	ENSG00000143105		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6219	protein-coding gene	gene with protein product		602420				16382104	Standard	NM_005549		Approved	Kv1.8	uc001dzt.1	Q16322	OTTHUMG00000022785	ENST00000369771.2:c.1303dupG	1.37:g.111060113_111060113dupC	ENSP00000358786:p.Lys435fs	Somatic		Capture	Illumina HiSeq	Phase_I	110861630	NM_005549		Frame_Shift_Ins	INS	ENST00000369771.2	37	CCDS826.1																																																																																				0.559	KCNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059081.1	NM_005549	
DENND2C	163259	broad.mit.edu	37	1	115130526	115130527	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:115130526_115130527insA	ENST00000393274.1	-	19	3103_3104	c.2478_2479insT	c.(2476-2481)tttgtgfs	p.V827fs	DENND2C_ENST00000481894.1_5'UTR|DENND2C_ENST00000393277.1_Frame_Shift_Ins_p.V715fs|DENND2C_ENST00000393276.3_Frame_Shift_Ins_p.V770fs	NM_001256404.1	NP_001243333.1	Q68D51	DEN2C_HUMAN	DENN/MADD domain containing 2C	827	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.V770fs*15(1)		NS(2)|breast(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|skin(3)	37	all_epithelial(7;9.54e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		ACCAACTCCACAAAAAACCTGA	0.436																																					p.V770fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2308_2309insT	1						.																																			114932050	SO:0001589	frameshift_variant	163259	exon16				CCDS875.1, CCDS58018.1	1p13.2-p13.1	2012-10-03			ENSG00000175984	ENSG00000175984		"""DENN/MADD domain containing"""	24748	protein-coding gene	gene with protein product							Standard	NM_198459		Approved	FLJ37099, DKFZp686G0351, DKFZp779P1149, dJ1156J9.1, RP5-1156J9.1	uc001efd.1	Q68D51	OTTHUMG00000011893	ENST00000393274.1:c.2479dupT	1.37:g.115130532_115130532dupA	ENSP00000376955:p.Val827fs	Somatic		Capture	Illumina HiSeq	Phase_I	114932049	NM_198459	B1AL26|Q5TCX6|Q6P3R3	Frame_Shift_Ins	INS	ENST00000393274.1	37	CCDS58018.1																																																																																				0.436	DENND2C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000314822.1	NM_198459	
DNAH14	127602	broad.mit.edu	37	1	225147936	225147937	+	Intron	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:225147936_225147937insA	ENST00000445597.2	+	6	748				DNAH14_ENST00000430092.1_Frame_Shift_Ins_p.RK100fs|DNAH14_ENST00000366849.1_Frame_Shift_Ins_p.RK100fs|DNAH14_ENST00000439375.2_Frame_Shift_Ins_p.RK100fs|DNAH14_ENST00000498360.1_3'UTR|DNAH14_ENST00000366848.1_Frame_Shift_Ins_p.RK100fs|DNAH14_ENST00000366850.3_Frame_Shift_Ins_p.RK100fs|DNAH14_ENST00000400952.3_Frame_Shift_Ins_p.RK100fs			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14						microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)	p.D103fs*10(2)		NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AAGTCAAGGAGAAAAAAGGATC	0.381																																					p.R100fs												.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.299_300insA	1						.																																			223214560	SO:0001627	intron_variant	127602	exon4			U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.749-4244->A	1.37:g.225147942_225147942dupA		Somatic		Capture	Illumina HiSeq	Phase_I	223214559	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Frame_Shift_Ins	INS	ENST00000445597.2	37																																																																																					0.381	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
LYST	1130	broad.mit.edu	37	1	235973203	235973204	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:235973203_235973204insT	ENST00000389794.3	-	5	1088_1089	c.914_915insA	c.(913-915)aacfs	p.N305fs	LYST_ENST00000389793.2_Frame_Shift_Ins_p.N305fs|LYST_ENST00000536965.1_Frame_Shift_Ins_p.N305fs			Q99698	LYST_HUMAN	lysosomal trafficking regulator	305					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)		p.N305fs*36(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			GACTCTCCAAGTTGTCGCTCAG	0.48																																					p.N305fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.915_916insA	1						.																																			234039827	SO:0001589	frameshift_variant	1130	exon5			U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.915dupA	1.37:g.235973205_235973205dupT	ENSP00000374444:p.Asn305fs	Somatic		Capture	Illumina HiSeq	Phase_I	234039826	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Frame_Shift_Ins	INS	ENST00000389794.3	37	CCDS31062.1																																																																																				0.480	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
CCDC27	148870	broad.mit.edu	37	1	3686432	3686433	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:3686432_3686433insT	ENST00000294600.2	+	11	1913_1914	c.1829_1830insT	c.(1828-1833)gacatcfs	p.I611fs	SMIM1_ENST00000444870.2_5'Flank	NM_152492.2	NP_689705.2	Q2M243	CCD27_HUMAN	coiled-coil domain containing 27	611								p.I611fs*17(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(2)|lung(17)|prostate(1)|skin(2)|urinary_tract(2)	36	all_cancers(77;0.0385)|Ovarian(185;0.0634)|Lung NSC(156;0.21)|all_lung(157;0.218)	all_epithelial(116;5.52e-17)|all_lung(118;1.04e-06)|Lung NSC(185;0.000214)|Renal(390;0.00357)|Breast(487;0.00446)|Hepatocellular(190;0.0218)|Lung SC(97;0.0367)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.127)		Epithelial(90;1.11e-38)|OV - Ovarian serous cystadenocarcinoma(86;1.35e-22)|GBM - Glioblastoma multiforme(42;3.46e-16)|Colorectal(212;1.17e-05)|COAD - Colon adenocarcinoma(227;5.76e-05)|Kidney(185;0.00036)|BRCA - Breast invasive adenocarcinoma(365;0.000696)|KIRC - Kidney renal clear cell carcinoma(229;0.00558)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.203)		TCTGACAATGACATCCTGGAAG	0.579																																					p.D610fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1829_1830insT	1						.																																			3676293	SO:0001589	frameshift_variant	148870	exon11				CCDS50.1	1p36.32	2008-02-05			ENSG00000162592	ENSG00000162592			26546	protein-coding gene	gene with protein product							Standard	NM_152492		Approved	FLJ32825	uc001akv.2	Q2M243	OTTHUMG00000003504	Exception_encountered	1.37:g.3686432_3686433insT	ENSP00000294600:p.Ile611fs	Somatic		Capture	Illumina HiSeq	Phase_I	3676292	NM_152492	Q5TBV3|Q96M50	Frame_Shift_Ins	INS	ENST00000294600.2	37	CCDS50.1																																																																																				0.579	CCDC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009740.1	NM_152492	
KIAA0040	9674	broad.mit.edu	37	1	175129490	175129491	+	3'UTR	INS	-	-	TG	rs148184244		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:175129490_175129491insTG	ENST00000423313.1	-	0	1195_1196				KIAA0040_ENST00000567124.1_5'Flank|KIAA0040_ENST00000545251.2_3'UTR|KIAA0040_ENST00000444639.1_3'UTR	NM_001162893.1|NM_001162895.1|NM_014656.2	NP_001156365.1|NP_001156367.1|NP_055471.2	Q15053	K0040_HUMAN	KIAA0040																		CTACCTGAATTTGTGTGTGTGT	0.421																																					.												.	.	0			.	1						.																																			173396114	SO:0001624	3_prime_UTR_variant	9674	.			D25539		1q24-q25	2012-11-29			ENSG00000235750	ENSG00000235750			28950	protein-coding gene	gene with protein product							Standard	NM_014656		Approved		uc001gkn.3	Q15053	OTTHUMG00000034880	ENST00000423313.1:c.*360->CA	1.37:g.175129499_175129500dupTG		Somatic		Capture	Illumina HiSeq	Phase_I	173396113	.	A8K9H6|Q2NKQ0	Frame_Shift_Ins	INS	ENST00000423313.1	37																																																																																					0.421	KIAA0040-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000084420.3	NM_014656	
UBE4B	10277	broad.mit.edu	37	1	10207124	10207124	+	Missense_Mutation	SNP	G	G	A	rs148514322		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:10207124G>A	ENST00000253251.8	+	18	3019	c.2180G>A	c.(2179-2181)cGc>cAc	p.R727H	UBE4B_ENST00000343090.6_Missense_Mutation_p.R856H|UBE4B_ENST00000377157.3_Missense_Mutation_p.R611H					ubiquitination factor E4B									p.R727H(1)		NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CTGCTGCTCCGCATCCTGGAC	0.517																																					p.R856H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2567A	1						.						186.0	171.0	176.0					1																	10207124		2203	4300	6503	10129711	SO:0001583	missense	10277	exon19			AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2180G>A	1.37:g.10207124G>A	ENSP00000253251:p.Arg727His	Somatic		Capture	Illumina HiSeq	Phase_I	10129711	NM_001105562		Missense_Mutation	SNP	ENST00000253251.8	37	CCDS110.1	.	.	.	.	.	.	.	.	.	.	G	34	5.322407	0.95708	.	.	ENSG00000130939	ENST00000253251;ENST00000377157;ENST00000343090	T;T;T	0.49139	0.79;0.79;0.79	5.68	5.68	0.88126	Ubiquitin conjugation factor E4, core (1);	0.049060	0.85682	D	0.000000	T	0.68668	0.3026	M	0.79926	2.475	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.997	P;P;P	0.58331	0.837;0.824;0.748	T	0.71484	-0.4579	10	0.59425	D	0.04	-11.928	19.8593	0.96777	0.0:0.0:1.0:0.0	.	727;856;727	A8K8S9;O95155;O95155-2	.;UBE4B_HUMAN;.	H	727;611;856	ENSP00000253251:R727H;ENSP00000366362:R611H;ENSP00000343001:R856H	ENSP00000253251:R727H	R	+	2	0	UBE4B	10129711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.615000	0.83006	2.700000	0.92200	0.558000	0.71614	CGC		0.517	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
CASZ1	54897	broad.mit.edu	37	1	10720015	10720015	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:10720015C>T	ENST00000377022.3	-	6	1401	c.1084G>A	c.(1084-1086)Gcc>Acc	p.A362T	CASZ1_ENST00000478728.2_5'Flank|CASZ1_ENST00000344008.5_Missense_Mutation_p.A362T	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	362					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.A362T(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)		AAGGCGATGGCCCCGCCCATG	0.642																																					p.A362T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1084A	1						.						49.0	53.0	52.0					1																	10720015		2203	4300	6503	10642602	SO:0001583	missense	54897	exon6			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.1084G>A	1.37:g.10720015C>T	ENSP00000366221:p.Ala362Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10642602	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	c	19.26	3.792563	0.70452	.	.	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.46	4.46	0.54185	.	0.058651	0.64402	D	0.000002	T	0.45975	0.1369	L	0.29908	0.895	0.34108	D	0.662668	D;P;P;P	0.52996	0.957;0.887;0.887;0.944	P;P;P;P	0.51415	0.669;0.535;0.535;0.572	T	0.61987	-0.6949	9	0.66056	D	0.02	-28.0871	12.6109	0.56549	0.1657:0.8342:0.0:0.0	.	386;362;362;362	B7Z1S3;B3KRV8;Q86V15-2;Q86V15	.;.;.;CASZ1_HUMAN	T	362	.	ENSP00000339445:A362T	A	-	1	0	CASZ1	10642602	0.996000	0.38824	1.000000	0.80357	0.950000	0.60333	3.384000	0.52478	2.223000	0.72356	0.306000	0.20318	GCC		0.642	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
COL11A1	1301	broad.mit.edu	37	1	103453263	103453263	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:103453263C>A	ENST00000370096.3	-	30	2740	c.2428G>T	c.(2428-2430)Gat>Tat	p.D810Y	COL11A1_ENST00000358392.2_Missense_Mutation_p.D822Y|COL11A1_ENST00000353414.4_Missense_Mutation_p.D771Y|COL11A1_ENST00000512756.1_Missense_Mutation_p.D694Y	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	810	Triple-helical region.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.D822Y(1)		NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		TCAGGGCCATCTTCCCCTCTT	0.458																																					p.D810Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2428T	1						.						89.0	85.0	86.0					1																	103453263		2203	4300	6503	103225851	SO:0001583	missense	1301	exon30			J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.2428G>T	1.37:g.103453263C>A	ENSP00000359114:p.Asp810Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	103225851	NM_001854	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.04|19.04	3.749895|3.749895	0.69533|0.69533	.|.	.|.	ENSG00000060718|ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756|ENST00000370090	D;D;D;D|.	0.94330|.	-3.4;-3.4;-3.36;-3.4|.	4.4|4.4	4.4|4.4	0.53042|0.53042	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.61937|0.61937	0.2387|0.2387	L|L	0.52573|0.52573	1.65|1.65	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.997;1.0;1.0;0.999|.	D;D;D;D|.	0.87578|.	0.994;0.997;0.998;0.995|.	T|T	0.61559|0.61559	-0.7038|-0.7038	10|6	0.87932|0.39692	D|T	0|0.17	.|.	17.5266|17.5266	0.87802|0.87802	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	694;771;822;810|.	E9PCU0;P12107-3;P12107-2;P12107|.	.;.;.;COBA1_HUMAN|.	Y|N	810;822;771;694|24	ENSP00000359114:D810Y;ENSP00000351163:D822Y;ENSP00000302551:D771Y;ENSP00000426533:D694Y|.	ENSP00000302551:D771Y|ENSP00000359108:K24N	D|K	-|-	1|3	0|2	COL11A1|COL11A1	103225851|103225851	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.625000|0.625000	0.37756|0.37756	7.132000|7.132000	0.77251|0.77251	2.422000|2.422000	0.82143|0.82143	0.467000|0.467000	0.42956|0.42956	GAT|AAG		0.458	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
PRMT6	55170	broad.mit.edu	37	1	107599778	107599778	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:107599778A>G	ENST00000370078.1	+	1	478	c.441A>G	c.(439-441)gaA>gaG	p.E147E	PRMT6_ENST00000361318.5_Silent_p.E88E			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	147	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)	p.E88E(1)		biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		AGTTGCCGGAACAGGTGGATG	0.652																																					p.E147E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A441G	1						.						82.0	95.0	91.0					1																	107599778		2195	4291	6486	107401301	SO:0001819	synonymous_variant	55170	exon1			AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"""Protein arginine methyltransferases"""	18241	protein-coding gene	gene with protein product		608274	"""HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"""	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.441A>G	1.37:g.107599778A>G		Somatic		Capture	Illumina HiSeq	Phase_I	107401301	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Silent	SNP	ENST00000370078.1	37	CCDS41360.2	.	.	.	.	.	.	.	.	.	.	A	5.195	0.221502	0.09863	.	.	ENSG00000198890	ENST00000540389	.	.	.	5.75	4.8	0.61643	.	.	.	.	.	T	0.55146	0.1902	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63065	-0.6720	5	0.87932	D	0	-8.3851	8.8839	0.35392	0.1693:0.0:0.8307:0.0	.	.	.	.	A	41	.	ENSP00000440829:T41A	T	+	1	0	PRMT6	107401301	0.963000	0.33076	1.000000	0.80357	0.007000	0.05969	1.471000	0.35365	1.419000	0.47118	-0.339000	0.08088	ACA		0.652	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137	
C1orf127	148345	broad.mit.edu	37	1	11008120	11008120	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:11008120G>T	ENST00000377008.4	-	11	2017	c.1571C>A	c.(1570-1572)cCc>cAc	p.P524H	C1orf127_ENST00000377004.4_Missense_Mutation_p.P691H			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	524								p.P524H(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCTCACCCTGGGCATCCCGGT	0.617																																					p.P691H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2072A	1						.						37.0	39.0	38.0					1																	11008120		2203	4300	6503	10930707	SO:0001583	missense	148345	exon12			AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1571C>A	1.37:g.11008120G>T	ENSP00000366207:p.Pro524His	Somatic		Capture	Illumina HiSeq	Phase_I	10930707	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.44|11.44	1.640852|1.640852	0.29157|0.29157	.|.	.|.	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|T;T	0.38887|0.52057	1.11;1.11|1.15;0.68	3.91|3.91	-7.82|-7.82	0.01205|0.01205	.|.	1.215770|1.215770	0.06222|0.06222	N|N	0.686947|0.686947	T|T	0.32675|0.32675	0.0837|0.0837	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B;B|.	0.14805|.	0.011;0.011;0.011|.	B;B;B|.	0.12156|.	0.007;0.007;0.007|.	T|T	0.52200|0.52200	-0.8607|-0.8607	10|8	0.72032|0.87932	D|D	0.01|0	0.3629|0.3629	9.516|9.516	0.39106|0.39106	0.1986:0.0:0.6661:0.1353|0.1986:0.0:0.6661:0.1353	.|.	542;516;524|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	H|T	691;524|526;643	ENSP00000366203:P691H;ENSP00000366207:P524H|ENSP00000387816:P526T;ENSP00000429704:P643T	ENSP00000366203:P691H|ENSP00000387816:P526T	P|P	-|-	2|1	0|0	C1orf127|C1orf127	10930707|10930707	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.024000|0.024000	0.10985|0.10985	-2.075000|-2.075000	0.01374|0.01374	-2.197000|-2.197000	0.00750|0.00750	0.467000|0.467000	0.42956|0.42956	CCC|CCA		0.617	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
PRMT6	55170	broad.mit.edu	37	1	107599898	107599898	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:107599898C>A	ENST00000370078.1	+	1	598	c.561C>A	c.(559-561)gcC>gcA	p.A187A	PRMT6_ENST00000361318.5_Silent_p.A128A			Q96LA8	ANM6_HUMAN	protein arginine methyltransferase 6	187	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				base-excision repair (GO:0006284)|histone H3-R2 methylation (GO:0034970)|histone H4-R3 methylation (GO:0043985)|histone methylation (GO:0016571)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	histone binding (GO:0042393)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H2A-R3 specific) (GO:0070612)|histone methyltransferase activity (H3-R2 specific) (GO:0070611)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)	p.A128A(1)		biliary_tract(1)|breast(2)|kidney(1)|large_intestine(4)|lung(5)|urinary_tract(1)	14		all_epithelial(167;0.000429)|all_lung(203;0.00122)|Lung NSC(277;0.00185)		Lung(183;0.0305)|Epithelial(280;0.0765)|Colorectal(144;0.0998)|all cancers(265;0.14)|LUSC - Lung squamous cell carcinoma(189;0.173)|BRCA - Breast invasive adenocarcinoma(282;0.242)		TCCTGCCGGCCTCCGCCGAGC	0.632																																					p.A187A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C561A	1						.						33.0	37.0	36.0					1																	107599898		2018	4174	6192	107401421	SO:0001819	synonymous_variant	55170	exon1			AK001421	CCDS41360.1, CCDS41360.2	1p13.2	2008-02-05	2006-02-16	2006-02-16	ENSG00000198890	ENSG00000198890		"""Protein arginine methyltransferases"""	18241	protein-coding gene	gene with protein product		608274	"""HMT1 hnRNP methyltransferase-like 6 (S. cerevisiae)"""	HRMT1L6		11724789	Standard	NM_018137		Approved	FLJ10559	uc010ous.2	Q96LA8	OTTHUMG00000010964	ENST00000370078.1:c.561C>A	1.37:g.107599898C>A		Somatic		Capture	Illumina HiSeq	Phase_I	107401421	NM_018137	A3KME1|B4DID8|Q5T5Y5|Q6DKI4|Q9NVR8	Silent	SNP	ENST00000370078.1	37	CCDS41360.2	.	.	.	.	.	.	.	.	.	.	C	12.21	1.869862	0.33069	.	.	ENSG00000198890	ENST00000540389	.	.	.	5.51	-5.03	0.02973	.	.	.	.	.	T	0.44932	0.1317	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61647	-0.7020	5	0.87932	D	0	-34.662	6.683	0.23131	0.0:0.3067:0.3289:0.3643	.	.	.	.	I	81	.	ENSP00000440829:L81I	L	+	1	0	PRMT6	107401421	0.000000	0.05858	0.984000	0.44739	0.820000	0.46376	-0.985000	0.03751	-0.492000	0.06687	-0.417000	0.06048	CTC		0.632	PRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030185.1	NM_018137	
CHI3L2	1117	broad.mit.edu	37	1	111778339	111778339	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:111778339G>T	ENST00000445067.2	+	8	1330	c.559G>T	c.(559-561)Ggg>Tgg	p.G187W	CHI3L2_ENST00000466741.1_Missense_Mutation_p.G108W|CHI3L2_ENST00000369744.2_Missense_Mutation_p.G177W|CHI3L2_ENST00000369748.4_Missense_Mutation_p.G187W|CHI3L2_ENST00000524472.1_Missense_Mutation_p.G108W			Q15782	CH3L2_HUMAN	chitinase 3-like 2	187					carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)	extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.G187W(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(8)|prostate(1)	19		all_cancers(81;1.89e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0171)|Colorectal(144;0.0387)|all cancers(265;0.0464)|LUSC - Lung squamous cell carcinoma(189;0.0872)|Epithelial(280;0.0994)|COAD - Colon adenocarcinoma(174;0.141)		CGTATCTGCAGGGAGGCAAAT	0.448																																					p.G108W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G322T	1						.						110.0	100.0	103.0					1																	111778339		2203	4300	6503	111579862	SO:0001583	missense	1117	exon5			U49835	CCDS30802.1, CCDS30803.1, CCDS41367.1	1p13.3	2008-02-05			ENSG00000064886	ENSG00000064886			1933	protein-coding gene	gene with protein product		601526				8702629	Standard	NM_001025197		Approved	YKL-39, YKL39	uc001eam.3	Q15782	OTTHUMG00000012174	ENST00000445067.2:c.559G>T	1.37:g.111778339G>T	ENSP00000437082:p.Gly187Trp	Somatic		Capture	Illumina HiSeq	Phase_I	111579862	NM_001025199	A6NNY3|B4DPR7|Q15749|Q15783|Q5VUV7|Q96F97	Missense_Mutation	SNP	ENST00000445067.2	37	CCDS30802.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.364288	0.41902	.	.	ENSG00000064886	ENST00000445067;ENST00000528451;ENST00000486561;ENST00000369744;ENST00000369748;ENST00000474304;ENST00000466741;ENST00000477185;ENST00000467038;ENST00000497587;ENST00000524472;ENST00000497220	T;T;T;T;T;T;T;T;T;T;T	0.06768	3.26;3.26;3.26;3.26;3.26;3.26;3.26;3.26;3.26;3.26;3.26	3.39	1.35	0.21983	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.355795	0.20465	N	0.091810	T	0.27098	0.0664	H	0.97077	3.935	0.36478	D	0.867676	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.29971	-0.9994	10	0.72032	D	0.01	-0.8102	9.5075	0.39056	0.0:0.0:0.6205:0.3794	.	108;177;187	B4DPR7;A6NNY3;Q15782	.;.;CH3L2_HUMAN	W	187;187;187;177;187;168;108;108;89;108;108;41	ENSP00000437082:G187W;ENSP00000436077:G187W;ENSP00000431968:G187W;ENSP00000358759:G177W;ENSP00000358763:G187W;ENSP00000437086:G108W;ENSP00000436272:G108W;ENSP00000431978:G89W;ENSP00000436006:G108W;ENSP00000432049:G108W;ENSP00000435250:G41W	ENSP00000358759:G177W	G	+	1	0	CHI3L2	111579862	1.000000	0.71417	0.485000	0.27403	0.466000	0.32739	2.834000	0.48167	0.190000	0.20209	0.561000	0.74099	GGG		0.448	CHI3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033669.4	NM_004000	
LRIG2	9860	broad.mit.edu	37	1	113662003	113662003	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:113662003A>C	ENST00000361127.5	+	17	3027	c.2829A>C	c.(2827-2829)aaA>aaC	p.K943N	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	943					innervation (GO:0060384)|regulation of platelet-derived growth factor receptor signaling pathway (GO:0010640)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.K943N(1)		breast(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(10)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	31	Lung SC(450;0.246)	all_cancers(81;1.56e-05)|all_epithelial(167;2.62e-05)|all_lung(203;0.000665)|Lung NSC(69;0.000986)		Lung(183;0.0279)|Colorectal(144;0.0885)|COAD - Colon adenocarcinoma(174;0.134)|all cancers(265;0.139)|Epithelial(280;0.143)|LUSC - Lung squamous cell carcinoma(189;0.15)		AAATGCCTAAAGAGACATATT	0.493																																					p.K943N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2829C	1						.						152.0	145.0	147.0					1																	113662003		2203	4300	6503	113463526	SO:0001583	missense	9860	exon17			AB018349	CCDS30808.1	1p13.1	2013-01-11			ENSG00000198799	ENSG00000198799		"""Immunoglobulin superfamily / I-set domain containing"""	20889	protein-coding gene	gene with protein product		608869					Standard	XM_005271369		Approved	KIAA0806	uc001edf.1	O94898	OTTHUMG00000012133	ENST00000361127.5:c.2829A>C	1.37:g.113662003A>C	ENSP00000355396:p.Lys943Asn	Somatic		Capture	Illumina HiSeq	Phase_I	113463526	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	10.68	1.418360	0.25552	.	.	ENSG00000198799	ENST00000361127	T	0.62498	0.02	5.3	1.13	0.20643	.	0.000000	0.85682	D	0.000000	T	0.33585	0.0868	L	0.60455	1.87	0.32198	N	0.578204	B	0.06786	0.001	B	0.10450	0.005	T	0.13495	-1.0507	10	0.26408	T	0.33	.	9.131	0.36846	0.6251:0.0:0.3749:0.0	.	943	O94898	LRIG2_HUMAN	N	943	ENSP00000355396:K943N	ENSP00000355396:K943N	K	+	3	2	LRIG2	113463526	1.000000	0.71417	0.997000	0.53966	0.254000	0.26022	0.898000	0.28404	0.260000	0.21731	0.482000	0.46254	AAA		0.493	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813	
MAGI3	260425	broad.mit.edu	37	1	114201751	114201751	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:114201751C>A	ENST00000307546.9	+	16	2754	c.2679C>A	c.(2677-2679)cgC>cgA	p.R893R	MAGI3_ENST00000369617.4_Silent_p.R918R|MAGI3_ENST00000369615.1_Silent_p.R893R|MAGI3_ENST00000369611.4_Silent_p.R893R	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	918	Interaction with LPAR2 and GRIN2B.|PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)	p.R893R(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CGGCTGACCGCTGTGGAAAAC	0.403																																					p.R893R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2679A	1						.						134.0	131.0	132.0					1																	114201751		2203	4300	6503	114003274	SO:0001819	synonymous_variant	260425	exon16			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2679C>A	1.37:g.114201751C>A		Somatic		Capture	Illumina HiSeq	Phase_I	114003274	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	De_novo_Start_OutOfFrame	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																				0.403	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
TRIM33	51592	broad.mit.edu	37	1	114976301	114976301	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:114976301T>C	ENST00000358465.2	-	5	1061	c.978A>G	c.(976-978)ctA>ctG	p.L326L	TRIM33_ENST00000450349.2_5'UTR|TRIM33_ENST00000369543.2_Silent_p.L326L	NM_015906.3	NP_056990.3	Q9UPN9	TRI33_HUMAN	tripartite motif containing 33	326	Necessary for oligomerization.				gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|R-SMAD binding (GO:0070412)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L326L(1)		breast(2)|central_nervous_system(5)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	48	all_epithelial(7;0.000132)|all_lung(7;0.00106)|Lung SC(450;0.184)	all_cancers(81;3.03e-08)|all_epithelial(167;3.24e-08)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTTCGCCAGTAGATTCTCAA	0.308			T	RET	papillary thyroid																																p.L326L			Dom	yes		1	1p13	51592	""" tripartite motif-containing 33 (PTC7,TIF1G)"""		E	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A978G	1						.						70.0	73.0	72.0					1																	114976301		2202	4298	6500	114777824	SO:0001819	synonymous_variant	51592	exon5			AF220136	CCDS872.1, CCDS873.1	1p13.1	2014-02-17	2011-01-25		ENSG00000197323	ENSG00000197323		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"", ""RING-type (C3HC4) zinc fingers"""	16290	protein-coding gene	gene with protein product	"""transcriptional intermediary factor 1 gamma"", ""ret-fused gene 7"""	605769	"""tripartite motif-containing 33"""			11331580, 10022127	Standard	XM_005270936		Approved	TIF1GAMMA, FLJ11429, KIAA1113, TIFGAMMA, RFG7, TF1G, TIF1G, PTC7	uc001eew.3	Q9UPN9	OTTHUMG00000011891	ENST00000358465.2:c.978A>G	1.37:g.114976301T>C		Somatic		Capture	Illumina HiSeq	Phase_I	114777824	NM_015906	O95855|Q5TG72|Q5TG73|Q5TG74|Q9C017|Q9UJ79	Silent	SNP	ENST00000358465.2	37	CCDS872.1	.	.	.	.	.	.	.	.	.	.	T	8.861	0.946970	0.18356	.	.	ENSG00000197323	ENST00000448034	.	.	.	5.13	0.183	0.15082	.	.	.	.	.	T	0.37433	0.1003	.	.	.	0.40318	D	0.978798	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	-4.4886	6.7391	0.23424	0.0:0.4042:0.1327:0.4631	.	.	.	.	C	63	.	.	Y	-	2	0	TRIM33	114777824	0.001000	0.12720	0.981000	0.43875	0.982000	0.71751	-0.990000	0.03732	-0.224000	0.09928	0.377000	0.23210	TAC		0.308	TRIM33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032854.1	NM_015906	
SIKE1	80143	broad.mit.edu	37	1	115321872	115321872	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:115321872G>A	ENST00000060969.5	-	3	368	c.299C>T	c.(298-300)gCt>gTt	p.A100V	SIKE1_ENST00000369528.5_Missense_Mutation_p.A104V|SIKE1_ENST00000506320.1_5'UTR			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	100					innate immune response (GO:0045087)	cytosol (GO:0005829)		p.A100V(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						AAGTTCCAAAGCATCCTGGTG	0.413																																					p.A100V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C299T	1						.						132.0	126.0	128.0					1																	115321872		2203	4300	6503	115123395	SO:0001583	missense	80143	exon3			AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"""suppressor of IKK epsilon"""	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.299C>T	1.37:g.115321872G>A	ENSP00000060969:p.Ala100Val	Somatic		Capture	Illumina HiSeq	Phase_I	115123395	NM_025073	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Missense_Mutation	SNP	ENST00000060969.5	37	CCDS878.1	.	.	.	.	.	.	.	.	.	.	G	36	5.695583	0.96802	.	.	ENSG00000052723	ENST00000369528;ENST00000060969	T;T	0.67171	-0.25;-0.25	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.79667	0.4485	M	0.73372	2.23	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.77629	-0.2516	10	0.51188	T	0.08	-7.7164	20.2052	0.98274	0.0:0.0:1.0:0.0	.	104;100	Q9BRV8-2;Q9BRV8	.;SIKE1_HUMAN	V	104;100	ENSP00000358541:A104V;ENSP00000060969:A100V	ENSP00000060969:A100V	A	-	2	0	SIKE1	115123395	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.880000	0.92407	2.873000	0.98535	0.563000	0.77884	GCT		0.413	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073	
MAD2L2	10459	broad.mit.edu	37	1	11734852	11734852	+	Missense_Mutation	SNP	G	G	A	rs142776270		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:11734852G>A	ENST00000235310.3	-	11	1544	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	MAD2L2_ENST00000376669.5_Missense_Mutation_p.R219C|MAD2L2_ENST00000376692.4_Missense_Mutation_p.R206C|MAD2L2_ENST00000376672.1_Missense_Mutation_p.R219C|MAD2L2_ENST00000376667.3_Missense_Mutation_p.R206C			Q9UI95	MD2L2_HUMAN	MAD2 mitotic arrest deficient-like 2 (yeast)	206	Mediates interaction with ipaB.				actin filament organization (GO:0007015)|DNA damage response, signal transduction resulting in transcription (GO:0042772)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|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 regulatory region DNA binding (GO:2000678)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|zeta DNA polymerase complex (GO:0016035)	JUN kinase binding (GO:0008432)|RNA polymerase II activating transcription factor binding (GO:0001102)	p.R206C(1)		kidney(1)|large_intestine(1)|lung(2)|ovary(1)	5	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.04e-06)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|Kidney(185;0.000733)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TTATGAGCGCGCTCTTCCACG	0.612								DNA polymerases (catalytic subunits)																													p.R206C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C616T	1						.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	85.0	78.0	81.0		616,616	1.8	1.0	1	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	MAD2L2	NM_001127325.1,NM_006341.3	180,180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	206/212,206/212	11734852	1,13005	2203	4300	6503	11657439	SO:0001583	missense	10459	exon9			AF139365	CCDS134.1	1p36	2013-01-17	2001-11-28		ENSG00000116670	ENSG00000116670		"""DNA polymerases"""	6764	protein-coding gene	gene with protein product	"""mitotic arrest deficient homolog-like 2"", ""polymerase (DNA-directed), zeta 2, accessory subunit"""	604094	"""MAD2 (mitotic arrest deficient, yeast, homolog)-like 2"""			10366450	Standard	NM_006341		Approved	MAD2B, REV7, POLZ2	uc009vnc.3	Q9UI95	OTTHUMG00000002231	ENST00000235310.3:c.616C>T	1.37:g.11734852G>A	ENSP00000235310:p.Arg206Cys	Somatic		Capture	Illumina HiSeq	Phase_I	11657439	NM_006341	B3KNE3|Q5TGW7|Q9UNA7|Q9Y6I6	Missense_Mutation	SNP	ENST00000235310.3	37	CCDS134.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.246933	0.22796	0.0	1.16E-4	ENSG00000116670	ENST00000376692;ENST00000235310;ENST00000376672;ENST00000376669;ENST00000376667	.	.	.	5.18	1.76	0.24704	DNA-binding HORMA (1);	0.159147	0.52532	D	0.000072	T	0.40956	0.1138	N	0.19112	0.55	0.80722	D	1	B	0.10296	0.003	B	0.04013	0.001	T	0.28964	-1.0027	9	0.51188	T	0.08	-14.132	12.752	0.57314	0.0:0.0:0.4532:0.5468	.	206	Q9UI95	MD2L2_HUMAN	C	206;206;219;219;206	.	ENSP00000235310:R206C	R	-	1	0	MAD2L2	11657439	1.000000	0.71417	0.980000	0.43619	0.335000	0.28730	1.567000	0.36407	0.508000	0.28173	0.655000	0.94253	CGC		0.612	MAD2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006344.2	NM_006341	
SLC22A15	55356	broad.mit.edu	37	1	116569566	116569566	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:116569566A>G	ENST00000369503.4	+	5	781	c.651A>G	c.(649-651)ttA>ttG	p.L217L	SLC22A15_ENST00000369502.1_Silent_p.L217L	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	217					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	transmembrane transporter activity (GO:0022857)	p.L217L(1)		endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|urinary_tract(1)	17	Lung SC(450;0.184)	all_cancers(81;3.17e-06)|all_epithelial(167;2.32e-06)|all_lung(203;9.81e-06)|Lung NSC(69;5.94e-05)		Lung(183;0.0171)|Colorectal(144;0.0686)|LUSC - Lung squamous cell carcinoma(189;0.0903)|all cancers(265;0.108)|COAD - Colon adenocarcinoma(174;0.111)|Epithelial(280;0.12)		ATGCCCTGTTAGGATACTTCA	0.478																																					p.L217L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A651G	1						.						188.0	174.0	178.0					1																	116569566		1905	4107	6012	116371089	SO:0001819	synonymous_variant	55356	exon5			AY145501	CCDS44198.1	1p12	2013-05-22	2008-01-11		ENSG00000163393	ENSG00000163393		"""Solute carriers"""	20301	protein-coding gene	gene with protein product		608275	"""solute carrier family 22 (organic cation transporter), member 15"""			12372408	Standard	NM_018420		Approved	FLIPT1	uc001egb.4	Q8IZD6	OTTHUMG00000012008	ENST00000369503.4:c.651A>G	1.37:g.116569566A>G		Somatic		Capture	Illumina HiSeq	Phase_I	116371089	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Silent	SNP	ENST00000369503.4	37	CCDS44198.1																																																																																				0.478	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420	
DRAXIN	374946	broad.mit.edu	37	1	11769364	11769364	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:11769364A>T	ENST00000294485.5	+	3	619	c.484A>T	c.(484-486)Atg>Ttg	p.M162L		NM_198545.3	NP_940947.3			dorsal inhibitory axon guidance protein																		CAGCTCCCTGATGAAGAAGGC	0.602																																					p.M162L												.	.	0			c.A484T	1						.						49.0	46.0	47.0					1																	11769364		2203	4300	6503	11691951	SO:0001583	missense	374946	exon3			AY358750	CCDS135.1	1p36.22	2012-08-20	2012-08-14	2012-08-14	ENSG00000162490	ENSG00000162490			25054	protein-coding gene	gene with protein product	"""dorsal repulsive axon guidance protein"", ""neural tissue-specific cysteine-rich protein"""	612682	"""chromosome 1 open reading frame 187"""	C1orf187		19150847	Standard	NM_198545		Approved	FLJ34999, Draxin, Neucrin	uc001asr.1	Q8NBI3	OTTHUMG00000002227	ENST00000294485.5:c.484A>T	1.37:g.11769364A>T	ENSP00000294485:p.Met162Leu	None		Capture	Illumina HiSeq	Phase_I	11691951	NM_198545		Missense_Mutation	SNP	ENST00000294485.5	37	CCDS135.1	.	.	.	.	.	.	.	.	.	.	a	10.53	1.375996	0.24857	.	.	ENSG00000162490	ENST00000294485	T	0.32753	1.44	5.42	5.42	0.78866	.	0.445681	0.24904	N	0.034666	T	0.19805	0.0476	L	0.37897	1.145	0.27827	N	0.9416	B	0.15473	0.013	B	0.17722	0.019	T	0.31166	-0.9953	10	0.05351	T	0.99	-25.3473	8.9472	0.35767	0.8232:0.0:0.0:0.1768	.	162	Q8NBI3	DRAXI_HUMAN	L	162	ENSP00000294485:M162L	ENSP00000294485:M162L	M	+	1	0	C1orf187	11691951	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.692000	0.47018	2.054000	0.61138	0.459000	0.35465	ATG		0.602	DRAXIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006325.1	NM_198545	
CLCN6	1185	broad.mit.edu	37	1	11898406	11898406	+	Silent	SNP	G	G	A	rs150497601		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:11898406G>A	ENST00000346436.6	+	21	2362	c.2310G>A	c.(2308-2310)ccG>ccA	p.P770P	CLCN6_ENST00000376496.3_Silent_p.P770P|CLCN6_ENST00000376487.3_Silent_p.P748P|NPPA-AS1_ENST00000446542.1_RNA|CLCN6_ENST00000312413.6_3'UTR	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	770					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)	p.P770P(1)		cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGCCAGCCGCGCCTCTCCT	0.632											OREG0013104	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P770P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2310A	1						.	G		1,4403	2.1+/-5.4	0,1,2201	56.0	55.0	55.0		2310	-10.8	0.4	1	dbSNP_134	55	0,8600		0,0,4300	no	coding-synonymous	CLCN6	NM_001286.2		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		770/870	11898406	1,13003	2202	4300	6502	11820993	SO:0001819	synonymous_variant	1185	exon21			X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.2310G>A	1.37:g.11898406G>A		Somatic	675	Capture	Illumina HiSeq	Phase_I	11820993	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																				0.632	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
ATP1A1	476	broad.mit.edu	37	1	116935541	116935541	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:116935541C>T	ENST00000295598.5	+	11	1650	c.1398C>T	c.(1396-1398)tcC>tcT	p.S466S	ATP1A1_ENST00000537345.1_Silent_p.S466S|ATP1A1_ENST00000369496.4_Silent_p.S435S	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	466					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.S466S(1)		NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GCTGTGGTTCCGTGAAGGAGA	0.493																																					p.S466S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1398T	1						.						169.0	144.0	153.0					1																	116935541		2203	4300	6503	116737064	SO:0001819	synonymous_variant	476	exon11			D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.1398C>T	1.37:g.116935541C>T		Somatic		Capture	Illumina HiSeq	Phase_I	116737064	NM_000701	B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Silent	SNP	ENST00000295598.5	37	CCDS887.1																																																																																				0.493	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5	NM_001160233	
PDE4DIP	9659	broad.mit.edu	37	1	144930951	144930951	+	Intron	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:144930951G>T	ENST00000369354.3	-	6	826				PDE4DIP_ENST00000313431.9_Missense_Mutation_p.P253H|PDE4DIP_ENST00000369349.3_Intron|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.P253H|PDE4DIP_ENST00000369359.4_Intron|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000369351.3_Intron|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000313382.9_Intron|PDE4DIP_ENST00000479408.2_Intron			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein						cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.P253H(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		CTGTTGTGGAGGGCTAGCCTG	0.507			T	PDGFRB	MPD																																p.P253H			Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	.	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)	c.C758A	1						.						148.0	143.0	145.0					1																	144930951		2203	4300	6503	143642308	SO:0001627	intron_variant	9659	exon1			AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.637-7130C>A	1.37:g.144930951G>T		Somatic		Capture	Illumina HiSeq	Phase_I	143642308	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	8.297	0.819089	0.16607	.	.	ENSG00000178104	ENST00000369353;ENST00000313431;ENST00000529945	T;T	0.12039	2.72;2.72	5.53	3.31	0.37934	.	.	.	.	.	T	0.05640	0.0148	L	0.36672	1.1	0.09310	N	0.999995	P	0.42649	0.786	B	0.41036	0.346	T	0.17992	-1.0351	9	0.66056	D	0.02	.	10.8646	0.46847	0.1815:0.0:0.8185:0.0	.	253	Q5VU43-2	.	H	253	ENSP00000316434:P253H;ENSP00000433392:P253H	ENSP00000316434:P253H	P	-	2	0	PDE4DIP	143642308	0.900000	0.30661	0.454000	0.27019	0.024000	0.10985	1.796000	0.38794	1.337000	0.45525	0.591000	0.81541	CCT		0.507	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
ITGA10	8515	broad.mit.edu	37	1	145528592	145528592	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:145528592G>A	ENST00000369304.3	+	5	564	c.389G>A	c.(388-390)cGt>cAt	p.R130H	ITGA10_ENST00000539363.1_Intron|ITGA10_ENST00000538811.1_Intron	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	130					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)	p.R130H(1)		NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CTCTGGTCTCGTGCTTGTGGC	0.587																																					p.R130H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G389A	1						.						125.0	114.0	118.0					1																	145528592		2203	4300	6503	144239949	SO:0001583	missense	8515	exon5			AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.389G>A	1.37:g.145528592G>A	ENSP00000358310:p.Arg130His	Somatic		Capture	Illumina HiSeq	Phase_I	144239949	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	G	9.792	1.178259	0.21787	.	.	ENSG00000143127	ENST00000369304;ENST00000543043	T	0.71461	-0.57	4.92	1.96	0.26148	.	0.248291	0.35646	N	0.003072	T	0.22551	0.0544	N	0.13098	0.295	0.80722	D	1	B;B	0.25312	0.123;0.075	B;B	0.24701	0.055;0.025	T	0.32719	-0.9896	10	0.02654	T	1	.	6.3609	0.21427	0.3894:0.0:0.6106:0.0	.	96;130	F5H3T9;O75578	.;ITA10_HUMAN	H	130;96	ENSP00000358310:R130H	ENSP00000358310:R130H	R	+	2	0	ITGA10	144239949	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	3.460000	0.53028	0.585000	0.29608	0.561000	0.74099	CGT		0.587	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
BCL9	607	broad.mit.edu	37	1	147096301	147096301	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:147096301G>T	ENST00000234739.3	+	10	4562	c.3822G>T	c.(3820-3822)caG>caT	p.Q1274H		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	1274	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|myotube differentiation involved in skeletal muscle regeneration (GO:0014908)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)		p.Q1274H(1)		breast(1)|large_intestine(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	7	all_hematologic(923;0.115)					CACACATGCAGGGGATGATGG	0.587			T	"""IGH@, IGL@"""	B-ALL																																p.Q1274H			Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3822T	1						.						46.0	45.0	46.0					1																	147096301		2203	4300	6503	145562925	SO:0001583	missense	607	exon10			Y13620	CCDS30833.1	1q21	2008-02-05			ENSG00000116128	ENSG00000116128			1008	protein-coding gene	gene with protein product		602597				9490669	Standard	NM_004326		Approved		uc001epq.3	O00512	OTTHUMG00000014031	ENST00000234739.3:c.3822G>T	1.37:g.147096301G>T	ENSP00000234739:p.Gln1274His	Somatic		Capture	Illumina HiSeq	Phase_I	145562925	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.546232	0.45383	.	.	ENSG00000116128	ENST00000234739	T	0.52754	0.65	5.26	3.39	0.38822	.	0.000000	0.85682	D	0.000000	T	0.29945	0.0749	L	0.47190	1.495	0.40650	D	0.982024	P;P	0.50943	0.94;0.94	P;P	0.48030	0.564;0.564	T	0.15896	-1.0421	10	0.87932	D	0	-8.5703	6.5652	0.22509	0.1498:0.0:0.7056:0.1447	.	1274;1274	Q1JQ81;O00512	.;BCL9_HUMAN	H	1274	ENSP00000234739:Q1274H	ENSP00000234739:Q1274H	Q	+	3	2	BCL9	145562925	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.490000	0.60319	0.607000	0.29982	0.650000	0.86243	CAG		0.587	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326	
BOLA1	51027	broad.mit.edu	37	1	149871871	149871871	+	Missense_Mutation	SNP	C	C	T	rs113958238	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:149871871C>T	ENST00000369153.2	+	3	923	c.259C>T	c.(259-261)Cgg>Tgg	p.R87W	BOLA1_ENST00000369150.1_Missense_Mutation_p.R87W|BOLA1_ENST00000369152.5_Missense_Mutation_p.R87W|BOLA1_ENST00000476344.1_3'UTR			Q9Y3E2	BOLA1_HUMAN	bolA family member 1	87						extracellular region (GO:0005576)|mitochondrion (GO:0005739)		p.R87W(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)	10	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			ACAACGACACCGGCTGGTCCA	0.682																																					p.R87W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C259T	1						.						34.0	33.0	33.0					1																	149871871		2203	4299	6502	148138495	SO:0001583	missense	51027	exon2			AF151901	CCDS939.1	1q21	2013-09-02	2013-09-02		ENSG00000178096	ENSG00000178096			24263	protein-coding gene	gene with protein product		613181	"""bolA-like 1 (E. coli)"", ""bolA homolog 1 (E. coli)"""			14718656	Standard	NM_016074		Approved	CGI-143	uc001etf.3	Q9Y3E2	OTTHUMG00000012087	ENST00000369153.2:c.259C>T	1.37:g.149871871C>T	ENSP00000358149:p.Arg87Trp	Somatic		Capture	Illumina HiSeq	Phase_I	148138495	NM_016074	B2R7K2|D3DUZ4|Q5QNY0	Missense_Mutation	SNP	ENST00000369153.2	37	CCDS939.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098808	0.56183	.	.	ENSG00000178096	ENST00000369153;ENST00000369152;ENST00000369150	T;T;T	0.74842	-0.88;-0.88;-0.88	5.35	4.43	0.53597	.	0.000000	0.85682	D	0.000000	D	0.90273	0.6958	H	0.99391	4.545	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92987	0.6411	10	0.87932	D	0	-38.0817	11.3882	0.49798	0.329:0.671:0.0:0.0	.	87	Q9Y3E2	BOLA1_HUMAN	W	87	ENSP00000358149:R87W;ENSP00000358148:R87W;ENSP00000358146:R87W	ENSP00000358146:R87W	R	+	1	2	BOLA1	148138495	1.000000	0.71417	1.000000	0.80357	0.049000	0.14656	1.691000	0.37721	1.376000	0.46267	-0.521000	0.04368	CGG		0.682	BOLA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033443.2	NM_016074	
PLEKHO1	51177	broad.mit.edu	37	1	150131699	150131699	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:150131699A>G	ENST00000369124.4	+	6	1489	c.1211A>G	c.(1210-1212)tAc>tGc	p.Y404C	PLEKHO1_ENST00000025469.6_Missense_Mutation_p.Y370C|PLEKHO1_ENST00000369126.1_Missense_Mutation_p.Y221C	NM_016274.4	NP_057358.2	Q53GL0	PKHO1_HUMAN	pleckstrin homology domain containing, family O member 1	404	Negative regulator of AP-1 activity.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.Y404C(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|skin(2)	22	Lung NSC(24;7.78e-28)|Breast(34;0.00211)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			CACAGTCAGTACCGGAAGAGC	0.562																																					p.Y404C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1211G	1						.						21.0	24.0	23.0					1																	150131699		2203	4300	6503	148398323	SO:0001583	missense	51177	exon6			AF073836	CCDS945.1	1q21.2	2013-01-10			ENSG00000023902	ENSG00000023902		"""Pleckstrin homology (PH) domain containing"""	24310	protein-coding gene	gene with protein product		608335				10799509	Standard	NM_016274		Approved	CKIP-1, OC120	uc001ett.3	Q53GL0	OTTHUMG00000012510	ENST00000369124.4:c.1211A>G	1.37:g.150131699A>G	ENSP00000358120:p.Tyr404Cys	Somatic		Capture	Illumina HiSeq	Phase_I	148398323	NM_016274	Q336K5|Q8IZ51|Q9NRV3|Q9UL48	Missense_Mutation	SNP	ENST00000369124.4	37	CCDS945.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.354088	0.61293	.	.	ENSG00000023902	ENST00000369126;ENST00000025469;ENST00000369124	T;T	0.59772	0.24;0.38	4.82	0.72	0.18214	.	0.247666	0.33938	N	0.004418	T	0.39784	0.1091	N	0.19112	0.55	0.45676	D	0.99859	D	0.67145	0.996	P	0.57371	0.819	T	0.44050	-0.9353	10	0.87932	D	0	-12.6209	9.6795	0.40061	0.4904:0.0:0.0:0.5096	.	404	Q53GL0	PKHO1_HUMAN	C	221;370;404	ENSP00000025469:Y370C;ENSP00000358120:Y404C	ENSP00000025469:Y370C	Y	+	2	0	PLEKHO1	148398323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.334000	0.43920	0.277000	0.22141	0.482000	0.46254	TAC		0.562	PLEKHO1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034962.1	NM_016274	
SETDB1	9869	broad.mit.edu	37	1	150915423	150915423	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:150915423A>G	ENST00000271640.5	+	7	959	c.769A>G	c.(769-771)Aag>Gag	p.K257E	SETDB1_ENST00000368969.4_Missense_Mutation_p.K257E|SETDB1_ENST00000368962.2_Missense_Mutation_p.K257E|SETDB1_ENST00000368963.1_Intron|SETDB1_ENST00000459773.1_Intron	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	257	Tudor 1.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)	p.K257E(2)		NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCCTGCTGACAAGCTGTATGT	0.478																																					p.K257E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A769G	1						.						124.0	119.0	121.0					1																	150915423		2203	4300	6503	149182047	SO:0001583	missense	9869	exon7			D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Tudor domain containing"""	10761	protein-coding gene	gene with protein product	"""tudor domain containing 21"""	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.769A>G	1.37:g.150915423A>G	ENSP00000271640:p.Lys257Glu	Somatic		Capture	Illumina HiSeq	Phase_I	149182047	NM_001145415	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	37	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660778	0.47572	.	.	ENSG00000143379	ENST00000271640;ENST00000368962;ENST00000534805;ENST00000368969;ENST00000498193;ENST00000413562	D;T;T;D;T	0.87412	-2.25;0.94;1.51;-2.25;1.24	6.11	4.96	0.65561	Tudor domain (1);	0.406039	0.30068	N	0.010500	T	0.62392	0.2424	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B	0.12013	0.001;0.001;0.001;0.005;0.003	B;B;B;B;B	0.09377	0.002;0.002;0.004;0.004;0.002	T	0.58934	-0.7548	10	0.07644	T	0.81	.	13.5209	0.61568	0.8699:0.1301:0.0:0.0	.	257;257;257;257;257	E9PRF4;E9PQM8;Q15047-2;Q15047-3;Q15047	.;.;.;.;SETB1_HUMAN	E	257;257;257;257;257;100	ENSP00000271640:K257E;ENSP00000357958:K257E;ENSP00000436148:K257E;ENSP00000357965:K257E;ENSP00000432348:K257E	ENSP00000271640:K257E	K	+	1	0	SETDB1	149182047	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.993000	0.70616	1.092000	0.41356	0.533000	0.62120	AAG		0.478	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		
FAM63A	55793	broad.mit.edu	37	1	150970119	150970119	+	Missense_Mutation	SNP	G	G	A	rs146551660		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:150970119G>A	ENST00000361936.5	-	10	2264	c.1310C>T	c.(1309-1311)aCg>aTg	p.T437M	FAM63A_ENST00000470877.1_5'Flank|FAM63A_ENST00000361738.6_Missense_Mutation_p.T485M|FAM63A_ENST00000312210.5_Missense_Mutation_p.T295M|FAM63A_ENST00000493834.2_Missense_Mutation_p.T342M	NM_018379.4	NP_060849	Q8N5J2	FA63A_HUMAN	family with sequence similarity 63, member A	437						extracellular vesicular exosome (GO:0070062)		p.T437M(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CAGGACCCGCGTCCGCATCCG	0.642																																					p.T437M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1310T	1						.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	30.0	31.0	31.0		884,1454,1025,884,1310	0.2	0.0	1	dbSNP_134	31	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	FAM63A	NM_001040217.2,NM_001163258.1,NM_001163259.1,NM_001163260.1,NM_018379.4	81,81,81,81,81	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	295/328,485/518,342/375,295/328,437/470	150970119	3,13003	2203	4300	6503	149236743	SO:0001583	missense	55793	exon10			BC032321	CCDS976.1, CCDS30854.1, CCDS53361.1, CCDS55635.1	1q21.2	2008-02-05			ENSG00000143409	ENSG00000143409			25648	protein-coding gene	gene with protein product						10718198	Standard	NM_001040217		Approved	FLJ11280	uc010pcn.2	Q8N5J2	OTTHUMG00000035061	ENST00000361936.5:c.1310C>T	1.37:g.150970119G>A	ENSP00000354814:p.Thr437Met	Somatic		Capture	Illumina HiSeq	Phase_I	149236743	NM_018379	B3KWP4|B3KWV8|B4DXF2|B4E1S4|D3DV09|J3KP53|Q5SZF0|Q9NUL9|Q9P2F7	Missense_Mutation	SNP	ENST00000361936.5	37	CCDS976.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.158|7.158	0.585191|0.585191	0.13749|0.13749	0.0|0.0	3.49E-4|3.49E-4	ENSG00000143409|ENSG00000143409	ENST00000497067|ENST00000312210;ENST00000361936;ENST00000361738;ENST00000493834	.|T;T;T;T	.|0.45668	.|0.92;0.91;0.89;0.92	0.199|0.199	0.199|0.199	0.15175|0.15175	.|.	.|1.647970	.|0.03506	.|N	.|0.218890	T|T	0.10208|0.10208	0.0250|0.0250	N|N	0.11560|0.11560	0.145|0.145	0.09310|0.09310	N|N	0.99999|0.99999	.|P;P	.|0.51791	.|0.948;0.855	.|B;B	.|0.41723	.|0.365;0.132	T|T	0.06197|0.06197	-1.0840|-1.0840	4|9	.|0.46703	.|T	.|0.11	2.9074|2.9074	.|.	.|.	.|.	.|.	.|485;437	.|Q8N5J2-3;Q8N5J2	.|.;FA63A_HUMAN	C|M	76|295;437;485;342	.|ENSP00000310923:T295M;ENSP00000354814:T437M;ENSP00000354669:T485M;ENSP00000437174:T342M	.|ENSP00000310923:T295M	R|T	-|-	1|2	0|0	FAM63A|FAM63A	149236743|149236743	0.000000|0.000000	0.05858|0.05858	0.048000|0.048000	0.18961|0.18961	0.003000|0.003000	0.03518|0.03518	0.099000|0.099000	0.15210|0.15210	0.300000|0.300000	0.22699|0.22699	0.306000|0.306000	0.20318|0.20318	CGC|ACG		0.642	FAM63A-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411753.1	NM_018379	
CGN	57530	broad.mit.edu	37	1	151496719	151496719	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:151496719G>A	ENST00000271636.7	+	7	1419	c.1286G>A	c.(1285-1287)cGc>cAc	p.R429H		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	423	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)	p.R429H(1)		NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			AACATGAAGCGCCTCTTGGAC	0.433																																					p.R429H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1286A	1						.						74.0	69.0	71.0					1																	151496719		2203	4300	6503	149763343	SO:0001583	missense	57530	exon7			AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1286G>A	1.37:g.151496719G>A	ENSP00000271636:p.Arg429His	Somatic		Capture	Illumina HiSeq	Phase_I	149763343	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471781	0.43942	.	.	ENSG00000143375	ENST00000271636	T	0.62498	0.02	4.95	1.1	0.20463	.	0.429980	0.25004	N	0.033881	T	0.14184	0.0343	N	0.08118	0	0.09310	N	0.999992	P	0.46327	0.876	B	0.34452	0.183	T	0.16867	-1.0388	10	0.51188	T	0.08	0.3796	5.7785	0.18294	0.1561:0.0:0.354:0.4899	.	423	Q9P2M7	CING_HUMAN	H	429	ENSP00000271636:R429H	ENSP00000271636:R429H	R	+	2	0	CGN	149763343	0.088000	0.21588	0.988000	0.46212	0.861000	0.49209	0.085000	0.14912	-0.071000	0.12886	-0.500000	0.04577	CGC		0.433	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
CELF3	11189	broad.mit.edu	37	1	151677587	151677587	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:151677587C>T	ENST00000290583.4	-	12	2121	c.1328G>A	c.(1327-1329)gGc>gAc	p.G443D	CELF3_ENST00000392706.3_Missense_Mutation_p.G238D|CELF3_ENST00000290585.4_Missense_Mutation_p.G393D|CELF3_ENST00000470688.1_5'UTR|RP11-98D18.1_ENST00000457548.1_RNA	NM_001172648.1|NM_007185.4	NP_001166119.1|NP_009116.3	Q5SZQ8	CELF3_HUMAN	CUGBP, Elav-like family member 3	443	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)	p.G443D(1)		central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)	21						GATCTGGAAGCCATTCATGGC	0.642																																					p.G443D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1328A	1						.						65.0	63.0	63.0					1																	151677587		2203	4300	6503	149944211	SO:0001583	missense	11189	exon12			U80759	CCDS1002.1, CCDS53367.1	1q21	2013-02-12	2010-02-19	2010-02-19	ENSG00000159409	ENSG00000159409		"""Trinucleotide (CAG) repeat containing"", ""RNA binding motif (RRM) containing"""	11967	protein-coding gene	gene with protein product	"""expanded repeat domain, CAG/CTG 4"", ""CAG repeat domain"", ""CUG-BP and ETR-3 like factor 3"""	612678	"""trinucleotide repeat containing 4"""	TNRC4		9225980	Standard	XM_005244859		Approved	CAGH4, BRUNOL1, ERDA4, MGC57297	uc001eys.2	Q5SZQ8	OTTHUMG00000013064	ENST00000290583.4:c.1328G>A	1.37:g.151677587C>T	ENSP00000290583:p.Gly443Asp	Somatic		Capture	Illumina HiSeq	Phase_I	149944211	NM_007185	B7ZKK6|O15414|Q499Y6|Q5SZQ7|Q6NVK0|Q8IZ98|Q9BZC2|Q9HB30	Missense_Mutation	SNP	ENST00000290583.4	37	CCDS1002.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	31|31	5.096081|5.096081	0.94197|0.94197	.|.	.|.	ENSG00000159409|ENSG00000159409	ENST00000420342|ENST00000290585;ENST00000290583;ENST00000392706	.|T;T;T	.|0.51071	.|1.76;1.76;0.72	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68824|0.68824	0.3043|0.3043	M|M	0.89095|0.89095	3.005|3.005	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.998;1.0;1.0;1.0;1.0	T|T	0.75451|0.75451	-0.3313|-0.3313	5|10	.|0.87932	.|D	.|0	-8.0434|-8.0434	15.5922|15.5922	0.76543|0.76543	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|238;393;442;443;442	.|B4DQL3;Q5SZQ7;Q5SZQ8-2;Q5SZQ8;Q5SZQ8-3	.|.;.;.;CELF3_HUMAN;.	T|D	444|393;443;238	.|ENSP00000290585:G393D;ENSP00000290583:G443D;ENSP00000376470:G238D	.|ENSP00000290583:G443D	A|G	-|-	1|2	0|0	CELF3|CELF3	149944211|149944211	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.981000|0.981000	0.71138|0.71138	7.651000|7.651000	0.83577|0.83577	2.540000|2.540000	0.85666|0.85666	0.655000|0.655000	0.94253|0.94253	GCT|GGC		0.642	CELF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036663.2	NM_007185	
HRNR	388697	broad.mit.edu	37	1	152191222	152191222	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152191222G>A	ENST00000368801.2	-	3	2958	c.2883C>T	c.(2881-2883)ggC>ggT	p.G961G	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	961					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.G961G(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGACCTAGAGCCGTGTTGTT	0.537																																					p.G961G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2883T	1						.						284.0	274.0	277.0					1																	152191222		2203	4300	6503	150457846	SO:0001819	synonymous_variant	388697	exon3			AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2883C>T	1.37:g.152191222G>A		Somatic		Capture	Illumina HiSeq	Phase_I	150457846	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																				0.537	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
FLG	2312	broad.mit.edu	37	1	152284366	152284366	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152284366G>A	ENST00000368799.1	-	3	3031	c.2996C>T	c.(2995-2997)gCa>gTa	p.A999V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	999	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.A999V(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)			GGAGCTGTCTGCAGAGTGCCC	0.562									Ichthyosis																												p.A999V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2996T	1						.						258.0	260.0	260.0					1																	152284366		2203	4300	6503	150550990	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.2996C>T	1.37:g.152284366G>A	ENSP00000357789:p.Ala999Val	Somatic		Capture	Illumina HiSeq	Phase_I	150550990	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	6.835	0.523220	0.13066	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00649	5.98	2.23	-0.136	0.13473	.	.	.	.	.	T	0.00300	0.0009	M	0.72479	2.2	0.09310	N	1	B	0.21225	0.053	B	0.09377	0.004	T	0.39623	-0.9605	9	0.27082	T	0.32	.	3.4852	0.07617	0.1776:0.2637:0.5586:0.0	.	999	P20930	FILA_HUMAN	V	999;206	ENSP00000357789:A999V	ENSP00000357789:A999V	A	-	2	0	FLG	150550990	0.001000	0.12720	0.001000	0.08648	0.048000	0.14542	0.265000	0.18515	0.154000	0.19237	0.291000	0.19559	GCA		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
FLG2	388698	broad.mit.edu	37	1	152326392	152326392	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152326392T>G	ENST00000388718.5	-	3	3942	c.3870A>C	c.(3868-3870)gaA>gaC	p.E1290D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1290					establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.E1290D(1)		NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTGAATGTGTTCTGAATGTC	0.478																																					p.E1290D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3870C	1						.						452.0	401.0	418.0					1																	152326392		2203	4300	6503	150593016	SO:0001583	missense	388698	exon3			AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.3870A>C	1.37:g.152326392T>G	ENSP00000373370:p.Glu1290Asp	Somatic		Capture	Illumina HiSeq	Phase_I	150593016	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	8.539	0.872746	0.17322	.	.	ENSG00000143520	ENST00000388718	T	0.03801	3.8	3.19	-2.35	0.06684	.	.	.	.	.	T	0.00845	0.0028	N	0.19112	0.55	0.09310	N	1	B	0.32425	0.371	B	0.30179	0.112	T	0.45934	-0.9227	9	0.18710	T	0.47	-0.0762	7.5444	0.27757	0.0:0.5259:0.0:0.4741	.	1290	Q5D862	FILA2_HUMAN	D	1290	ENSP00000373370:E1290D	ENSP00000373370:E1290D	E	-	3	2	FLG2	150593016	0.000000	0.05858	0.000000	0.03702	0.355000	0.29361	-0.351000	0.07711	-0.325000	0.08577	0.165000	0.16767	GAA		0.478	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
LCE3D	84648	broad.mit.edu	37	1	152552351	152552351	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152552351C>A	ENST00000368787.3	-	2	118	c.62G>T	c.(61-63)tGt>tTt	p.C21F		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	21					keratinization (GO:0031424)			p.C21F(1)		breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		CTTTGGGGGACACTTGGGTGA	0.612																																					p.C21F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G62T	1						.						102.0	110.0	107.0					1																	152552351		2203	4300	6503	150818975	SO:0001583	missense	84648	exon2			BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.62G>T	1.37:g.152552351C>A	ENSP00000357776:p.Cys21Phe	Somatic		Capture	Illumina HiSeq	Phase_I	150818975	NM_032563	Q3MIL1	Missense_Mutation	SNP	ENST00000368787.3	37	CCDS1014.1	.	.	.	.	.	.	.	.	.	.	C	10.34	1.324292	0.24080	.	.	ENSG00000163202	ENST00000368787	T	0.11385	2.78	3.9	3.9	0.45041	.	.	.	.	.	T	0.21427	0.0516	.	.	.	0.35103	D	0.765382	D	0.76494	0.999	D	0.80764	0.994	T	0.01566	-1.1323	8	0.87932	D	0	.	11.5409	0.50665	0.0:1.0:0.0:0.0	.	21	Q9BYE3	LCE3D_HUMAN	F	21	ENSP00000357776:C21F	ENSP00000357776:C21F	C	-	2	0	LCE3D	150818975	0.976000	0.34144	1.000000	0.80357	0.973000	0.67179	1.046000	0.30354	2.167000	0.68274	0.655000	0.94253	TGT		0.612	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
LCE2C	353140	broad.mit.edu	37	1	152648578	152648578	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152648578C>T	ENST00000368783.1	+	2	142	c.87C>T	c.(85-87)ccC>ccT	p.P29P	LCE2B_ENST00000417924.2_Intron	NM_178429.2	NP_848516.1	Q5TA81	LCE2C_HUMAN	late cornified envelope 2C	29	Cys-rich.				keratinization (GO:0031424)			p.P29P(1)		endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)	13	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			ctaagtgtccccccaaATGCC	0.592																																					p.P29P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C87T	1						.						119.0	127.0	124.0					1																	152648578		2203	4300	6503	150915202	SO:0001819	synonymous_variant	353140	exon2				CCDS1019.1	1q21.3	2008-02-05			ENSG00000187180	ENSG00000187180		"""Late cornified envelopes"""	29460	protein-coding gene	gene with protein product		612611				11698679	Standard	NM_178429		Approved	LEP11	uc001fah.4	Q5TA81	OTTHUMG00000012389	ENST00000368783.1:c.87C>T	1.37:g.152648578C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150915202	NM_178429		Silent	SNP	ENST00000368783.1	37	CCDS1019.1																																																																																				0.592	LCE2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034509.1	NM_178429	
KPRP	448834	broad.mit.edu	37	1	152732421	152732421	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:152732421C>T	ENST00000606109.1	+	1	385	c.357C>T	c.(355-357)taC>taT	p.Y119Y	KPRP_ENST00000368773.1_Silent_p.Y119Y			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	119	Gln-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)		p.Y119Y(1)		NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGGTGTCCTACGTGCAGTGCG	0.488																																					p.Y119Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C357T	1						.						266.0	252.0	257.0					1																	152732421		2203	4300	6503	150999045	SO:0001819	synonymous_variant	448834	exon2			AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.357C>T	1.37:g.152732421C>T		Somatic		Capture	Illumina HiSeq	Phase_I	150999045	NM_001025231		Silent	SNP	ENST00000606109.1	37	CCDS30862.1																																																																																				0.488	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
INTS3	65123	broad.mit.edu	37	1	153730181	153730181	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:153730181T>C	ENST00000318967.2	+	10	1659	c.1091T>C	c.(1090-1092)cTg>cCg	p.L364P	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000456435.1_Missense_Mutation_p.L158P|INTS3_ENST00000435409.2_Missense_Mutation_p.L364P|INTS3_ENST00000512605.1_Missense_Mutation_p.L158P	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	365					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)		p.L364P(1)		breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AATGAAGTACTGAGTTCAGAT	0.537																																					p.L364P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1091C	1						.						129.0	106.0	114.0					1																	153730181		2203	4300	6503	151996805	SO:0001583	missense	65123	exon10			BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.1091T>C	1.37:g.153730181T>C	ENSP00000318641:p.Leu364Pro	Somatic		Capture	Illumina HiSeq	Phase_I	151996805	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384262	0.82792	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.74	4.74	0.60224	.	0.000000	0.64402	D	0.000006	T	0.75817	0.3901	M	0.87827	2.91	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.997;0.998;0.997	T	0.79759	-0.1668	9	0.54805	T	0.06	.	12.232	0.54492	0.0:0.0:0.0:1.0	.	158;365;364	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	P	364;158;364;158	.	ENSP00000318641:L364P	L	+	2	0	INTS3	151996805	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.949000	0.75971	1.994000	0.58287	0.374000	0.22700	CTG		0.537	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
TPM3	7170	broad.mit.edu	37	1	154145398	154145398	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:154145398A>G	ENST00000368530.2	-	5	744	c.552T>C	c.(550-552)gcT>gcC	p.A184A	TPM3_ENST00000271850.7_Silent_p.A184A|TPM3_ENST00000341372.3_Silent_p.A122A|TPM3_ENST00000328159.4_Silent_p.A147A|TPM3_ENST00000330188.9_Silent_p.A147A|TPM3_ENST00000368531.2_Silent_p.A147A|TPM3_ENST00000469717.1_5'UTR|TPM3_ENST00000323144.7_Silent_p.A147A|TPM3_ENST00000368533.3_Silent_p.A147A|TPM3_ENST00000302206.5_Silent_p.A57A|TPM3_ENST00000341485.5_Silent_p.A131A	NM_152263.2	NP_689476.2	P06753	TPM3_HUMAN	tropomyosin 3	184					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle thin filament tropomyosin (GO:0005862)|stress fiber (GO:0001725)		p.A147A(1)	TPM3/NTRK1_ENST00000392302(70)|TPM3/ALK(33)	breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)					CTGCCAGCTCAGCTCGTTCCT	0.458			T	"""NTRK1, ALK, ROS1"""	"""papillary thyroid, ALCL, NSCLC"""																																p.A147A			Dom	yes		1	1q22-q23	7170	tropomyosin 3		"""E, L"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T441C	1						.						176.0	158.0	164.0					1																	154145398		2203	4300	6503	152412022	SO:0001819	synonymous_variant	7170	exon4			BC008425	CCDS1060.1, CCDS41400.1, CCDS41401.1, CCDS41402.1, CCDS41403.1, CCDS60274.1, CCDS60275.1, CCDS72922.1	1q21.2	2014-09-17			ENSG00000143549	ENSG00000143549		"""Tropomyosins"""	12012	protein-coding gene	gene with protein product		191030		NEM1		1829807	Standard	NM_153649		Approved	TRK	uc001fec.2	P06753	OTTHUMG00000035853	ENST00000368530.2:c.552T>C	1.37:g.154145398A>G		Somatic		Capture	Illumina HiSeq	Phase_I	152412022	NM_001043351	D3DV71|P12324|Q2QD06|Q5VU58|Q5VU63|Q5VU66|Q5VU71|Q5VU72|Q8TCG3|Q969Q2|Q9NQH8	Silent	SNP	ENST00000368530.2	37	CCDS41403.1																																																																																				0.458	TPM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087271.2	NM_152263	
ADAM15	8751	broad.mit.edu	37	1	155030433	155030433	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:155030433A>G	ENST00000356955.2	+	14	1624	c.1523A>G	c.(1522-1524)gAt>gGt	p.D508G	ADAM15_ENST00000449910.2_Missense_Mutation_p.D508G|ADAM15_ENST00000360674.4_Missense_Mutation_p.D508G|ADAM15_ENST00000531455.1_Missense_Mutation_p.D518G|ADAM15_ENST00000359280.4_Missense_Mutation_p.D508G|ADAM15_ENST00000355956.2_Missense_Mutation_p.D508G|ADAM15_ENST00000368412.3_Missense_Mutation_p.D508G|ADAM15_ENST00000271836.6_Missense_Mutation_p.D508G|ADAM15_ENST00000447332.3_Missense_Mutation_p.D492G|ADAM15_ENST00000368410.2_Missense_Mutation_p.D214G|ADAM15_ENST00000368413.1_Missense_Mutation_p.D214G|ADAM15_ENST00000472434.1_3'UTR	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	508	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)	p.D508G(1)		NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			AGCCTAGGGGATGGCGAGCCC	0.642																																					p.D508G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1523G	1						.						96.0	94.0	95.0					1																	155030433		2203	4300	6503	153297057	SO:0001583	missense	8751	exon14			U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1523A>G	1.37:g.155030433A>G	ENSP00000349436:p.Asp508Gly	Somatic		Capture	Illumina HiSeq	Phase_I	153297057	NM_207195	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	A	17.77	3.470875	0.63625	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	4.92	4.92	0.64577	ADAM, cysteine-rich (2);Blood coagulation inhibitor, Disintegrin (1);	0.161338	0.28841	N	0.013973	T	0.51805	0.1696	M	0.89840	3.065	0.47441	D	0.999424	P;P;P;P;P;P;P;P;P;P;P	0.50156	0.929;0.929;0.932;0.897;0.76;0.913;0.855;0.76;0.76;0.916;0.798	P;P;P;P;P;P;P;P;P;D;P	0.64237	0.842;0.842;0.808;0.874;0.519;0.755;0.755;0.755;0.755;0.923;0.842	T	0.61931	-0.6961	10	0.72032	D	0.01	.	12.6131	0.56561	1.0:0.0:0.0:0.0	.	518;525;492;508;508;508;508;508;508;508;505	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444;Q59GF2	.;.;.;.;.;.;.;.;.;ADA15_HUMAN;.	G	508;508;508;508;508;508;214;508;214;518	ENSP00000349436:D508G;ENSP00000403843:D508G;ENSP00000352226:D508G;ENSP00000353892:D508G;ENSP00000357397:D508G;ENSP00000348227:D508G;ENSP00000357395:D214G;ENSP00000271836:D508G;ENSP00000357398:D214G;ENSP00000432927:D518G	ENSP00000271836:D508G	D	+	2	0	ADAM15	153297057	1.000000	0.71417	0.891000	0.34965	0.304000	0.27724	7.783000	0.85696	2.070000	0.61991	0.529000	0.55759	GAT		0.642	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
EFNA3	1944	broad.mit.edu	37	1	155058631	155058631	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:155058631C>A	ENST00000368408.3	+	4	606	c.536C>A	c.(535-537)cCc>cAc	p.P179H	EFNA3_ENST00000505139.1_Missense_Mutation_p.P174H|EFNA3_ENST00000556931.1_Missense_Mutation_p.P174H|EFNA3_ENST00000418360.2_Intron|EFNA3_ENST00000498667.1_3'UTR	NM_004952.4	NP_004943.1	P52797	EFNA3_HUMAN	ephrin-A3	179					axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|ephrin receptor signaling pathway (GO:0048013)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ephrin receptor binding (GO:0046875)|transmembrane-ephrin receptor activity (GO:0005005)	p.P179H(1)		breast(1)|central_nervous_system(1)|large_intestine(1)|lung(2)	5	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		all cancers(21;5.67e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000284)|LUSC - Lung squamous cell carcinoma(543;0.193)			AAGCCGGTCCCCACTCTCCCC	0.677											OREG0013850	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P179H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C536A	1						.						38.0	38.0	38.0					1																	155058631		2203	4298	6501	153325255	SO:0001583	missense	1944	exon4			BC017722	CCDS1090.1	1q21-q22	2011-03-09			ENSG00000143590	ENSG00000143590		"""Ephrins"""	3223	protein-coding gene	gene with protein product		601381		EPLG3		8660976	Standard	NM_004952		Approved	LERK3, Ehk1-L	uc001fhf.3	P52797	OTTHUMG00000035313	ENST00000368408.3:c.536C>A	1.37:g.155058631C>A	ENSP00000357393:p.Pro179His	Somatic	220	Capture	Illumina HiSeq	Phase_I	153325255	NM_004952	B7ZAD3|D3DV85|Q0VGC9|Q5SR70	Missense_Mutation	SNP	ENST00000368408.3	37	CCDS1090.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966024	0.74131	.	.	ENSG00000143590;ENSG00000143590;ENSG00000251246	ENST00000556931;ENST00000368408;ENST00000505139	D;D;D	0.94184	-3.37;-3.32;-3.37	4.51	4.51	0.55191	.	0.505440	0.18087	N	0.152103	D	0.91095	0.7197	N	0.24115	0.695	0.80722	D	1	D;D	0.76494	0.99;0.999	P;P	0.58454	0.709;0.839	D	0.92050	0.5647	10	0.59425	D	0.04	-12.2167	15.1743	0.72899	0.0:1.0:0.0:0.0	.	174;179	B4DXG7;P52797	.;EFNA3_HUMAN	H	174;179;174	ENSP00000450814:P174H;ENSP00000357393:P179H;ENSP00000426741:P174H	ENSP00000357393:P179H	P	+	2	0	RP11-540D14.8;EFNA3	153325255	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.142000	0.50601	2.525000	0.85131	0.456000	0.33151	CCC		0.677	EFNA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085429.1	NM_004952	
FDPS	2224	broad.mit.edu	37	1	155279945	155279945	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:155279945G>A	ENST00000356657.6	+	3	450	c.288G>A	c.(286-288)gaG>gaA	p.E96E	FDPS_ENST00000487002.1_3'UTR|FDPS_ENST00000368356.4_Silent_p.E96E|FDPS_ENST00000447866.1_Silent_p.E30E	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	96					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.E96E(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	TGCTGACTGAGGATGAGATGG	0.512																																					p.E96E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G288A	1						.						67.0	66.0	67.0					1																	155279945		2203	4300	6503	153546569	SO:0001819	synonymous_variant	2224	exon3			J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"""farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"""	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.288G>A	1.37:g.155279945G>A		Somatic		Capture	Illumina HiSeq	Phase_I	153546569	NM_002004	D3DV91|E9PCI9|Q96G29	Silent	SNP	ENST00000356657.6	37	CCDS1110.1																																																																																				0.512	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004	
KIAA0907	22889	broad.mit.edu	37	1	155899582	155899582	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:155899582A>G	ENST00000368321.3	-	3	328	c.305T>C	c.(304-306)cTg>cCg	p.L102P	KIAA0907_ENST00000482337.1_5'UTR|KIAA0907_ENST00000368320.3_Missense_Mutation_p.L102P|KIAA0907_ENST00000368319.3_Missense_Mutation_p.L102P	NM_014949.2	NP_055764.2	Q7Z7F0	K0907_HUMAN	KIAA0907	102							RNA binding (GO:0003723)	p.L102P(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|urinary_tract(1)	21	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;8.82e-06)			AGCTACCACCAGGTCATCCTT	0.413																																					p.L102P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T305C	1						.						158.0	142.0	148.0					1																	155899582		2203	4300	6503	154166206	SO:0001583	missense	22889	exon3			BC062637	CCDS30885.1	1q22	2012-11-30			ENSG00000132680	ENSG00000132680			29145	protein-coding gene	gene with protein product						10048485	Standard	NM_014949		Approved	BLOM7	uc001fmi.1	Q7Z7F0	OTTHUMG00000014103	ENST00000368321.3:c.305T>C	1.37:g.155899582A>G	ENSP00000357304:p.Leu102Pro	Somatic		Capture	Illumina HiSeq	Phase_I	154166206	NM_014949	O94981|Q7L7Q2|Q7Z7E9|Q8TBQ0	Missense_Mutation	SNP	ENST00000368321.3	37	CCDS30885.1	.	.	.	.	.	.	.	.	.	.	A	17.32	3.358929	0.61403	.	.	ENSG00000132680	ENST00000368321;ENST00000368320;ENST00000368319	.	.	.	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000001	T	0.43590	0.1254	L	0.55213	1.73	0.80722	D	1	B;P;B;B;B;B	0.43578	0.172;0.811;0.172;0.347;0.106;0.376	B;B;B;B;B;B	0.43536	0.048;0.423;0.032;0.111;0.09;0.187	T	0.36939	-0.9727	9	0.22706	T	0.39	-7.7714	15.1035	0.72303	1.0:0.0:0.0:0.0	.	102;102;102;102;102;102	D3DVA4;Q7Z7F0-4;A8K1I7;Q7Z7F0-3;Q7Z7F0-2;Q7Z7F0	.;.;.;.;.;K0907_HUMAN	P	102	.	ENSP00000357302:L102P	L	-	2	0	KIAA0907	154166206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.735000	0.91549	2.234000	0.73211	0.460000	0.39030	CTG		0.413	KIAA0907-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039583.1	NM_014949	
BGLAP	632	broad.mit.edu	37	1	156212041	156212041	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:156212041C>A	ENST00000368272.4	+	1	289	c.19C>A	c.(19-21)Ctc>Atc	p.L7I	PMF1_ENST00000567140.1_Intron|PMF1-BGLAP_ENST00000490491.1_Intron|PMF1-BGLAP_ENST00000368276.4_Intron|PMF1_ENST00000565805.1_Intron|PMF1-BGLAP_ENST00000320139.5_Intron|PAQR6_ENST00000492619.1_5'Flank	NM_199173.4	NP_954642.1	P02818	OSTCN_HUMAN	bone gamma-carboxyglutamate (gla) protein	7					bone development (GO:0060348)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cell aging (GO:0007569)|cellular response to growth factor stimulus (GO:0071363)|cellular response to vitamin D (GO:0071305)|odontogenesis (GO:0042476)|osteoblast development (GO:0002076)|osteoblast differentiation (GO:0001649)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of osteoclast differentiation (GO:0045670)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to gravity (GO:0009629)|response to hydroxyisoflavone (GO:0033594)|response to mechanical stimulus (GO:0009612)|response to testosterone (GO:0033574)|response to vitamin D (GO:0033280)|response to vitamin K (GO:0032571)|response to zinc ion (GO:0010043)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|perikaryon (GO:0043204)|rough endoplasmic reticulum (GO:0005791)	calcium ion binding (GO:0005509)|hydroxyapatite binding (GO:0046848)|structural constituent of bone (GO:0008147)|structural molecule activity (GO:0005198)	p.L7I(1)		large_intestine(3)|lung(1)|urinary_tract(1)	5	Hepatocellular(266;0.158)				Gallium nitrate(DB05260)|Menadione(DB00170)|Phylloquinone(DB01022)	CCTCACACTCCTCGCCCTATT	0.657																																					p.L7I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C19A	1						.						79.0	62.0	68.0					1																	156212041		2202	4299	6501	154478665	SO:0001583	missense	632	exon1			X04143	CCDS1134.1	1q22	2014-05-13	2008-08-01		ENSG00000242252	ENSG00000242252			1043	protein-coding gene	gene with protein product	"""osteocalcin"""	112260				2785029, 2394711	Standard	NM_199173		Approved	OCN	uc001fnt.3	P02818	OTTHUMG00000014819	ENST00000368272.4:c.19C>A	1.37:g.156212041C>A	ENSP00000357255:p.Leu7Ile	Somatic		Capture	Illumina HiSeq	Phase_I	154478665	NM_199173	Q5TCK6	Missense_Mutation	SNP	ENST00000368272.4	37	CCDS1134.1	.	.	.	.	.	.	.	.	.	.	C	6.419	0.445425	0.12164	.	.	ENSG00000242252	ENST00000368272	T	0.58797	0.31	4.77	2.86	0.33363	.	.	.	.	.	T	0.22205	0.0535	L	0.58810	1.83	0.09310	N	1	P	0.39424	0.673	B	0.31191	0.125	T	0.14200	-1.0481	9	0.10111	T	0.7	.	7.9136	0.29806	0.0:0.7514:0.1597:0.089	.	7	P02818	OSTCN_HUMAN	I	7	ENSP00000357255:L7I	ENSP00000357255:L7I	L	+	1	0	BGLAP	154478665	0.047000	0.20315	0.057000	0.19452	0.098000	0.18820	0.219000	0.17641	0.580000	0.29522	0.561000	0.74099	CTC		0.657	BGLAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040867.2	NM_199173	
PEAR1	375033	broad.mit.edu	37	1	156876652	156876652	+	Silent	SNP	C	C	T	rs142345759		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:156876652C>T	ENST00000338302.3	+	7	849	c.624C>T	c.(622-624)ccC>ccT	p.P208P	PEAR1_ENST00000292357.7_Silent_p.P208P			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	208					recognition of apoptotic cell (GO:0043654)	integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.P208P(1)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(6)|lung(22)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)	43	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCTTCTGCCCCGCAGAGAGAA	0.587																																					p.P208P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C624T	1						.						34.0	36.0	35.0					1																	156876652		2203	4300	6503	155143276	SO:0001819	synonymous_variant	375033	exon6			AK098809	CCDS30892.1	1q23.1	2008-02-05	2007-10-25	2007-10-25	ENSG00000187800	ENSG00000187800			33631	protein-coding gene	gene with protein product		610278	"""multiple EGF-like-domains 12"""	MEGF12		15851471	Standard	NM_001080471		Approved	JEDI, FLJ00193	uc001fqj.1	Q5VY43	OTTHUMG00000041293	ENST00000338302.3:c.624C>T	1.37:g.156876652C>T		Somatic		Capture	Illumina HiSeq	Phase_I	155143276	NM_001080471	Q8TEK2	Silent	SNP	ENST00000338302.3	37	CCDS30892.1																																																																																				0.587	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471	
SPTA1	6708	broad.mit.edu	37	1	158597503	158597503	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:158597503A>G	ENST00000368147.4	-	40	5756	c.5576T>C	c.(5575-5577)aTg>aCg	p.M1859T		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1859					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.M1859T(1)		NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCATGCTTCATTAGCAAGCT	0.398																																					p.M1859T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T5576C	1						.						148.0	132.0	137.0					1																	158597503		1852	4093	5945	156864127	SO:0001583	missense	6708	exon40			M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.5576T>C	1.37:g.158597503A>G	ENSP00000357129:p.Met1859Thr	Somatic		Capture	Illumina HiSeq	Phase_I	156864127	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	10.13	1.264548	0.23136	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.46451	0.87;0.87	5.55	3.21	0.36854	.	0.500994	0.14895	N	0.292127	T	0.09335	0.0230	N	0.08118	0	0.29413	N	0.861094	B	0.10296	0.003	B	0.04013	0.001	T	0.20806	-1.0264	10	0.72032	D	0.01	.	8.2708	0.31842	0.1341:0.0:0.1359:0.73	.	1859	P02549	SPTA1_HUMAN	T	1859	ENSP00000357130:M1859T;ENSP00000357129:M1859T	ENSP00000357129:M1859T	M	-	2	0	SPTA1	156864127	1.000000	0.71417	0.990000	0.47175	0.605000	0.37080	2.801000	0.47908	0.525000	0.28522	-1.321000	0.01291	ATG		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
ACKR1	2532	broad.mit.edu	37	1	159175893	159175893	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:159175893C>T	ENST00000368122.2	+	2	1343	c.664C>T	c.(664-666)Cca>Tca	p.P222S	DARC_ENST00000368121.2_Missense_Mutation_p.P224S|CTA-134P22.2_ENST00000609696.1_RNA|DARC_ENST00000537147.1_Missense_Mutation_p.P222S	NM_002036.3	NP_002027.2	Q16570	ACKR1_HUMAN		222					chemokine-mediated signaling pathway (GO:0070098)|defense response (GO:0006952)|inflammatory response (GO:0006954)|regulation of chemokine production (GO:0032642)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-C chemokine binding (GO:0019957)|G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.P222S(1)		large_intestine(2)|lung(1)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	8	all_hematologic(112;0.0429)					TGTCTTGTTGCCATTGGGTTT	0.542																																					p.P222S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C664T	1						.						87.0	75.0	79.0					1																	159175893		2203	4300	6503	157442517	SO:0001583	missense	2532	exon2																														ENST00000368122.2:c.664C>T	1.37:g.159175893C>T	ENSP00000357104:p.Pro222Ser	Somatic		Capture	Illumina HiSeq	Phase_I	157442517	NM_002036	A8YPG5|O75898|Q16300|Q8WWE3|Q9UJP0|Q9UKZ5|Q9UKZ6|Q9UQE1	Missense_Mutation	SNP	ENST00000368122.2	37	CCDS1183.1	.	.	.	.	.	.	.	.	.	.	C	13.18	2.160007	0.38119	.	.	ENSG00000213088	ENST00000368122;ENST00000537147;ENST00000359381;ENST00000368121	T;T;T	0.55930	0.49;0.49;0.49	5.22	4.31	0.51392	.	0.274191	0.19310	U	0.117407	T	0.52853	0.1760	L	0.46157	1.445	0.35659	D	0.81237	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.58059	-0.7703	10	0.52906	T	0.07	-8.2922	10.0642	0.42292	0.0:0.907:0.0:0.093	.	224;222	Q5Y7A1;Q16570	.;DUFFY_HUMAN	S	222;222;222;224	ENSP00000357104:P222S;ENSP00000441985:P222S;ENSP00000357103:P224S	ENSP00000352341:P222S	P	+	1	0	DARC	157442517	0.999000	0.42202	0.870000	0.34147	0.083000	0.17756	2.199000	0.42715	1.346000	0.45694	-0.142000	0.14014	CCA		0.542	DARC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090338.2		
KCNJ9	3765	broad.mit.edu	37	1	160053948	160053948	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:160053948G>A	ENST00000368088.3	+	2	370	c.128G>A	c.(127-129)cGc>cAc	p.R43H		NM_004983.2	NP_004974.2	Q92806	KCNJ9_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 9	43					synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein activated inward rectifier potassium channel activity (GO:0015467)	p.R43H(1)		biliary_tract(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|skin(2)	16	all_cancers(52;5.86e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GAGACATACCGCTACCTGACG	0.687																																					p.R43H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G128A	1						.						71.0	45.0	53.0					1																	160053948		2203	4299	6502	158320572	SO:0001583	missense	3765	exon2			U52152	CCDS1194.1	1q23.2	2011-07-05			ENSG00000162728	ENSG00000162728		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6270	protein-coding gene	gene with protein product		600932				8575783, 16382105	Standard	NM_004983		Approved	Kir3.3, GIRK3	uc001fuy.1	Q92806	OTTHUMG00000024072	ENST00000368088.3:c.128G>A	1.37:g.160053948G>A	ENSP00000357067:p.Arg43His	Somatic		Capture	Illumina HiSeq	Phase_I	158320572	NM_004983	Q5JW75	Missense_Mutation	SNP	ENST00000368088.3	37	CCDS1194.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939689	0.92526	.	.	ENSG00000162728	ENST00000368088	D	0.96856	-4.15	4.53	4.53	0.55603	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.000000	0.85682	D	0.000000	D	0.98385	0.9463	M	0.92219	3.285	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.99777	1.1026	10	0.87932	D	0	.	16.0432	0.80698	0.0:0.0:1.0:0.0	.	43	Q92806	IRK9_HUMAN	H	43	ENSP00000357067:R43H	ENSP00000357067:R43H	R	+	2	0	KCNJ9	158320572	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.730000	0.98797	2.036000	0.60181	0.430000	0.28490	CGC		0.687	KCNJ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060628.1	NM_004983	
ATP1A4	480	broad.mit.edu	37	1	160125871	160125871	+	Missense_Mutation	SNP	G	G	A	rs61734683	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:160125871G>A	ENST00000368081.4	+	4	919	c.448G>A	c.(448-450)Gtc>Atc	p.V150I		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	150					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)	p.V150I(1)		breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CGTGGTCATCGTCACTGGCTG	0.498													A|||	64	0.0127796	0.0461	0.0043	5008	,	,		19734	0.0		0.0	False		,,,				2504	0.0				p.V150I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G448A	1						.	A	ILE/VAL	119,4287	815.4+/-416.2	4,111,2088	156.0	129.0	138.0		448	3.3	0.4	1	dbSNP_129	138	2,8598	819.2+/-406.8	0,2,4298	yes	missense	ATP1A4	NM_144699.3	29	4,113,6386	AA,AG,GG		0.0233,2.7009,0.9303	benign	150/1030	160125871	121,12885	2203	4300	6503	158392495	SO:0001583	missense	480	exon4			BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.448G>A	1.37:g.160125871G>A	ENSP00000357060:p.Val150Ile	Somatic		Capture	Illumina HiSeq	Phase_I	158392495	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Missense_Mutation	SNP	ENST00000368081.4	37	CCDS1197.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	A	0.035	-1.313645	0.01331	0.027009	2.33E-4	ENSG00000132681	ENST00000368081	D	0.88818	-2.43	4.46	3.32	0.38043	ATPase, P-type, ATPase-associated domain (1);	0.205123	0.39544	N	0.001330	T	0.50633	0.1627	N	0.04724	-0.175	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.51795	-0.8660	10	0.02654	T	1	.	7.4045	0.26983	0.8146:0.0:0.1854:0.0	rs61734683	150	Q13733	AT1A4_HUMAN	I	150	ENSP00000357060:V150I	ENSP00000357060:V150I	V	+	1	0	ATP1A4	158392495	0.012000	0.17670	0.370000	0.25965	0.023000	0.10783	0.013000	0.13310	0.249000	0.21456	-0.521000	0.04368	GTC		0.498	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
MPZ	4359	broad.mit.edu	37	1	161277147	161277147	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:161277147C>A	ENST00000533357.1	-	2	201	c.135G>T	c.(133-135)cgG>cgT	p.R45R	MPZ_ENST00000491222.2_5'UTR|MPZ_ENST00000526189.1_5'Flank|MPZ_ENST00000360451.6_Silent_p.R55R|MPZ_ENST00000336559.4_Silent_p.R45R	NM_000530.6	NP_000521.2	P25189	MYP0_HUMAN	myelin protein zero	45	Ig-like V-type.				cell death (GO:0008219)|cell-cell junction maintenance (GO:0045217)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			central_nervous_system(1)|large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	10	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)	Breast(1374;0.181)	BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCAGGGTCACCCGGGAGCCCA	0.612																																					p.R45R												.	.	0			c.G135T	1						.						57.0	49.0	52.0					1																	161277147		2203	4300	6503	159543771	SO:0001819	synonymous_variant	4359	exon2			BC006491	CCDS1229.1, CCDS1229.2	1q22	2014-09-17	2008-08-01		ENSG00000158887	ENSG00000158887		"""Immunoglobulin superfamily / V-set domain containing"""	7225	protein-coding gene	gene with protein product		159440	"""Charcot-Marie-Tooth neuropathy 1B"""	CMT1, CMT1B		7693129	Standard	NM_000530		Approved	HMSNIB	uc001gaf.4	P25189	OTTHUMG00000034341	ENST00000533357.1:c.135G>T	1.37:g.161277147C>A		None		Capture	Illumina HiSeq	Phase_I	159543771	NM_000530	Q16072|Q5VTH4|Q92677|Q9BR67	Silent	SNP	ENST00000533357.1	37	CCDS1229.2																																																																																				0.612	MPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082987.2	NM_000530	
HSPA6	3310	broad.mit.edu	37	1	161495842	161495842	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:161495842G>A	ENST00000309758.4	+	1	1807	c.1394G>A	c.(1393-1395)gGc>gAc	p.G465D	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	465					ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|protein refolding (GO:0042026)|response to unfolded protein (GO:0006986)	blood microparticle (GO:0072562)|centriole (GO:0005814)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)	p.G465D(1)		endometrium(3)|large_intestine(5)|lung(9)|prostate(2)|skin(2)	21	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GAACTCAGTGGCATCCCTCCT	0.562																																					p.G465D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1394A	1						.						83.0	82.0	82.0					1																	161495842		2203	4300	6503	159762466	SO:0001583	missense	3310	exon1				CCDS1231.1	1q23.3	2011-09-02	2002-08-29		ENSG00000173110	ENSG00000173110		"""Heat shock proteins / HSP70"""	5239	protein-coding gene	gene with protein product		140555	"""heat shock 70kD protein 6 (HSP70B')"""			1346391	Standard	NM_002155		Approved		uc001gaq.3	P17066	OTTHUMG00000034461	ENST00000309758.4:c.1394G>A	1.37:g.161495842G>A	ENSP00000310219:p.Gly465Asp	Somatic		Capture	Illumina HiSeq	Phase_I	159762466	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	17.29	3.352761	0.61293	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01295	5.04	3.5	2.57	0.30868	.	0.182059	0.26082	N	0.026450	T	0.04048	0.0113	M	0.87097	2.86	0.43076	D	0.994729	D	0.71674	0.998	D	0.76575	0.988	T	0.08722	-1.0708	10	0.87932	D	0	.	8.1108	0.30914	0.1232:0.0:0.8768:0.0	.	465	P17066	HSP76_HUMAN	D	465;441	ENSP00000310219:G465D	ENSP00000310219:G465D	G	+	2	0	HSPA6	159762466	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	5.619000	0.67729	0.650000	0.30769	0.591000	0.81541	GGC		0.562	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155	
NOS1AP	9722	broad.mit.edu	37	1	162124265	162124265	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:162124265G>A	ENST00000361897.5	+	2	578	c.176G>A	c.(175-177)cGg>cAg	p.R59Q	MIR4654_ENST00000577581.1_RNA|NOS1AP_ENST00000530878.1_Splice_Site_p.R59Q	NM_001164757.1|NM_014697.2	NP_001158229.1|NP_055512.1	O75052	CAPON_HUMAN	nitric oxide synthase 1 (neuronal) adaptor protein	59	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				regulation of apoptotic process (GO:0042981)|regulation of nitric oxide biosynthetic process (GO:0045428)|regulation of nitric-oxide synthase activity (GO:0050999)		nitric-oxide synthase binding (GO:0050998)	p.R59Q(2)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(2)	32	all_hematologic(112;0.203)		BRCA - Breast invasive adenocarcinoma(70;0.0537)			CGCCGGATACGGGTGAGTGGC	0.602																																					p.R59Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G176A	1						.						77.0	67.0	70.0					1																	162124265		2203	4300	6503	160390889	SO:0001630	splice_region_variant	9722	exon2			AB007933	CCDS1237.1, CCDS44267.1, CCDS53421.1	1q23.3	2010-08-20			ENSG00000198929	ENSG00000198929			16859	protein-coding gene	gene with protein product	"""C-terminal PDZ domain ligand of neuronal nitric oxide synthase"""	605551				9455484, 9459447	Standard	NM_001126060		Approved	KIAA0464, CAPON	uc001gbv.2	O75052	OTTHUMG00000024049	ENST00000361897.5:c.177+1G>A	1.37:g.162124265G>A		Somatic		Capture	Illumina HiSeq	Phase_I	160390889	NM_001164757	B7ZLF5|O43564|Q3T551|Q5VU95	Missense_Mutation	SNP	ENST00000361897.5	37	CCDS1237.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.839470	0.51057	.	.	ENSG00000198929	ENST00000530878;ENST00000361897	T;T	0.19938	2.11;2.11	5.36	5.36	0.76844	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.311888	0.33895	N	0.004453	T	0.16514	0.0397	L	0.54323	1.7	.	.	.	P;P;P	0.50710	0.938;0.497;0.497	P;B;B	0.45343	0.477;0.408;0.343	T	0.02512	-1.1148	9	0.54805	T	0.06	.	14.594	0.68392	0.0:0.0:1.0:0.0	.	59;59;59	E9PSG0;B7ZLF5;O75052	.;.;CAPON_HUMAN	Q	59	ENSP00000431586:R59Q;ENSP00000355133:R59Q	ENSP00000355133:R59Q	R	+	2	0	NOS1AP	160390889	1.000000	0.71417	0.997000	0.53966	0.538000	0.34931	5.789000	0.69029	2.497000	0.84241	0.462000	0.41574	CGG		0.602	NOS1AP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060555.2	NM_014697	Missense_Mutation
DDR2	4921	broad.mit.edu	37	1	162748468	162748468	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:162748468T>C	ENST00000367922.3	+	18	2820	c.2382T>C	c.(2380-2382)gaT>gaC	p.D794D	DDR2_ENST00000367921.3_Silent_p.D794D|RN7SL861P_ENST00000473793.2_RNA	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	794	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|chondrocyte proliferation (GO:0035988)|collagen fibril organization (GO:0030199)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|endochondral bone growth (GO:0003416)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein autophosphorylation (GO:0046777)|regulation of bone mineralization (GO:0030500)|regulation of extracellular matrix disassembly (GO:0010715)|signal transduction (GO:0007165)	apical plasma membrane (GO:0016324)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.D794D(1)		central_nervous_system(2)|kidney(1)|lung(2)|ovary(1)|skin(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.113)		Regorafenib(DB08896)	AGCTGTCAGATGAACAGGTTA	0.483																																					p.D794D	NSCLC(161;314 2006 8283 19651 23192)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2382C	1						.						148.0	143.0	145.0					1																	162748468		2203	4300	6503	161015092	SO:0001819	synonymous_variant	4921	exon18			AK095975	CCDS1241.1	1q12-q23	2009-07-10	2008-01-23		ENSG00000162733	ENSG00000162733	2.7.10.1		2731	protein-coding gene	gene with protein product		191311	"""discoidin domain receptor family, member 2"""	TYRO10, NTRKR3		9659899	Standard	XM_005245221		Approved	TKT	uc001gcg.3	Q16832	OTTHUMG00000034423	ENST00000367922.3:c.2382T>C	1.37:g.162748468T>C		Somatic		Capture	Illumina HiSeq	Phase_I	161015092	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																				0.483	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182	
UCK2	7371	broad.mit.edu	37	1	165876943	165876943	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:165876943G>A	ENST00000367879.4	+	7	972	c.669G>A	c.(667-669)caG>caA	p.Q223Q	UCK2_ENST00000470820.1_Silent_p.Q73Q|UCK2_ENST00000372212.4_3'UTR|UCK2_ENST00000462329.1_3'UTR|UCK2_ENST00000469256.2_Silent_p.Q73Q	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	223					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TCATCGTGCAGCACATCCAGG	0.607																																					p.Q223Q												.	.	0			c.G669A	1						.						140.0	113.0	122.0					1																	165876943		2203	4300	6503	164143567	SO:0001819	synonymous_variant	7371	exon7			AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.669G>A	1.37:g.165876943G>A		None		Capture	Illumina HiSeq	Phase_I	164143567	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																				0.607	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
ILDR2	387597	broad.mit.edu	37	1	166927228	166927228	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:166927228C>T	ENST00000271417.3	-	2	212	c.157G>A	c.(157-159)Gtt>Att	p.V53I	ILDR2_ENST00000469934.2_Missense_Mutation_p.V53I|ILDR2_ENST00000528703.1_Missense_Mutation_p.V53I|ILDR2_ENST00000526687.1_Missense_Mutation_p.V53I|ILDR2_ENST00000529071.1_Missense_Mutation_p.V53I|ILDR2_ENST00000525740.1_Missense_Mutation_p.V53I|ILDR2_ENST00000529387.1_Missense_Mutation_p.V53I	NM_199351.2	NP_955383.1	Q71H61	ILDR2_HUMAN	immunoglobulin-like domain containing receptor 2	53	Ig-like V-type.				cell differentiation (GO:0030154)|homeostasis of number of cells within a tissue (GO:0048873)|insulin secretion (GO:0030073)|pancreas development (GO:0031016)|response to glucose (GO:0009749)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)		p.V53I(1)		NS(3)|breast(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	22						CACTGCACAACTGCAGGCTGA	0.562																																					p.V53I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G157A	1						.						169.0	145.0	153.0					1																	166927228		2203	4300	6503	165193852	SO:0001583	missense	387597	exon2			AF503509	CCDS1256.1	1q24.1	2008-12-18	2008-12-18	2008-12-18	ENSG00000143195	ENSG00000143195			18131	protein-coding gene	gene with protein product	"""LISCH-like"""		"""chromosome 1 open reading frame 32"""	C1orf32			Standard	NM_199351		Approved		uc001gdx.2	Q71H61	OTTHUMG00000034320	ENST00000271417.3:c.157G>A	1.37:g.166927228C>T	ENSP00000271417:p.Val53Ile	Somatic		Capture	Illumina HiSeq	Phase_I	165193852	NM_199351		Missense_Mutation	SNP	ENST00000271417.3	37	CCDS1256.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.087243	0.36855	.	.	ENSG00000143195	ENST00000271417;ENST00000525740;ENST00000529387;ENST00000469934;ENST00000529071;ENST00000526687;ENST00000528703	T;T;T;T;T;T;T	0.42900	4.76;0.96;0.96;0.96;4.76;4.76;4.76	5.48	5.48	0.80851	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.43255	0.1239	L	0.40543	1.245	0.53688	D	0.999974	D	0.76494	0.999	D	0.76071	0.987	T	0.14839	-1.0458	10	0.09338	T	0.73	.	19.3452	0.94359	0.0:1.0:0.0:0.0	.	53	Q71H61	ILDR2_HUMAN	I	53	ENSP00000271417:V53I;ENSP00000436120:V53I;ENSP00000431316:V53I;ENSP00000437008:V53I;ENSP00000436882:V53I;ENSP00000434273:V53I;ENSP00000432750:V53I	ENSP00000271417:V53I	V	-	1	0	ILDR2	165193852	1.000000	0.71417	0.097000	0.21041	0.941000	0.58515	6.080000	0.71299	2.545000	0.85829	0.563000	0.77884	GTT		0.562	ILDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082880.2	NM_199351	
CCDC181	57821	broad.mit.edu	37	1	169388275	169388275	+	Missense_Mutation	SNP	C	C	A	rs374590445		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:169388275C>A	ENST00000367806.3	-	4	1343	c.1191G>T	c.(1189-1191)aaG>aaT	p.K397N	CCDC181_ENST00000491570.1_5'UTR|CCDC181_ENST00000545005.1_Missense_Mutation_p.K397N|CCDC181_ENST00000367805.3_Missense_Mutation_p.K397N	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	397						nucleus (GO:0005634)		p.K397N(1)									CTTCAATTTCCTTTGCTCGCT	0.338																																					p.K397N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1191T	1						.						172.0	166.0	168.0					1																	169388275		2203	4300	6503	167654899	SO:0001583	missense	57821	exon4			AL049687	CCDS1279.1, CCDS72979.1	1q24	2013-03-14	2013-03-14	2013-03-14	ENSG00000117477	ENSG00000117477			28051	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 114"""	C1orf114			Standard	XM_005245381		Approved	FLJ25846	uc001gfz.1	Q5TID7	OTTHUMG00000035448	ENST00000367806.3:c.1191G>T	1.37:g.169388275C>A	ENSP00000356780:p.Lys397Asn	Somatic		Capture	Illumina HiSeq	Phase_I	167654899	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		.	.	.	.	.	.	.	.	.	.	C	19.35	3.810336	0.70797	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005	T;T;T	0.28454	1.69;1.61;1.69	6.02	3.07	0.35406	.	0.050715	0.85682	D	0.000000	T	0.39655	0.1086	M	0.76002	2.32	0.38517	D	0.948635	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.988;0.999;0.999	T	0.46119	-0.9214	9	0.87932	D	0	-19.5588	9.1874	0.37178	0.0:0.6945:0.0:0.3055	.	397;397;397	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	N	397	ENSP00000356779:K397N;ENSP00000356780:K397N;ENSP00000442297:K397N	ENSP00000356779:K397N	K	-	3	2	C1orf114	167654899	0.998000	0.40836	0.999000	0.59377	0.997000	0.91878	0.479000	0.22228	0.383000	0.24910	0.650000	0.86243	AAG		0.338	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179	
MROH9	80133	broad.mit.edu	37	1	170961417	170961417	+	Missense_Mutation	SNP	G	G	A	rs371741888		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:170961417G>A	ENST00000367758.3	+	12	1240	c.1141G>A	c.(1141-1143)Gta>Ata	p.V381I	MROH9_ENST00000367759.4_Missense_Mutation_p.V381I	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	381								p.V381I(1)									GGAGGACACCGTAACGGAAGG	0.473																																					p.V381I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1141A	1						.						156.0	160.0	159.0					1																	170961417		1990	4155	6145	169228041	SO:0001583	missense	80133	exon12			AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1141G>A	1.37:g.170961417G>A	ENSP00000356732:p.Val381Ile	Somatic		Capture	Illumina HiSeq	Phase_I	169228041	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	.	.	.	.	.	.	.	.	.	.	g	5.115	0.206809	0.09704	.	.	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.15017	4.07;2.46	5.61	-11.2	0.00127	.	2.101470	0.02171	N	0.059686	T	0.01558	0.0050	N	0.19112	0.55	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.31364	-0.9946	10	0.13853	T	0.58	6.9975	2.6339	0.04952	0.5008:0.1762:0.1361:0.1869	.	381;381	F5GWX6;Q5TGP6	.;CA129_HUMAN	I	381	ENSP00000356733:V381I;ENSP00000356732:V381I	ENSP00000356732:V381I	V	+	1	0	C1orf129	169228041	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.692000	0.00198	-3.327000	0.00186	-2.062000	0.00397	GTA		0.473	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
METTL13	51603	broad.mit.edu	37	1	171752952	171752952	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:171752952A>G	ENST00000361735.3	+	2	492	c.226A>G	c.(226-228)Aac>Gac	p.N76D	METTL13_ENST00000367737.5_Missense_Mutation_p.N76D|METTL13_ENST00000458517.1_Missense_Mutation_p.N75D|METTL13_ENST00000362019.3_5'UTR	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	76							methyltransferase activity (GO:0008168)	p.N76D(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						GGATATAGTGAACATCGACAT	0.483																																					p.N76D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A226G	1						.						175.0	162.0	167.0					1																	171752952		2203	4300	6503	170019575	SO:0001583	missense	51603	exon2			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.226A>G	1.37:g.171752952A>G	ENSP00000354920:p.Asn76Asp	Somatic		Capture	Illumina HiSeq	Phase_I	170019575	NM_001007239	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.445733	0.84101	.	.	ENSG00000010165	ENST00000458517;ENST00000367737;ENST00000361735	T;T;T	0.63255	0.38;-0.03;0.38	5.28	5.28	0.74379	Methyltransferase type 11 (1);	0.000000	0.85682	D	0.000000	T	0.77605	0.4155	M	0.87269	2.87	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.80764	0.993;0.96;0.994	T	0.82641	-0.0357	10	0.72032	D	0.01	-14.7823	14.87	0.70450	1.0:0.0:0.0:0.0	.	75;76;76	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	D	75;76;76	ENSP00000401955:N75D;ENSP00000356711:N76D;ENSP00000354920:N76D	ENSP00000354920:N76D	N	+	1	0	METTL13	170019575	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.774000	0.91767	1.973000	0.57446	0.533000	0.62120	AAC		0.483	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
METTL13	51603	broad.mit.edu	37	1	171757062	171757062	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:171757062C>T	ENST00000361735.3	+	4	1567	c.1301C>T	c.(1300-1302)tCt>tTt	p.S434F	METTL13_ENST00000466643.1_3'UTR|METTL13_ENST00000367737.5_Missense_Mutation_p.S278F|METTL13_ENST00000458517.1_Missense_Mutation_p.S433F|METTL13_ENST00000362019.3_Missense_Mutation_p.S348F	NM_015935.4	NP_057019.3	Q8N6R0	MET13_HUMAN	methyltransferase like 13	434							methyltransferase activity (GO:0008168)	p.S434F(1)		breast(3)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(8)|lung(17)|stomach(3)	41						AAGGATGTGTCTCACAAAGGT	0.547																																					p.S348F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1043T	1						.						121.0	85.0	97.0					1																	171757062		2203	4300	6503	170023685	SO:0001583	missense	51603	exon4			AF132936	CCDS1299.1, CCDS1300.1, CCDS30936.1	1q24-q25.3	2009-02-23	2009-02-23	2009-02-23	ENSG00000010165	ENSG00000010165			24248	protein-coding gene	gene with protein product			"""KIAA0859"""	KIAA0859		10810093, 10048485	Standard	NM_001007239		Approved	CGI-01	uc001ghz.3	Q8N6R0	OTTHUMG00000034912	ENST00000361735.3:c.1301C>T	1.37:g.171757062C>T	ENSP00000354920:p.Ser434Phe	Somatic		Capture	Illumina HiSeq	Phase_I	170023685	NM_014955	A6NFK0|A8K6S5|O94940|Q53EZ6|Q5TGP9|Q5TGQ0|Q8N2P8|Q96J11|Q96SQ0|Q9Y2Z1|Q9Y3M6	Missense_Mutation	SNP	ENST00000361735.3	37	CCDS1299.1	.	.	.	.	.	.	.	.	.	.	C	12.44	1.939508	0.34189	.	.	ENSG00000010165	ENST00000458517;ENST00000362019;ENST00000367737;ENST00000361735	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.44	3.5	0.40072	.	0.457593	0.24838	N	0.035198	T	0.32882	0.0844	L	0.29908	0.895	0.26368	N	0.976936	P;D;P	0.65815	0.731;0.995;0.731	B;P;B	0.59643	0.342;0.861;0.299	T	0.29427	-1.0012	10	0.48119	T	0.1	-4.3131	15.2971	0.73916	0.0:0.7337:0.2663:0.0	.	433;278;434	B4E2X3;Q8N6R0-1;Q8N6R0	.;.;MTL13_HUMAN	F	433;348;278;434	ENSP00000401955:S433F;ENSP00000355393:S348F;ENSP00000356711:S278F;ENSP00000354920:S434F	ENSP00000354920:S434F	S	+	2	0	METTL13	170023685	0.923000	0.31300	0.531000	0.27976	0.639000	0.38242	2.204000	0.42761	0.606000	0.29965	-0.176000	0.13171	TCT		0.547	METTL13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084528.5	NM_014955	
GNB1	2782	broad.mit.edu	37	1	1721912	1721912	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:1721912T>C	ENST00000378609.4	-	9	952	c.621A>G	c.(619-621)tcA>tcG	p.S207S		NM_001282539.1|NM_002074.3	NP_001269468.1|NP_002065.1	P62873	GBB1_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 1	207					adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|blood coagulation (GO:0007596)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(3)|skin(1)	12	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.62e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;1.14e-35)|OV - Ovarian serous cystadenocarcinoma(86;7.31e-23)|GBM - Glioblastoma multiforme(42;3.1e-07)|COAD - Colon adenocarcinoma(227;0.000323)|Colorectal(212;0.000374)|Kidney(185;0.00392)|BRCA - Breast invasive adenocarcinoma(365;0.00573)|STAD - Stomach adenocarcinoma(132;0.0072)|KIRC - Kidney renal clear cell carcinoma(229;0.0482)|Lung(427;0.236)		AGAGTTTGGCTGAAGCATCAC	0.557																																					p.S207S												.	.	0			c.A621G	1						.						131.0	103.0	112.0					1																	1721912		2203	4300	6503	1711772	SO:0001819	synonymous_variant	2782	exon9			BC004186	CCDS34.1, CCDS72685.1	1p36.33	2013-01-10			ENSG00000078369	ENSG00000078369		"""WD repeat domain containing"""	4396	protein-coding gene	gene with protein product		139380					Standard	NM_002074		Approved		uc001aif.3	P62873	OTTHUMG00000000940	ENST00000378609.4:c.621A>G	1.37:g.1721912T>C		None		Capture	Illumina HiSeq	Phase_I	1711772	NM_002074	B1AJZ7|P04697|P04901|Q1RMY8	Silent	SNP	ENST00000378609.4	37	CCDS34.1	.	.	.	.	.	.	.	.	.	.	T	10.83	1.460168	0.26248	.	.	ENSG00000078369	ENST00000424622	.	.	.	5.43	-4.75	0.03239	.	.	.	.	.	T	0.37892	0.1020	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39941	-0.9589	4	.	.	.	-5.8948	2.0809	0.03635	0.218:0.394:0.103:0.285	.	.	.	.	R	65	.	.	Q	-	2	0	GNB1	1711772	0.417000	0.25432	0.984000	0.44739	0.991000	0.79684	-0.326000	0.07965	-0.553000	0.06158	-0.250000	0.11733	CAG		0.557	GNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002762.3	NM_002074	
DNM3	26052	broad.mit.edu	37	1	172376953	172376953	+	Missense_Mutation	SNP	G	G	A	rs183558699		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:172376953G>A	ENST00000355305.5	+	21	2739	c.2582G>A	c.(2581-2583)cGc>cAc	p.R861H	DNM3_ENST00000358155.4_Missense_Mutation_p.R855H|PIGC_ENST00000484368.1_Intron|DNM3_ENST00000367731.1_Missense_Mutation_p.R851H			Q9UQ16	DYN3_HUMAN	dynamin 3	861					endocytosis (GO:0006897)|filopodium assembly (GO:0046847)|GTP catabolic process (GO:0006184)|synapse assembly (GO:0007416)	dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.R855H(1)		NS(1)|breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(16)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						ACTATAATCCGCCCACTAGAA	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		20911	0.001		0.0	False		,,,				2504	0.0				p.R855H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2564A	1						.						218.0	214.0	215.0					1																	172376953		1879	4105	5984	170643576	SO:0001583	missense	26052	exon21			AL136712	CCDS44276.1, CCDS60356.1	1q24.1	2013-01-10			ENSG00000197959	ENSG00000197959		"""Pleckstrin homology (PH) domain containing"""	29125	protein-coding gene	gene with protein product	"""Dyna III"""	611445				10048485	Standard	NM_015569		Approved	KIAA0820	uc001gie.4	Q9UQ16	OTTHUMG00000034913	ENST00000355305.5:c.2582G>A	1.37:g.172376953G>A	ENSP00000347457:p.Arg861His	Somatic		Capture	Illumina HiSeq	Phase_I	170643576	NM_015569	A9Z1Y1|O14982|O95555|Q1MTM8|Q5W129|Q6P2G1|Q9H0P3|Q9H548|Q9NQ68|Q9NQN6	Missense_Mutation	SNP	ENST00000355305.5	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	20.9	4.066789	0.76301	.	.	ENSG00000197959	ENST00000359070;ENST00000358155;ENST00000355305;ENST00000367731	T;T;T	0.52526	0.66;0.66;0.66	5.83	5.83	0.93111	.	0.259771	0.35739	N	0.003006	T	0.57388	0.2050	L	0.49126	1.545	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.59005	-0.7535	10	0.87932	D	0	.	16.8531	0.85999	0.0:0.0:1.0:0.0	.	851;855	Q9UQ16-2;Q9UQ16-3	.;.	H	865;855;861;851	ENSP00000350876:R855H;ENSP00000347457:R861H;ENSP00000356705:R851H	ENSP00000347457:R861H	R	+	2	0	DNM3	170643576	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.534000	0.60622	2.770000	0.95276	0.655000	0.94253	CGC		0.413	DNM3-003	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000084531.1	NM_015569	
TNN	63923	broad.mit.edu	37	1	175092583	175092583	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:175092583A>G	ENST00000239462.4	+	12	2811	c.2698A>G	c.(2698-2700)Atg>Gtg	p.M900V		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	900	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)		p.M900V(1)		NS(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|liver(1)|lung(81)|ovary(5)|prostate(6)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	156		Breast(1374;0.000962)		KIRC - Kidney renal clear cell carcinoma(1967;0.00198)		GACGGAGAATATGGCCACTGT	0.502																																					p.M900V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2698G	1						.						63.0	62.0	62.0					1																	175092583		2203	4300	6503	173359206	SO:0001583	missense	63923	exon12			AK127044	CCDS30943.1	1q23-q24	2013-02-11			ENSG00000120332	ENSG00000120332		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	22942	protein-coding gene	gene with protein product							Standard	NM_022093		Approved		uc001gkl.1	Q9UQP3	OTTHUMG00000034882	ENST00000239462.4:c.2698A>G	1.37:g.175092583A>G	ENSP00000239462:p.Met900Val	Somatic		Capture	Illumina HiSeq	Phase_I	173359206	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	A	6.243	0.413041	0.11812	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.56275	0.47	4.98	2.38	0.29361	Fibronectin, type III (4);	0.344482	0.29480	N	0.012024	T	0.35335	0.0928	N	0.19112	0.55	0.21762	N	0.999554	B	0.14012	0.009	B	0.23150	0.044	T	0.32241	-0.9914	10	0.59425	D	0.04	.	8.5064	0.33190	0.6907:0.0:0.0:0.3093	.	900	Q9UQP3	TENN_HUMAN	V	900;723	ENSP00000239462:M900V	ENSP00000239462:M900V	M	+	1	0	TNN	173359206	0.000000	0.05858	0.939000	0.37840	0.349000	0.29174	0.433000	0.21477	0.787000	0.33731	0.379000	0.24179	ATG		0.502	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527	
TNR	7143	broad.mit.edu	37	1	175292549	175292549	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:175292549G>A	ENST00000367674.2	-	23	4729	c.4021C>T	c.(4021-4023)Cgc>Tgc	p.R1341C	TNR_ENST00000263525.2_Missense_Mutation_p.R1341C|RP3-518E13.2_ENST00000569593.1_RNA			Q92752	TENR_HUMAN	tenascin R	1341	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.R1341C(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TTGTAGGGGCGCATCTTCATT	0.512																																					p.R1341C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4021T	1						.						175.0	152.0	160.0					1																	175292549		2203	4300	6503	173559172	SO:0001583	missense	7143	exon23			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.4021C>T	1.37:g.175292549G>A	ENSP00000356646:p.Arg1341Cys	Somatic		Capture	Illumina HiSeq	Phase_I	173559172	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.001319	0.74818	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.81078	-1.45;-1.45	5.37	4.43	0.53597	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);	0.000000	0.85682	D	0.000000	D	0.94275	0.8161	H	0.99464	4.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96325	0.9239	10	0.87932	D	0	.	14.6178	0.68560	0.0:0.0:0.8484:0.1516	.	1341	Q92752	TENR_HUMAN	C	1341;1341;1251	ENSP00000356646:R1341C;ENSP00000263525:R1341C	ENSP00000263525:R1341C	R	-	1	0	TNR	173559172	1.000000	0.71417	0.998000	0.56505	0.833000	0.47200	4.167000	0.58209	1.200000	0.43188	0.561000	0.74099	CGC		0.512	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
TNR	7143	broad.mit.edu	37	1	175365922	175365922	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:175365922C>T	ENST00000367674.2	-	5	1706	c.998G>A	c.(997-999)cGa>cAa	p.R333Q	TNR_ENST00000263525.2_Missense_Mutation_p.R333Q			Q92752	TENR_HUMAN	tenascin R	333	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)		p.R333Q(1)		NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					ACCAGCCACTCGCAAGTCCTC	0.572																																					p.R333Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G998A	1						.						77.0	81.0	79.0					1																	175365922		2203	4300	6503	173632545	SO:0001583	missense	7143	exon5			X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.998G>A	1.37:g.175365922C>T	ENSP00000356646:p.Arg333Gln	Somatic		Capture	Illumina HiSeq	Phase_I	173632545	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.410397	0.42715	.	.	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.66280	-0.2;-0.2	5.95	5.95	0.96441	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.165319	0.40385	N	0.001119	T	0.65698	0.2716	L	0.40543	1.245	0.42214	D	0.991825	D	0.61697	0.99	P	0.54664	0.758	T	0.57136	-0.7863	10	0.10377	T	0.69	.	19.9698	0.97280	0.0:1.0:0.0:0.0	.	333	Q92752	TENR_HUMAN	Q	333	ENSP00000356646:R333Q;ENSP00000263525:R333Q	ENSP00000263525:R333Q	R	-	2	0	TNR	173632545	0.991000	0.36638	1.000000	0.80357	0.998000	0.95712	1.766000	0.38491	2.817000	0.96982	0.563000	0.77884	CGA		0.572	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
RASAL2	9462	broad.mit.edu	37	1	178427543	178427543	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:178427543G>T	ENST00000462775.1	+	12	2818	c.2693G>T	c.(2692-2694)gGg>gTg	p.G898V	RASAL2_ENST00000448150.3_Missense_Mutation_p.G1028V|RASAL2_ENST00000367649.3_Missense_Mutation_p.G1039V	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	898					negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Ras GTPase activator activity (GO:0005099)	p.G1028V(1)|p.G1039V(1)		biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						CGTAGCACCGGGAGCATGTCA	0.632																																					p.G1039V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3116T	1						.						55.0	56.0	56.0					1																	178427543		2203	4300	6503	176694166	SO:0001583	missense	9462	exon14			AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.2693G>T	1.37:g.178427543G>T	ENSP00000420558:p.Gly898Val	Somatic		Capture	Illumina HiSeq	Phase_I	176694166	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.621477	0.66787	.	.	ENSG00000075391	ENST00000448150;ENST00000367649;ENST00000462775	T;T;T	0.15718	2.4;2.4;2.4	5.46	4.55	0.56014	.	0.257336	0.37530	N	0.002042	T	0.33990	0.0882	L	0.50333	1.59	0.80722	D	1	P;D;P	0.76494	0.78;0.999;0.527	P;D;B	0.78314	0.509;0.991;0.313	T	0.02326	-1.1176	10	0.31617	T	0.26	.	13.8799	0.63676	0.0729:0.0:0.9271:0.0	.	1028;898;1039	B1AKC7;Q9UJF2;F8W755	.;NGAP_HUMAN;.	V	1028;1039;898	ENSP00000407768:G1028V;ENSP00000356621:G1039V;ENSP00000420558:G898V	ENSP00000356621:G1039V	G	+	2	0	RASAL2	176694166	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	3.536000	0.53582	1.295000	0.44724	0.591000	0.81541	GGG		0.632	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	
RALGPS2	55103	broad.mit.edu	37	1	178854287	178854287	+	Silent	SNP	G	G	A	rs372147647		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:178854287G>A	ENST00000367635.3	+	12	1319	c.981G>A	c.(979-981)ccG>ccA	p.P327P	RALGPS2_ENST00000477383.1_3'UTR|RALGPS2_ENST00000367634.2_Silent_p.P327P	NM_152663.3	NP_689876.2	Q86X27	RGPS2_HUMAN	Ral GEF with PH domain and SH3 binding motif 2	327					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.P327P(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						CACAGACACCGCCATCCCCTC	0.423																																					p.P327P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G981A	1						.	G		1,4405	2.1+/-5.4	0,1,2202	76.0	78.0	77.0		981	-11.2	0.0	1		77	0,8600		0,0,4300	no	coding-synonymous	RALGPS2	NM_152663.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		327/584	178854287	1,13005	2203	4300	6503	177120910	SO:0001819	synonymous_variant	55103	exon12			AK098470	CCDS1325.1, CCDS65733.1	1q24	2013-01-11			ENSG00000116191	ENSG00000116191		"""Pleckstrin homology (PH) domain containing"""	30279	protein-coding gene	gene with protein product						10747847, 12102558	Standard	NM_152663		Approved	KIAA0351, FLJ10244, FLJ25604	uc001glz.3	Q86X27	OTTHUMG00000035076	ENST00000367635.3:c.981G>A	1.37:g.178854287G>A		Somatic		Capture	Illumina HiSeq	Phase_I	177120910	NM_152663	B7Z7B1|Q5T5Z1|Q5VZ67|Q9NW78	Silent	SNP	ENST00000367635.3	37	CCDS1325.1	.	.	.	.	.	.	.	.	.	.	G	8.090	0.774211	0.16051	2.27E-4	0.0	ENSG00000116191	ENST00000415888	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.30135	0.0755	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.39057	-0.9632	4	.	.	.	.	0.7112	0.00925	0.3991:0.1994:0.1644:0.237	.	.	.	.	T	65	.	.	A	+	1	0	RALGPS2	177120910	0.000000	0.05858	0.002000	0.10522	0.917000	0.54804	-2.710000	0.00818	-2.460000	0.00537	-1.309000	0.01313	GCC		0.423	RALGPS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084926.2	NM_152663	
TOR3A	64222	broad.mit.edu	37	1	179054950	179054950	+	Silent	SNP	C	C	T	rs369007016		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:179054950C>T	ENST00000367627.3	+	3	1313	c.561C>T	c.(559-561)gaC>gaT	p.D187D	TOR3A_ENST00000495145.1_3'UTR|TOR3A_ENST00000352445.6_Silent_p.D187D	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	187					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.D187D(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						TGTATCGGGACGGGCTGATGA	0.592																																					p.D187D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C561T	1						.	C		0,4406		0,0,2203	102.0	80.0	88.0		561	-11.1	0.0	1		88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TOR3A	NM_022371.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		187/398	179054950	1,13005	2203	4300	6503	177321573	SO:0001819	synonymous_variant	64222	exon3			BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.561C>T	1.37:g.179054950C>T		Somatic		Capture	Illumina HiSeq	Phase_I	177321573	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Silent	SNP	ENST00000367627.3	37	CCDS1329.1																																																																																				0.592	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
ABL2	27	broad.mit.edu	37	1	179077038	179077038	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:179077038C>A	ENST00000502732.1	-	12	3567	c.3364G>T	c.(3364-3366)Ggc>Tgc	p.G1122C	ABL2_ENST00000504405.1_Missense_Mutation_p.G983C|ABL2_ENST00000512653.1_Missense_Mutation_p.G1107C|ABL2_ENST00000344730.3_Missense_Mutation_p.G1004C|ABL2_ENST00000408940.3_Missense_Mutation_p.G1086C|ABL2_ENST00000507173.1_Missense_Mutation_p.G998C|ABL2_ENST00000367623.4_Missense_Mutation_p.G1101C|ABL2_ENST00000511413.1_Missense_Mutation_p.G1019C	NM_001168236.1|NM_001168237.1|NM_001168238.1|NM_007314.3	NP_001161708.1|NP_001161709.1|NP_001161710.1|NP_009298.1	P42684	ABL2_HUMAN	ABL proto-oncogene 2, non-receptor tyrosine kinase	1122	F-actin-binding. {ECO:0000250}.				actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular protein modification process (GO:0006464)|cellular response to retinoic acid (GO:0071300)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phospholipase C activity (GO:0010863)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)	p.G1086C(1)		breast(8)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	65					Adenosine triphosphate(DB00171)|Dasatinib(DB01254)	TCCACATAGCCTGAGCAGTAG	0.547			T	ETV6	AML																																p.G983C			Dom	yes		1	1q24-q25	27	v-abl Abelson murine leukemia viral oncogene homolog 2		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2947T	1						.						85.0	76.0	79.0					1																	179077038		2203	4300	6503	177343661	SO:0001583	missense	27	exon12			M14904	CCDS30947.1, CCDS41441.1, CCDS44282.1, CCDS44283.1, CCDS41441.2, CCDS53435.1, CCDS53436.1, CCDS53437.1, CCDS53438.1	1q25.2	2014-06-26	2014-06-26		ENSG00000143322	ENSG00000143322		"""SH2 domain containing"""	77	protein-coding gene	gene with protein product	"""Abelson-related gene"""	164690	"""v-abl Abelson murine leukemia viral oncogene homolog 2 (arg, Abelson-related gene)"", ""v-abl Abelson murine leukemia viral oncogene homolog 2"", ""c-abl oncogene 2, non-receptor tyrosine kinase"""	ABLL		3787260	Standard	NM_001136001		Approved	ARG	uc001gmi.4	P42684	OTTHUMG00000035199	ENST00000502732.1:c.3364G>T	1.37:g.179077038C>A	ENSP00000427562:p.Gly1122Cys	Somatic		Capture	Illumina HiSeq	Phase_I	177343661	NM_001168239	A0M8X0|B7UEF2|B7UEF3|B7UEF4|B7UEF5|Q5T0X6|Q5W0C5|Q6NZY6|Q7Z301	Missense_Mutation	SNP	ENST00000502732.1	37	CCDS30947.1	.	.	.	.	.	.	.	.	.	.	C	16.20	3.057106	0.55325	.	.	ENSG00000143322	ENST00000502732;ENST00000408940;ENST00000344730;ENST00000512653;ENST00000504405;ENST00000367623;ENST00000507173;ENST00000511413	T;T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.65	5.65	0.86999	F-actin binding (2);	0.000000	0.53938	D	0.000057	T	0.53997	0.1831	L	0.56769	1.78	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	1.0;0.991;0.991;0.999;1.0;1.0;1.0;0.991	T	0.48222	-0.9054	10	0.46703	T	0.11	.	18.7287	0.91726	0.0:1.0:0.0:0.0	.	1101;998;1019;983;1122;1107;1086;1004	P42684-6;P42684-7;P42684-5;P42684-4;P42684;P42684-3;D1MPS6;P42684-10	.;.;.;.;ABL2_HUMAN;.;.;.	C	1122;1086;1004;1107;983;1101;998;1019	ENSP00000427562:G1122C;ENSP00000386152:G1086C;ENSP00000339209:G1004C;ENSP00000423578:G1107C;ENSP00000426831:G983C;ENSP00000356595:G1101C;ENSP00000423413:G998C;ENSP00000424697:G1019C	ENSP00000339209:G1004C	G	-	1	0	ABL2	177343661	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.218000	0.51192	2.655000	0.90218	0.655000	0.94253	GGC		0.547	ABL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085174.3	NM_005158	
TDRD5	163589	broad.mit.edu	37	1	179561902	179561902	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:179561902G>A	ENST00000367614.1	+	2	511	c.152G>A	c.(151-153)cGg>cAg	p.R51Q	TDRD5_ENST00000294848.8_Missense_Mutation_p.R51Q|TDRD5_ENST00000444136.1_Missense_Mutation_p.R51Q|RP11-545A16.4_ENST00000567150.1_RNA	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	51	HTH OST-type 1. {ECO:0000255|PROSITE- ProRule:PRU00975}.				DNA methylation involved in gamete generation (GO:0043046)|P granule organization (GO:0030719)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|pi-body (GO:0071546)		p.R51Q(1)		NS(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(44)|ovary(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)	77						CTTGGGTATCGGTCCACTATG	0.473																																					p.R51Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G152A	1						.						193.0	173.0	180.0					1																	179561902		2203	4300	6503	177828525	SO:0001583	missense	163589	exon2			AK092142	CCDS1332.1, CCDS55663.1	1q24.2	2013-01-23			ENSG00000162782	ENSG00000162782		"""Tudor domain containing"""	20614	protein-coding gene	gene with protein product							Standard	NM_001199085		Approved	FLJ34823, TUDOR3	uc010pnp.2	Q8NAT2	OTTHUMG00000035259	ENST00000367614.1:c.152G>A	1.37:g.179561902G>A	ENSP00000356586:p.Arg51Gln	Somatic		Capture	Illumina HiSeq	Phase_I	177828525	NM_001199085	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.521026	0.85495	.	.	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.42513	0.97;0.97;0.97	5.91	5.91	0.95273	.	0.152863	0.40640	N	0.001055	T	0.55114	0.1900	L	0.48642	1.525	0.35049	D	0.760427	D;D	0.89917	1.0;1.0	D;D	0.68765	0.958;0.96	T	0.64407	-0.6415	10	0.54805	T	0.06	-12.4631	12.2082	0.54365	0.0776:0.0:0.9224:0.0	.	51;51	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	Q	51	ENSP00000356586:R51Q;ENSP00000294848:R51Q;ENSP00000406052:R51Q	ENSP00000294848:R51Q	R	+	2	0	TDRD5	177828525	0.134000	0.22483	0.990000	0.47175	0.993000	0.82548	2.514000	0.45503	2.793000	0.96121	0.655000	0.94253	CGG		0.473	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
LAMC2	3918	broad.mit.edu	37	1	183194775	183194775	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:183194775C>A	ENST00000264144.4	+	8	1051	c.986C>A	c.(985-987)cCc>cAc	p.P329H	LAMC2_ENST00000493293.1_Missense_Mutation_p.P329H	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	329	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)	p.P329H(1)		breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						AATTGGAGCCCCCAGCTGAGT	0.393																																					p.P329H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C986A	1						.						107.0	117.0	114.0					1																	183194775		2203	4300	6503	181461398	SO:0001583	missense	3918	exon8			Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.986C>A	1.37:g.183194775C>A	ENSP00000264144:p.Pro329His	Somatic		Capture	Illumina HiSeq	Phase_I	181461398	NM_018891	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.656527	0.88154	.	.	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.36699	1.24;1.24	5.06	5.06	0.68205	Laminin B type IV (2);Laminin B, subgroup (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000002	T	0.66147	0.2760	M	0.85197	2.74	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.73026	-0.4112	10	0.87932	D	0	.	18.4349	0.90642	0.0:1.0:0.0:0.0	.	329;329;329	Q2M1N2;Q13753;Q13753-2	.;LAMC2_HUMAN;.	H	329	ENSP00000432063:P329H;ENSP00000264144:P329H	ENSP00000264144:P329H	P	+	2	0	LAMC2	181461398	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.501000	0.73691	2.336000	0.79503	0.655000	0.94253	CCC		0.393	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
COLGALT2	23127	broad.mit.edu	37	1	184006369	184006369	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:184006369C>T	ENST00000361927.4	-	1	494	c.123G>A	c.(121-123)gaG>gaA	p.E41E	COLGALT2_ENST00000546159.1_Silent_p.E41E	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	41					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)	p.E41E(1)									AAACCACCGGCTCCTCTCCGT	0.726																																					p.E41E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G123A	1						.						10.0	11.0	11.0					1																	184006369		2156	4257	6413	182272992	SO:0001819	synonymous_variant	23127	exon1			AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 17"", ""glycosyltransferase 25 domain containing 2"""	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.123G>A	1.37:g.184006369C>T		Somatic		Capture	Illumina HiSeq	Phase_I	182272992	NM_015101	O60327|Q9BZR0	Silent	SNP	ENST00000361927.4	37	CCDS1360.1																																																																																				0.726	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101	
HMCN1	83872	broad.mit.edu	37	1	186106636	186106636	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:186106636G>T	ENST00000271588.4	+	88	13818	c.13589G>T	c.(13588-13590)gGt>gTt	p.G4530V	HMCN1_ENST00000367492.2_Missense_Mutation_p.G4530V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4530	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.G4530V(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						GCAGTTCATGGTGGATTTTCC	0.428																																					p.G4530V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G13589T	1						.						46.0	48.0	47.0					1																	186106636		2203	4300	6503	184373259	SO:0001583	missense	83872	exon88			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13589G>T	1.37:g.186106636G>T	ENSP00000271588:p.Gly4530Val	Somatic		Capture	Illumina HiSeq	Phase_I	184373259	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.922211	0.92319	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.62364	0.03;0.03	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	D	0.86847	0.6031	H	0.97758	4.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.87454	0.2403	10	0.27082	T	0.32	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	4530	Q96RW7	HMCN1_HUMAN	V	4530	ENSP00000271588:G4530V;ENSP00000356462:G4530V	ENSP00000271588:G4530V	G	+	2	0	HMCN1	184373259	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.414000	0.97362	2.729000	0.93468	0.650000	0.86243	GGT		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HMCN1	83872	broad.mit.edu	37	1	186158894	186158894	+	Nonsense_Mutation	SNP	C	C	T	rs193921043		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:186158894C>T	ENST00000271588.4	+	107	17021	c.16792C>T	c.(16792-16794)Cga>Tga	p.R5598*	HMCN1_ENST00000367492.2_Nonsense_Mutation_p.R5481*	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5598					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.R5598*(2)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ACGACCACTACGAGAAGCAGA	0.473																																					p.R5598X												.	.	2	Substitution - Nonsense(2)	large_intestine(1)|pancreas(1)	c.C16792T	1						.						113.0	98.0	103.0					1																	186158894		2203	4300	6503	184425517	SO:0001587	stop_gained	83872	exon107			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.16792C>T	1.37:g.186158894C>T	ENSP00000271588:p.Arg5598*	Somatic		Capture	Illumina HiSeq	Phase_I	184425517	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Nonsense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	57	28.798362	0.99974	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	.	.	.	5.91	5.91	0.95273	.	0.418418	0.27147	N	0.020711	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	.	.	.	X	5598;5481	.	ENSP00000271588:R5598X	R	+	1	2	HMCN1	184425517	0.995000	0.38212	0.375000	0.26029	0.772000	0.43724	5.970000	0.70431	2.793000	0.96121	0.655000	0.94253	CGA		0.473	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
IGSF21	84966	broad.mit.edu	37	1	18704816	18704816	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:18704816C>T	ENST00000251296.1	+	10	1783	c.1400C>T	c.(1399-1401)aCg>aTg	p.T467M		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	467			T -> M (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.			extracellular region (GO:0005576)		p.T467M(2)		endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		CTGGAGCTGACGTGAAGGCAC	0.552																																					p.T467M												IGSF21,large_intestine,colon,Substitution - Missense,0 	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1400T	1						.						40.0	37.0	38.0					1																	18704816		2203	4300	6503	18577403	SO:0001583	missense	84966	exon10			AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.1400C>T	1.37:g.18704816C>T	ENSP00000251296:p.Thr467Met	Somatic		Capture	Illumina HiSeq	Phase_I	18577403	NM_032880	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	37	CCDS184.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586484	0.86851	.	.	ENSG00000117154	ENST00000251296	T	0.64991	-0.13	5.39	5.39	0.77823	.	0.193239	0.43416	D	0.000575	T	0.71779	0.3380	L	0.34521	1.04	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.74352	-0.3693	10	0.87932	D	0	-0.943	18.1078	0.89526	0.0:1.0:0.0:0.0	.	467	Q96ID5	IGS21_HUMAN	M	467	ENSP00000251296:T467M	ENSP00000251296:T467M	T	+	2	0	IGSF21	18577403	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.718000	0.68455	2.709000	0.92574	0.561000	0.74099	ACG		0.552	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880	
PTGS2	5743	broad.mit.edu	37	1	186643808	186643808	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:186643808G>C	ENST00000367468.5	-	10	1628	c.1492C>G	c.(1492-1494)Cct>Gct	p.P498A	PTGS2_ENST00000490885.2_5'UTR	NM_000963.2	NP_000954.1	P35354	PGH2_HUMAN	prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)	498					anagen (GO:0042640)|angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|brown fat cell differentiation (GO:0050873)|cellular component movement (GO:0006928)|cellular response to ATP (GO:0071318)|cellular response to hypoxia (GO:0071456)|cellular response to mechanical stimulus (GO:0071260)|cellular response to UV (GO:0034644)|cyclooxygenase pathway (GO:0019371)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|inflammatory response (GO:0006954)|learning (GO:0007612)|lipoxygenase pathway (GO:0019372)|maintenance of blood-brain barrier (GO:0035633)|memory (GO:0007613)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of synaptic transmission, dopaminergic (GO:0032227)|ovulation (GO:0030728)|positive regulation of apoptotic process (GO:0043065)|positive regulation of brown fat cell differentiation (GO:0090336)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of fever generation (GO:0031622)|positive regulation of fibroblast growth factor production (GO:0090271)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasoconstriction (GO:0045907)|positive regulation vascular endothelial growth factor production (GO:0010575)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|regulation of blood pressure (GO:0008217)|regulation of inflammatory response (GO:0050727)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to fatty acid (GO:0070542)|response to fructose (GO:0009750)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to manganese ion (GO:0010042)|response to oxidative stress (GO:0006979)|response to tumor necrosis factor (GO:0034612)|response to vitamin D (GO:0033280)|sensory perception of pain (GO:0019233)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|neuron projection (GO:0043005)|nucleus (GO:0005634)|protein complex (GO:0043234)	arachidonate 15-lipoxygenase activity (GO:0050473)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|lipid binding (GO:0008289)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)|prostaglandin-endoperoxide synthase activity (GO:0004666)	p.P498A(2)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	27					Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Aldesleukin(DB00041)|Aminosalicylic Acid(DB00233)|Antipyrine(DB01435)|Antrafenine(DB01419)|Balsalazide(DB01014)|Bromfenac(DB00963)|Bumetanide(DB00887)|Carprofen(DB00821)|Celecoxib(DB00482)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Clodronate(DB00720)|Dapsone(DB00250)|Desmopressin(DB00035)|Diclofenac(DB00586)|Diflunisal(DB00861)|Dihomo-gamma-linolenic acid(DB00154)|Drospirenone(DB01395)|Etanercept(DB00005)|Etodolac(DB00749)|Etoposide(DB00773)|Etoricoxib(DB01628)|Fenoprofen(DB00573)|Flurbiprofen(DB00712)|Ginseng(DB01404)|Ibuprofen(DB01050)|Icosapent(DB00159)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Ketorolac(DB00465)|Lenalidomide(DB00480)|Lornoxicam(DB06725)|Lumiracoxib(DB01283)|Magnesium salicylate(DB01397)|Meclofenamic acid(DB00939)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Mesalazine(DB00244)|Nabumetone(DB00461)|Naproxen(DB00788)|Nepafenac(DB06802)|Niflumic Acid(DB04552)|Nonoxynol-9(DB06804)|Oxaprozin(DB00991)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pomalidomide(DB08910)|Risedronate(DB00884)|Salicylate-sodium(DB01398)|Salicylic acid(DB00936)|Salsalate(DB01399)|Sulfasalazine(DB00795)|Sulindac(DB00605)|Suprofen(DB00870)|Tafluprost(DB08819)|Tenoxicam(DB00469)|Tetrahydrobiopterin(DB00360)|Thalidomide(DB01041)|Tiaprofenic acid(DB01600)|Tolmetin(DB00500)|Triamcinolone(DB00620)|Trisalicylate-choline(DB01401)	TCTGGCCGAGGCTTTTCTACC	0.478																																					p.P498A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1492G	1						.						99.0	98.0	98.0					1																	186643808		2203	4300	6503	184910431	SO:0001583	missense	5743	exon10			D28235	CCDS1371.1	1q25.2-q25.3	2008-02-05			ENSG00000073756	ENSG00000073756	1.14.99.1		9605	protein-coding gene	gene with protein product		600262				1380156	Standard	NM_000963		Approved	COX2	uc001gsb.3	P35354	OTTHUMG00000035473	ENST00000367468.5:c.1492C>G	1.37:g.186643808G>C	ENSP00000356438:p.Pro498Ala	Somatic		Capture	Illumina HiSeq	Phase_I	184910431	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	37	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.380380	0.42207	.	.	ENSG00000073756	ENST00000367468	T	0.68624	-0.34	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	L	0.46741	1.465	0.80722	D	1	B	0.18741	0.03	B	0.15870	0.014	T	0.56529	-0.7964	10	0.15952	T	0.53	-16.2191	19.6891	0.95991	0.0:0.0:1.0:0.0	.	498	P35354	PGH2_HUMAN	A	498	ENSP00000356438:P498A	ENSP00000356438:P498A	P	-	1	0	PTGS2	184910431	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.466000	0.73543	2.641000	0.89580	0.650000	0.86243	CCT		0.478	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963	
BRINP3	339479	broad.mit.edu	37	1	190067542	190067542	+	Missense_Mutation	SNP	T	T	C	rs372106848		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:190067542T>C	ENST00000367462.3	-	8	2138	c.1907A>G	c.(1906-1908)aAt>aGt	p.N636S	BRINP3_ENST00000534846.1_Missense_Mutation_p.N534S	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	636					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)		p.N636S(1)									ATTGGGACCATTGGACTTGAT	0.413																																					p.N636S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1907G	1						.						188.0	199.0	195.0					1																	190067542		2203	4300	6503	188334165	SO:0001583	missense	339479	exon8			AB111893	CCDS1373.1	1q31.1	2013-09-18	2013-09-18	2013-09-18	ENSG00000162670	ENSG00000162670			22393	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member C"""	FAM5C		16018821, 15193423	Standard	NM_199051		Approved	DBCCR1L, DBCCR1L1	uc001gse.1	Q76B58	OTTHUMG00000035533	ENST00000367462.3:c.1907A>G	1.37:g.190067542T>C	ENSP00000356432:p.Asn636Ser	Somatic		Capture	Illumina HiSeq	Phase_I	188334165	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	0.003	-2.408796	0.00193	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.16457	2.61;2.34	5.64	-5.2	0.02823	.	0.159137	0.42053	N	0.000766	T	0.05318	0.0141	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23154	-1.0196	10	0.27785	T	0.31	.	13.9769	0.64279	0.0:0.5798:0.0:0.4202	.	534;636	B7Z260;Q76B58	.;FAM5C_HUMAN	S	636;534	ENSP00000356432:N636S;ENSP00000438022:N534S	ENSP00000356432:N636S	N	-	2	0	FAM5C	188334165	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.297000	0.08276	-1.357000	0.02180	-0.297000	0.09499	AAT		0.413	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051	
CFHR2	3080	broad.mit.edu	37	1	196928086	196928086	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:196928086A>C	ENST00000367415.5	+	5	789	c.689A>C	c.(688-690)tAt>tCt	p.Y230S	CFHR2_ENST00000476712.2_Missense_Mutation_p.Y214S|CFHR2_ENST00000496448.1_3'UTR|CFHR2_ENST00000367421.3_Missense_Mutation_p.Y230S	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	230	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)		p.Y230S(1)		large_intestine(2)|ovary(1)|skin(3)	6						CAAAAGCTTTATTCAAGAACA	0.299																																					p.Y230S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A689C	1						.						52.0	55.0	54.0					1																	196928086		2202	4292	6494	195194709	SO:0001583	missense	3080	exon5			X64877	CCDS30959.1	1q31.3	2008-02-05	2004-08-09	2006-02-28	ENSG00000080910	ENSG00000080910		"""Complement system"""	4890	protein-coding gene	gene with protein product		600889	"""H factor (complement)-like 3"""	HFL3, CFHL2		1533657, 7672821	Standard	NM_005666		Approved	FHR2	uc001gtq.1	P36980	OTTHUMG00000036518	ENST00000367415.5:c.689A>C	1.37:g.196928086A>C	ENSP00000356385:p.Tyr230Ser	Somatic		Capture	Illumina HiSeq	Phase_I	195194709	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	.	.	.	.	.	.	.	.	.	.	.	14.13	2.442375	0.43326	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	D;D	0.84298	-1.83;-1.83	3.52	3.52	0.40303	Complement control module (2);Sushi/SCR/CCP (2);	0.000000	0.31145	N	0.008167	D	0.91633	0.7356	M	0.87381	2.88	0.09310	N	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.977;0.992	D	0.83516	0.0083	10	0.40728	T	0.16	.	10.0435	0.42173	1.0:0.0:0.0:0.0	.	203;230	P36980-2;P36980	.;FHR2_HUMAN	S	230	ENSP00000356391:Y230S;ENSP00000356385:Y230S	ENSP00000356385:Y230S	Y	+	2	0	CFHR2	195194709	0.086000	0.21541	0.013000	0.15412	0.004000	0.04260	1.955000	0.40372	1.454000	0.47793	0.443000	0.29094	TAT		0.299	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666	
DENND1B	163486	broad.mit.edu	37	1	197614826	197614826	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:197614826G>A	ENST00000367396.3	-	9	724	c.555C>T	c.(553-555)ccC>ccT	p.P185P	DENND1B_ENST00000235453.4_Silent_p.P155P|DENND1B_ENST00000400967.2_Silent_p.P155P	NM_144977.4	NP_659414.2	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B	185	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.P155P(1)		NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						TTACACTCTCGGGTATTGTTG	0.289																																					p.P185P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C555T	1						.						43.0	40.0	41.0					1																	197614826		1790	4055	5845	195881449	SO:0001819	synonymous_variant	163486	exon9			BC016588	CCDS41452.2, CCDS72996.1, CCDS72997.1	1q31.3	2012-10-03	2005-08-17	2005-08-17	ENSG00000213047	ENSG00000213047		"""DENN/MADD domain containing"""	28404	protein-coding gene	gene with protein product		613292	"""family with sequence similarity 31, member B"", ""chromosome 1 open reading frame 218"""	FAM31B, C1orf218		12477932	Standard	NM_144977		Approved	MGC27044, FLJ20054	uc021pgu.1	Q6P3S1	OTTHUMG00000035653	ENST00000367396.3:c.555C>T	1.37:g.197614826G>A		Somatic		Capture	Illumina HiSeq	Phase_I	195881449	NM_001195215	B5MD89|D3PFD5|Q5T3B8|Q5T3B9|Q5T3C1|Q5TAI8|Q6B0I8|Q8NDT1|Q8TBE6|Q9H774|Q9NXU2	Silent	SNP	ENST00000367396.3	37	CCDS41452.2																																																																																				0.289	DENND1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086539.1	NM_144977	
TNNT2	7139	broad.mit.edu	37	1	201328371	201328371	+	Silent	SNP	G	G	A	rs45503195		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:201328371G>A	ENST00000509001.1	-	16	1120	c.834C>T	c.(832-834)cgC>cgT	p.R278R	TNNT2_ENST00000367317.4_Silent_p.R278R|TNNT2_ENST00000360372.4_Silent_p.R273R|TNNT2_ENST00000458432.2_Silent_p.R287R|TNNT2_ENST00000236918.7_Silent_p.R283R|TNNT2_ENST00000367320.2_Silent_p.R245R|TNNT2_ENST00000460780.1_5'UTR|TNNT2_ENST00000367322.1_Silent_p.R275R|TNNT2_ENST00000421663.2_Silent_p.R281R|TNNT2_ENST00000367315.2_Silent_p.R275R|TNNT2_ENST00000367318.5_Silent_p.R278R	NM_001276347.1	NP_001263276.1	P45379	TNNT2_HUMAN	troponin T type 2 (cardiac)	288					ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|muscle filament sliding (GO:0030049)|negative regulation of ATPase activity (GO:0032780)|positive regulation of ATPase activity (GO:0032781)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytosol (GO:0005829)|sarcomere (GO:0030017)|striated muscle thin filament (GO:0005865)|troponin complex (GO:0005861)	actin binding (GO:0003779)|structural constituent of cytoskeleton (GO:0005200)|tropomyosin binding (GO:0005523)|troponin C binding (GO:0030172)|troponin I binding (GO:0031013)	p.R275R(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|liver(1)|lung(9)	20						TAGCCTTCCCGCGGGTCTTGG	0.632																																					p.R285R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C855T	1						.						42.0	40.0	41.0					1																	201328371		2203	4299	6502	199594994	SO:0001819	synonymous_variant	7139	exon16			X74819	CCDS30968.1, CCDS30969.1, CCDS60390.1, CCDS73002.1, CCDS73003.1	1q32	2014-09-17	2005-09-12		ENSG00000118194	ENSG00000118194			11949	protein-coding gene	gene with protein product		191045	"""troponin T2, cardiac"", ""cardiomyopathy, hypertrophic 2"", ""cardiomyopathy, dilated 1D (autosomal dominant)"""	CMH2, CMD1D		8088824, 8205619, 9482583	Standard	NM_001001430		Approved	CMPD2	uc001gwf.4	P45379	OTTHUMG00000035733	ENST00000509001.1:c.834C>T	1.37:g.201328371G>A		Somatic		Capture	Illumina HiSeq	Phase_I	199594994	NM_000364	A2TDB9|A8K3K6|O60214|Q99596|Q99597|Q9BUF6|Q9UM96	Silent	SNP	ENST00000509001.1	37	CCDS30969.1																																																																																				0.632	TNNT2-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360358.1	NM_000364	
OTUD3	23252	broad.mit.edu	37	1	20230832	20230832	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:20230832G>A	ENST00000375120.3	+	5	680	c.679G>A	c.(679-681)Gac>Aac	p.D227N		NM_015207.1	NP_056022.1	Q5T2D3	OTUD3_HUMAN	OTU deubiquitinase 3	227					protein K11-linked deubiquitination (GO:0035871)|protein K6-linked deubiquitination (GO:0044313)		ubiquitin-specific protease activity (GO:0004843)	p.D227N(1)		breast(1)|kidney(2)|large_intestine(4)|lung(1)|skin(1)	9		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000276)|Lung NSC(340;0.000338)|Breast(348;0.000812)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|COAD - Colon adenocarcinoma(152;1.12e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000142)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.000408)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		CTCTGAAGACGACCTGAGAGA	0.373																																					p.D227N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G679A	1						.						164.0	159.0	161.0					1																	20230832		1908	4133	6041	20103419	SO:0001583	missense	23252	exon5			AB007928	CCDS41279.1	1p36.13	2014-02-24	2014-02-24		ENSG00000169914	ENSG00000169914		"""OTU domain containing"""	29038	protein-coding gene	gene with protein product		611758	"""OTU domain containing 3"""			9455484, 23827681	Standard	NM_015207		Approved	KIAA0459, DUBA4	uc001bcs.4	Q5T2D3	OTTHUMG00000002696	ENST00000375120.3:c.679G>A	1.37:g.20230832G>A	ENSP00000364261:p.Asp227Asn	Somatic		Capture	Illumina HiSeq	Phase_I	20103419	NM_015207	O75047	Missense_Mutation	SNP	ENST00000375120.3	37	CCDS41279.1	.	.	.	.	.	.	.	.	.	.	G	15.00	2.703960	0.48412	.	.	ENSG00000169914	ENST00000375120	T	0.21734	1.99	5.09	3.19	0.36642	.	0.475823	0.23922	N	0.043234	T	0.10723	0.0262	L	0.34521	1.04	0.25980	N	0.982386	P	0.42993	0.797	B	0.24701	0.055	T	0.20174	-1.0283	10	0.19147	T	0.46	.	10.6878	0.45854	0.1602:0.0:0.8398:0.0	.	227	Q5T2D3	OTUD3_HUMAN	N	227	ENSP00000364261:D227N	ENSP00000364261:D227N	D	+	1	0	OTUD3	20103419	0.997000	0.39634	0.818000	0.32626	0.871000	0.50021	3.216000	0.51176	0.527000	0.28560	0.591000	0.81541	GAC		0.373	OTUD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007655.1		
LMOD1	25802	broad.mit.edu	37	1	201915384	201915384	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:201915384T>G	ENST00000367288.4	-	1	331	c.85A>C	c.(85-87)Atg>Ctg	p.M29L		NM_012134.2	NP_036266.2	P29536	LMOD1_HUMAN	leiomodin 1 (smooth muscle)	29					muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)		p.M29L(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26						AGCTCCTCCATCTCCTCGGGA	0.597																																					p.M29L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A85C	1						.						44.0	50.0	48.0					1																	201915384		2022	4167	6189	200182007	SO:0001583	missense	25802	exon1			X54162	CCDS53457.1	1q32.1	2008-05-22			ENSG00000163431	ENSG00000163431			6647	protein-coding gene	gene with protein product		602715					Standard	NM_012134		Approved	64kD, D1, 1D	uc021phl.1	P29536	OTTHUMG00000035802	ENST00000367288.4:c.85A>C	1.37:g.201915384T>G	ENSP00000356257:p.Met29Leu	Somatic		Capture	Illumina HiSeq	Phase_I	200182007	NM_012134	B1APV6|C4AMB1|Q68EN2	Missense_Mutation	SNP	ENST00000367288.4	37	CCDS53457.1	.	.	.	.	.	.	.	.	.	.	T	18.49	3.634316	0.67130	.	.	ENSG00000163431	ENST00000367288;ENST00000400965;ENST00000412469	T	0.17054	2.3	5.93	4.81	0.61882	.	0.138411	0.33110	N	0.005268	T	0.08537	0.0212	N	0.12502	0.225	0.43874	D	0.996489	B;B	0.17465	0.007;0.022	B;B	0.12837	0.008;0.008	T	0.15549	-1.0433	10	0.09084	T	0.74	-56.1528	9.98	0.41809	0.0:0.0792:0.0:0.9208	.	29;29	B4E3S9;P29536	.;LMOD1_HUMAN	L	29	ENSP00000356257:M29L	ENSP00000356257:M29L	M	-	1	0	LMOD1	200182007	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.966000	0.29331	1.083000	0.41159	0.459000	0.35465	ATG		0.597	LMOD1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087085.2		
KDM5B	10765	broad.mit.edu	37	1	202777306	202777306	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:202777306G>T	ENST00000367265.3	-	1	1292	c.128C>A	c.(127-129)gCg>gAg	p.A43E	PCAT6_ENST00000553157.1_RNA|RP11-480I12.10_ENST00000564127.1_RNA|PCAT6_ENST00000425295.1_RNA|PCAT6_ENST00000417262.1_RNA|KDM5B_ENST00000367264.2_Missense_Mutation_p.A43E	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	43	JmjN. {ECO:0000255|PROSITE- ProRule:PRU00537}.				histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)	p.A43E(1)		breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						GAAGGGGTCCGCGAACTCTTC	0.711																																					p.A43E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C128A	1						.						37.0	50.0	46.0					1																	202777306		2203	4300	6503	201043929	SO:0001583	missense	10765	exon1			AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.128C>A	1.37:g.202777306G>T	ENSP00000356234:p.Ala43Glu	Somatic		Capture	Illumina HiSeq	Phase_I	201043929	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	g	13.94	2.386851	0.42308	.	.	ENSG00000117139	ENST00000367265;ENST00000367264	T;T	0.20598	2.06;2.06	3.68	3.68	0.42216	Transcription factor jumonji, JmjN (3);	0.294777	0.30781	U	0.008896	T	0.10594	0.0259	N	0.11724	0.165	0.48696	D	0.999691	P;B	0.51537	0.946;0.437	B;B	0.41466	0.358;0.262	T	0.07328	-1.0778	10	0.06099	T	0.92	-2.6034	14.171	0.65510	0.0:0.0:1.0:0.0	.	43;43	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	E	43	ENSP00000356234:A43E;ENSP00000356233:A43E	ENSP00000356233:A43E	A	-	2	0	KDM5B	201043929	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.951000	0.40333	1.581000	0.49865	0.298000	0.19748	GCG		0.711	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
FMOD	2331	broad.mit.edu	37	1	203317083	203317083	+	Missense_Mutation	SNP	G	G	A	rs376310218		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:203317083G>A	ENST00000354955.4	-	2	779	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	FMOD_ENST00000493296.1_Intron	NM_002023.4	NP_002014.2	Q06828	FMOD_HUMAN	fibromodulin	106					carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor complex assembly (GO:0007181)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)		p.R106C(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	17			BRCA - Breast invasive adenocarcinoma(75;0.171)			TACTTCATGCGGGAGGGAACG	0.577																																					p.R106C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C316T	1						.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	100.0	84.0	89.0		316	5.2	1.0	1		89	0,8600		0,0,4300	no	missense	FMOD	NM_002023.3	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	106/377	203317083	1,13005	2203	4300	6503	201583706	SO:0001583	missense	2331	exon2			U05291	CCDS30976.1	1q32	2008-02-05			ENSG00000122176	ENSG00000122176		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	3774	protein-coding gene	gene with protein product	"""fibromodulin proteoglycan"""	600245				7851907	Standard	NM_002023		Approved	SLRR2E	uc001gzr.3	Q06828	OTTHUMG00000035910	ENST00000354955.4:c.316C>T	1.37:g.203317083G>A	ENSP00000347041:p.Arg106Cys	Somatic		Capture	Illumina HiSeq	Phase_I	201583706	NM_002023	Q15331|Q8IV47	Missense_Mutation	SNP	ENST00000354955.4	37	CCDS30976.1	.	.	.	.	.	.	.	.	.	.	G	18.15	3.558793	0.65538	2.27E-4	0.0	ENSG00000122176	ENST00000435105;ENST00000354955;ENST00000539467	T	0.59083	0.29	5.16	5.16	0.70880	Leucine-rich repeat-containing N-terminal (1);	0.124753	0.53938	D	0.000055	T	0.76765	0.4033	M	0.85630	2.765	0.58432	D	0.999999	D	0.89917	1.0	D	0.80764	0.994	T	0.79785	-0.1657	10	0.59425	D	0.04	-11.0048	12.3546	0.55167	0.0:0.0:0.8313:0.1687	.	106	Q06828	FMOD_HUMAN	C	93;106;86	ENSP00000347041:R106C	ENSP00000347041:R106C	R	-	1	0	FMOD	201583706	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.102000	0.57776	2.398000	0.81561	0.563000	0.77884	CGC		0.577	FMOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087472.1	NM_002023	
NFASC	23114	broad.mit.edu	37	1	204948576	204948576	+	Missense_Mutation	SNP	G	G	A	rs562163063		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:204948576G>A	ENST00000401399.1	+	18	2264	c.2065G>A	c.(2065-2067)Gtc>Atc	p.V689I	NFASC_ENST00000360049.4_Missense_Mutation_p.V685I|NFASC_ENST00000339876.6_Missense_Mutation_p.V689I|NFASC_ENST00000404907.1_Missense_Mutation_p.V685I|NFASC_ENST00000367170.4_Missense_Mutation_p.V689I|NFASC_ENST00000367171.4_Missense_Mutation_p.V674I|NFASC_ENST00000513543.1_Missense_Mutation_p.V685I|NFASC_ENST00000338586.6_Missense_Mutation_p.V689I|NFASC_ENST00000539706.1_Missense_Mutation_p.V685I|NFASC_ENST00000404076.1_Missense_Mutation_p.V668I|NFASC_ENST00000338515.6_Missense_Mutation_p.V689I|NFASC_ENST00000367169.4_Missense_Mutation_p.V689I|NFASC_ENST00000367172.4_Missense_Mutation_p.V689I			O94856	NFASC_HUMAN	neurofascin	689	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.V685I(2)|p.V689I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			TAACTCAGCCGTCCTCCGGCT	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		18674	0.0		0.001	False		,,,				2504	0.0				p.V700I												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.G2098A	1						.						107.0	104.0	105.0					1																	204948576		2203	4300	6503	203215199	SO:0001583	missense	23114	exon17			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.2065G>A	1.37:g.204948576G>A	ENSP00000385637:p.Val689Ile	Somatic		Capture	Illumina HiSeq	Phase_I	203215199	NM_001160331	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	.	.	.	.	.	.	.	.	.	.	G	0.497	-0.872707	0.02570	.	.	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.59224	0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28;0.28	5.43	0.154	0.14901	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.452189	0.18437	N	0.141253	T	0.27489	0.0675	N	0.11255	0.115	0.19300	N	0.999973	B;B;B;B;B;B	0.33022	0.127;0.001;0.008;0.099;0.394;0.008	B;B;B;B;B;B	0.23150	0.044;0.002;0.01;0.012;0.012;0.005	T	0.14117	-1.0484	10	0.22706	T	0.39	.	6.4211	0.21744	0.4377:0.1188:0.4434:0.0	.	689;700;685;674;689;685	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3	NFASC_HUMAN;.;.;.;.;.	I	689;674;689;689;689;689;700;685;685;689;668;689;685;685;676	ENSP00000356140:V689I;ENSP00000356139:V674I;ENSP00000356138:V689I;ENSP00000342128:V689I;ENSP00000344786:V689I;ENSP00000343509:V689I;ENSP00000438614:V685I;ENSP00000353154:V685I;ENSP00000356137:V689I;ENSP00000385676:V668I;ENSP00000385637:V689I;ENSP00000384061:V685I;ENSP00000425908:V685I;ENSP00000415031:V676I	ENSP00000295776:V700I	V	+	1	0	NFASC	203215199	0.038000	0.19896	0.100000	0.21137	0.135000	0.20990	0.371000	0.20450	-0.226000	0.09899	-0.136000	0.14681	GTC		0.587	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
PM20D1	148811	broad.mit.edu	37	1	205819088	205819088	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:205819088C>T	ENST00000367136.4	-	1	157	c.113G>A	c.(112-114)cGa>cAa	p.R38Q	PM20D1_ENST00000460624.1_5'UTR	NM_152491.4	NP_689704.4	Q6GTS8	P20D1_HUMAN	peptidase M20 domain containing 1	38					negative regulation of neuron death (GO:1901215)|regulation of defense response to virus by host (GO:0050691)|regulation of viral process (GO:0050792)	extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|peptidase activity (GO:0008233)	p.R38Q(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(1)	28	Breast(84;0.201)		BRCA - Breast invasive adenocarcinoma(75;0.0252)			AGAAGGGATTCGCGACGCCCT	0.592																																					p.R38Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G113A	1						.						90.0	92.0	91.0					1																	205819088		2203	4300	6503	204085711	SO:0001583	missense	148811	exon1				CCDS1460.1	1q32.1	2008-02-05			ENSG00000162877	ENSG00000162877			26518	protein-coding gene	gene with protein product							Standard	NM_152491		Approved	FLJ32569, Cps1	uc001hdj.3	Q6GTS8	OTTHUMG00000035999	ENST00000367136.4:c.113G>A	1.37:g.205819088C>T	ENSP00000356104:p.Arg38Gln	Somatic		Capture	Illumina HiSeq	Phase_I	204085711	NM_152491	Q6P4E3|Q96DM4	Missense_Mutation	SNP	ENST00000367136.4	37	CCDS1460.1	.	.	.	.	.	.	.	.	.	.	C	10.51	1.371743	0.24857	.	.	ENSG00000162877	ENST00000367136	T	0.06294	3.32	5.27	2.33	0.28932	.	0.385756	0.27927	N	0.017288	T	0.05456	0.0144	L	0.51422	1.61	0.19945	N	0.999943	B	0.21688	0.059	B	0.14023	0.01	T	0.44651	-0.9314	10	0.10902	T	0.67	.	6.9349	0.24461	0.0:0.7049:0.0:0.2951	.	38	Q6GTS8	P20D1_HUMAN	Q	38	ENSP00000356104:R38Q	ENSP00000356104:R38Q	R	-	2	0	PM20D1	204085711	0.670000	0.27512	0.819000	0.32651	0.487000	0.33371	0.365000	0.20348	0.327000	0.23409	-0.136000	0.14681	CGA		0.592	PM20D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087736.1	NM_152491	
SRGAP2	23380	broad.mit.edu	37	1	206566199	206566199	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:206566199C>T	ENST00000414007.1	+	2	220	c.220C>T	c.(220-222)Cgc>Tgc	p.R74C	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	214	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)	p.R74C(1)		NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					GGCCAACGTTCGCATTGAGGA	0.532																																					p.S127L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C380T	1						.						72.0	71.0	71.0					1																	206566199		2165	4275	6440	204632822	SO:0001583	missense	23380	exon3			AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.220C>T	1.37:g.206566199C>T	ENSP00000390898:p.Arg74Cys	Somatic		Capture	Illumina HiSeq	Phase_I	204632822	NM_001170637		Missense_Mutation	SNP	ENST00000414007.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.141870|4.141870	0.77775|0.77775	.|.	.|.	ENSG00000163486|ENSG00000163486	ENST00000414359;ENST00000414007|ENST00000295713	T|.	0.55760|.	0.5|.	5.36|5.36	4.39|4.39	0.52855|0.52855	.|.	0.235557|.	0.39544|.	N|.	0.001325|.	T|T	0.62889|0.62889	0.2465|0.2465	.|.	.|.	.|.	0.45502|.	D|.	0.998463|.	D;P;D|.	0.56968|.	0.978;0.905;0.975|.	B;P;P|.	0.48571|.	0.306;0.556;0.582|.	T|T	0.69476|0.69476	-0.5135|-0.5135	8|3	0.62326|.	D|.	0.03|.	.|.	13.3626|13.3626	0.60665|0.60665	0.2364:0.7636:0.0:0.0|0.2364:0.7636:0.0:0.0	.|.	61;214;214|.	B4DDU0;O75044;B7Z3G4|.	.;FNBP2_HUMAN;.|.	C|L	128;74|127	ENSP00000390898:R74C|.	ENSP00000390898:R74C|.	R|S	+|+	1|2	0|0	SRGAP2|SRGAP2	204632822|204632822	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.856000|0.856000	0.48823|0.48823	2.561000|2.561000	0.45905|0.45905	2.483000|2.483000	0.83821|0.83821	0.455000|0.455000	0.32223|0.32223	CGC|TCG		0.532	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
CR1	1378	broad.mit.edu	37	1	207783030	207783030	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:207783030A>T	ENST00000367049.4	+	37	6292	c.6292A>T	c.(6292-6294)Agg>Tgg	p.R2098W	CR1_ENST00000367053.1_Missense_Mutation_p.R1648W|CR1_ENST00000367051.1_Missense_Mutation_p.R1648W|CR1_ENST00000400960.2_Missense_Mutation_p.R1648W|CR1_ENST00000367052.1_Missense_Mutation_p.R1648W	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1648					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)	p.R1653W(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						ACACTGCTCCAGGGGTGAGTG	0.498																																					p.R2098W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6292T	1						.						18.0	18.0	18.0					1																	207783030		1949	4154	6103	205849653	SO:0001583	missense	1378	exon37			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6292A>T	1.37:g.207783030A>T	ENSP00000356016:p.Arg2098Trp	Somatic		Capture	Illumina HiSeq	Phase_I	205849653	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	A	14.30	2.493684	0.44352	.	.	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	2.41	1.19	0.21007	Complement control module (1);Sushi/SCR/CCP (1);	.	.	.	.	T	0.69958	0.3169	M	0.92219	3.285	0.25209	N	0.98999	D;D;D	0.89917	0.993;0.999;1.0	P;D;D	0.76575	0.633;0.988;0.973	T	0.56673	-0.7940	9	0.66056	D	0.02	.	5.2958	0.15751	0.6999:0.3001:0.0:0.0	.	1648;1648;2098	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	W	1648;1648;1648;1648;2098	ENSP00000356019:R1648W;ENSP00000356018:R1648W;ENSP00000356020:R1648W;ENSP00000383744:R1648W;ENSP00000356016:R2098W	ENSP00000356016:R2098W	R	+	1	2	CR1	205849653	0.000000	0.05858	0.984000	0.44739	0.360000	0.29518	-0.012000	0.12699	0.315000	0.23110	0.260000	0.18958	AGG		0.498	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
FAM43B	163933	broad.mit.edu	37	1	20879559	20879559	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:20879559G>A	ENST00000332947.4	+	1	628	c.93G>A	c.(91-93)tcG>tcA	p.S31S		NM_207334.2	NP_997217.1	Q6ZT52	FA43B_HUMAN	family with sequence similarity 43, member B	31								p.S31S(1)		large_intestine(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00979)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.000399)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)		CCTACACGTCGCTGCTCTCCA	0.677																																					p.S31S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G93A	1						.						38.0	39.0	39.0					1																	20879559		2203	4300	6503	20752146	SO:0001819	synonymous_variant	163933	exon1			AK126900	CCDS209.1	1p36.12	2014-08-14			ENSG00000183114	ENSG00000183114			31791	protein-coding gene	gene with protein product						21461611	Standard	NM_207334		Approved	FLJ44952	uc001bdj.3	Q6ZT52	OTTHUMG00000057491	ENST00000332947.4:c.93G>A	1.37:g.20879559G>A		Somatic		Capture	Illumina HiSeq	Phase_I	20752146	NM_207334	A5PKT8|A5PL01	Silent	SNP	ENST00000332947.4	37	CCDS209.1																																																																																				0.677	FAM43B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127759.1	NM_207334	
CD34	947	broad.mit.edu	37	1	208062548	208062548	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:208062548G>A	ENST00000310833.7	-	6	1086	c.765C>T	c.(763-765)agC>agT	p.S255S	CD34_ENST00000537704.1_Silent_p.S120S|CD34_ENST00000367036.3_Silent_p.S97S|CD34_ENST00000356522.4_Silent_p.S255S|CD34_ENST00000485761.1_5'UTR	NM_001025109.1	NP_001020280.1	P28906	CD34_HUMAN	CD34 molecule	255					cell motility (GO:0048870)|cell proliferation (GO:0008283)|endothelial cell proliferation (GO:0001935)|endothelium development (GO:0003158)|extracellular vesicular exosome assembly (GO:0071971)|glomerular endothelium development (GO:0072011)|glomerular filtration (GO:0003094)|glutamate metabolic process (GO:0006536)|hematopoietic stem cell proliferation (GO:0071425)|hemopoiesis (GO:0030097)|leukocyte migration (GO:0050900)|mesangial cell-matrix adhesion (GO:0035759)|metanephric glomerular mesangial cell differentiation (GO:0072254)|negative regulation of blood coagulation (GO:0030195)|negative regulation of cellular response to heat (GO:1900035)|negative regulation of cellular response to hypoxia (GO:1900038)|negative regulation of gene expression (GO:0010629)|negative regulation of interleukin-2 secretion (GO:1900041)|negative regulation of neuron death (GO:1901215)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of tumor necrosis factor production (GO:0032720)|paracrine signaling (GO:0038001)|positive regulation of angiogenesis (GO:0045766)|positive regulation of gene expression (GO:0010628)|positive regulation of glial cell line-derived neurotrophic factor secretion (GO:1900168)|positive regulation of granulocyte colony-stimulating factor production (GO:0071657)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of odontogenesis (GO:0042482)|positive regulation of transforming growth factor beta production (GO:0071636)|positive regulation of vasculogenesis (GO:2001214)|regulation of blood pressure (GO:0008217)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|stem cell proliferation (GO:0072089)|tissue homeostasis (GO:0001894)|transdifferentiation (GO:0060290)|vascular wound healing (GO:0061042)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|glomerular endothelium fenestra (GO:0036053)|integral component of plasma membrane (GO:0005887)|intercellular bridge (GO:0045171)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|sulfate binding (GO:0043199)|transcription factor binding (GO:0008134)	p.S255S(1)		kidney(2)|large_intestine(2)|lung(8)|ovary(1)	13						GTTGGAGTTTGCTGGAAATTT	0.478																																					p.S255S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C765T	1						.						108.0	112.0	110.0					1																	208062548		2203	4300	6503	206129171	SO:0001819	synonymous_variant	947	exon6			M81104	CCDS31011.1, CCDS31012.1	1q32	2008-02-05	2006-03-28		ENSG00000174059	ENSG00000174059		"""CD molecules"""	1662	protein-coding gene	gene with protein product		142230	"""CD34 antigen"""			1370171, 1374051	Standard	NM_001025109		Approved		uc001hgw.1	P28906	OTTHUMG00000036565	ENST00000310833.7:c.765C>T	1.37:g.208062548G>A		Somatic		Capture	Illumina HiSeq	Phase_I	206129171	NM_001773	A8K664|Q15970|Q15971|Q5JTA3|Q5JTA4|Q9UJB1	Silent	SNP	ENST00000310833.7	37	CCDS31011.1																																																																																				0.478	CD34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088933.1	NM_001773	
SERTAD4	56256	broad.mit.edu	37	1	210415073	210415073	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:210415073C>T	ENST00000367012.3	+	4	692	c.462C>T	c.(460-462)tgC>tgT	p.C154C	SERTAD4_ENST00000490620.1_3'UTR	NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	154						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		TCCCTGCCTGCTCTTTCAATG	0.448																																					p.C154C												.	.	0			c.C462T	1						.						136.0	140.0	139.0					1																	210415073		2203	4300	6503	208481696	SO:0001819	synonymous_variant	56256	exon4			BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.462C>T	1.37:g.210415073C>T		None		Capture	Illumina HiSeq	Phase_I	208481696	NM_019605	B2RD32	Silent	SNP	ENST00000367012.3	37	CCDS1494.1																																																																																				0.448	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605	
EIF4G3	8672	broad.mit.edu	37	1	21268015	21268015	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:21268015T>C	ENST00000264211.8	-	8	1658	c.1464A>G	c.(1462-1464)caA>caG	p.Q488Q	EIF4G3_ENST00000374937.3_Silent_p.Q494Q|EIF4G3_ENST00000400422.1_Silent_p.Q488Q|EIF4G3_ENST00000374935.3_Intron|EIF4G3_ENST00000356916.3_Silent_p.Q499Q|EIF4G3_ENST00000536266.1_Silent_p.Q92Q|EIF4G3_ENST00000544689.1_5'UTR|EIF4G3_ENST00000374927.4_Silent_p.Q488Q|EIF4G3_ENST00000374933.3_5'Flank|EIF4G3_ENST00000602326.1_Silent_p.Q494Q	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	488					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.Q488Q(1)|p.Q494Q(1)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		AATTTAAGTTTTGAGAATCCA	0.398																																					p.Q488Q												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A1464G	1						.						195.0	200.0	198.0					1																	21268015		2203	4300	6503	21140602	SO:0001819	synonymous_variant	8672	exon9			AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.1464A>G	1.37:g.21268015T>C		Somatic		Capture	Illumina HiSeq	Phase_I	21140602	NM_003760	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Silent	SNP	ENST00000264211.8	37	CCDS214.1																																																																																				0.398	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
TRAF5	7188	broad.mit.edu	37	1	211534447	211534447	+	Silent	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:211534447T>G	ENST00000261464.5	+	7	693	c.639T>G	c.(637-639)gcT>gcG	p.A213A	TRAF5_ENST00000462410.1_3'UTR|TRAF5_ENST00000336184.2_Silent_p.A213A|TRAF5_ENST00000427925.2_Intron|TRAF5_ENST00000367004.3_Silent_p.A213A	NM_001033910.2	NP_001029082.1	O00463	TRAF5_HUMAN	TNF receptor-associated factor 5	213					apoptotic process (GO:0006915)|positive regulation of cell proliferation (GO:0008284)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	CD40 receptor complex (GO:0035631)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)	signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.A213A(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				OV - Ovarian serous cystadenocarcinoma(81;0.00946)|all cancers(67;0.0808)|Epithelial(68;0.144)		AACACCTGGCTGTATGTCCTG	0.433																																					p.A213A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T639G	1						.						188.0	161.0	170.0					1																	211534447		2203	4300	6503	209601070	SO:0001819	synonymous_variant	7188	exon7			AB000509	CCDS1497.1	1q32	2008-02-05			ENSG00000082512	ENSG00000082512		"""RING-type (C3HC4) zinc fingers"""	12035	protein-coding gene	gene with protein product		602356				9126477	Standard	NM_001033910		Approved	RNF84	uc001hii.3	O00463	OTTHUMG00000036997	ENST00000261464.5:c.639T>G	1.37:g.211534447T>G		Somatic		Capture	Illumina HiSeq	Phase_I	209601070	NM_004619	B4DIS9|B4E0A2|Q6FHY1	Silent	SNP	ENST00000261464.5	37	CCDS1497.1																																																																																				0.433	TRAF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089825.1	NM_004619	
RPS6KC1	26750	broad.mit.edu	37	1	213414680	213414680	+	Missense_Mutation	SNP	T	T	A	rs187036422		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:213414680T>A	ENST00000366960.3	+	11	2011	c.1861T>A	c.(1861-1863)Ttg>Atg	p.L621M	RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.L409M|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.L324M|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.L609M	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	621					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.L621M(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		TGGAGAAAAATTGTATAGTCT	0.383																																					p.L621M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1861A	1						.						49.0	54.0	52.0					1																	213414680		2203	4300	6503	211481303	SO:0001583	missense	26750	exon11			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.1861T>A	1.37:g.213414680T>A	ENSP00000355927:p.Leu621Met	Somatic		Capture	Illumina HiSeq	Phase_I	211481303	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	T	9.093	1.002157	0.19121	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.44482	1.35;1.38;1.38;0.92	5.19	1.49	0.22878	.	0.670497	0.14856	N	0.294369	T	0.37812	0.1017	M	0.65975	2.015	0.26647	N	0.972179	P;B;B	0.35033	0.481;0.042;0.042	B;B;B	0.36608	0.229;0.046;0.046	T	0.31861	-0.9928	10	0.52906	T	0.07	-23.3486	4.4637	0.11678	0.1508:0.2889:0.0:0.5603	.	409;621;609	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	M	409;621;609;324	ENSP00000442306:L409M;ENSP00000355927:L621M;ENSP00000355926:L609M;ENSP00000439282:L324M	ENSP00000355926:L609M	L	+	1	2	RPS6KC1	211481303	0.000000	0.05858	0.996000	0.52242	0.988000	0.76386	-0.368000	0.07543	-0.011000	0.14247	0.455000	0.32223	TTG		0.383	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
RPS6KC1	26750	broad.mit.edu	37	1	213415975	213415975	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:213415975C>T	ENST00000366960.3	+	12	3035	c.2885C>T	c.(2884-2886)gCc>gTc	p.A962V	RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.A750V|RPS6KC1_ENST00000543354.1_3'UTR|RPS6KC1_ENST00000366959.3_Missense_Mutation_p.A950V	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	962	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)	p.A962V(1)		breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GACAGCGATGCCATAGAGAGA	0.393																																					p.A962V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2885T	1						.						129.0	116.0	120.0					1																	213415975		2203	4300	6503	211482598	SO:0001583	missense	26750	exon12			AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2885C>T	1.37:g.213415975C>T	ENSP00000355927:p.Ala962Val	Somatic		Capture	Illumina HiSeq	Phase_I	211482598	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.050753	0.75960	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959	T;T;T	0.61040	0.14;0.14;0.14	5.96	5.05	0.67936	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64594	0.2612	N	0.20881	0.62	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.999;0.999	T	0.69628	-0.5094	10	0.72032	D	0.01	-47.8128	15.3845	0.74687	0.0:0.9333:0.0:0.0667	.	750;962;950	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	V	750;962;950	ENSP00000442306:A750V;ENSP00000355927:A962V;ENSP00000355926:A950V	ENSP00000355926:A950V	A	+	2	0	RPS6KC1	211482598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.294000	0.78760	1.533000	0.49186	0.655000	0.94253	GCC		0.393	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
SPATA17	128153	broad.mit.edu	37	1	217955579	217955579	+	Missense_Mutation	SNP	C	C	T	rs200145412		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:217955579C>T	ENST00000366933.4	+	8	842	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	RP11-415L24.1_ENST00000415765.1_RNA	NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	263						cytoplasm (GO:0005737)		p.R263W(1)		endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GCCAACGTTGCGGGTGGCAGA	0.453																																					p.R263W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C787T	1						.						92.0	95.0	94.0					1																	217955579		2203	4300	6503	216022202	SO:0001583	missense	128153	exon8			AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.787C>T	1.37:g.217955579C>T	ENSP00000355900:p.Arg263Trp	Somatic		Capture	Illumina HiSeq	Phase_I	216022202	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	C	17.79	3.475316	0.63737	.	.	ENSG00000162814	ENST00000366933	T	0.61510	0.1	4.73	-2.29	0.06805	.	0.224021	0.37530	N	0.002041	T	0.69548	0.3123	M	0.81942	2.565	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.63233	-0.6683	10	0.62326	D	0.03	-20.1943	7.058	0.25109	0.1875:0.5633:0.0:0.2492	.	263	Q96L03	SPT17_HUMAN	W	263	ENSP00000355900:R263W	ENSP00000355900:R263W	R	+	1	2	SPATA17	216022202	1.000000	0.71417	0.000000	0.03702	0.531000	0.34715	0.845000	0.27668	-1.105000	0.03011	-1.969000	0.00466	CGG		0.453	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
HSPG2	3339	broad.mit.edu	37	1	22201196	22201196	+	Silent	SNP	C	C	T	rs550724412		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:22201196C>T	ENST00000374695.3	-	27	3520	c.3441G>A	c.(3439-3441)acG>acA	p.T1147T		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1147	Laminin EGF-like 5; second part. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.T1147T(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGCCACTGGGCGTGCGTGTGT	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16595	0.0		0.0	False		,,,				2504	0.0				p.T1147T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3441A	1						.						39.0	41.0	40.0					1																	22201196		2202	4299	6501	22073783	SO:0001819	synonymous_variant	3339	exon27			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3441G>A	1.37:g.22201196C>T		Somatic		Capture	Illumina HiSeq	Phase_I	22073783	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	8.277	0.814592	0.16607	.	.	ENSG00000142798	ENST00000427897	.	.	.	5.02	-3.63	0.04529	.	.	.	.	.	T	0.18215	0.0437	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29731	-1.0002	4	.	.	.	.	1.7401	0.02950	0.1147:0.3514:0.2255:0.3084	.	.	.	.	T	2	.	.	A	-	1	0	HSPG2	22073783	0.000000	0.05858	0.781000	0.31783	0.945000	0.59286	-0.631000	0.05496	-0.066000	0.12998	-0.301000	0.09380	GCC		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
DUSP10	11221	broad.mit.edu	37	1	221879716	221879716	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:221879716C>T	ENST00000366899.3	-	3	1142	c.904G>A	c.(904-906)Gcg>Acg	p.A302T	DUSP10_ENST00000323825.3_5'UTR|DUSP10_ENST00000544095.1_5'UTR|DUSP10_ENST00000468085.1_5'UTR	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	302					inactivation of MAPK activity (GO:0000188)|JNK cascade (GO:0007254)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of respiratory burst involved in inflammatory response (GO:0060266)|oligodendrocyte differentiation (GO:0048709)|protein dephosphorylation (GO:0006470)|regulation of adaptive immune response (GO:0002819)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	MAP kinase phosphatase activity (GO:0033549)|MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.A302T(1)		NS(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				GBM - Glioblastoma multiforme(131;0.0103)		CTCGAGGCCGCGGATGCGCCG	0.582																																					p.A302T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G904A	1						.						66.0	75.0	72.0					1																	221879716		2203	4300	6503	219946339	SO:0001583	missense	11221	exon3			AB026436	CCDS1528.1	1q41	2011-06-09			ENSG00000143507	ENSG00000143507		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3065	protein-coding gene	gene with protein product		608867				10391943, 10597297	Standard	NM_007207		Approved	MKP-5, MKP5	uc001hmy.2	Q9Y6W6	OTTHUMG00000037269	ENST00000366899.3:c.904G>A	1.37:g.221879716C>T	ENSP00000355866:p.Ala302Thr	Somatic		Capture	Illumina HiSeq	Phase_I	219946339	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Missense_Mutation	SNP	ENST00000366899.3	37	CCDS1528.1	.	.	.	.	.	.	.	.	.	.	C	18.32	3.598682	0.66332	.	.	ENSG00000143507	ENST00000366899;ENST00000418487	T	0.02472	4.28	5.44	5.44	0.79542	.	0.260060	0.36932	N	0.002339	T	0.03263	0.0095	N	0.19112	0.55	0.80722	D	1	B	0.20261	0.043	B	0.17098	0.017	T	0.58025	-0.7709	10	0.33940	T	0.23	.	19.622	0.95660	0.0:1.0:0.0:0.0	.	302	Q9Y6W6	DUS10_HUMAN	T	302;247	ENSP00000355866:A302T	ENSP00000355866:A302T	A	-	1	0	DUSP10	219946339	1.000000	0.71417	0.813000	0.32504	0.956000	0.61745	4.488000	0.60300	2.702000	0.92279	0.591000	0.81541	GCG		0.582	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207	
CCDC185	164127	broad.mit.edu	37	1	223568473	223568473	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:223568473G>A	ENST00000366875.3	+	1	1759	c.1656G>A	c.(1654-1656)aaG>aaA	p.K552K		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		552								p.K552K(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		AAGCCGAGAAGGAGGAAAAGT	0.522																																					p.K552K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1656A	1						.						101.0	105.0	104.0					1																	223568473		2203	4300	6503	221635096	SO:0001819	synonymous_variant	164127	exon1																														ENST00000366875.3:c.1656G>A	1.37:g.223568473G>A		Somatic		Capture	Illumina HiSeq	Phase_I	221635096	NM_152610	Q8N746|Q8NA93	Silent	SNP	ENST00000366875.3	37	CCDS1537.1																																																																																				0.522	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1		
URB2	9816	broad.mit.edu	37	1	229779333	229779333	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:229779333T>G	ENST00000258243.2	+	5	3824	c.3688T>G	c.(3688-3690)Ttg>Gtg	p.L1230V		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1230						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.L1230V(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						TTTGGGAGCCTTGTTCACCCA	0.453																																					p.L1230V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3688G	1						.						161.0	151.0	154.0					1																	229779333		2203	4300	6503	227845956	SO:0001583	missense	9816	exon5			D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.3688T>G	1.37:g.229779333T>G	ENSP00000258243:p.Leu1230Val	Somatic		Capture	Illumina HiSeq	Phase_I	227845956	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917225	0.33815	.	.	ENSG00000135763	ENST00000258243	T	0.52057	0.68	5.36	-2.83	0.05769	.	0.072600	0.56097	D	0.000037	T	0.29389	0.0732	N	0.20986	0.625	0.18873	N	0.999981	P	0.46064	0.872	B	0.43360	0.417	T	0.39251	-0.9623	9	.	.	.	-15.2919	9.8516	0.41059	0.0:0.5707:0.1207:0.3086	.	1230	Q14146	URB2_HUMAN	V	1230	ENSP00000258243:L1230V	.	L	+	1	2	URB2	227845956	0.002000	0.14202	0.036000	0.18154	0.307000	0.27823	-0.357000	0.07651	-0.399000	0.07668	-0.274000	0.10170	TTG		0.453	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
PGBD5	79605	broad.mit.edu	37	1	230468601	230468601	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:230468601G>A	ENST00000525115.1	-	5	1078	c.1055C>T	c.(1054-1056)cCg>cTg	p.P352L	PGBD5_ENST00000321327.2_Missense_Mutation_p.P451L|PGBD5_ENST00000391860.1_Missense_Mutation_p.P306L|PGBD5_ENST00000530424.1_5'UTR			Q8N414	PGBD5_HUMAN	piggyBac transposable element derived 5	352						integral component of membrane (GO:0016021)		p.P451L(1)		biliary_tract(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(2)|skin(1)	33	Breast(184;0.0397)	Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;0.201)		CTGCTGCACCGGGGAGTAGGC	0.627																																					p.P352L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1055T	1						.						157.0	132.0	141.0					1																	230468601		2203	4300	6503	228535224	SO:0001583	missense	79605	exon5			AK021475		1q42.13	2008-02-05			ENSG00000177614	ENSG00000177614			19405	protein-coding gene	gene with protein product							Standard	NM_001258311		Approved	DKFZp761A0620, FLJ11413	uc031psq.1	Q8N414	OTTHUMG00000037759	ENST00000525115.1:c.1055C>T	1.37:g.230468601G>A	ENSP00000431404:p.Pro352Leu	Somatic		Capture	Illumina HiSeq	Phase_I	228535224	NM_024554	A0PJF3|B9EK58|Q5SR37|Q6PJN2	Missense_Mutation	SNP	ENST00000525115.1	37		.	.	.	.	.	.	.	.	.	.	-	33	5.235456	0.95240	.	.	ENSG00000177614	ENST00000391860;ENST00000321327;ENST00000525115	T;T;T	0.20738	2.08;2.08;2.05	5.62	5.62	0.85841	.	0.048784	0.85682	D	0.000000	T	0.35537	0.0935	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.67231	0.889;0.95	T	0.07888	-1.0749	10	0.59425	D	0.04	-30.9378	19.7826	0.96422	0.0:0.0:1.0:0.0	.	352;42	Q8N414;B4DM72	PGBD5_HUMAN;.	L	306;451;352	ENSP00000375733:P306L;ENSP00000322530:P451L;ENSP00000431404:P352L	ENSP00000322530:P451L	P	-	2	0	PGBD5	228535224	1.000000	0.71417	0.938000	0.37757	0.860000	0.49131	9.542000	0.98086	2.679000	0.91253	0.579000	0.79373	CCG		0.627	PGBD5-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382617.1	NM_024554	
COG2	22796	broad.mit.edu	37	1	230827255	230827255	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:230827255A>G	ENST00000366669.4	+	17	2175	c.2060A>G	c.(2059-2061)gAc>gGc	p.D687G	COG2_ENST00000534989.1_Missense_Mutation_p.D628G|COG2_ENST00000535166.1_Missense_Mutation_p.D571G|COG2_ENST00000366668.3_Missense_Mutation_p.D686G|COG2_ENST00000546013.1_Missense_Mutation_p.D376G	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	687					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)	p.D687G(1)		NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GGCATGAGCGACGACGACAAA	0.542																																					p.D687G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2060G	1						.						83.0	83.0	83.0					1																	230827255		2203	4300	6503	228893878	SO:0001583	missense	22796	exon17			Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.2060A>G	1.37:g.230827255A>G	ENSP00000355629:p.Asp687Gly	Somatic		Capture	Illumina HiSeq	Phase_I	228893878	NM_007357	Q86U99	Missense_Mutation	SNP	ENST00000366669.4	37	CCDS1584.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.624283	0.66901	.	.	ENSG00000135775	ENST00000366669;ENST00000535166;ENST00000366668;ENST00000534989;ENST00000546013	T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55	5.59	5.59	0.84812	COG complex component, COG2, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.78438	0.4283	M	0.91717	3.235	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.83824	0.0248	10	0.87932	D	0	-24.9764	15.4361	0.75149	1.0:0.0:0.0:0.0	.	686;687	Q86U99;Q14746	.;COG2_HUMAN	G	687;571;686;628;376	ENSP00000355629:D687G;ENSP00000445724:D571G;ENSP00000355628:D686G;ENSP00000440349:D628G;ENSP00000442147:D376G	ENSP00000355628:D686G	D	+	2	0	COG2	228893878	1.000000	0.71417	0.732000	0.30844	0.111000	0.19643	9.078000	0.94023	2.140000	0.66376	0.459000	0.35465	GAC		0.542	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
DISC1	27185	broad.mit.edu	37	1	231902894	231902894	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:231902894G>A	ENST00000602281.1	+	5	1330	c.1277G>A	c.(1276-1278)gGa>gAa	p.G426E	DISC1_ENST00000602873.1_Missense_Mutation_p.G76E|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000366633.3_Missense_Mutation_p.G426E|DISC1_ENST00000439617.2_Missense_Mutation_p.G426E|DISC1_ENST00000537876.1_Missense_Mutation_p.G426E|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000539444.1_Missense_Mutation_p.G426E|DISC1_ENST00000366636.4_Missense_Mutation_p.G426E|DISC1_ENST00000535983.1_Missense_Mutation_p.G426E	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	426	Interaction with TRAF3IP1.				canonical Wnt signaling pathway (GO:0060070)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cerebral cortex radially oriented cell migration (GO:0021799)|microtubule cytoskeleton organization (GO:0000226)|mitochondrial calcium ion homeostasis (GO:0051560)|neuron migration (GO:0001764)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neuron projection development (GO:0010975)|regulation of synapse maturation (GO:0090128)|TOR signaling (GO:0031929)	cell junction (GO:0030054)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|postsynaptic membrane (GO:0045211)		p.G426E(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(173;0.0208)|Prostate(94;0.0975)				AGGGCCAGCGGAGATGACACC	0.493																																					p.G426E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1277A	1						.						148.0	136.0	140.0					1																	231902894		2203	4300	6503	229969517	SO:0001583	missense	27185	exon5			AF222980	CCDS31055.1, CCDS31056.1, CCDS53482.1, CCDS53483.1, CCDS53484.1, CCDS59205.1, CCDS59206.1, CCDS59207.1	1q42.1	2008-02-05			ENSG00000162946	ENSG00000162946			2888	protein-coding gene	gene with protein product		605210				10814723	Standard	NM_001164550		Approved		uc010pxh.2	Q9NRI5	OTTHUMG00000037835	ENST00000602281.1:c.1277G>A	1.37:g.231902894G>A	ENSP00000473425:p.Gly426Glu	Somatic		Capture	Illumina HiSeq	Phase_I	229969517	NM_001164539	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	G	5.171	0.217043	0.09810	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.10960	3.21;3.03;3.03;2.84;3.21;2.85;2.85;2.82	3.74	3.74	0.42951	.	1.149810	0.06723	N	0.775319	T	0.07324	0.0185	L	0.36672	1.1	0.09310	N	1	B;B;P;B;P;B;B;B;B;B;B;B;P;B;B;B;B;B	0.39022	0.004;0.008;0.655;0.169;0.655;0.4;0.169;0.047;0.138;0.138;0.4;0.138;0.655;0.066;0.4;0.066;0.4;0.4	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.35039	0.009;0.019;0.194;0.056;0.194;0.121;0.051;0.022;0.055;0.055;0.121;0.055;0.194;0.03;0.121;0.03;0.121;0.121	T	0.11155	-1.0599	10	0.05436	T	0.98	1.0566	6.0192	0.19620	0.1824:0.0:0.8176:0.0	.	458;458;426;426;426;426;426;76;426;426;426;426;426;426;426;426;426;426	C4P096;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	E	426;426;426;458;426;426;426;426;426;426	ENSP00000403888:G426E;ENSP00000355596:G426E;ENSP00000443996:G426E;ENSP00000440909:G426E;ENSP00000355593:G426E;ENSP00000440953:G426E;ENSP00000295051:G426E;ENSP00000441193:G426E	ENSP00000295051:G426E	G	+	2	0	DISC1	229969517	0.138000	0.22547	0.042000	0.18584	0.010000	0.07245	0.897000	0.28390	2.063000	0.61619	0.655000	0.94253	GGA		0.493	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662	
SIPA1L2	57568	broad.mit.edu	37	1	232581487	232581487	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:232581487G>A	ENST00000366630.1	-	10	3499	c.3141C>T	c.(3139-3141)ctC>ctT	p.L1047L	SIPA1L2_ENST00000308942.4_Silent_p.L121L|SIPA1L2_ENST00000262861.4_Silent_p.L1047L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1047					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)	p.L1047L(1)		NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				CCTCGCTGTCGAGTTTATATT	0.577																																					p.L1047L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3141T	1						.						88.0	90.0	89.0					1																	232581487		1877	4110	5987	230648110	SO:0001819	synonymous_variant	57568	exon9			AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.3141C>T	1.37:g.232581487G>A		Somatic		Capture	Illumina HiSeq	Phase_I	230648110	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																				0.577	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
PCNXL2	80003	broad.mit.edu	37	1	233334732	233334732	+	Missense_Mutation	SNP	C	C	T	rs535193160		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:233334732C>T	ENST00000258229.9	-	15	3253	c.3019G>A	c.(3019-3021)Gtc>Atc	p.V1007I	PCNXL2_ENST00000488780.2_Missense_Mutation_p.V140I	NM_014801.3	NP_055616.3	A6NKB5	PCX2_HUMAN	pecanex-like 2 (Drosophila)	1007						integral component of membrane (GO:0016021)		p.V1007I(1)		NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(7)|large_intestine(19)|lung(30)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86		all_cancers(173;0.0347)|Prostate(94;0.137)				GCAGCCAAGACGCTCCGGGCC	0.498													c|||	1	0.000199681	0.0	0.0	5008	,	,		16326	0.0		0.0	False		,,,				2504	0.001				p.V1007I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3019A	1						.						14.0	17.0	16.0					1																	233334732		1975	4156	6131	231401355	SO:0001583	missense	80003	exon15			AK055374	CCDS44335.1	1q42.2	2008-02-05	2001-11-28		ENSG00000135749	ENSG00000135749			8736	protein-coding gene	gene with protein product			"""pecanex (Drosophila)-like 2"""			12477932	Standard	NM_014801		Approved	KIAA0435, FLJ11383	uc001hvl.2	A6NKB5	OTTHUMG00000037824	ENST00000258229.9:c.3019G>A	1.37:g.233334732C>T	ENSP00000258229:p.Val1007Ile	Somatic		Capture	Illumina HiSeq	Phase_I	231401355	NM_014801	O43162|Q5T9Z8|Q5TDF1|Q8TEP4|Q96HP9|Q9HAL8	Missense_Mutation	SNP	ENST00000258229.9	37	CCDS44335.1	.	.	.	.	.	.	.	.	.	.	c	0.260	-1.000340	0.02128	.	.	ENSG00000135749	ENST00000258229;ENST00000488780;ENST00000518351	T;T	0.39592	3.17;1.07	5.33	-7.75	0.01236	.	.	.	.	.	T	0.14313	0.0346	N	0.13043	0.29	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31833	-0.9929	9	0.02654	T	1	.	2.3231	0.04216	0.2915:0.2503:0.0671:0.3911	.	1007	A6NKB5	PCX2_HUMAN	I	1007;140;176	ENSP00000258229:V1007I;ENSP00000429231:V176I	ENSP00000258229:V1007I	V	-	1	0	PCNXL2	231401355	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.087000	0.14958	-1.738000	0.01348	-4.854000	0.00002	GTC		0.498	PCNXL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092480.3	NM_014801	
NID1	4811	broad.mit.edu	37	1	236157046	236157046	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:236157046G>A	ENST00000264187.6	-	13	2736	c.2654C>T	c.(2653-2655)gCg>gTg	p.A885V	NID1_ENST00000366595.3_Missense_Mutation_p.A752V	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	885	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				basement membrane organization (GO:0071711)|cell-matrix adhesion (GO:0007160)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|positive regulation of cell-substrate adhesion (GO:0010811)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|cell periphery (GO:0071944)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|laminin binding (GO:0043236)|proteoglycan binding (GO:0043394)	p.A885V(1)		breast(4)|endometrium(9)|kidney(1)|large_intestine(23)|lung(20)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(1)	66	Ovarian(103;0.0544)|Breast(184;0.23)	all_cancers(173;0.00491)|Prostate(94;0.184)|Acute lymphoblastic leukemia(190;0.229)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Urokinase(DB00013)	CTGGGTGGGCGCGTAGTGCCC	0.706																																					p.A885V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2654T	1						.						29.0	30.0	30.0					1																	236157046		2202	4299	6501	234223669	SO:0001583	missense	4811	exon13			BC045606	CCDS1608.1	1q43	2011-05-08	2005-06-02	2005-06-02	ENSG00000116962	ENSG00000116962			7821	protein-coding gene	gene with protein product		131390	"""nidogen (enactin)"""	NID		2471408, 7557988	Standard	NM_002508		Approved	entactin	uc001hxo.3	P14543	OTTHUMG00000040071	ENST00000264187.6:c.2654C>T	1.37:g.236157046G>A	ENSP00000264187:p.Ala885Val	Somatic		Capture	Illumina HiSeq	Phase_I	234223669	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Missense_Mutation	SNP	ENST00000264187.6	37	CCDS1608.1	.	.	.	.	.	.	.	.	.	.	G	11.54	1.670522	0.29693	.	.	ENSG00000116962	ENST00000264187;ENST00000366595	T;T	0.64260	-0.09;-0.09	5.69	-8.57	0.00900	Thyroglobulin type-1 (6);	1.133540	0.06249	N	0.691694	T	0.40119	0.1104	N	0.05383	-0.06	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.39921	-0.9590	10	0.17832	T	0.49	.	19.8499	0.96734	0.8747:0.0:0.1253:0.0	.	752;885	P14543-2;P14543	.;NID1_HUMAN	V	885;752	ENSP00000264187:A885V;ENSP00000355554:A752V	ENSP00000264187:A885V	A	-	2	0	NID1	234223669	0.000000	0.05858	0.000000	0.03702	0.572000	0.35998	-1.930000	0.01557	-1.664000	0.01479	-0.378000	0.06908	GCG		0.706	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508	
FMN2	56776	broad.mit.edu	37	1	240370368	240370368	+	Silent	SNP	C	C	T	rs140392779		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:240370368C>T	ENST00000319653.9	+	5	2486	c.2256C>T	c.(2254-2256)ggC>ggT	p.G752G		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	752					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.G895G(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			CGGAAGAGGGCGGGGTGCTGA	0.547																																					p.G752G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2256T	1						.	T		0,4406		0,0,2203	44.0	42.0	43.0		2256	-7.8	0.0	1	dbSNP_134	43	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FMN2	NM_020066.4		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		752/1723	240370368	3,13003	2203	4300	6503	238436991	SO:0001819	synonymous_variant	56776	exon5			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.2256C>T	1.37:g.240370368C>T		Somatic		Capture	Illumina HiSeq	Phase_I	238436991	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.547	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
CHML	1122	broad.mit.edu	37	1	241798095	241798095	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:241798095T>C	ENST00000366553.1	-	1	1137	c.974A>G	c.(973-975)tAc>tGc	p.Y325C	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	325					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.Y325C(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			AGTTTTTAAGTATTCTGAAAA	0.338																																					p.Y325C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A974G	1						.						115.0	118.0	117.0					1																	241798095		2203	4299	6502	239864718	SO:0001583	missense	1122	exon1			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.974A>G	1.37:g.241798095T>C	ENSP00000355511:p.Tyr325Cys	Somatic		Capture	Illumina HiSeq	Phase_I	239864718	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	T	14.34	2.506649	0.44558	.	.	ENSG00000203668	ENST00000366553	T	0.60548	0.18	4.96	4.96	0.65561	.	0.114862	0.64402	U	0.000018	T	0.70996	0.3288	.	.	.	0.42422	D	0.992646	D	0.76494	0.999	D	0.66716	0.946	T	0.74487	-0.3649	9	0.72032	D	0.01	-9.6176	8.2979	0.31997	0.176:0.0:0.0:0.8239	.	325	P26374	RAE2_HUMAN	C	325	ENSP00000355511:Y325C	ENSP00000355511:Y325C	Y	-	2	0	CHML	239864718	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	2.022000	0.41030	2.222000	0.72286	0.533000	0.62120	TAC		0.338	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
CHML	1122	broad.mit.edu	37	1	241798773	241798773	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:241798773G>C	ENST00000366553.1	-	1	459	c.296C>G	c.(295-297)aCa>aGa	p.T99R	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	99					intracellular protein transport (GO:0006886)|protein geranylgeranylation (GO:0018344)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	GTPase activator activity (GO:0005096)|Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)	p.T99R(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(4)|skin(3)|stomach(1)	26	Ovarian(103;0.103)|all_lung(81;0.23)	all_cancers(173;0.0231)	OV - Ovarian serous cystadenocarcinoma(106;0.0125)			AAAAGCTTCTGTGTGTTGAAT	0.438																																					p.T99R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C296G	1						.						207.0	208.0	208.0					1																	241798773		2203	4299	6502	239865396	SO:0001583	missense	1122	exon1			X64728	CCDS31073.1	1q43	2013-09-19			ENSG00000203668	ENSG00000203668			1941	protein-coding gene	gene with protein product		118825				7981670	Standard	NM_001821		Approved	REP-2	uc001hzd.3	P26374	OTTHUMG00000039690	ENST00000366553.1:c.296C>G	1.37:g.241798773G>C	ENSP00000355511:p.Thr99Arg	Somatic		Capture	Illumina HiSeq	Phase_I	239865396	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	G	0.486	-0.877457	0.02550	.	.	ENSG00000203668	ENST00000366553	T	0.58652	0.32	4.77	-2.35	0.06684	.	1.294060	0.05204	U	0.505455	T	0.40423	0.1116	.	.	.	0.09310	N	1	B	0.28208	0.203	B	0.28849	0.095	T	0.24119	-1.0169	9	0.17832	T	0.49	3.2416	10.0234	0.42057	0.7486:0.0:0.2514:0.0	.	99	P26374	RAE2_HUMAN	R	99	ENSP00000355511:T99R	ENSP00000355511:T99R	T	-	2	0	CHML	239865396	0.000000	0.05858	0.003000	0.11579	0.226000	0.24999	0.043000	0.13971	-0.482000	0.06782	-0.781000	0.03364	ACA		0.438	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821	
CEP170	9859	broad.mit.edu	37	1	243328306	243328306	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:243328306C>T	ENST00000366542.1	-	13	3007	c.2956G>A	c.(2956-2958)Gaa>Aaa	p.E986K	CEP170_ENST00000366544.1_Missense_Mutation_p.E888K|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000490813.1_5'Flank|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000366543.1_Missense_Mutation_p.E888K	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	986	Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)		p.E986K(1)		NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TCCATTTTTTCCCTAGCACCT	0.413																																					p.E888K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2662A	1						.						38.0	36.0	37.0					1																	243328306		1827	4059	5886	241394929	SO:0001583	missense	9859	exon12			AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2956G>A	1.37:g.243328306C>T	ENSP00000355500:p.Glu986Lys	Somatic		Capture	Illumina HiSeq	Phase_I	241394929	NM_001042405	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	C	17.32	3.359966	0.61403	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543	T;T;T	0.60040	0.45;0.43;0.22	4.89	4.89	0.63831	.	0.149328	0.64402	D	0.000017	T	0.58836	0.2150	M	0.65498	2.005	0.80722	D	1	B;B;B;B	0.32829	0.386;0.184;0.184;0.229	B;B;B;B	0.34489	0.184;0.066;0.066;0.119	T	0.61262	-0.7098	10	0.41790	T	0.15	-7.7476	17.0433	0.86495	0.0:1.0:0.0:0.0	.	949;888;888;986	B1ARM6;Q5SW79-3;Q5SW79-2;Q5SW79	.;.;.;CE170_HUMAN	K	986;888;888	ENSP00000355500:E986K;ENSP00000355502:E888K;ENSP00000355501:E888K	ENSP00000355500:E986K	E	-	1	0	CEP170	241394929	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	7.243000	0.78219	2.248000	0.74166	0.555000	0.69702	GAA		0.413	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
AHCTF1	25909	broad.mit.edu	37	1	247014594	247014594	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:247014594C>T	ENST00000391829.2	-	33	4837	c.4714G>A	c.(4714-4716)Gac>Aac	p.D1572N	AHCTF1_ENST00000366508.1_Missense_Mutation_p.D1607N|AHCTF1_ENST00000326225.3_Missense_Mutation_p.D1581N|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1572	Disordered. {ECO:0000250}.|Mediates transcriptional activity. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1572N(1)		NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TCAGCAGTGTCTTTGTTATCA	0.378																																					p.D1581N	Colon(145;197 1800 4745 15099 26333)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4741A	1						.						117.0	110.0	113.0					1																	247014594		2203	4300	6503	245081217	SO:0001583	missense	25909	exon33				CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.4714G>A	1.37:g.247014594C>T	ENSP00000375705:p.Asp1572Asn	Somatic		Capture	Illumina HiSeq	Phase_I	245081217	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		.	.	.	.	.	.	.	.	.	.	C	13.62	2.291853	0.40594	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.44083	0.93;0.93;0.94	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.61763	0.2373	M	0.68952	2.095	0.35193	D	0.773544	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.97110	1.0;0.984;0.965	T	0.68682	-0.5344	10	0.46703	T	0.11	-17.7768	13.2493	0.60041	0.0:0.9279:0.0:0.0721	.	433;1607;1572	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	N	1607;1581;1572	ENSP00000355464:D1607N;ENSP00000355465:D1581N;ENSP00000375705:D1572N	ENSP00000355465:D1581N	D	-	1	0	AHCTF1	245081217	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	2.786000	0.47790	2.941000	0.99782	0.655000	0.94253	GAC		0.378	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
SAMD11	148398	broad.mit.edu	37	1	874447	874447	+	Missense_Mutation	SNP	G	G	A	rs374848064		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:874447G>A	ENST00000342066.3	+	6	541	c.458G>A	c.(457-459)cGc>cAc	p.R153H		NM_152486.2	NP_689699	Q96NU1	SAM11_HUMAN	sterile alpha motif domain containing 11	153					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)		p.R153H(1)		breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.74e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000472)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		AGGCTGGGCCGCTCCCCCCGT	0.622																																					p.R153H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G458A	1						.	G	HIS/ARG	0,4404		0,0,2202	38.0	34.0	36.0		458	0.8	1.0	1		36	2,8596		0,2,4297	no	missense	SAMD11	NM_152486.2	29	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	benign	153/682	874447	2,13000	2202	4299	6501	864310	SO:0001583	missense	148398	exon6			BC024295	CCDS2.2	1p36.33	2013-01-10			ENSG00000187634	ENSG00000187634		"""Sterile alpha motif (SAM) domain containing"""	28706	protein-coding gene	gene with protein product						12477932	Standard	NM_152486		Approved	MGC45873	uc001abw.1	Q96NU1	OTTHUMG00000040719	ENST00000342066.3:c.458G>A	1.37:g.874447G>A	ENSP00000342313:p.Arg153His	Somatic		Capture	Illumina HiSeq	Phase_I	864310	NM_152486	A2AA76|I7FV78|I7FV81|I7G0Z6|Q5SV96|Q5SV99|Q5SVA0|Q8N195|Q8TB59	Missense_Mutation	SNP	ENST00000342066.3	37	CCDS2.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	2.147|2.147	-0.395400|-0.395400	0.04899|0.04899	0.0|0.0	2.33E-4|2.33E-4	ENSG00000187634|ENSG00000187634	ENST00000341065|ENST00000420190;ENST00000342066	.|.	.|.	.|.	4.1|4.1	0.8|0.8	0.18672|0.18672	.|.	.|0.242197	.|0.34802	.|N	.|0.003671	T|T	0.21550|0.21550	0.0519|0.0519	N|N	0.12182|0.12182	0.205|0.205	0.23823|0.23823	N|N	0.996748|0.996748	.|B;B	.|0.10296	.|0.001;0.003	.|B;B	.|0.04013	.|0.001;0.001	T|T	0.17198|0.17198	-1.0377|-1.0377	5|9	.|0.44086	.|T	.|0.13	-2.0739|-2.0739	8.3975|8.3975	0.32566|0.32566	0.0907:0.3064:0.6029:0.0|0.0907:0.3064:0.6029:0.0	.|.	.|153;153	.|Q96NU1-1;Q96NU1	.|.;SAM11_HUMAN	T|H	77|153	.|.	.|ENSP00000342313:R153H	A|R	+|+	1|2	0|0	SAMD11|SAMD11	864310|864310	0.012000|0.012000	0.17670|0.17670	0.998000|0.998000	0.56505|0.56505	0.657000|0.657000	0.38888|0.38888	0.763000|0.763000	0.26517|0.26517	0.441000|0.441000	0.26529|0.26529	-0.424000|-0.424000	0.05967|0.05967	GCT|CGC		0.622	SAMD11-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276866.2	NM_152486	
WRAP73	49856	broad.mit.edu	37	1	3563259	3563259	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:3563259G>A	ENST00000270708.7	-	3	383	c.310C>T	c.(310-312)Cgc>Tgc	p.R104C	WRAP73_ENST00000378322.3_Missense_Mutation_p.R104C	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	104						centrosome (GO:0005813)|cytoplasm (GO:0005737)		p.R104C(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						AGAATGTGGCGCCCGTCCGGG	0.577																																					p.R104C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C310T	1						.						96.0	108.0	104.0					1																	3563259		2203	4300	6503	3553119	SO:0001583	missense	49856	exon3			AB034912, EF494669	CCDS48.1	1p36.3	2013-05-21	2011-04-13	2011-04-13	ENSG00000116213	ENSG00000116213		"""WD repeat domain containing"""	12759	protein-coding gene	gene with protein product		606040	"""WD repeat domain 8"""	WDR8			Standard	NM_017818		Approved		uc001ako.3	Q9P2S5	OTTHUMG00000000612	ENST00000270708.7:c.310C>T	1.37:g.3563259G>A	ENSP00000270708:p.Arg104Cys	Somatic		Capture	Illumina HiSeq	Phase_I	3553119	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	37	CCDS48.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907416	0.92107	.	.	ENSG00000116213	ENST00000270708;ENST00000378322;ENST00000424367;ENST00000419924	T;T;T	0.06768	3.26;3.27;3.27	5.18	5.18	0.71444	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.28830	0.0715	M	0.69248	2.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;1.0;1.0	T	0.00837	-1.1546	10	0.56958	D	0.05	-47.3659	17.6804	0.88241	0.0:0.0:1.0:0.0	.	104;104;104	B4DYE9;Q9P2S5;Q5T0D5	.;WRP73_HUMAN;.	C	104	ENSP00000270708:R104C;ENSP00000367573:R104C;ENSP00000416192:R104C	ENSP00000270708:R104C	R	-	1	0	WRAP73	3553119	1.000000	0.71417	0.986000	0.45419	0.944000	0.59088	7.856000	0.86956	2.401000	0.81631	0.655000	0.94253	CGC		0.577	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1		
CHD5	26038	broad.mit.edu	37	1	6202223	6202223	+	Missense_Mutation	SNP	C	C	T	rs567329094		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:6202223C>T	ENST00000262450.3	-	15	2500	c.2401G>A	c.(2401-2403)Gcc>Acc	p.A801T	CHD5_ENST00000378021.1_5'UTR	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.A801T(2)		breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		CTCCGAATGGCGTTGTCCTCA	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		18654	0.0		0.0	False		,,,				2504	0.001				p.A801T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2401A	1						.						169.0	158.0	162.0					1																	6202223		2203	4300	6503	6124810	SO:0001583	missense	26038	exon15			AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.2401G>A	1.37:g.6202223C>T	ENSP00000262450:p.Ala801Thr	Somatic		Capture	Illumina HiSeq	Phase_I	6124810	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.021467	0.93462	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	D	0.91407	-2.84	4.07	4.07	0.47477	DEAD-like helicase (2);SNF2-related (1);	0.073472	0.53938	D	0.000051	D	0.91744	0.7389	L	0.28344	0.845	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.92805	0.6259	10	0.54805	T	0.06	-22.6321	16.6218	0.84932	0.0:1.0:0.0:0.0	.	801	Q8TDI0	CHD5_HUMAN	T	801;317;209;209	ENSP00000262450:A801T	ENSP00000262450:A801T	A	-	1	0	CHD5	6124810	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	7.693000	0.84214	1.977000	0.57605	0.561000	0.74099	GCC		0.577	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
GPR153	387509	broad.mit.edu	37	1	6310603	6310603	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:6310603G>A	ENST00000377893.2	-	5	1320	c.1061C>T	c.(1060-1062)gCc>gTc	p.A354V		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	354						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.A354V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CCTATCTAGGGCCACAAAATC	0.617																																					p.A354V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1061T	1						.						40.0	34.0	36.0					1																	6310603		2197	4297	6494	6233190	SO:0001583	missense	387509	exon5			AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.1061C>T	1.37:g.6310603G>A	ENSP00000367125:p.Ala354Val	Somatic		Capture	Illumina HiSeq	Phase_I	6233190	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.266669	0.59540	.	.	ENSG00000158292	ENST00000377893	T	0.28895	1.59	5.17	2.23	0.28157	.	0.310621	0.34223	N	0.004142	T	0.21145	0.0509	L	0.36672	1.1	0.36035	D	0.839681	B	0.09022	0.002	B	0.08055	0.003	T	0.09079	-1.0691	10	0.46703	T	0.11	-15.7151	6.8249	0.23876	0.166:0.1451:0.6889:0.0	.	354	Q6NV75	GP153_HUMAN	V	354	ENSP00000367125:A354V	ENSP00000367125:A354V	A	-	2	0	GPR153	6233190	1.000000	0.71417	0.998000	0.56505	0.884000	0.51177	3.128000	0.50492	0.189000	0.20188	0.455000	0.32223	GCC		0.617	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
CAMTA1	23261	broad.mit.edu	37	1	7700472	7700472	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:7700472G>A	ENST00000303635.7	+	7	730	c.523G>A	c.(523-525)Gtc>Atc	p.V175I	CAMTA1_ENST00000439411.2_Missense_Mutation_p.V175I	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	175					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.V175I(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		CCCCGACATCGTCCTGGTGCA	0.652			T	WWTR1	epitheliod hemangioendothelioma																																p.V175I			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G523A	1						.						103.0	88.0	93.0					1																	7700472		2203	4300	6503	7623059	SO:0001583	missense	23261	exon7			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.523G>A	1.37:g.7700472G>A	ENSP00000306522:p.Val175Ile	Somatic		Capture	Illumina HiSeq	Phase_I	7623059	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	G	35	5.451319	0.96205	.	.	ENSG00000171735	ENST00000303635;ENST00000439411	T;T	0.45276	0.9;0.91	5.5	5.5	0.81552	CG-1 (2);	0.000000	0.64402	D	0.000001	T	0.71846	0.3388	M	0.88105	2.93	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.77512	-0.2560	10	0.87932	D	0	-24.7416	19.3963	0.94608	0.0:0.0:1.0:0.0	.	175	Q9Y6Y1	CMTA1_HUMAN	I	175	ENSP00000306522:V175I;ENSP00000402561:V175I	ENSP00000306522:V175I	V	+	1	0	CAMTA1	7623059	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.764000	0.98949	2.575000	0.86900	0.563000	0.77884	GTC		0.652	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
CAMTA1	23261	broad.mit.edu	37	1	7797386	7797386	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:7797386G>A	ENST00000303635.7	+	15	3621	c.3414G>A	c.(3412-3414)tcG>tcA	p.S1138S	CAMTA1_ENST00000439411.2_Silent_p.S1138S	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1138					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S1138S(1)		breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		GGGCCATCTCGATTCCCGACT	0.572			T	WWTR1	epitheliod hemangioendothelioma																																p.S1138S			Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3414A	1						.						98.0	99.0	99.0					1																	7797386		2203	4300	6503	7719973	SO:0001819	synonymous_variant	23261	exon15			AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3414G>A	1.37:g.7797386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	7719973	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Silent	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	G	1.196	-0.633820	0.03584	.	.	ENSG00000171735	ENST00000495233	.	.	.	5.91	-11.8	0.00035	.	.	.	.	.	T	0.43389	0.1245	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55068	-0.8198	4	.	.	.	-16.0717	7.6387	0.28282	0.0639:0.4407:0.3258:0.1696	.	.	.	.	Q	95	.	.	R	+	2	0	CAMTA1	7719973	0.006000	0.16342	0.092000	0.20876	0.367000	0.29736	-1.065000	0.03458	-2.365000	0.00606	-1.824000	0.00597	CGA		0.572	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
ERRFI1	54206	broad.mit.edu	37	1	8073928	8073928	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:8073928C>T	ENST00000377482.5	-	4	954	c.731G>A	c.(730-732)cGa>cAa	p.R244Q	ERRFI1_ENST00000469499.1_3'UTR|ERRFI1_ENST00000467067.1_3'UTR|ERRFI1_ENST00000474874.1_Intron	NM_018948.3	NP_061821.1	Q9UJM3	ERRFI_HUMAN	ERBB receptor feedback inhibitor 1	244					lung alveolus development (GO:0048286)|lung epithelium development (GO:0060428)|lung vasculature development (GO:0060426)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of protein autophosphorylation (GO:0031953)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of keratinocyte differentiation (GO:0045616)|response to stress (GO:0006950)|skin morphogenesis (GO:0043589)	cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|Rho GTPase activator activity (GO:0005100)	p.R244Q(1)		breast(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(3)|ovary(1)|prostate(1)|skin(2)	16	Ovarian(185;0.06)|all_lung(157;0.151)	all_epithelial(116;1.76e-16)|all_lung(118;3.66e-05)|Lung NSC(185;0.000163)|Renal(390;0.000469)|Colorectal(325;0.0033)|Breast(348;0.0044)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.11)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.33e-70)|GBM - Glioblastoma multiforme(8;8.05e-37)|Colorectal(212;6.23e-08)|COAD - Colon adenocarcinoma(227;6.9e-06)|Kidney(185;4.89e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.000985)|READ - Rectum adenocarcinoma(331;0.0642)		TCTTAATCTTCGGTGGGTCTG	0.478																																					p.R244Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G731A	1						.						56.0	57.0	57.0					1																	8073928		2203	4300	6503	7996515	SO:0001583	missense	54206	exon4			BC025337	CCDS94.1	1p36.23	2008-02-05			ENSG00000116285	ENSG00000116285			18185	protein-coding gene	gene with protein product		608069				10749885, 2780291, 12226756, 11003669	Standard	NM_018948		Approved	MIG-6, GENE-33, RALT	uc001aoz.3	Q9UJM3	OTTHUMG00000001221	ENST00000377482.5:c.731G>A	1.37:g.8073928C>T	ENSP00000366702:p.Arg244Gln	Somatic		Capture	Illumina HiSeq	Phase_I	7996515	NM_018948	B2RDX9|Q9NTG9|Q9UD05	Missense_Mutation	SNP	ENST00000377482.5	37	CCDS94.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.009878	0.75046	.	.	ENSG00000116285	ENST00000377482	T	0.18960	2.18	5.52	4.61	0.57282	.	0.054901	0.64402	N	0.000001	T	0.20414	0.0491	M	0.76002	2.32	0.80722	D	1	P	0.43519	0.809	B	0.27608	0.081	T	0.08310	-1.0728	10	0.34782	T	0.22	-20.0239	13.541	0.61674	0.0:0.9251:0.0:0.0749	.	244	Q9UJM3	ERRFI_HUMAN	Q	244	ENSP00000366702:R244Q	ENSP00000366702:R244Q	R	-	2	0	ERRFI1	7996515	1.000000	0.71417	0.860000	0.33809	0.995000	0.86356	7.137000	0.77295	1.321000	0.45227	0.561000	0.74099	CGA		0.478	ERRFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003617.1	NM_018948	
H6PD	9563	broad.mit.edu	37	1	9323915	9323915	+	Missense_Mutation	SNP	C	C	T	rs371234309		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:9323915C>T	ENST00000377403.2	+	5	1665	c.1363C>T	c.(1363-1365)Cgg>Tgg	p.R455W	H6PD_ENST00000602477.1_Missense_Mutation_p.R466W	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	455	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)	p.R455W(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TGTGCGGGAGCGGGACGCCCA	0.597																																					p.R455W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1363T	1						.						66.0	76.0	73.0					1																	9323915		2203	4300	6503	9246502	SO:0001583	missense	9563	exon5			AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1363C>T	1.37:g.9323915C>T	ENSP00000366620:p.Arg455Trp	Somatic		Capture	Illumina HiSeq	Phase_I	9246502	NM_004285	Q4TT33|Q66I35|Q68DT3	Missense_Mutation	SNP	ENST00000377403.2	37	CCDS101.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.208574	0.39003	.	.	ENSG00000049239	ENST00000377403	D	0.98362	-4.89	5.53	3.5	0.40072	.	0.417173	0.26731	N	0.022784	D	0.96318	0.8799	L	0.53249	1.67	0.36148	D	0.847271	D	0.69078	0.997	P	0.46208	0.507	D	0.95836	0.8862	10	0.54805	T	0.06	-5.7783	6.2376	0.20772	0.3537:0.5496:0.0:0.0967	.	455	O95479	G6PE_HUMAN	W	455	ENSP00000366620:R455W	ENSP00000366620:R455W	R	+	1	2	H6PD	9246502	0.996000	0.38824	0.844000	0.33320	0.173000	0.22820	2.717000	0.47227	1.332000	0.45431	0.561000	0.74099	CGG		0.597	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
PRDM2	7799	broad.mit.edu	37	1	14108749	14108749	+	Frame_Shift_Del	DEL	A	A	-	rs141416335|rs57173229		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:14108749delA	ENST00000235372.7	+	8	5315	c.4459delA	c.(4459-4461)aaafs	p.K1489fs	PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000311066.5_Frame_Shift_Del_p.K1489fs|PRDM2_ENST00000503842.1_Intron|PRDM2_ENST00000413440.1_Frame_Shift_Del_p.K1288fs|PRDM2_ENST00000343137.4_Frame_Shift_Del_p.K1288fs	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	1489					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.V1490fs*74(1)		endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(16)|lung(20)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	55	Ovarian(185;0.249)	all_lung(284;2.56e-05)|Lung NSC(185;4.94e-05)|Renal(390;0.000147)|Breast(348;0.000162)|Colorectal(325;0.00058)|Ovarian(437;0.00965)|Hepatocellular(190;0.0245)|Myeloproliferative disorder(586;0.0255)	GBM - Glioblastoma multiforme(2;0.00182)	UCEC - Uterine corpus endometrioid carcinoma (279;0.00224)|Colorectal(212;3.23e-08)|BRCA - Breast invasive adenocarcinoma(304;2.16e-05)|COAD - Colon adenocarcinoma(227;2.53e-05)|Kidney(185;0.000762)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00446)|READ - Rectum adenocarcinoma(331;0.0276)|Lung(427;0.145)		TTCTCCTCCCAAAAAAAAAGT	0.463																																					p.K1286fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3856delA	1						.						141.0	165.0	157.0					1																	14108749		2203	4300	6503	13981336	SO:0001589	frameshift_variant	7799	exon3			U17838	CCDS150.1, CCDS151.1, CCDS30603.1, CCDS44061.1	1p36	2011-07-01			ENSG00000116731	ENSG00000116731		"""Chromatin-modifying enzymes / K-methyltransferases"""	9347	protein-coding gene	gene with protein product	"""retinoblastoma protein-binding zinc finger protein"", ""retinoblastoma protein-interacting zinc finger protein"", ""MTE-binding protein"", ""zinc-finger DNA-binding protein"", ""GATA-3 binding protein G3B"""	601196				7538672	Standard	NM_012231		Approved	RIZ, RIZ1, RIZ2, KMT8, MTB-ZF, HUMHOXY1	uc001avi.3	Q13029	OTTHUMG00000007917	ENST00000235372.7:c.4459delA	1.37:g.14108749delA	ENSP00000235372:p.Lys1489fs	Germline		Capture	Illumina HiSeq	Phase_I	13981336	NM_001007257	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Frame_Shift_Del	DEL	ENST00000235372.7	37	CCDS150.1																																																																																				0.463	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231	
RUNX3	864	broad.mit.edu	37	1	25228901	25228901	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:25228901G>A	ENST00000308873.6	-	5	968	c.960C>T	c.(958-960)agC>agT	p.S320S	RUNX3_ENST00000399916.1_Silent_p.S334S|RUNX3_ENST00000496967.1_5'Flank|RUNX3_ENST00000338888.3_Silent_p.S334S|RUNX3_ENST00000540420.1_Silent_p.S227S	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	320	Pro/Ser/Thr-rich.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S320S(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		GGAAGGGCCCGCTCTGGTTCT	0.692																																					p.S334S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1002T	1						.						22.0	30.0	27.0					1																	25228901		2201	4299	6500	25101488	SO:0001819	synonymous_variant	864	exon6			BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.960C>T	1.37:g.25228901G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25101488	NM_001031680	B1AJV5|Q12969|Q13760	Silent	SNP	ENST00000308873.6	37	CCDS257.1																																																																																				0.692	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350	
RUNX3	864	broad.mit.edu	37	1	25233840	25233840	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:25233840G>A	ENST00000308873.6	-	4	621	c.613C>T	c.(613-615)Cgc>Tgc	p.R205C	RUNX3_ENST00000399916.1_Missense_Mutation_p.R219C|RUNX3_ENST00000496967.1_5'UTR|RUNX3_ENST00000338888.3_Missense_Mutation_p.R219C|RUNX3_ENST00000540420.1_Missense_Mutation_p.R112C	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	205	Pro/Ser/Thr-rich.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R205C(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		ACCCGCATGCGCAGCCGTTCC	0.657																																					p.R219C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C655T	1						.						68.0	60.0	62.0					1																	25233840		2203	4300	6503	25106427	SO:0001583	missense	864	exon5			BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.613C>T	1.37:g.25233840G>A	ENSP00000308051:p.Arg205Cys	Somatic		Capture	Illumina HiSeq	Phase_I	25106427	NM_001031680	B1AJV5|Q12969|Q13760	Missense_Mutation	SNP	ENST00000308873.6	37	CCDS257.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.588602	0.66105	.	.	ENSG00000020633	ENST00000399916;ENST00000308873;ENST00000338888;ENST00000540420	D;D;D;D	0.97378	-4.36;-4.35;-4.36;-3.98	4.58	4.58	0.56647	.	0.173987	0.40385	N	0.001104	D	0.96377	0.8818	L	0.54323	1.7	0.47994	D	0.999561	D;D	0.69078	0.997;0.997	P;P	0.50754	0.649;0.649	D	0.96399	0.9295	10	0.72032	D	0.01	-30.2288	13.3915	0.60827	0.0:0.1577:0.8423:0.0	.	219;205	B1AJV5;Q13761	.;RUNX3_HUMAN	C	219;205;219;112	ENSP00000382800:R219C;ENSP00000308051:R205C;ENSP00000343477:R219C;ENSP00000444872:R112C	ENSP00000308051:R205C	R	-	1	0	RUNX3	25106427	1.000000	0.71417	0.994000	0.49952	0.830000	0.47004	3.651000	0.54431	2.396000	0.81511	0.555000	0.69702	CGC		0.657	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350	
RUNX3	864	broad.mit.edu	37	1	25254126	25254126	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:25254126G>A	ENST00000308873.6	-	2	386	c.378C>T	c.(376-378)gcC>gcT	p.A126A	RUNX3_ENST00000399916.1_Silent_p.A140A|RUNX3_ENST00000496967.1_5'UTR|RUNX3_ENST00000338888.3_Silent_p.A140A|RUNX3_ENST00000540420.1_Silent_p.A33A	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	126	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				axon guidance (GO:0007411)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|hair follicle morphogenesis (GO:0031069)|interferon-gamma production (GO:0032609)|negative regulation of cell cycle (GO:0045786)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peripheral nervous system neuron development (GO:0048935)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A126A(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(3)	18		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.000946)|all_lung(284;0.00131)|Ovarian(437;0.00764)|Breast(348;0.0148)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;2.85e-26)|Colorectal(126;4.35e-08)|COAD - Colon adenocarcinoma(152;1.92e-06)|GBM - Glioblastoma multiforme(114;0.000102)|STAD - Stomach adenocarcinoma(196;0.000766)|KIRC - Kidney renal clear cell carcinoma(1967;0.00148)|BRCA - Breast invasive adenocarcinoma(304;0.00173)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.136)		TCTTCATGACGGCCGAGGCAT	0.602																																					p.A140A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C420T	1						.						137.0	120.0	126.0					1																	25254126		2203	4300	6503	25126713	SO:0001819	synonymous_variant	864	exon3			BC013362	CCDS257.1, CCDS30633.1	1p36	2008-02-05			ENSG00000020633	ENSG00000020633			10473	protein-coding gene	gene with protein product		600210		CBFA3		7835892	Standard	NM_001031680		Approved	AML2, PEBP2A3	uc001bjq.3	Q13761	OTTHUMG00000003316	ENST00000308873.6:c.378C>T	1.37:g.25254126G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25126713	NM_001031680	B1AJV5|Q12969|Q13760	Silent	SNP	ENST00000308873.6	37	CCDS257.1																																																																																				0.602	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350	
RHCE	6006	broad.mit.edu	37	1	25718568	25718568	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:25718568G>A	ENST00000294413.7	-	4	609	c.551C>T	c.(550-552)gCc>gTc	p.A184V	RHCE_ENST00000374352.2_Missense_Mutation_p.A168V|RHCE_ENST00000455194.1_Intron|RHCE_ENST00000349438.4_Missense_Mutation_p.A184V|RHCE_ENST00000413854.1_Missense_Mutation_p.A184V|RHCE_ENST00000243186.6_Missense_Mutation_p.A184V|RHCE_ENST00000340849.4_Intron|RHCE_ENST00000346452.4_Intron|RHCE_ENST00000425135.1_Missense_Mutation_p.A184V|RHCE_ENST00000349320.3_Missense_Mutation_p.A168V	NM_020485.4	NP_065231	P18577	RHCE_HUMAN	Rh blood group, CcEe antigens	184						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)	p.A184V(1)		endometrium(8)|large_intestine(6)|lung(3)	17		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0426)|OV - Ovarian serous cystadenocarcinoma(117;2.12e-27)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|STAD - Stomach adenocarcinoma(196;0.00035)|KIRC - Kidney renal clear cell carcinoma(1967;0.000769)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|GBM - Glioblastoma multiforme(114;0.00458)|READ - Rectum adenocarcinoma(331;0.0649)		CAGGCACCAGGCCACAGTCAG	0.532																																					p.A184V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C551T	1						.						260.0	208.0	225.0					1																	25718568		2203	4300	6503	25591155	SO:0001583	missense	6006	exon4			BC075081	CCDS30634.1, CCDS30635.1, CCDS30636.1, CCDS30637.1	1p36.11	2014-09-17	2006-02-23		ENSG00000188672	ENSG00000188672		"""CD molecules"", ""Blood group antigens"""	10008	protein-coding gene	gene with protein product		111700	"""Rhesus blood group, CcEe antigens"""	RH		8220426	Standard	NM_138618		Approved	CD240CE	uc001bkf.3	P18577	OTTHUMG00000007650	ENST00000294413.7:c.551C>T	1.37:g.25718568G>A	ENSP00000294413:p.Ala184Val	Somatic		Capture	Illumina HiSeq	Phase_I	25591155	NM_020485	A7DW68|B7UDF3|B7UDF4|B7UDF5|B7UDF6|B7UDF7|B7UDF8|B7UDF9|B7UDG0|B7UDG1|B7UDG2|B7UDG3|Q02163|Q02164|Q02165|Q16160|Q2MJW0|Q2VC86|Q3LTM6|Q6AZX5|Q6J2U3|Q7RU06|Q8IZT2|Q8IZT3|Q8IZT4|Q8IZT5|Q9UD13|Q9UD14|Q9UD15|Q9UD16|Q9UD73|Q9UD74|Q9UEC2|Q9UEC3|Q9UPN0	Missense_Mutation	SNP	ENST00000294413.7	37	CCDS30635.1	.	.	.	.	.	.	.	.	.	.	g	13.46	2.243830	0.39697	.	.	ENSG00000188672	ENST00000413854;ENST00000374352;ENST00000243186;ENST00000425135;ENST00000349320;ENST00000294413;ENST00000447203;ENST00000349438	T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47	3.99	2.08	0.27032	Ammonium transporter AmtB-like (3);	0.323114	0.32687	N	0.005776	T	0.47060	0.1425	M	0.72894	2.215	0.38140	D	0.938422	B;B;D	0.76494	0.215;0.364;0.999	B;B;D	0.85130	0.3;0.395;0.997	T	0.46317	-0.9200	10	0.59425	D	0.04	-3.6828	4.9231	0.13880	0.111:0.0:0.6804:0.2086	.	168;184;184	Q5VSJ9;Q5VSJ8;P18577	.;.;RHCE_HUMAN	V	184;168;184;184;168;184;184;184	ENSP00000415417:A184V;ENSP00000363472:A168V;ENSP00000243186:A184V;ENSP00000392809:A184V;ENSP00000311185:A168V;ENSP00000294413:A184V;ENSP00000334570:A184V	ENSP00000243186:A184V	A	-	2	0	RHCE	25591155	0.965000	0.33210	0.711000	0.30485	0.171000	0.22731	1.643000	0.37217	0.435000	0.26365	0.561000	0.74099	GCC		0.532	RHCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020312.2	NM_020485	
MAN1C1	57134	broad.mit.edu	37	1	26073272	26073272	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:26073272G>A	ENST00000374332.4	+	3	1081	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	MAN1C1_ENST00000473891.1_3'UTR|MAN1C1_ENST00000374329.1_Missense_Mutation_p.V22M|MAN1C1_ENST00000263979.3_Missense_Mutation_p.V71M	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	251					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.V251M(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(7)|pancreas(1)|prostate(1)|skin(2)	25		Colorectal(325;3.78e-05)|Lung NSC(340;0.000181)|all_lung(284;0.000245)|Renal(390;0.000714)|Ovarian(437;0.00159)|Breast(348;0.0156)|Myeloproliferative disorder(586;0.0257)|all_neural(195;0.0515)|Esophageal squamous(538;0.232)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0574)|OV - Ovarian serous cystadenocarcinoma(117;2.46e-25)|Colorectal(126;1.15e-07)|COAD - Colon adenocarcinoma(152;4.31e-06)|STAD - Stomach adenocarcinoma(196;0.00125)|BRCA - Breast invasive adenocarcinoma(304;0.00141)|KIRC - Kidney renal clear cell carcinoma(1967;0.00146)|GBM - Glioblastoma multiforme(114;0.0149)|READ - Rectum adenocarcinoma(331;0.0803)		CCACCTGAACGTGGTGAGTCA	0.622																																					p.V251M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G751A	1						.						45.0	37.0	40.0					1																	26073272		2203	4300	6503	25945859	SO:0001583	missense	57134	exon3			AF261655	CCDS265.1	1p35	2008-02-05			ENSG00000117643	ENSG00000117643			19080	protein-coding gene	gene with protein product						10915796	Standard	XM_005245945		Approved	HMIC	uc001bkm.2	Q9NR34	OTTHUMG00000004417	ENST00000374332.4:c.751G>A	1.37:g.26073272G>A	ENSP00000363452:p.Val251Met	Somatic		Capture	Illumina HiSeq	Phase_I	25945859	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.840606	0.51057	.	.	ENSG00000117643	ENST00000374332;ENST00000374331;ENST00000263979;ENST00000374329	T;T;T	0.72505	-0.66;-0.66;-0.66	4.93	4.93	0.64822	.	0.140115	0.49305	D	0.000142	T	0.73682	0.3618	L	0.57536	1.79	0.40283	D	0.978412	D	0.61080	0.989	P	0.49451	0.611	T	0.76564	-0.2913	10	0.46703	T	0.11	.	16.3004	0.82807	0.0:0.0:1.0:0.0	.	251	Q9NR34	MA1C1_HUMAN	M	251;71;71;22	ENSP00000363452:V251M;ENSP00000263979:V71M;ENSP00000363449:V22M	ENSP00000263979:V71M	V	+	1	0	MAN1C1	25945859	1.000000	0.71417	0.996000	0.52242	0.900000	0.52787	4.295000	0.59049	2.448000	0.82819	0.462000	0.41574	GTG		0.622	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379	
PAQR7	164091	broad.mit.edu	37	1	26190120	26190120	+	Missense_Mutation	SNP	C	C	T	rs149765684	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:26190120C>T	ENST00000374296.3	-	2	877	c.211G>A	c.(211-213)Gag>Aag	p.E71K	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	71					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|response to steroid hormone (GO:0048545)|steroid hormone mediated signaling pathway (GO:0043401)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)	p.E71K(1)		breast(3)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.00038)|all_lung(284;0.00051)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0505)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.16e-25)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000724)|BRCA - Breast invasive adenocarcinoma(304;0.000965)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0136)|READ - Rectum adenocarcinoma(331;0.0649)		TTCACGGCCTCGTTGTGCTGC	0.642																																					p.E71K	Esophageal Squamous(111;1206 1556 18433 19151 38418)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G211A	1						.	C	LYS/GLU	0,4406		0,0,2203	53.0	56.0	55.0		211	3.8	1.0	1	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PAQR7	NM_178422.5	56	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	71/347	26190120	2,13004	2203	4300	6503	26062707	SO:0001583	missense	164091	exon2				CCDS267.1	1p35.3	2012-08-10			ENSG00000182749	ENSG00000182749			23146	protein-coding gene	gene with protein product	"""membrane progestin receptor alpha"""	607779					Standard	NM_178422		Approved	mSR, MPRA	uc001bkx.3	Q86WK9	OTTHUMG00000007373	ENST00000374296.3:c.211G>A	1.37:g.26190120C>T	ENSP00000363414:p.Glu71Lys	Somatic		Capture	Illumina HiSeq	Phase_I	26062707	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	37	CCDS267.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.935751	0.92458	0.0	2.33E-4	ENSG00000182749	ENST00000374296	T	0.42131	0.98	4.75	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.67069	0.2854	M	0.87827	2.91	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.73534	-0.3952	10	0.87932	D	0	-20.4821	12.3268	0.55015	0.0:0.9159:0.0:0.0841	.	71	Q86WK9	MPRA_HUMAN	K	71	ENSP00000363414:E71K	ENSP00000363414:E71K	E	-	1	0	PAQR7	26062707	1.000000	0.71417	0.987000	0.45799	0.975000	0.68041	7.585000	0.82584	1.360000	0.45960	0.655000	0.94253	GAG		0.642	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422	
CATSPER4	378807	broad.mit.edu	37	1	26526548	26526548	+	Splice_Site	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:26526548A>G	ENST00000456354.2	+	7	1053	c.986A>G	c.(985-987)gAg>gGg	p.E329G		NM_198137.1	NP_937770.1	Q7RTX7	CTSR4_HUMAN	cation channel, sperm associated 4	329					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.E329G(1)		NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)	27		all_cancers(24;2.05e-18)|Colorectal(325;0.000147)|Renal(390;0.00211)|all_lung(284;0.00218)|Lung NSC(340;0.00239)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0589)|all_neural(195;0.0687)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;3.52e-26)|Colorectal(126;1.34e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.000755)|BRCA - Breast invasive adenocarcinoma(304;0.000995)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00878)|READ - Rectum adenocarcinoma(331;0.0649)		ACCTTTAGTGAGGTGCGTGGG	0.502																																					p.E329G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A986G	1						.						138.0	83.0	101.0					1																	26526548		2203	4300	6503	26399135	SO:0001630	splice_region_variant	378807	exon7			BN000273	CCDS30645.1	1p35.3	2011-07-05			ENSG00000188782	ENSG00000188782		"""Voltage-gated ion channels / Cation channels, sperm associated"""	23220	protein-coding gene	gene with protein product		609121				12932298, 17227845, 16382101	Standard	NM_198137		Approved		uc010oez.2	Q7RTX7	OTTHUMG00000003383	ENST00000456354.2:c.987+1A>G	1.37:g.26526548A>G		Somatic		Capture	Illumina HiSeq	Phase_I	26399135	NM_198137	A1A4W6|Q5VY71	Missense_Mutation	SNP	ENST00000456354.2	37	CCDS30645.1	.	.	.	.	.	.	.	.	.	.	A	15.07	2.723161	0.48728	.	.	ENSG00000188782	ENST00000338855;ENST00000456354	D;D	0.97665	-4.48;-4.47	4.64	4.64	0.57946	.	0.493610	0.18781	N	0.131340	D	0.93533	0.7936	L	0.33485	1.01	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.09377	0.002;0.004	D	0.90681	0.4605	10	0.42905	T	0.14	-12.4839	11.0076	0.47644	1.0:0.0:0.0:0.0	.	329;313	Q7RTX7;Q7RTX7-2	CTSR4_HUMAN;.	G	329	ENSP00000341006:E329G;ENSP00000390423:E329G	ENSP00000341006:E329G	E	+	2	0	CATSPER4	26399135	0.999000	0.42202	0.970000	0.41538	0.017000	0.09413	2.646000	0.46630	2.036000	0.60181	0.383000	0.25322	GAG		0.502	CATSPER4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019849.2	NM_198137	Missense_Mutation
UBXN11	91544	broad.mit.edu	37	1	26608890	26608891	+	Frame_Shift_Del	DEL	CC	CC	-	rs376181141		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	CC	CC	CC	-	CC	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:26608890_26608891delCC	ENST00000374222.1	-	16	1926_1927	c.1462_1463delGG	c.(1462-1464)ggtfs	p.G488fs	UBXN11_ENST00000314675.7_Frame_Shift_Del_p.G368fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.G455fs|UBXN11_ENST00000374221.3_Frame_Shift_Del_p.G488fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.G455fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.G245fs			Q5T124	UBX11_HUMAN	UBX domain protein 11	488	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.|Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						gggaccgggaccgggacaggga	0.713																																					p.368_368del												.	.	0			c.1102_1103del	1						.																																			26481478	SO:0001589	frameshift_variant	91544	exon11			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1462_1463delGG	1.37:g.26608890_26608891delCC	ENSP00000363339:p.Gly488fs	Germline		Capture	Illumina HiSeq	Phase_I	26481477	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Frame_Shift_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																				0.713	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
UBXN11	91544	broad.mit.edu	37	1	26608893	26608896	+	Frame_Shift_Del	DEL	GGAC	GGAC	-	rs72872911|rs367932248|rs534102934	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GGAC	GGAC	GGAC	-	GGAC	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:26608893_26608896delGGAC	ENST00000374222.1	-	16	1921_1924	c.1457_1460delGTCC	c.(1456-1461)tgtcccfs	p.CP486fs	UBXN11_ENST00000314675.7_Frame_Shift_Del_p.CP366fs|UBXN11_ENST00000357089.4_Frame_Shift_Del_p.CP453fs|UBXN11_ENST00000374221.3_Frame_Shift_Del_p.CP486fs|UBXN11_ENST00000374217.2_Frame_Shift_Del_p.CP453fs|UBXN11_ENST00000374223.1_Frame_Shift_Del_p.CP243fs			Q5T124	UBX11_HUMAN	UBX domain protein 11	486	Pro-rich.		C -> CPGPGPGPS. {ECO:0000269|PubMed:15498874}.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						accgggaccgggacagggaccagg	0.716																																					p.366_367del												.	.	0			c.1097_1100del	1						.																																			26481483	SO:0001589	frameshift_variant	91544	exon11			AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1457_1460delGTCC	1.37:g.26608893_26608896delGGAC	ENSP00000363339:p.Cys486fs	Germline		Capture	Illumina HiSeq	Phase_I	26481480	NM_001077262	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Frame_Shift_Del	DEL	ENST00000374222.1	37	CCDS41288.1																																																																																				0.716	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ARID1A	8289	broad.mit.edu	37	1	27058020	27058020	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:27058020G>T	ENST00000324856.7	+	3	2099	c.1728G>T	c.(1726-1728)caG>caT	p.Q576H	ARID1A_ENST00000374152.2_Missense_Mutation_p.Q193H|ARID1A_ENST00000457599.2_Missense_Mutation_p.Q576H	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	576					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.Q576H(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TCTCCCAGCAGGCTGCGTATC	0.632			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.Q576H			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1728T	1						.						148.0	147.0	148.0					1																	27058020		2203	4300	6503	26930607	SO:0001583	missense	8289	exon3			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.1728G>T	1.37:g.27058020G>T	ENSP00000320485:p.Gln576His	Somatic		Capture	Illumina HiSeq	Phase_I	26930607	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	G	14.86	2.661949	0.47572	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02631	4.42;4.22;4.25	5.31	5.31	0.75309	.	0.361307	0.29551	N	0.011834	T	0.03783	0.0107	N	0.08118	0	0.80722	D	1	P;D;P	0.54964	0.947;0.969;0.947	P;P;P	0.54100	0.556;0.742;0.556	T	0.68066	-0.5507	10	0.25106	T	0.35	-6.8248	15.5313	0.75964	0.0:0.0:0.8616:0.1384	.	576;576;230	O14497;O14497-2;Q4LE49	ARI1A_HUMAN;.;.	H	576;576;193	ENSP00000320485:Q576H;ENSP00000387636:Q576H;ENSP00000363267:Q193H	ENSP00000320485:Q576H	Q	+	3	2	ARID1A	26930607	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.376000	0.52417	2.755000	0.94549	0.563000	0.77884	CAG		0.632	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
MAP3K6	9064	broad.mit.edu	37	1	27685318	27685318	+	Missense_Mutation	SNP	C	C	T	rs550309860		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:27685318C>T	ENST00000493901.1	-	20	2704	c.2465G>A	c.(2464-2466)gGc>gAc	p.G822D	MAP3K6_ENST00000357582.2_Missense_Mutation_p.G822D|MAP3K6_ENST00000374040.3_Missense_Mutation_p.G814D	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	822	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)	p.G814D(1)		breast(4)|central_nervous_system(2)|lung(3)|ovary(1)	10		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.69e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00132)|KIRC - Kidney renal clear cell carcinoma(1967;0.00163)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		CCCGCGTGGGCCCTGGTCAAT	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		20056	0.0		0.0	False		,,,				2504	0.001				p.G822D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2465A	1						.						83.0	75.0	78.0					1																	27685318		2203	4300	6503	27557905	SO:0001583	missense	9064	exon19			AF100318	CCDS299.1, CCDS72738.1	1p36.11	2011-06-09			ENSG00000142733	ENSG00000142733		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6858	protein-coding gene	gene with protein product	"""apoptosis signal regulating kinase 2"""	604468				9875215	Standard	XM_005246029		Approved	MAPKKK6, ASK2, MEKK6	uc001bny.1	O95382	OTTHUMG00000004631	ENST00000493901.1:c.2465G>A	1.37:g.27685318C>T	ENSP00000419591:p.Gly822Asp	Somatic		Capture	Illumina HiSeq	Phase_I	27557905	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Missense_Mutation	SNP	ENST00000493901.1	37	CCDS299.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.246583|5.246583	0.95305|0.95305	.|.	.|.	ENSG00000142733|ENSG00000142733	ENST00000472410|ENST00000374040;ENST00000493901;ENST00000545447;ENST00000357582	.|T;T;T	.|0.29142	.|1.58;1.58;1.58	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|.	.|.	.|.	.|.	T|T	0.50531|0.50531	0.1621|0.1621	L|L	0.42686|0.42686	1.345|1.345	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|0.999;1.0	T|T	0.40572|0.40572	-0.9556|-0.9556	5|9	.|0.54805	.|T	.|0.06	.|.	18.8993|18.8993	0.92435|0.92435	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|814;822	.|O95382-3;O95382	.|.;M3K6_HUMAN	T|D	546|814;822;545;822	.|ENSP00000363152:G814D;ENSP00000419591:G822D;ENSP00000350195:G822D	.|ENSP00000350195:G822D	A|G	-|-	1|2	0|0	MAP3K6|MAP3K6	27557905|27557905	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	7.466000|7.466000	0.80914|0.80914	2.768000|2.768000	0.95171|0.95171	0.561000|0.561000	0.74099|0.74099	GCC|GGC		0.582	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672	
XKR8	55113	broad.mit.edu	37	1	28293668	28293668	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:28293668T>C	ENST00000373884.5	+	3	1753	c.1145T>C	c.(1144-1146)tTc>tCc	p.F382S		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	382					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.F382S(1)		endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		CAGAAGTTTTTCCCCAAGGCT	0.572																																					p.F382S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1145C	1						.						57.0	57.0	57.0					1																	28293668		2203	4300	6503	28166255	SO:0001583	missense	55113	exon3			AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.1145T>C	1.37:g.28293668T>C	ENSP00000362991:p.Phe382Ser	Somatic		Capture	Illumina HiSeq	Phase_I	28166255	NM_018053		Missense_Mutation	SNP	ENST00000373884.5	37	CCDS315.1	.	.	.	.	.	.	.	.	.	.	T	14.26	2.482473	0.44147	.	.	ENSG00000158156	ENST00000373884	.	.	.	4.86	4.86	0.63082	.	0.814594	0.11008	N	0.609778	T	0.64294	0.2585	M	0.66939	2.045	0.30667	N	0.753733	D	0.89917	1.0	D	0.66196	0.942	T	0.61118	-0.7127	9	0.46703	T	0.11	.	10.7541	0.46225	0.0:0.0:0.0:1.0	.	382	Q9H6D3	XKR8_HUMAN	S	382	.	ENSP00000362991:F382S	F	+	2	0	XKR8	28166255	0.910000	0.30920	0.654000	0.29608	0.126000	0.20510	5.205000	0.65186	2.042000	0.60477	0.482000	0.46254	TTC		0.572	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
MED18	54797	broad.mit.edu	37	1	28661264	28661264	+	Missense_Mutation	SNP	G	G	A	rs146026180		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:28661264G>A	ENST00000373842.4	+	3	619	c.410G>A	c.(409-411)cGt>cAt	p.R137H	MED18_ENST00000479574.1_3'UTR|MED18_ENST00000398997.2_Missense_Mutation_p.R137H	NM_001127350.1|NM_017638.2	NP_001120822.1|NP_060108.2	Q9BUE0	MED18_HUMAN	mediator complex subunit 18	137						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.R137H(1)		endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7		Colorectal(325;0.000147)|Lung NSC(340;0.000818)|all_lung(284;0.000996)|Renal(390;0.00357)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|all_neural(195;0.0557)|Ovarian(437;0.113)		OV - Ovarian serous cystadenocarcinoma(117;2.36e-22)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00299)|BRCA - Breast invasive adenocarcinoma(304;0.0141)|READ - Rectum adenocarcinoma(331;0.0649)		CATTTGTTCCGTAAGGGCATC	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		22450	0.001		0.0	False		,,,				2504	0.0				p.R137H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G410A	1						.						162.0	146.0	152.0					1																	28661264		2203	4300	6503	28533851	SO:0001583	missense	54797	exon3			BC002694	CCDS322.1	1p35.3	2007-07-30	2007-07-30		ENSG00000130772	ENSG00000130772			25944	protein-coding gene	gene with protein product		612384	"""mediator of RNA polymerase II transcription, subunit 18 homolog (S. cerevisiae)"""			15175163	Standard	NM_001127350		Approved	FLJ20045, p28b	uc009vtg.3	Q9BUE0	OTTHUMG00000003537	ENST00000373842.4:c.410G>A	1.37:g.28661264G>A	ENSP00000362948:p.Arg137His	Somatic		Capture	Illumina HiSeq	Phase_I	28533851	NM_017638	D3DPM1|Q9NXU9	Missense_Mutation	SNP	ENST00000373842.4	37	CCDS322.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	25.0	4.594887	0.86953	.	.	ENSG00000130772	ENST00000373842;ENST00000398997	.	.	.	5.84	5.84	0.93424	Mediator complex, subunit Med18, metazoa/fungi (1);	0.000000	0.85682	D	0.000000	T	0.61924	0.2386	L	0.60455	1.87	0.30886	N	0.730845	D	0.69078	0.997	P	0.61477	0.889	T	0.66097	-0.6008	9	0.66056	D	0.02	-14.0269	14.4202	0.67177	0.0:0.0:0.8517:0.1483	.	137	Q9BUE0	MED18_HUMAN	H	137	.	ENSP00000362948:R137H	R	+	2	0	MED18	28533851	1.000000	0.71417	0.989000	0.46669	0.958000	0.62258	7.785000	0.85724	2.756000	0.94617	0.655000	0.94253	CGT		0.493	MED18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009856.1	NM_017638	
MARCKSL1	65108	broad.mit.edu	37	1	32800306	32800306	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:32800306C>A	ENST00000329421.7	-	2	825	c.480G>T	c.(478-480)gaG>gaT	p.E160D		NM_023009.6	NP_075385.1	P49006	MRP_HUMAN	MARCKS-like 1	160					positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.E160E(1)|p.E160D(1)		breast(1)|large_intestine(3)|lung(1)|ovary(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				CTGCACTAGCCTCTGCCCCCT	0.677																																					p.E160D												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|breast(1)	c.G480T	1						.						43.0	42.0	42.0					1																	32800306		2203	4300	6503	32572893	SO:0001583	missense	65108	exon2			AF031640	CCDS361.1	1p35.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000175130	ENSG00000175130			7142	protein-coding gene	gene with protein product		602940	"""MARCKS-like protein"""	MLP		9598313	Standard	NM_023009		Approved	F52, MacMARCKS, MLP1	uc001bvd.4	P49006	OTTHUMG00000007589	ENST00000329421.7:c.480G>T	1.37:g.32800306C>A	ENSP00000362638:p.Glu160Asp	Somatic		Capture	Illumina HiSeq	Phase_I	32572893	NM_023009	D3DPQ0|Q5TEE6|Q6NXS5	Missense_Mutation	SNP	ENST00000329421.7	37	CCDS361.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919816	0.52653	.	.	ENSG00000175130	ENST00000329421	T	0.31510	1.49	5.16	3.25	0.37280	.	0.121074	0.53938	D	0.000042	T	0.37404	0.1002	N	0.24115	0.695	0.48452	D	0.999659	D	0.65815	0.995	D	0.67231	0.95	T	0.18650	-1.0330	10	0.48119	T	0.1	-13.6009	12.4551	0.55700	0.0:0.8541:0.0:0.1459	.	160	P49006	MRP_HUMAN	D	160	ENSP00000362638:E160D	ENSP00000362638:E160D	E	-	3	2	MARCKSL1	32572893	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.439000	0.35013	1.340000	0.45581	0.556000	0.70494	GAG		0.677	MARCKSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020059.3	NM_023009	
SYNC	81493	broad.mit.edu	37	1	33160579	33160579	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:33160579C>T	ENST00000409190.3	-	2	1578	c.1120G>A	c.(1120-1122)Gct>Act	p.A374T	SYNC_ENST00000373484.3_Missense_Mutation_p.A374T	NM_030786.2	NP_110413	Q9H7C4	SYNCI_HUMAN	syncoilin, intermediate filament protein	374	Coil 2.				intermediate filament-based process (GO:0045103)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	structural molecule activity (GO:0005198)	p.A43T(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						GGTCTCAGAGCCTCCTTCATT	0.567																																					p.A374T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1120A	1						.						119.0	122.0	121.0					1																	33160579		2203	4300	6503	32933166	SO:0001583	missense	81493	exon2			AK024707	CCDS367.2, CCDS53294.1	1p35.1	2013-01-16	2008-09-19	2008-09-19	ENSG00000162520	ENSG00000162520		"""Intermediate filaments type III"""	28897	protein-coding gene	gene with protein product		611750	"""syncoilin, intermediate filament 1"""	SYNC1		11053421	Standard	NM_030786		Approved	SYNCOILIN	uc001bvt.2	Q9H7C4	OTTHUMG00000008087	ENST00000409190.3:c.1120G>A	1.37:g.33160579C>T	ENSP00000386439:p.Ala374Thr	Somatic		Capture	Illumina HiSeq	Phase_I	32933166	NM_001161708	B4DNK8|B4DY58|C9IY41	Missense_Mutation	SNP	ENST00000409190.3	37	CCDS367.2	.	.	.	.	.	.	.	.	.	.	C	4.662	0.122991	0.08931	.	.	ENSG00000162520	ENST00000373484;ENST00000409190	D;D	0.88124	-2.34;-2.34	4.0	2.99	0.34606	Filament (1);	0.244283	0.36703	N	0.002449	T	0.75199	0.3817	N	0.19112	0.55	0.26901	N	0.967117	B;B	0.25390	0.061;0.125	B;B	0.24848	0.056;0.053	T	0.59616	-0.7421	10	0.13853	T	0.58	-0.877	11.6684	0.51387	0.1776:0.8223:0.0:0.0	.	374;374	Q9H7C4-2;Q9H7C4	.;SYNCI_HUMAN	T	374	ENSP00000362583:A374T;ENSP00000386439:A374T	ENSP00000362583:A374T	A	-	1	0	SYNC	32933166	0.974000	0.33945	0.998000	0.56505	0.371000	0.29859	1.244000	0.32778	1.965000	0.57142	0.491000	0.48974	GCT		0.567	SYNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022129.3	NM_030786	
CSMD2	114784	broad.mit.edu	37	1	34158547	34158547	+	De_novo_Start_OutOfFrame	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:34158547C>A	ENST00000373388.2	-	0	874				CSMD2_ENST00000373380.1_Missense_Mutation_p.E218D|CSMD2_ENST00000373381.4_Missense_Mutation_p.E1345D			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2							integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TGCAGCCGGCCTCTGCTTCGA	0.562																																					p.E1305D												.	.	0			c.G3915T	1						.						158.0	147.0	151.0					1																	34158547		2203	4300	6503	33931134			114784	exon25			AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373388.2:c.-1669G>T	1.37:g.34158547C>A		None		Capture	Illumina HiSeq	Phase_I	33931134	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Missense_Mutation	SNP	ENST00000373388.2	37		.	.	.	.	.	.	.	.	.	.	C	0.949	-0.707128	0.03230	.	.	ENSG00000121904	ENST00000373381;ENST00000373380	T;T	0.59772	0.24;0.24	5.52	-7.27	0.01461	CUB (5);	0.373499	0.27451	N	0.019310	T	0.19846	0.0477	N	0.11255	0.115	0.43965	D	0.996644	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.002	T	0.42783	-0.9431	10	0.02654	T	1	.	2.2366	0.04010	0.2213:0.2549:0.3546:0.1692	.	218;1305;1345	Q7Z408-2;Q7Z408;E7EUA6	.;CSMD2_HUMAN;.	D	1345;218	ENSP00000362479:E1345D;ENSP00000362478:E218D	ENSP00000241312:E1305D	E	-	3	2	CSMD2	33931134	0.001000	0.12720	0.701000	0.30321	0.979000	0.70002	-1.424000	0.02448	-1.247000	0.02507	-1.085000	0.02201	GAG		0.562	CSMD2-202	KNOWN	basic	protein_coding	protein_coding		NM_052896	
PSMB2	5690	broad.mit.edu	37	1	36074882	36074882	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:36074882A>G	ENST00000373237.3	-	4	824	c.413T>C	c.(412-414)cTg>cCg	p.L138P		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	138					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)	threonine-type endopeptidase activity (GO:0004298)	p.L138P(1)		endometrium(1)|large_intestine(2)	3		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)			Bortezomib(DB00188)|Carfilzomib(DB08889)	ACTGAGAGTCAGGAAGGCACC	0.557																																					p.L113P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T338C	1						.						71.0	67.0	68.0					1																	36074882		2203	4300	6503	35847469	SO:0001583	missense	5690	exon4			D26599	CCDS394.1, CCDS72755.1	1p34.2	2008-02-05			ENSG00000126067	ENSG00000126067		"""Proteasome (prosome, macropain) subunits"""	9539	protein-coding gene	gene with protein product		602175				7918633	Standard	NM_002794		Approved	HC7-I	uc001bzf.2	P49721	OTTHUMG00000004169	ENST00000373237.3:c.413T>C	1.37:g.36074882A>G	ENSP00000362334:p.Leu138Pro	Somatic		Capture	Illumina HiSeq	Phase_I	35847469	NM_001199779	D3DPS0|P31145|Q9BWZ9	Missense_Mutation	SNP	ENST00000373237.3	37	CCDS394.1	.	.	.	.	.	.	.	.	.	.	A	27.7	4.857546	0.91433	.	.	ENSG00000126067	ENST00000373237	T	0.22539	1.95	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.76574	2.34	0.80722	D	1	D;D;D	0.76494	0.99;0.988;0.999	D;D;D	0.78314	0.959;0.958;0.991	T	0.50048	-0.8873	10	0.87932	D	0	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	113;138;170	B7Z478;P49721;Q59FJ0	.;PSB2_HUMAN;.	P	138	ENSP00000362334:L138P	ENSP00000362334:L138P	L	-	2	0	PSMB2	35847469	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.170000	0.94795	2.311000	0.77944	0.533000	0.62120	CTG		0.557	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794	
AGO4	192670	broad.mit.edu	37	1	36282591	36282591	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:36282591A>T	ENST00000373210.3	+	2	373	c.128A>T	c.(127-129)gAt>gTt	p.D43V		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	43					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)	p.D43V(1)									CCTAAAATAGATGTGTATCAC	0.413																																					p.D43V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A128T	1						.						114.0	114.0	114.0					1																	36282591		2203	4300	6503	36055178	SO:0001583	missense	192670	exon2			AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.128A>T	1.37:g.36282591A>T	ENSP00000362306:p.Asp43Val	Somatic		Capture	Illumina HiSeq	Phase_I	36055178	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	37	CCDS397.1	.	.	.	.	.	.	.	.	.	.	A	18.18	3.566035	0.65651	.	.	ENSG00000134698	ENST00000373210	T	0.10005	2.92	5.35	5.35	0.76521	Argonaute/Dicer protein, PAZ (1);	0.000000	0.85682	D	0.000000	T	0.19005	0.0456	M	0.83483	2.645	0.80722	D	1	B	0.09022	0.002	B	0.12156	0.007	T	0.02064	-1.1220	10	0.33940	T	0.23	-9.0475	15.3337	0.74234	1.0:0.0:0.0:0.0	.	43	Q9HCK5	AGO4_HUMAN	V	43	ENSP00000362306:D43V	ENSP00000362306:D43V	D	+	2	0	EIF2C4	36055178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.282000	0.95840	2.040000	0.60383	0.533000	0.62120	GAT		0.413	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
AGO1	26523	broad.mit.edu	37	1	36360812	36360812	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:36360812C>T	ENST00000373204.4	+	8	1175	c.962C>T	c.(961-963)cCc>cTc	p.P321L	AGO1_ENST00000373206.1_Missense_Mutation_p.P246L	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	321	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.P321L(1)									CTCAAGTATCCCCATCTGCCC	0.478																																					p.P321L												.	.	1	Substitution - Missense(1)	skin(1)	c.C962T	1						.						138.0	121.0	127.0					1																	36360812		2203	4300	6503	36133399	SO:0001583	missense	26523	exon8			AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.962C>T	1.37:g.36360812C>T	ENSP00000362300:p.Pro321Leu	None		Capture	Illumina HiSeq	Phase_I	36133399	NM_012199	Q5TA57|Q6P4S0	Missense_Mutation	SNP	ENST00000373204.4	37	CCDS398.1	.	.	.	.	.	.	.	.	.	.	C	36	5.802617	0.96960	.	.	ENSG00000092847	ENST00000373206;ENST00000373204	T;T	0.35973	2.38;1.28	6.17	6.17	0.99709	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.69360	0.3102	M	0.93638	3.44	0.80722	D	1	P	0.48911	0.917	P	0.57720	0.826	T	0.75434	-0.3319	10	0.87932	D	0	-12.376	20.8794	0.99867	0.0:1.0:0.0:0.0	.	321	Q9UL18	AGO1_HUMAN	L	246;321	ENSP00000362302:P246L;ENSP00000362300:P321L	ENSP00000362300:P321L	P	+	2	0	EIF2C1	36133399	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	CCC		0.478	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3		
AGO3	192669	broad.mit.edu	37	1	36470047	36470047	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:36470047A>G	ENST00000373191.4	+	6	1113	c.764A>G	c.(763-765)cAt>cGt	p.H255R	RP4-665N4.8_ENST00000466576.2_RNA|AGO3_ENST00000246314.6_Missense_Mutation_p.H21R	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	255	PAZ. {ECO:0000255|HAMAP-Rule:MF_03032}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)	p.H255R(1)									ACTGATTCTCATCGGGTAAAA	0.333																																					p.H21R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A62G	1						.						102.0	97.0	99.0					1																	36470047		2203	4300	6503	36242634	SO:0001583	missense	192669	exon4			AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.764A>G	1.37:g.36470047A>G	ENSP00000362287:p.His255Arg	Somatic		Capture	Illumina HiSeq	Phase_I	36242634	NM_177422	B1ALI0|Q5TA55|Q9H1U6	Missense_Mutation	SNP	ENST00000373191.4	37	CCDS399.1	.	.	.	.	.	.	.	.	.	.	A	15.65	2.896777	0.52121	.	.	ENSG00000126070	ENST00000373191;ENST00000246314	T;T	0.13089	2.62;2.62	5.56	5.56	0.83823	Argonaute/Dicer protein, PAZ (4);	0.000000	0.85682	D	0.000000	T	0.12561	0.0305	L	0.28115	0.83	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.03829	-1.1000	10	0.66056	D	0.02	-2.6781	15.7042	0.77565	1.0:0.0:0.0:0.0	.	255	Q9H9G7	AGO3_HUMAN	R	255;21	ENSP00000362287:H255R;ENSP00000246314:H21R	ENSP00000246314:H21R	H	+	2	0	EIF2C3	36242634	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.307000	0.96226	2.119000	0.64992	0.377000	0.23210	CAT		0.333	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
THRAP3	9967	broad.mit.edu	37	1	36754721	36754721	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:36754721C>T	ENST00000354618.5	+	5	1325	c.1101C>T	c.(1099-1101)acC>acT	p.T367T	THRAP3_ENST00000469141.2_Silent_p.T367T	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	367	Required for mRNA decay activity.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.T367T(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AAACAAATACCGATAAAGAAA	0.363			T	USP6	aneurysmal bone cysts																																p.T367T	Pancreas(129;785 1795 20938 23278 32581)		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1101T	1						.						48.0	52.0	50.0					1																	36754721		2197	4298	6495	36527308	SO:0001819	synonymous_variant	9967	exon5			AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.1101C>T	1.37:g.36754721C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36527308	NM_005119	D3DPS5|Q5VTK6	Silent	SNP	ENST00000354618.5	37	CCDS405.1																																																																																				0.363	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
SNIP1	79753	broad.mit.edu	37	1	38006206	38006206	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:38006206C>T	ENST00000296215.6	-	3	550	c.478G>A	c.(478-480)Ggg>Agg	p.G160R	SNIP1_ENST00000468040.1_5'UTR	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1	160	Arg-rich.				I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.G160R(1)		breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				TGACCCTGCCCACTCCCAGGC	0.582																																					p.G160R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G478A	1						.						121.0	125.0	124.0					1																	38006206		2203	4300	6503	37778793	SO:0001583	missense	79753	exon3				CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225	ENST00000296215.6:c.478G>A	1.37:g.38006206C>T	ENSP00000296215:p.Gly160Arg	Somatic		Capture	Illumina HiSeq	Phase_I	37778793	NM_024700	Q96SP9|Q9H9T7	Missense_Mutation	SNP	ENST00000296215.6	37	CCDS419.1	.	.	.	.	.	.	.	.	.	.	C	5.150	0.213230	0.09757	.	.	ENSG00000163877	ENST00000296215;ENST00000436196	T	0.16897	2.31	5.25	5.25	0.73442	.	0.227351	0.44285	D	0.000469	T	0.12689	0.0308	N	0.24115	0.695	0.40423	D	0.979869	B	0.19445	0.036	B	0.12837	0.008	T	0.12837	-1.0532	10	0.14656	T	0.56	-11.6691	17.2058	0.86917	0.0:1.0:0.0:0.0	.	160	Q8TAD8	SNIP1_HUMAN	R	160;144	ENSP00000296215:G160R	ENSP00000296215:G160R	G	-	1	0	SNIP1	37778793	0.213000	0.23551	0.950000	0.38849	0.305000	0.27757	3.261000	0.51530	2.733000	0.93635	0.655000	0.94253	GGG		0.582	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2	NM_024700	
MTF1	4520	broad.mit.edu	37	1	38288175	38288175	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:38288175delG	ENST00000373036.4	-	9	1525	c.1385delC	c.(1384-1386)cctfs	p.P462fs		NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	462	Pro-rich.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.P462fs*83(1)		endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TAAGAGAGCAGGGGGGTTGCC	0.602																																					p.P462fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1385delC	1						.						39.0	40.0	40.0					1																	38288175		2203	4300	6503	38060762	SO:0001589	frameshift_variant	4520	exon9			BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.1385delC	1.37:g.38288175delG	ENSP00000362127:p.Pro462fs	Somatic		Capture	Illumina HiSeq	Phase_I	38060762	NM_005955	B2RAK6|Q96CB1	Frame_Shift_Del	DEL	ENST00000373036.4	37	CCDS30676.1																																																																																				0.602	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955	
INPP5B	3633	broad.mit.edu	37	1	38409491	38409491	+	Missense_Mutation	SNP	G	G	A	rs200033881		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:38409491G>A	ENST00000373026.1	-	3	227	c.227C>T	c.(226-228)tCg>tTg	p.S76L	INPP5B_ENST00000373024.3_Missense_Mutation_p.S76L|INPP5B_ENST00000373023.2_Missense_Mutation_p.S76L|INPP5B_ENST00000373021.1_Missense_Mutation_p.S76L			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	76	PH.				in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)	p.S113L(1)|p.S76L(1)		breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AAAATCCCGCGAGACTGGCAC	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		18040	0.0		0.0	False		,,,				2504	0.001				p.S76L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C227T	1						.	G	LEU/SER	0,3896		0,0,1948	91.0	90.0	90.0		227	5.2	0.5	1		90	1,8291		0,1,4145	no	missense	INPP5B	NM_005540.2	145	0,1,6093	AA,AG,GG		0.0121,0.0,0.0082	possibly-damaging	76/914	38409491	1,12187	1948	4146	6094	38182078	SO:0001583	missense	3633	exon4			M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.227C>T	1.37:g.38409491G>A	ENSP00000362117:p.Ser76Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38182078	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	G	18.27	3.587583	0.66105	0.0	1.21E-4	ENSG00000204084	ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024;ENST00000373021	D;D;D;T	0.92858	-3.12;-3.12;-3.11;0.64	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000018	D	0.94778	0.8314	M	0.62723	1.935	0.80722	D	1	P;D;P	0.89917	0.916;1.0;0.88	B;D;B	0.69142	0.213;0.962;0.344	D	0.94961	0.8108	10	0.72032	D	0.01	.	14.5153	0.67816	0.0:0.0:1.0:0.0	.	76;76;76	P32019;B1ARF3;P32019-2	I5P2_HUMAN;.;.	L	76	ENSP00000362114:S76L;ENSP00000362117:S76L;ENSP00000362115:S76L;ENSP00000362112:S76L	ENSP00000362112:S76L	S	-	2	0	INPP5B	38182078	1.000000	0.71417	0.529000	0.27951	0.750000	0.42670	5.904000	0.69886	2.556000	0.86216	0.462000	0.41574	TCG		0.577	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
SMAP2	64744	broad.mit.edu	37	1	40882609	40882609	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:40882609G>A	ENST00000539317.1	+	9	958	c.765G>A	c.(763-765)atG>atA	p.M255I		NM_001198980.1	NP_001185909.1	Q8WU79	SMAP2_HUMAN	small ArfGAP2	335					regulation of ARF GTPase activity (GO:0032312)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.M335I(1)		central_nervous_system(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24	Lung NSC(20;1.56e-05)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;1.04e-17)			CCATGGCCATGCCTGCAGGCT	0.572																																					p.M330I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G990A	1						.						55.0	50.0	51.0					1																	40882609		2203	4300	6503	40655196	SO:0001583	missense	64744	exon9			AL137764	CCDS451.1, CCDS55592.1, CCDS55593.1, CCDS72763.1	1p35.3-p34.1	2008-09-22	2008-09-05	2008-01-09	ENSG00000084070	ENSG00000084070		"""ADP-ribosylation factor GTPase activating proteins"""	25082	protein-coding gene	gene with protein product			"""stromal membrane-associated protein 1-like"", ""stromal membrane-associated GTPase-activating protein 2"""	SMAP1L		16571680	Standard	NM_001198978		Approved		uc001cfj.3	Q8WU79	OTTHUMG00000007301	ENST00000539317.1:c.765G>A	1.37:g.40882609G>A	ENSP00000442835:p.Met255Ile	Somatic		Capture	Illumina HiSeq	Phase_I	40655196	NM_001198979	B2R7T1|B7Z5B5|B7Z8V2|D3DPV2|Q5QPL2|Q96C93|Q9NST2|Q9UJL8	Missense_Mutation	SNP	ENST00000539317.1	37	CCDS55593.1	.	.	.	.	.	.	.	.	.	.	G	12.87	2.067744	0.36470	.	.	ENSG00000084070	ENST00000372718;ENST00000372708;ENST00000539317	T;T;T	0.38560	1.13;1.13;1.13	6.17	4.19	0.49359	.	0.630727	0.19284	N	0.118063	T	0.19805	0.0476	N	0.04669	-0.19	0.36256	D	0.854255	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14868	-1.0457	10	0.19590	T	0.45	-18.4575	10.9298	0.47211	0.0:0.1304:0.721:0.1485	.	305;335	Q8WU79-2;Q8WU79	.;SMAP2_HUMAN	I	335;305;255	ENSP00000361803:M335I;ENSP00000361793:M305I;ENSP00000442835:M255I	ENSP00000361793:M305I	M	+	3	0	SMAP2	40655196	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.490000	0.22403	2.941000	0.99782	0.655000	0.94253	ATG		0.572	SMAP2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022733	
HIVEP3	59269	broad.mit.edu	37	1	42047804	42047804	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:42047804G>A	ENST00000372583.1	-	4	3550	c.2665C>T	c.(2665-2667)Cgc>Tgc	p.R889C	HIVEP3_ENST00000460604.1_5'Flank|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R889C|HIVEP3_ENST00000429157.2_Missense_Mutation_p.R889C|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R889C	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	889	No DNA binding activity or transactivation activity, but complete prevention of TRAF-dependent NF-Kappa-B activation; associates with TRAF2 and JUN. {ECO:0000250}.				positive regulation of transcription, DNA-templated (GO:0045893)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R889C(1)		NS(2)|breast(3)|central_nervous_system(5)|endometrium(13)|kidney(3)|large_intestine(13)|lung(33)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	85	Ovarian(52;0.00769)|all_hematologic(146;0.109)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0367)				GTCTGGCTGCGCTGGGGCCAT	0.597																																					p.R889C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2665T	1						.						54.0	63.0	60.0					1																	42047804		2203	4300	6503	41820391	SO:0001583	missense	59269	exon4			AF278765	CCDS463.1, CCDS44124.1	1p34	2013-01-08	2001-11-28		ENSG00000127124	ENSG00000127124		"""Zinc fingers, C2H2-type"""	13561	protein-coding gene	gene with protein product	"""kappabinding protein-1"""	606649	"""human immunodeficiency virus type I enhancer-binding protein 3"""			11161801	Standard	NR_038260		Approved	KRC, KBP1, KBP-1, SHN3, FLJ16752, KIAA1555, ZAS3, Schnurri-3, ZNF40C	uc001cha.4	Q5T1R4	OTTHUMG00000006361	ENST00000372583.1:c.2665C>T	1.37:g.42047804G>A	ENSP00000361664:p.Arg889Cys	Somatic		Capture	Illumina HiSeq	Phase_I	41820391	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.679130	0.68042	.	.	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.61859	0.07;0.07;0.07;0.07	4.95	4.95	0.65309	.	0.000000	0.53938	D	0.000060	T	0.73466	0.3590	M	0.76727	2.345	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.76107	-0.3080	10	0.87932	D	0	2.8066	11.1037	0.48190	0.0:0.0:0.6936:0.3063	.	889;889	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	C	889	ENSP00000361665:R889C;ENSP00000361664:R889C;ENSP00000247584:R889C;ENSP00000410828:R889C	ENSP00000247584:R889C	R	-	1	0	HIVEP3	41820391	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.841000	0.69409	2.562000	0.86427	0.462000	0.41574	CGC		0.597	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503	
PPCS	79717	broad.mit.edu	37	1	42925370	42925370	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:42925370G>A	ENST00000372561.3	+	3	716	c.709G>A	c.(709-711)Gcc>Acc	p.A237T	PPCS_ENST00000455780.1_Missense_Mutation_p.A64T|PPCS_ENST00000472013.1_3'UTR|PPCS_ENST00000372556.3_3'UTR|PPCS_ENST00000372562.1_Missense_Mutation_p.A64T	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	237					coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)	p.A237T(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GACTGACCCCGCCATTGTAAT	0.408																																					p.A64T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G190A	1						.						87.0	84.0	85.0					1																	42925370		1844	4097	5941	42697957	SO:0001583	missense	79717	exon3			AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.709G>A	1.37:g.42925370G>A	ENSP00000361642:p.Ala237Thr	Somatic		Capture	Illumina HiSeq	Phase_I	42697957	NM_001077447	Q3KQT2|Q5VVM0	Missense_Mutation	SNP	ENST00000372561.3	37	CCDS41311.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.777723	0.31502	.	.	ENSG00000127125	ENST00000372562;ENST00000455780;ENST00000372561	.	.	.	6.01	0.507	0.16967	DNA/pantothenate metabolism flavoprotein, C-terminal (3);	0.739769	0.14050	N	0.344821	T	0.13500	0.0327	N	0.02751	-0.505	0.19775	N	0.999952	B	0.06786	0.001	B	0.04013	0.001	T	0.23511	-1.0186	9	0.30078	T	0.28	-2.2439	6.6093	0.22743	0.2016:0.0:0.2539:0.5445	.	237	Q9HAB8	PPCS_HUMAN	T	64;64;237	.	ENSP00000361642:A237T	A	+	1	0	PPCS	42697957	0.000000	0.05858	0.926000	0.36857	0.946000	0.59487	0.103000	0.15292	0.506000	0.28125	-0.275000	0.10095	GCC		0.408	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664	
YBX1	4904	broad.mit.edu	37	1	43166630	43166630	+	Missense_Mutation	SNP	G	G	A	rs200741644		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:43166630G>A	ENST00000321358.7	+	7	1058	c.919G>A	c.(919-921)Gat>Aat	p.D307N		NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	307					CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.D307N(1)		large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AAAAGCAGCCGATCCACCAGC	0.562																																					p.D307N												.	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G919A	1						.						56.0	58.0	57.0					1																	43166630		2203	4299	6502	42939217	SO:0001583	missense	4904	exon7			BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"""nuclease sensitive element binding protein 1"""	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.919G>A	1.37:g.43166630G>A	ENSP00000361626:p.Asp307Asn	Germline		Capture	Illumina HiSeq	Phase_I	42939217	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Missense_Mutation	SNP	ENST00000321358.7	37	CCDS470.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735579	0.69189	.	.	ENSG00000065978	ENST00000321358;ENST00000318612	T	0.31510	1.49	5.39	5.39	0.77823	.	0.236880	0.49916	N	0.000136	T	0.22044	0.0531	N	0.17379	0.485	0.54753	D	0.999989	B	0.25312	0.123	B	0.15052	0.012	T	0.04078	-1.0979	10	0.62326	D	0.03	-3.4519	16.6483	0.85182	0.0:0.0:1.0:0.0	.	307	P67809	YBOX1_HUMAN	N	307;297	ENSP00000361626:D307N	ENSP00000361621:D297N	D	+	1	0	YBX1	42939217	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.018000	0.93657	2.505000	0.84491	0.557000	0.71058	GAT		0.562	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559	
CDC20	991	broad.mit.edu	37	1	43828742	43828742	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:43828742G>A	ENST00000372462.1	+	10	1645	c.1442G>A	c.(1441-1443)cGg>cAg	p.R481Q	ELOVL1_ENST00000470769.1_5'Flank|CDC20_ENST00000310955.6_Missense_Mutation_p.R481Q			Q12834	CDC20_HUMAN	cell division cycle 20	481					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle (GO:0007049)|mitotic cell cycle (GO:0000278)|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 cell proliferation (GO:0008284)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic plasticity (GO:0031915)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of dendrite development (GO:0050773)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|spindle (GO:0005819)	enzyme binding (GO:0019899)|protein C-terminus binding (GO:0008022)	p.R481Q(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	15	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GCGCGGCGGCGGGAGCGGGAG	0.562																																					p.R481Q	Esophageal Squamous(137;1154 1759 10362 10401 46925)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1442A	1						.						72.0	82.0	79.0					1																	43828742		2203	4300	6503	43601329	SO:0001583	missense	991	exon11			U05340	CCDS484.1	1p34.1	2013-01-17	2013-01-17		ENSG00000117399	ENSG00000117399		"""WD repeat domain containing"""	1723	protein-coding gene	gene with protein product		603618	"""CDC20 (cell division cycle 20, S. cerevisiae, homolog)"", ""CDC20 cell division cycle 20 homolog (S. cerevisiae)"", ""cell division cycle 20 homolog (S. cerevisiae)"""			7513050, 9353311	Standard	NM_001255		Approved	p55CDC, CDC20A	uc001cix.3	Q12834	OTTHUMG00000007420	ENST00000372462.1:c.1442G>A	1.37:g.43828742G>A	ENSP00000361540:p.Arg481Gln	Somatic		Capture	Illumina HiSeq	Phase_I	43601329	NM_001255	B2R6Z6|D3DPJ1|Q5JUY4|Q9BW56|Q9UQI9	Missense_Mutation	SNP	ENST00000372462.1	37	CCDS484.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.925483	0.73213	.	.	ENSG00000117399	ENST00000437896;ENST00000310955;ENST00000372462	T;T	0.54866	0.55;0.55	5.62	5.62	0.85841	.	0.361900	0.27917	N	0.017321	T	0.22666	0.0547	N	0.04203	-0.255	0.34602	D	0.716583	P	0.40398	0.716	B	0.25614	0.062	T	0.37033	-0.9723	10	0.56958	D	0.05	-22.993	7.3444	0.26656	0.2017:0.0:0.7983:0.0	.	481	Q12834	CDC20_HUMAN	Q	457;481;481	ENSP00000308450:R481Q;ENSP00000361540:R481Q	ENSP00000308450:R481Q	R	+	2	0	CDC20	43601329	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.195000	0.65131	2.639000	0.89480	0.561000	0.74099	CGG		0.562	CDC20-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019488.1	NM_001255	
SZT2	23334	broad.mit.edu	37	1	43907463	43907463	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:43907463C>A	ENST00000562955.1	+	54	7545	c.7545C>A	c.(7543-7545)acC>acA	p.T2515T	SZT2_ENST00000372442.1_Silent_p.T1673T	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2572					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)		p.T1673T(2)		NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CTGGAGACACCAGTGTCCGCA	0.527																																					p.T1673T												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C5019A	1						.						102.0	84.0	90.0					1																	43907463		2203	4300	6503	43680050	SO:0001819	synonymous_variant	23334	exon40			AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.7545C>A	1.37:g.43907463C>A		Somatic		Capture	Illumina HiSeq	Phase_I	43680050	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																				0.527	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
KDM4A	9682	broad.mit.edu	37	1	44126006	44126006	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:44126006G>A	ENST00000372396.3	+	4	486	c.352G>A	c.(352-354)Gag>Aag	p.E118K	KDM4A_ENST00000463151.1_3'UTR	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A	118					cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E118*(1)|p.E118K(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						TGAAGAGCTCGAGCGGAAAta	0.403																																					p.E118K												.	.	2	Substitution - Nonsense(1)|Substitution - Missense(1)	large_intestine(1)|lung(1)	c.G352A	1						.						90.0	86.0	87.0					1																	44126006		2203	4300	6503	43898593	SO:0001583	missense	9682	exon4			AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.352G>A	1.37:g.44126006G>A	ENSP00000361473:p.Glu118Lys	Somatic		Capture	Illumina HiSeq	Phase_I	43898593	NM_014663	Q5VVB1	Missense_Mutation	SNP	ENST00000372396.3	37	CCDS491.1	.	.	.	.	.	.	.	.	.	.	G	36	5.848906	0.97023	.	.	ENSG00000066135	ENST00000372396	T	0.46063	0.88	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.77205	0.4096	H	0.95437	3.67	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	T	0.82816	-0.0270	10	0.87932	D	0	0.0731	20.5827	0.99408	0.0:0.0:1.0:0.0	.	118;118	B4DT38;O75164	.;KDM4A_HUMAN	K	118	ENSP00000361473:E118K	ENSP00000361473:E118K	E	+	1	0	KDM4A	43898593	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	9.187000	0.94912	2.941000	0.99782	0.655000	0.94253	GAG		0.403	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663	
PLK3	1263	broad.mit.edu	37	1	45268943	45268943	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:45268943T>C	ENST00000372201.4	+	8	1191	c.952T>C	c.(952-954)Tac>Cac	p.Y318H	PLK3_ENST00000465443.1_3'UTR	NM_004073.2	NP_004064.2	Q9H4B4	PLK3_HUMAN	polo-like kinase 3	318					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cytoplasmic microtubule organization (GO:0031122)|endomitotic cell cycle (GO:0007113)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi disassembly (GO:0090166)|mitotic cell cycle checkpoint (GO:0007093)|mitotic G1/S transition checkpoint (GO:0044819)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process involved in cellular response to hypoxia (GO:2000777)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell division (GO:0051302)|regulation of cytokinesis (GO:0032465)|response to osmotic stress (GO:0006970)|response to radiation (GO:0009314)|response to reactive oxygen species (GO:0000302)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi stack (GO:0005795)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)	p.Y279H(1)		endometrium(4)|large_intestine(2)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TCCCTAGGGCTACACCCCCGA	0.572																																					p.Y318H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T952C	1						.						60.0	64.0	63.0					1																	45268943		2203	4300	6503	45041530	SO:0001583	missense	1263	exon8			AJ293866	CCDS515.1	1p34.1	2013-01-18	2010-06-24	2004-01-28	ENSG00000173846	ENSG00000173846			2154	protein-coding gene	gene with protein product		602913	"""cytokine-inducible kinase"", ""polo-like kinase 3 (Drosophila)"""	CNK		8702627	Standard	NM_004073		Approved	FNK, PRK	uc001cmn.3	Q9H4B4	OTTHUMG00000008491	ENST00000372201.4:c.952T>C	1.37:g.45268943T>C	ENSP00000361275:p.Tyr318His	Somatic		Capture	Illumina HiSeq	Phase_I	45041530	NM_004073	Q15767|Q5JR99|Q96CV1	Missense_Mutation	SNP	ENST00000372201.4	37	CCDS515.1	.	.	.	.	.	.	.	.	.	.	T	18.26	3.585485	0.66105	.	.	ENSG00000173846	ENST00000372201;ENST00000543983	T	0.24350	1.86	5.52	5.52	0.82312	Protein kinase-like domain (1);	.	.	.	.	T	0.46541	0.1398	M	0.71581	2.175	0.54753	D	0.999988	D	0.55605	0.972	P	0.58928	0.848	T	0.45687	-0.9244	9	0.56958	D	0.05	-16.8734	14.8191	0.70059	0.0:0.0:0.0:1.0	.	318	Q9H4B4	PLK3_HUMAN	H	318;293	ENSP00000361275:Y318H	ENSP00000361275:Y318H	Y	+	1	0	PLK3	45041530	1.000000	0.71417	1.000000	0.80357	0.618000	0.37518	7.698000	0.84413	2.103000	0.63969	0.459000	0.35465	TAC		0.572	PLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023429.1	NM_004073	
PTCH2	8643	broad.mit.edu	37	1	45292921	45292921	+	Missense_Mutation	SNP	C	C	T	rs112613379	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:45292921C>T	ENST00000372192.3	-	16	2562	c.2432G>A	c.(2431-2433)cGc>cAc	p.R811H	PTCH2_ENST00000447098.2_Missense_Mutation_p.R811H	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	811					epidermis development (GO:0008544)|hair cycle (GO:0042633)|negative regulation of smoothened signaling pathway (GO:0045879)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|smoothened binding (GO:0005119)	p.R811H(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(19)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	50	Acute lymphoblastic leukemia(166;0.155)					AGAGCCATTGCGGTACGAGTG	0.622									Basal Cell Nevus syndrome				C|||	2	0.000399361	0.0008	0.0	5008	,	,		18032	0.0		0.001	False		,,,				2504	0.0				p.R811H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2432A	1						.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	69.0	77.0	74.0		2432,2432	4.9	1.0	1	dbSNP_132	74	0,8600		0,0,4300	no	missense,missense	PTCH2	NM_001166292.1,NM_003738.4	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	811/1147,811/1204	45292921	1,13005	2203	4300	6503	45065508	SO:0001583	missense	8643	exon16	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	AF091501	CCDS516.1, CCDS53312.1	1p34.1	2010-06-24	2010-06-24		ENSG00000117425	ENSG00000117425			9586	protein-coding gene	gene with protein product		603673	"""patched (Drosophila) homolog 2"", ""patched homolog 2 (Drosophila)"""			9811851, 9931336	Standard	NM_003738		Approved		uc010olf.2	Q9Y6C5	OTTHUMG00000008490	ENST00000372192.3:c.2432G>A	1.37:g.45292921C>T	ENSP00000361266:p.Arg811His	Somatic		Capture	Illumina HiSeq	Phase_I	45065508	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.72	3.685143	0.68157	2.27E-4	0.0	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.84370	-1.84;-1.84	4.93	4.93	0.64822	.	0.131649	0.35320	N	0.003285	D	0.88923	0.6569	L	0.58101	1.795	0.52501	D	0.999954	D;D	0.65815	0.982;0.995	P;P	0.56088	0.707;0.791	D	0.88348	0.2979	10	0.40728	T	0.16	-17.3707	18.5308	0.90992	0.0:1.0:0.0:0.0	.	811;811	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	H	811	ENSP00000389703:R811H;ENSP00000361266:R811H	ENSP00000361266:R811H	R	-	2	0	PTCH2	45065508	0.997000	0.39634	1.000000	0.80357	0.979000	0.70002	1.403000	0.34612	2.445000	0.82738	0.557000	0.71058	CGC		0.622	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738	
TESK2	10420	broad.mit.edu	37	1	45810995	45810995	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:45810995G>A	ENST00000372086.3	-	11	1633	c.1233C>T	c.(1231-1233)ggC>ggT	p.G411G	TESK2_ENST00000486676.1_5'UTR|TESK2_ENST00000341771.6_Silent_p.G382G|TESK2_ENST00000372084.1_Silent_p.G382G|TESK2_ENST00000538496.1_Silent_p.G328G	NM_007170.2	NP_009101.2	Q96S53	TESK2_HUMAN	testis-specific kinase 2	411					actin cytoskeleton organization (GO:0030036)|focal adhesion assembly (GO:0048041)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)	p.G395G(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|pancreas(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	32	Acute lymphoblastic leukemia(166;0.155)					ACTTGATCTTGCCCCCCATGA	0.572																																					p.G411G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1233T	1						.						44.0	46.0	45.0					1																	45810995		1900	4112	6012	45583582	SO:0001819	synonymous_variant	10420	exon11			AJ132545	CCDS41323.1	1p32	2010-04-27			ENSG00000070759	ENSG00000070759	2.7.12.1		11732	protein-coding gene	gene with protein product		604746				10512679	Standard	NM_007170		Approved		uc001cns.1	Q96S53	OTTHUMG00000007680	ENST00000372086.3:c.1233C>T	1.37:g.45810995G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45583582	NM_007170	Q5T422|Q5T423|Q8N520|Q9Y3Q6	Silent	SNP	ENST00000372086.3	37	CCDS41323.1																																																																																				0.572	TESK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020523.1	NM_007170	
MMACHC	25974	broad.mit.edu	37	1	45973111	45973111	+	Silent	SNP	G	G	A	rs369883781		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:45973111G>A	ENST00000401061.4	+	2	445	c.165G>A	c.(163-165)acG>acA	p.T55T		NM_015506.2	NP_056321.2	Q9Y4U1	MMAC_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblC type, with homocystinuria	55					cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)	p.T55T(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8	Acute lymphoblastic leukemia(166;0.155)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TACTCAGCACGCCTGCCATGT	0.587																																					p.T55T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G165A	1						.	G		0,4096		0,0,2048	52.0	55.0	54.0		165	-3.4	1.0	1		54	1,8423		0,1,4211	no	coding-synonymous	MMACHC	NM_015506.2		0,1,6259	AA,AG,GG		0.0119,0.0,0.0080		55/283	45973111	1,12519	2048	4212	6260	45745698	SO:0001819	synonymous_variant	25974	exon2				CCDS41324.1	1p34.1	2011-05-12			ENSG00000132763	ENSG00000132763			24525	protein-coding gene	gene with protein product		609831				16311595	Standard	NM_015506		Approved	DKFZP564I122, cblC	uc009vxv.3	Q9Y4U1	OTTHUMG00000007742	ENST00000401061.4:c.165G>A	1.37:g.45973111G>A		Somatic		Capture	Illumina HiSeq	Phase_I	45745698	NM_015506	Q5T157|Q9BRQ7	Silent	SNP	ENST00000401061.4	37	CCDS41324.1																																																																																				0.587	MMACHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020864.2	NM_015506	
RAD54L	8438	broad.mit.edu	37	1	46739342	46739342	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:46739342T>C	ENST00000371975.4	+	14	2207	c.1533T>C	c.(1531-1533)cgT>cgC	p.R511R	RAD54L_ENST00000442598.1_Silent_p.R511R	NM_003579.3	NP_003570.2	Q92698	RAD54_HUMAN	RAD54-like (S. cerevisiae)	511	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				chromosome organization (GO:0051276)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R511R(1)		breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		CCCGAAGCCGTAGCAGTGACA	0.542								Direct reversal of damage;Homologous recombination																													p.R511R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1533C	1						.						70.0	75.0	74.0					1																	46739342		2203	4300	6503	46511929	SO:0001819	synonymous_variant	8438	exon15			X97795	CCDS532.1	1p32	2008-02-05	2001-11-28		ENSG00000085999	ENSG00000085999			9826	protein-coding gene	gene with protein product		603615	"""RAD54 (S.cerevisiae)-like"""			8805304	Standard	NM_003579		Approved	hHR54, hRAD54, RAD54A	uc009vye.2	Q92698	OTTHUMG00000007772	ENST00000371975.4:c.1533T>C	1.37:g.46739342T>C		Somatic		Capture	Illumina HiSeq	Phase_I	46511929	NM_001142548	Q5TE31|Q6IUY3	Silent	SNP	ENST00000371975.4	37	CCDS532.1																																																																																				0.542	RAD54L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021272.1	NM_003579	
FAAH	2166	broad.mit.edu	37	1	46879146	46879146	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:46879146G>A	ENST00000243167.8	+	15	1723	c.1639G>A	c.(1639-1641)Gtg>Atg	p.V547M		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	547					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)	p.V547M(1)		breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	GGGGCTGCCGGTGGCCGTGCA	0.602																																					p.V547M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1639A	1						.						141.0	102.0	115.0					1																	46879146		2203	4300	6503	46651733	SO:0001583	missense	2166	exon15			U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1639G>A	1.37:g.46879146G>A	ENSP00000243167:p.Val547Met	Somatic		Capture	Illumina HiSeq	Phase_I	46651733	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	.	.	.	.	.	.	.	.	.	.	G	15.84	2.952643	0.53293	.	.	ENSG00000117480	ENST00000243167	T	0.63417	-0.04	5.38	4.47	0.54385	Amidase signature domain (2);	0.680145	0.13523	N	0.381563	D	0.84763	0.5544	H	0.94620	3.56	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.86946	0.2082	10	0.87932	D	0	-11.8348	14.1015	0.65059	0.0729:0.0:0.9271:0.0	.	547	O00519	FAAH1_HUMAN	M	547	ENSP00000243167:V547M	ENSP00000243167:V547M	V	+	1	0	FAAH	46651733	1.000000	0.71417	0.866000	0.34008	0.166000	0.22503	6.173000	0.71937	1.283000	0.44513	-0.258000	0.10820	GTG		0.602	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
MROH7	374977	broad.mit.edu	37	1	55174703	55174703	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:55174703C>T	ENST00000421030.2	+	23	3969	c.3684C>T	c.(3682-3684)tgC>tgT	p.C1228C	MROH7-TTC4_ENST00000414150.2_Silent_p.C1228C|MROH7_ENST00000454855.2_Silent_p.C746C|MROH7_ENST00000409996.1_Silent_p.C796C	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	1228						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.C1228C(1)|p.C1225C(1)									TGGTCCCCTGCATGGAGAGCA	0.522																																					p.C1228C												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3684T	1						.						123.0	122.0	123.0					1																	55174703		1917	4111	6028	54947291	SO:0001819	synonymous_variant	374977	exon23			AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.3684C>T	1.37:g.55174703C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54947291	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	37	CCDS41342.2																																																																																				0.522	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
C8B	732	broad.mit.edu	37	1	57422574	57422574	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:57422574C>T	ENST00000371237.4	-	3	325	c.259G>A	c.(259-261)Gcc>Acc	p.A87T	C8B_ENST00000543257.1_Missense_Mutation_p.A35T|C8B_ENST00000535057.1_Missense_Mutation_p.A25T	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	87	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)		p.A87T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						AGCAAGTAGGCATACCTGTAC	0.512																																					p.A87T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G259A	1						.						112.0	102.0	105.0					1																	57422574		2203	4300	6503	57195162	SO:0001583	missense	732	exon3			M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.259G>A	1.37:g.57422574C>T	ENSP00000360281:p.Ala87Thr	Somatic		Capture	Illumina HiSeq	Phase_I	57195162	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	.	.	.	.	.	.	.	.	.	.	C	9.711	1.156984	0.21454	.	.	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	T;T;T	0.27104	2.23;2.23;1.69	5.33	3.91	0.45181	.	0.281030	0.39475	N	0.001354	T	0.21590	0.0520	L	0.47716	1.5	0.22489	N	0.999056	B;B;B	0.20550	0.026;0.046;0.007	B;B;B	0.23419	0.027;0.046;0.011	T	0.17806	-1.0357	10	0.45353	T	0.12	-4.1951	7.1264	0.25473	0.1482:0.7243:0.0:0.1274	.	35;25;87	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	T	87;35;25	ENSP00000360281:A87T;ENSP00000442548:A35T;ENSP00000440113:A25T	ENSP00000360281:A87T	A	-	1	0	C8B	57195162	0.004000	0.15560	0.097000	0.21041	0.481000	0.33189	0.561000	0.23515	0.905000	0.36596	0.591000	0.81541	GCC		0.512	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
DOCK7	85440	broad.mit.edu	37	1	63084513	63084513	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:63084513C>T	ENST00000340370.5	-	14	1563	c.1546G>A	c.(1546-1548)Gca>Aca	p.A516T	DOCK7_ENST00000404627.2_Missense_Mutation_p.A516T|DOCK7_ENST00000251157.5_Missense_Mutation_p.A516T	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	516					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						TTTTCAGGTGCGGGAGAAATG	0.373																																					p.A516T												.	.	0			c.G1546A	1						.						121.0	131.0	128.0					1																	63084513		2203	4300	6503	62857101	SO:0001583	missense	85440	exon14				CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.1546G>A	1.37:g.63084513C>T	ENSP00000340742:p.Ala516Thr	None		Capture	Illumina HiSeq	Phase_I	62857101	NM_033407	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	31	5.095001	0.94197	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.36520	1.25;1.25;1.25	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.53722	0.1814	M	0.80183	2.485	0.58432	D	0.999999	D;D;P;D;P	0.64830	0.98;0.971;0.914;0.994;0.927	P;P;P;P;B	0.59487	0.666;0.726;0.489;0.858;0.342	T	0.56086	-0.8037	10	0.54805	T	0.06	.	19.2632	0.93975	0.0:1.0:0.0:0.0	.	516;516;516;516;516	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	T	516	ENSP00000251157:A516T;ENSP00000340742:A516T;ENSP00000384446:A516T	ENSP00000251157:A516T	A	-	1	0	DOCK7	62857101	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.700000	0.68318	2.785000	0.95823	0.650000	0.86243	GCA		0.373	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
RAVER2	55225	broad.mit.edu	37	1	65273154	65273154	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:65273154A>G	ENST00000294428.3	+	9	1755	c.1677A>G	c.(1675-1677)tcA>tcG	p.S559S	RAVER2_ENST00000371072.4_Silent_p.S546S|RAVER2_ENST00000430964.2_Intron			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	559						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.S546S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						AGATAAGTTCAGGGGTAAGAA	0.398																																					p.S546S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1638G	1						.						43.0	46.0	45.0					1																	65273154		1852	4111	5963	65045742	SO:0001819	synonymous_variant	55225	exon9			AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.1677A>G	1.37:g.65273154A>G		Somatic		Capture	Illumina HiSeq	Phase_I	65045742	NM_018211	Q6P141|Q9NPV7	Silent	SNP	ENST00000294428.3	37																																																																																					0.398	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211	
RAVER2	55225	broad.mit.edu	37	1	65280513	65280513	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:65280513A>G	ENST00000294428.3	+	11	1997	c.1919A>G	c.(1918-1920)gAt>gGt	p.D640G	RAVER2_ENST00000371072.4_Missense_Mutation_p.D627G|RAVER2_ENST00000430964.2_Missense_Mutation_p.D179G			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	640						cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D627G(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	24						CCTTTTGGTGATTATGCACAG	0.363																																					p.D627G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1880G	1						.						93.0	87.0	89.0					1																	65280513		1840	4102	5942	65053101	SO:0001583	missense	55225	exon11			AB046799	CCDS41345.1	1p31.3	2013-02-12			ENSG00000162437	ENSG00000162437		"""RNA binding motif (RRM) containing"""	25577	protein-coding gene	gene with protein product		609953				16051233	Standard	NM_018211		Approved	KIAA1579, FLJ10770	uc001dbs.2	Q9HCJ3	OTTHUMG00000009102	ENST00000294428.3:c.1919A>G	1.37:g.65280513A>G	ENSP00000294428:p.Asp640Gly	Somatic		Capture	Illumina HiSeq	Phase_I	65053101	NM_018211	Q6P141|Q9NPV7	Missense_Mutation	SNP	ENST00000294428.3	37		.	.	.	.	.	.	.	.	.	.	A	8.594	0.885315	0.17540	.	.	ENSG00000162437	ENST00000371072;ENST00000294428;ENST00000430964	T;T	0.36699	1.26;1.24	5.28	5.28	0.74379	.	0.109180	0.64402	D	0.000010	T	0.20210	0.0486	L	0.55481	1.735	0.39795	D	0.972494	B;B	0.24186	0.06;0.099	B;B	0.22753	0.018;0.041	T	0.04767	-1.0928	10	0.30854	T	0.27	-11.3426	13.7323	0.62794	1.0:0.0:0.0:0.0	.	640;627	Q9HCJ3;Q9HCJ3-2	RAVR2_HUMAN;.	G	627;640;179	ENSP00000360112:D627G;ENSP00000294428:D640G	ENSP00000294428:D640G	D	+	2	0	RAVER2	65053101	0.997000	0.39634	0.710000	0.30468	0.007000	0.05969	3.901000	0.56303	2.118000	0.64928	0.472000	0.43445	GAT		0.363	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211	
FUBP1	8880	broad.mit.edu	37	1	78429978	78429978	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:78429978delT	ENST00000370768.2	-	11	982	c.901delA	c.(901-903)atafs	p.I301fs	FUBP1_ENST00000370767.1_Frame_Shift_Del_p.I301fs|FUBP1_ENST00000436586.2_Frame_Shift_Del_p.I322fs	NM_003902.3	NP_003893.2	Q96AE4	FUBP1_HUMAN	far upstream element (FUSE) binding protein 1	301	KH 3. {ECO:0000255|PROSITE- ProRule:PRU00117}.				positive regulation of gene expression (GO:0010628)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)	p.I301fs*22(1)		central_nervous_system(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(3)	17						TCATTTTGTATTTTTTTGATC	0.348			"""F, N"""		oligodendroglioma																																p.I301fs			Rec	yes		1	1p13.1	8880	far upstream element (FUSE) binding protein 1		O	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.901delA	1						.						84.0	82.0	83.0					1																	78429978		2203	4300	6503	78202566	SO:0001589	frameshift_variant	8880	exon11			U05040	CCDS683.1	1p31.1	2008-02-05			ENSG00000162613	ENSG00000162613			4004	protein-coding gene	gene with protein product		603444		FUBP		8125259	Standard	XM_005271309		Approved	FBP	uc001dii.3	Q96AE4	OTTHUMG00000040799	ENST00000370768.2:c.901delA	1.37:g.78429978delT	ENSP00000359804:p.Ile301fs	Somatic		Capture	Illumina HiSeq	Phase_I	78202566	NM_003902	Q12828	Frame_Shift_Del	DEL	ENST00000370768.2	37	CCDS683.1																																																																																				0.348	FUBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098030.3	NM_003902	
BCL10	8915	broad.mit.edu	37	1	85733523	85733523	+	Silent	SNP	C	C	T	rs139473915		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:85733523C>T	ENST00000370580.1	-	3	1226	c.489G>A	c.(487-489)acG>acA	p.T163T		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	163					adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.T163T(1)		haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		AAAAAAAGGGCGTCGTGCTGG	0.433			T	IGH@	MALT								C|||	1	0.000199681	0.0	0.0	5008	,	,		16153	0.0		0.001	False		,,,				2504	0.0				p.T163T	NSCLC(34;993 1034 12176 32621 50182)		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G489A	1						.	C		4,4402	8.1+/-20.4	0,4,2199	101.0	104.0	103.0		489	0.5	0.8	1	dbSNP_134	103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BCL10	NM_003921.4		0,5,6498	TT,TC,CC		0.0116,0.0908,0.0384		163/234	85733523	5,13001	2203	4300	6503	85506111	SO:0001819	synonymous_variant	8915	exon3			AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.489G>A	1.37:g.85733523C>T		Somatic		Capture	Illumina HiSeq	Phase_I	85506111	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																				0.433	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
SH3GLB1	51100	broad.mit.edu	37	1	87200293	87200293	+	Missense_Mutation	SNP	G	G	T	rs200907097		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:87200293G>T	ENST00000370558.4	+	6	903	c.579G>T	c.(577-579)caG>caT	p.Q193H	SH3GLB1_ENST00000482504.1_Missense_Mutation_p.Q214H|SH3GLB1_ENST00000535010.1_Missense_Mutation_p.Q93H	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1	193	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)	p.Q193H(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		AGTCTGAACAGGAATTAAGAA	0.338																																					p.Q193H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G579T	1						.						46.0	47.0	47.0					1																	87200293		2201	4299	6500	86972881	SO:0001583	missense	51100	exon6			AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	10833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 70"""	609287	"""SH3-domain, GRB2-like, endophilin B1"""			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.579G>T	1.37:g.87200293G>T	ENSP00000473267:p.Gln193His	Somatic		Capture	Illumina HiSeq	Phase_I	86972881	NM_016009	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Missense_Mutation	SNP	ENST00000370558.4	37	CCDS710.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930838	0.73327	.	.	ENSG00000097033	ENST00000212369;ENST00000535010;ENST00000482504	T;T	0.32753	1.44;1.44	4.97	4.97	0.65823	BAR (3);IRSp53/MIM homology domain (IMD) (1);	0.000000	0.85682	D	0.000000	T	0.27866	0.0686	N	0.21097	0.63	0.80722	D	1	D;D;B	0.55800	0.973;0.967;0.003	P;P;B	0.57548	0.823;0.73;0.012	T	0.05886	-1.0858	10	0.46703	T	0.11	0.204	18.2378	0.89956	0.0:0.0:1.0:0.0	.	93;214;193	B4E182;Q9Y371-2;Q9Y371	.;.;SHLB1_HUMAN	H	193;93;214	ENSP00000441355:Q93H;ENSP00000418744:Q214H	ENSP00000212369:Q193H	Q	+	3	2	SH3GLB1	86972881	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.296000	0.72751	2.316000	0.78162	0.561000	0.74099	CAG		0.338	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009	
GBP1	2633	broad.mit.edu	37	1	89524576	89524576	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:89524576T>C	ENST00000370473.4	-	5	798	c.579A>G	c.(577-579)ggA>ggG	p.G193G		NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	193	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)	p.G193G(1)		endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		TGAGGGGTTGTCCATCTGCTT	0.448																																					p.G193G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A579G	1						.						190.0	176.0	181.0					1																	89524576		2203	4300	6503	89297164	SO:0001819	synonymous_variant	2633	exon5			BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"""guanylate binding protein 1, interferon-inducible, 67kDa"""			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.579A>G	1.37:g.89524576T>C		Somatic		Capture	Illumina HiSeq	Phase_I	89297164	NM_002053	D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	CCDS718.1																																																																																				0.448	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053	
ZNF644	84146	broad.mit.edu	37	1	91404135	91404135	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:91404135T>A	ENST00000370440.1	-	3	2993	c.2776A>T	c.(2776-2778)Agt>Tgt	p.S926C	ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000337393.5_Missense_Mutation_p.S926C			Q9H582	ZN644_HUMAN	zinc finger protein 644	926					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S926C(1)		breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		AAGTTGTTACTTCCAGTATCT	0.363																																					p.S926C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2776T	1						.						54.0	55.0	54.0					1																	91404135		2203	4299	6502	91176723	SO:0001583	missense	84146	exon3			AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2776A>T	1.37:g.91404135T>A	ENSP00000359469:p.Ser926Cys	Somatic		Capture	Illumina HiSeq	Phase_I	91176723	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	37	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	9.700	1.154247	0.21371	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.00591	6.35;6.35	5.84	3.48	0.39840	.	0.399613	0.29884	N	0.010959	T	0.00178	0.0005	N	0.14661	0.345	0.21527	N	0.999652	B	0.26876	0.162	B	0.30855	0.121	T	0.45483	-0.9258	10	0.56958	D	0.05	-3.2427	4.4931	0.11824	0.1365:0.2583:0.0:0.6051	.	926	Q9H582	ZN644_HUMAN	C	926;926;498	ENSP00000359469:S926C;ENSP00000337008:S926C	ENSP00000337008:S926C	S	-	1	0	ZNF644	91176723	0.859000	0.29813	1.000000	0.80357	0.964000	0.63967	-0.063000	0.11655	0.460000	0.27045	0.482000	0.46254	AGT		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
HFM1	164045	broad.mit.edu	37	1	91784693	91784693	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:91784693A>T	ENST00000370425.3	-	25	2852	c.2754T>A	c.(2752-2754)tgT>tgA	p.C918*	HFM1_ENST00000370424.3_Nonsense_Mutation_p.C597*|HFM1_ENST00000294696.5_Nonsense_Mutation_p.C150*|HFM1_ENST00000462405.1_5'UTR	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	918	SEC63.				resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)	p.C918*(1)		breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		TACACCTAAAACATTTAGCTA	0.348																																					p.C918X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T2754A	1						.						66.0	69.0	68.0					1																	91784693		2203	4300	6503	91557281	SO:0001587	stop_gained	164045	exon25			AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2754T>A	1.37:g.91784693A>T	ENSP00000359454:p.Cys918*	Somatic		Capture	Illumina HiSeq	Phase_I	91557281	NM_001017975	B1B0B6|Q8N9Q0	Nonsense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	A	39	7.874968	0.98537	.	.	ENSG00000162669	ENST00000370425;ENST00000294696;ENST00000370424;ENST00000370421	.	.	.	5.14	3.99	0.46301	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.791	0.40706	0.8616:0.0:0.1384:0.0	.	.	.	.	X	918;150;597;602	.	ENSP00000294696:C150X	C	-	3	2	HFM1	91557281	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.011000	0.40922	2.065000	0.61736	0.528000	0.53228	TGT		0.348	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
GFI1	2672	broad.mit.edu	37	1	92948984	92948984	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:92948984G>T	ENST00000370332.1	-	2	379	c.61C>A	c.(61-63)Cca>Aca	p.P21T	GFI1_ENST00000294702.5_Missense_Mutation_p.P21T|GFI1_ENST00000483490.1_5'UTR|GFI1_ENST00000427103.1_Missense_Mutation_p.P21T	NM_001127215.1	NP_001120687.1	Q99684	GFI1_HUMAN	growth factor independent 1 transcription repressor	21					auditory receptor cell differentiation (GO:0042491)|cell fate commitment (GO:0045165)|cellular response to lipopolysaccharide (GO:0071222)|inner ear morphogenesis (GO:0042472)|mechanosensory behavior (GO:0007638)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cell fate specification (GO:0009996)|negative regulation of neuron projection development (GO:0010977)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vitamin D biosynthetic process (GO:0010957)|positive regulation of cell fate specification (GO:0042660)|positive regulation of interleukin-6-mediated signaling pathway (GO:0070105)|regulation of toll-like receptor signaling pathway (GO:0034121)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|viral process (GO:0016032)	nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.P21T(1)		autonomic_ganglia(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15		all_lung(203;0.00292)|Lung NSC(277;0.0115)|all_neural(321;0.185)|Glioma(108;0.203)		OV - Ovarian serous cystadenocarcinoma(397;9.04e-07)|Epithelial(280;1.17e-05)|all cancers(265;5.61e-05)|GBM - Glioblastoma multiforme(16;0.0191)		TCTGGTCCTGGGGAGCGCGGC	0.657																																					p.P21T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C61A	1						.						69.0	57.0	61.0					1																	92948984		2203	4300	6503	92721572	SO:0001583	missense	2672	exon2			U67369	CCDS30773.1	1p22	2014-09-17	2007-10-04		ENSG00000162676	ENSG00000162676		"""Zinc fingers, C2H2-type"""	4237	protein-coding gene	gene with protein product		600871	"""growth factor independent 1"""	ZNF163		7789186	Standard	NM_005263		Approved	GFI1A, GFI-1	uc001dov.4	Q99684	OTTHUMG00000010897	ENST00000370332.1:c.61C>A	1.37:g.92948984G>T	ENSP00000359357:p.Pro21Thr	Somatic		Capture	Illumina HiSeq	Phase_I	92721572	NM_001127215	Q8N564	Missense_Mutation	SNP	ENST00000370332.1	37	CCDS30773.1	.	.	.	.	.	.	.	.	.	.	G	13.58	2.278953	0.40294	.	.	ENSG00000162676	ENST00000370332;ENST00000427103;ENST00000294702	T;T;T	0.08896	3.04;3.04;3.04	5.36	5.36	0.76844	.	0.369567	0.25439	N	0.030670	T	0.03477	0.0100	L	0.54323	1.7	0.29269	N	0.870803	P	0.43477	0.808	B	0.36464	0.225	T	0.41875	-0.9484	10	0.14656	T	0.56	-31.7455	14.5855	0.68320	0.0:0.0:1.0:0.0	.	21	Q99684	GFI1_HUMAN	T	21	ENSP00000359357:P21T;ENSP00000399719:P21T;ENSP00000294702:P21T	ENSP00000294702:P21T	P	-	1	0	GFI1	92721572	0.002000	0.14202	1.000000	0.80357	0.845000	0.48019	0.725000	0.25970	2.500000	0.84329	0.561000	0.74099	CCA		0.657	GFI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030054.1	NM_005263	
ARHGAP29	9411	broad.mit.edu	37	1	94650983	94650983	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:94650983G>A	ENST00000260526.6	-	17	2017	c.1835C>T	c.(1834-1836)aCa>aTa	p.T612I	ARHGAP29_ENST00000482481.1_5'UTR	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	612					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)	p.T612I(1)		NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		AAACTTGTGTGTGAGAGCTGC	0.373																																					p.T612I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1835T	1						.						153.0	142.0	146.0					1																	94650983		2203	4300	6503	94423571	SO:0001583	missense	9411	exon17				CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.1835C>T	1.37:g.94650983G>A	ENSP00000260526:p.Thr612Ile	Somatic		Capture	Illumina HiSeq	Phase_I	94423571	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.191383	0.78902	.	.	ENSG00000137962	ENST00000260526	D	0.84516	-1.86	5.7	4.74	0.60224	Protein kinase C-like, phorbol ester/diacylglycerol binding (2);	0.000000	0.39687	N	0.001283	D	0.91212	0.7231	M	0.76170	2.325	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.988;0.994	D	0.91774	0.5430	10	0.87932	D	0	-23.9357	18.3296	0.90264	0.0:0.1284:0.8716:0.0	.	612;612	F8VWZ8;Q52LW3	.;RHG29_HUMAN	I	612	ENSP00000260526:T612I	ENSP00000260526:T612I	T	-	2	0	ARHGAP29	94423571	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.786000	0.69006	2.698000	0.92095	0.655000	0.94253	ACA		0.373	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
TRMT13	54482	broad.mit.edu	37	1	100606529	100606529	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:100606529delA	ENST00000370141.2	+	7	629	c.623delA	c.(622-624)gaafs	p.E208fs		NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	208					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)	p.V210fs*5(1)									AAAGATGCTGAAAAAGTTCAC	0.358																																					p.E208fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.623delA	1						.						105.0	104.0	104.0					1																	100606529		2203	4300	6503	100379117	SO:0001589	frameshift_variant	54482	exon7			BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.623delA	1.37:g.100606529delA	ENSP00000359160:p.Glu208fs	Somatic		Capture	Illumina HiSeq	Phase_I	100379117	NM_019083	Q5VVL0|Q9NW65	Frame_Shift_Del	DEL	ENST00000370141.2	37	CCDS765.1																																																																																				0.358	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
FNDC7	163479	broad.mit.edu	37	1	109276138	109276138	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:109276138delA	ENST00000370017.3	+	10	2401	c.2124delA	c.(2122-2124)ccafs	p.P708fs	RP11-293A10.3_ENST00000437400.2_RNA|FNDC7_ENST00000271311.2_Frame_Shift_Del_p.P709fs	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	708	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)		p.I478fs*4(1)		breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		CTTTCTGTCCAAAAAAAATAT	0.363																																					p.P708fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2124delA	1						.						65.0	66.0	66.0					1																	109276138		2203	4300	6503	109077661	SO:0001589	frameshift_variant	163479	exon10				CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.2124delA	1.37:g.109276138delA	ENSP00000359034:p.Pro708fs	Somatic		Capture	Illumina HiSeq	Phase_I	109077661	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Frame_Shift_Del	DEL	ENST00000370017.3	37	CCDS44185.1																																																																																				0.363	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
ZNF687	57592	broad.mit.edu	37	1	151261079	151261079	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:151261079delC	ENST00000368879.2	+	3	2289	c.2191delC	c.(2191-2193)cccfs	p.P732fs		NM_020832.1	NP_065883.1	Q8N1G0	ZN687_HUMAN	zinc finger protein 687	732					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.H733fs*30(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)			TAAGAATCGACCCCCCCATGT	0.577																																					p.P731fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2191delC	1						.						117.0	98.0	105.0					1																	151261079		2203	4300	6503	149527703	SO:0001589	frameshift_variant	57592	exon3				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.2191delC	1.37:g.151261079delC	ENSP00000357874:p.Pro732fs	Somatic		Capture	Illumina HiSeq	Phase_I	149527703	NM_020832	D3DV17|Q68DQ8|Q9H937|Q9P2A7	Frame_Shift_Del	DEL	ENST00000368879.2	37																																																																																					0.577	ZNF687-201	KNOWN	basic	protein_coding	protein_coding		NM_020832	
USF1	7391	broad.mit.edu	37	1	161011524	161011524	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:161011524delC	ENST00000368021.3	-	6	593	c.389delG	c.(388-390)ggtfs	p.G130fs	TSTD1_ENST00000423014.2_5'Flank|USF1_ENST00000435396.1_Frame_Shift_Del_p.G71fs|TSTD1_ENST00000318289.10_5'Flank|USF1_ENST00000368019.1_Splice_Site|TSTD1_ENST00000368023.3_5'Flank|TSTD1_ENST00000368024.1_5'Flank|F11R_ENST00000289779.3_5'Flank|USF1_ENST00000368020.1_Frame_Shift_Del_p.G130fs	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	130					carbon catabolite regulation of transcription (GO:0045990)|cellular response to insulin stimulus (GO:0032869)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|late viral transcription (GO:0019086)|lipid homeostasis (GO:0055088)|negative regulation of fibrinolysis (GO:0051918)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter by glucose (GO:0000430)|response to hypoxia (GO:0001666)|response to UV (GO:0009411)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)	p.G130fs*33(1)		central_nervous_system(1)|large_intestine(3)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	all_cancers(52;6.73e-18)|Breast(13;0.012)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CGATGTGGTACCCCCTGCCCC	0.592											OREG0013936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G130fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.389delG	1						.						87.0	82.0	84.0					1																	161011524		2203	4300	6503	159278148	SO:0001589	frameshift_variant	7391	exon6			BC035505	CCDS1214.1	1q22-q23	2013-05-21			ENSG00000158773	ENSG00000158773		"""Basic helix-loop-helix proteins"""	12593	protein-coding gene	gene with protein product		191523				8486371	Standard	NM_007122		Approved	UEF, MLTFI, bHLHb11	uc031pqv.1	P22415	OTTHUMG00000031472	ENST00000368021.3:c.389delG	1.37:g.161011524delC	ENSP00000357000:p.Gly130fs	Somatic	1813	Capture	Illumina HiSeq	Phase_I	159278148	NM_007122	B2RBZ4|Q5SY46|Q7Z5Y1	Frame_Shift_Del	DEL	ENST00000368021.3	37	CCDS1214.1																																																																																				0.592	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122	
PRDX6	9588	broad.mit.edu	37	1	173454618	173454618	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:173454618delA	ENST00000340385.5	+	3	503	c.371delA	c.(370-372)gaafs	p.E124fs	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	124	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)	p.K125fs*5(1)		NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						GAGAAGGATGAAAAGGGCATG	0.468																																					p.E124fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.371delA	1						.						137.0	128.0	131.0					1																	173454618		2203	4300	6503	171721241	SO:0001589	frameshift_variant	9588	exon3			D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.371delA	1.37:g.173454618delA	ENSP00000342026:p.Glu124fs	Somatic		Capture	Illumina HiSeq	Phase_I	171721241	NM_004905	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Frame_Shift_Del	DEL	ENST00000340385.5	37	CCDS1307.1																																																																																				0.468	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905	
HMCN1	83872	broad.mit.edu	37	1	185969318	185969318	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:185969318delT	ENST00000271588.4	+	26	4245	c.4016delT	c.(4015-4017)gtgfs	p.V1339fs	HMCN1_ENST00000367492.2_Frame_Shift_Del_p.V1339fs	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1339	Ig-like C2-type 10.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)	p.V1339fs*22(1)		NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TACATCTGTGTGGCAGTCAAT	0.433																																					p.V1339fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4016delT	1						.						126.0	113.0	117.0					1																	185969318		2203	4300	6503	184235941	SO:0001589	frameshift_variant	83872	exon26			AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.4016delT	1.37:g.185969318delT	ENSP00000271588:p.Val1339fs	Somatic		Capture	Illumina HiSeq	Phase_I	184235941	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Frame_Shift_Del	DEL	ENST00000271588.4	37	CCDS30956.1																																																																																				0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
TPR	7175	broad.mit.edu	37	1	186291530	186291530	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:186291530delA	ENST00000367478.4	-	45	6677	c.6381delT	c.(6379-6381)tttfs	p.F2127fs		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	2127					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)	p.F2114fs*65(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		CTTCATCATCAAAAAAATGCT	0.338			T	NTRK1	papillary thyroid																																p.F2127fs			Dom	yes		1	1q25	7175	translocated promoter region		E	.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6381delT	1						.						96.0	90.0	92.0					1																	186291530		1859	4095	5954	184558153	SO:0001589	frameshift_variant	7175	exon45			U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.6381delT	1.37:g.186291530delA	ENSP00000356448:p.Phe2127fs	Somatic		Capture	Illumina HiSeq	Phase_I	184558153	NM_003292	Q15655|Q5SWY0|Q99968	Frame_Shift_Del	DEL	ENST00000367478.4	37	CCDS41446.1																																																																																				0.338	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
ASPM	259266	broad.mit.edu	37	1	197091290	197091290	+	Splice_Site	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:197091290delT	ENST00000367409.4	-	15	3996	c.3740delA	c.(3739-3741)aag>ag	p.K1247fs	ASPM_ENST00000294732.7_Splice_Site_p.K1247fs|ASPM_ENST00000367408.1_Splice_Site_p.K497fs	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1247					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)		p.K1247fs*21(1)		breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTTACTTACCTTTTCATCTGG	0.294																																					p.K1247fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3740delA	1						.						32.0	33.0	33.0					1																	197091290		2199	4289	6488	195357913	SO:0001630	splice_region_variant	259266	exon15			AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.3741+1A>-	1.37:g.197091290delT		Somatic		Capture	Illumina HiSeq	Phase_I	195357913	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Frame_Shift_Del	DEL	ENST00000367409.4	37	CCDS1389.1																																																																																				0.294	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	Frame_Shift_Del
ZC3H11A	9877	broad.mit.edu	37	1	203816590	203816590	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:203816590delA	ENST00000545588.1	+	12	5148	c.1321delA	c.(1321-1323)aaafs	p.K442fs	ZC3H11A_ENST00000367214.1_Frame_Shift_Del_p.K442fs|ZC3H11A_ENST00000367212.3_Frame_Shift_Del_p.K442fs|ZC3H11A_ENST00000367210.1_Frame_Shift_Del_p.K442fs|ZC3H11A_ENST00000332127.4_Frame_Shift_Del_p.K442fs	NM_001271675.1	NP_001258604.1	O75152	ZC11A_HUMAN	zinc finger CCCH-type containing 11A	442					poly(A)+ mRNA export from nucleus (GO:0016973)		metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.T443fs*2(1)		central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32	all_cancers(21;0.0904)|all_epithelial(62;0.234)		BRCA - Breast invasive adenocarcinoma(75;0.109)			TAGTGAAATTAAAAAAACAGT	0.428																																					p.K441fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1321delA	1						.						64.0	71.0	69.0					1																	203816590		2203	4299	6502	202083213	SO:0001589	frameshift_variant	9877	exon15				CCDS30978.1	1q32.1	2012-07-05	2005-06-02	2005-06-02	ENSG00000058673	ENSG00000058673		"""Zinc fingers, CCCH-type domain containing"""	29093	protein-coding gene	gene with protein product		613513	"""zinc finger CCCH-type domain containing 11A"""	ZC3HDC11A		9734811	Standard	NM_014827		Approved	KIAA0663	uc001hac.3	O75152	OTTHUMG00000035909	ENST00000545588.1:c.1321delA	1.37:g.203816590delA	ENSP00000438527:p.Lys442fs	Somatic		Capture	Illumina HiSeq	Phase_I	202083213	NM_014827	Q6AHY4|Q6AHY9|Q6AW79|Q6AWA1|Q6PJK4|Q86XZ7	Frame_Shift_Del	DEL	ENST00000545588.1	37	CCDS30978.1																																																																																				0.428	ZC3H11A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087471.3	NM_014827	
OR2M7	391196	broad.mit.edu	37	1	248487096	248487096	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr1:248487096A>G	ENST00000317965.2	-	1	803	c.775T>C	c.(775-777)Tgc>Cgc	p.C259R		NM_001004691.1	NP_001004691.1	Q8NG81	OR2M7_HUMAN	olfactory receptor, family 2, subfamily M, member 7	259						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C259R(1)		breast(1)|endometrium(6)|large_intestine(3)|lung(29)|skin(3)	42	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GGCTGAATGCACATGAACAAA	0.468																																					p.C259R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T775C	1						.						174.0	157.0	163.0					1																	248487096		2203	4300	6503	246553719	SO:0001583	missense	391196	exon1			BK004486	CCDS31111.1	1q44	2012-08-09			ENSG00000177186	ENSG00000177186		"""GPCR / Class A : Olfactory receptors"""	19594	protein-coding gene	gene with protein product							Standard	NM_001004691		Approved		uc010pzk.2	Q8NG81	OTTHUMG00000040461	ENST00000317965.2:c.775T>C	1.37:g.248487096A>G	ENSP00000324557:p.Cys259Arg	Somatic		Capture	Illumina HiSeq	Phase_I	246553719	NM_001004691	B2RNL0|Q6IEX6	Missense_Mutation	SNP	ENST00000317965.2	37	CCDS31111.1	.	.	.	.	.	.	.	.	.	.	A	0.655	-0.808054	0.02819	.	.	ENSG00000177186	ENST00000317965	T	0.00063	8.78	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.29868	U	0.011000	T	0.00109	0.0003	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30736	-0.9968	10	0.87932	D	0	.	8.684	0.34225	1.0:0.0:0.0:0.0	.	259	Q8NG81	OR2M7_HUMAN	R	259	ENSP00000324557:C259R	ENSP00000324557:C259R	C	-	1	0	OR2M7	246553719	0.016000	0.18221	0.003000	0.11579	0.017000	0.09413	2.797000	0.47877	0.708000	0.31955	0.163000	0.16589	TGC		0.468	OR2M7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097357.1	NM_001004691	
SNAP25	6616	broad.mit.edu	37	20	10277646	10277646	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:10277646C>T	ENST00000254976.2	+	6	566	c.355C>T	c.(355-357)Cgt>Tgt	p.R119C	SNAP25_ENST00000495883.1_3'UTR|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25-AS1_ENST00000421143.2_RNA|SNAP25_ENST00000304886.2_Missense_Mutation_p.R119C	NM_130811.2	NP_570824.1	P60880	SNP25_HUMAN	synaptosomal-associated protein, 25kDa	119					energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long-term synaptic potentiation (GO:0060291)|neurotransmitter secretion (GO:0007269)|neurotransmitter uptake (GO:0001504)|regulation of establishment of protein localization (GO:0070201)|regulation of insulin secretion (GO:0050796)|regulation of neuron projection development (GO:0010975)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|SNARE complex (GO:0031201)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex (GO:0070032)|trans-Golgi network (GO:0005802)	calcium-dependent protein binding (GO:0048306)	p.R119C(1)		endometrium(1)|large_intestine(2)|lung(8)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	18					Botulinum Toxin Type A(DB00083)	CCAGCCTGCTCGTGTAGTGGA	0.517																																					p.R119C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C355T	20						.						76.0	71.0	73.0					20																	10277646		2203	4300	6503	10225646	SO:0001583	missense	6616	exon6				CCDS13109.1, CCDS13110.1	20p12-p11.2	2008-08-01	2002-08-29		ENSG00000132639	ENSG00000132639			11132	protein-coding gene	gene with protein product	"""resistance to inhibitors of cholinesterase 4 homolog"""	600322	"""synaptosomal-associated protein, 25kD"""	SNAP		8661740, 10692432	Standard	NM_003081		Approved	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2	uc002wnr.2	P60880	OTTHUMG00000031863	ENST00000254976.2:c.355C>T	20.37:g.10277646C>T	ENSP00000254976:p.Arg119Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10225646	NM_130811	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Missense_Mutation	SNP	ENST00000254976.2	37	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989702	0.74589	.	.	ENSG00000132639	ENST00000254976;ENST00000304886	.	.	.	5.86	5.86	0.93980	SNAP-25 (1);	0.000000	0.85682	D	0.000000	D	0.84669	0.5523	M	0.85945	2.785	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79108	0.984;0.992	D	0.85515	0.1200	9	0.62326	D	0.03	-2.2047	20.1996	0.98256	0.0:1.0:0.0:0.0	.	119;119	P60880-2;P60880	.;SNP25_HUMAN	C	119	.	ENSP00000254976:R119C	R	+	1	0	SNAP25	10225646	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.818000	0.86416	2.776000	0.95493	0.650000	0.86243	CGT		0.517	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811	
JAG1	182	broad.mit.edu	37	20	10629720	10629720	+	Missense_Mutation	SNP	C	C	T	rs201667840		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:10629720C>T	ENST00000254958.5	-	11	1899	c.1384G>A	c.(1384-1386)Gcc>Acc	p.A462T	JAG1_ENST00000423891.2_Missense_Mutation_p.A303T|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	462	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)	p.A462T(4)		biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CGACAGGAGGCGTCATTCTGA	0.353									Alagille Syndrome				C|||	1	0.000199681	0.0	0.0	5008	,	,		18871	0.0		0.001	False		,,,				2504	0.0				p.A462T												.	.	4	Substitution - Missense(4)	large_intestine(4)	c.G1384A	20						.						51.0	54.0	53.0					20																	10629720		2203	4300	6503	10577720	SO:0001583	missense	182	exon11	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.1384G>A	20.37:g.10629720C>T	ENSP00000254958:p.Ala462Thr	Somatic		Capture	Illumina HiSeq	Phase_I	10577720	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	29.8	5.033955	0.93575	.	.	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.94232	-3.38;-3.38	6.07	6.07	0.98685	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.047852	0.85682	D	0.000000	D	0.97337	0.9129	M	0.93062	3.375	0.52099	D	0.999949	D	0.69078	0.997	P	0.59424	0.857	D	0.97462	1.0035	10	0.87932	D	0	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	462	P78504	JAG1_HUMAN	T	462;303	ENSP00000254958:A462T;ENSP00000389519:A303T	ENSP00000254958:A462T	A	-	1	0	JAG1	10577720	1.000000	0.71417	0.949000	0.38748	0.981000	0.71138	7.786000	0.85741	2.884000	0.98904	0.655000	0.94253	GCC		0.353	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
ISM1	140862	broad.mit.edu	37	20	13279713	13279713	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:13279713G>A	ENST00000262487.4	+	6	1008	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	334	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)		p.T334T(1)		NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						CCTACAGCACGGCCGACATCT	0.582																																					p.T334T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1002A	20						.						46.0	52.0	50.0					20																	13279713		2112	4234	6346	13227713	SO:0001819	synonymous_variant	140862	exon6			AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"""chromosome 20 open reading frame 82"", ""isthmin 1 homolog (zebrafish)"""	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.1002G>A	20.37:g.13279713G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13227713	NM_080826	Q8WVH9	Silent	SNP	ENST00000262487.4	37	CCDS46579.1																																																																																				0.582	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2		
SIRPB1	10326	broad.mit.edu	37	20	1552456	1552456	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:1552456C>T	ENST00000381605.4	-	3	725	c.661G>A	c.(661-663)Gtt>Att	p.V221I	SIRPB1_ENST00000262929.5_Intron|SIRPB1_ENST00000381603.3_Intron|RP4-576H24.4_ENST00000564763.1_Intron	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	221	Ig-like C1-type 1.				cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)		p.V221I(1)		central_nervous_system(2)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	31						TGAGAGTGAACGTCCCCACGG	0.587																																					p.V221I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G661A	20						.						159.0	138.0	145.0					20																	1552456		2203	4300	6503	1500456	SO:0001583	missense	10326	exon3			Y10376	CCDS13019.1, CCDS42850.1, CCDS46571.1	20p13	2013-01-11			ENSG00000101307	ENSG00000101307		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	15928	protein-coding gene	gene with protein product		603889				9062191, 16339511	Standard	NM_001083910		Approved	SIRP-BETA-1, CD172b	uc010gai.3	O00241	OTTHUMG00000031676	ENST00000381605.4:c.661G>A	20.37:g.1552456C>T	ENSP00000371018:p.Val221Ile	Somatic		Capture	Illumina HiSeq	Phase_I	1500456	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Missense_Mutation	SNP	ENST00000381605.4	37	CCDS13019.1	.	.	.	.	.	.	.	.	.	.	.	7.428	0.638069	0.14386	.	.	ENSG00000101307	ENST00000381605	T	0.00608	6.25	2.47	-0.459	0.12179	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.118916	0.37530	N	0.002059	T	0.00468	0.0015	L	0.31845	0.965	0.09310	N	1	B	0.27765	0.188	B	0.32022	0.139	T	0.47169	-0.9138	10	0.18276	T	0.48	.	4.7091	0.12863	0.0:0.5033:0.0:0.4967	.	221	O00241	SIRB1_HUMAN	I	221	ENSP00000371018:V221I	ENSP00000371018:V221I	V	-	1	0	SIRPB1	1500456	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.425000	0.07017	-0.004000	0.14419	-0.467000	0.05162	GTT		0.587	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
NDUFAF5	79133	broad.mit.edu	37	20	13765886	13765886	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:13765886T>C	ENST00000378106.5	+	1	291	c.172T>C	c.(172-174)Tgg>Cgg	p.W58R	ESF1_ENST00000202816.1_5'Flank|NDUFAF5_ENST00000475968.1_3'UTR|NDUFAF5_ENST00000463598.1_Missense_Mutation_p.W58R	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	58					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)	p.W58R(1)									ACAGAAGAACTGGGCAGCCCG	0.642																																					p.W58R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T172C	20						.						19.0	23.0	22.0					20																	13765886		2203	4300	6503	13713886	SO:0001583	missense	79133	exon1				CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"""Mitochondrial respiratory chain complex assembly factors"""	15899	protein-coding gene	gene with protein product		612360	"""chromosome 20 open reading frame 7"""	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.172T>C	20.37:g.13765886T>C	ENSP00000367346:p.Trp58Arg	Somatic		Capture	Illumina HiSeq	Phase_I	13713886	NM_001039375	A8K166|Q6GPH3|Q9H6F4	Missense_Mutation	SNP	ENST00000378106.5	37	CCDS13118.1	.	.	.	.	.	.	.	.	.	.	T	8.768	0.925314	0.18056	.	.	ENSG00000101247	ENST00000378106;ENST00000536501;ENST00000463598	T;T	0.35421	1.31;1.31	5.7	5.7	0.88788	.	0.060590	0.64402	D	0.000001	T	0.17874	0.0429	N	0.04746	-0.17	0.80722	D	1	B;B;B	0.12013	0.005;0.003;0.001	B;B;B	0.15484	0.013;0.006;0.001	T	0.10800	-1.0614	10	0.02654	T	1	-2.4218	15.6352	0.76946	0.0:0.0:0.0:1.0	.	58;58;58	Q5TEU4-2;Q5TEU4;B3KR61	.;CT007_HUMAN;.	R	58	ENSP00000367346:W58R;ENSP00000420497:W58R	ENSP00000437325:W58R	W	+	1	0	C20orf7	13713886	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.959000	0.70339	2.170000	0.68504	0.482000	0.46254	TGG		0.642	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375	
BANF2	140836	broad.mit.edu	37	20	17716439	17716439	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:17716439T>C	ENST00000246090.5	+	4	518	c.256T>C	c.(256-258)Tgt>Cgt	p.C86R	BANF2_ENST00000467330.1_3'UTR|BANF2_ENST00000545418.2_Missense_Mutation_p.C93R|BANF2_ENST00000377805.3_Missense_Mutation_p.C86R	NM_178477.4	NP_848572.3	Q9H503	BAFL_HUMAN	barrier to autointegration factor 2	86						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.C86R(1)		large_intestine(1)|lung(1)|prostate(3)|skin(1)	6						CAAGGAGTGGTGTGCCTGCTT	0.552																																					p.C86R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T256C	20						.						157.0	131.0	139.0					20																	17716439		2203	4300	6503	17664439	SO:0001583	missense	140836	exon4			BC054871	CCDS13129.1, CCDS54449.1	20p12.1	2007-12-17	2007-12-17	2007-12-17	ENSG00000125888	ENSG00000125888			16172	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 179"""	C20orf179			Standard	NM_178477		Approved	dJ803K15.1, BAF-L, BAFL, BAF2	uc010zrs.1	Q9H503	OTTHUMG00000031949	ENST00000246090.5:c.256T>C	20.37:g.17716439T>C	ENSP00000246090:p.Cys86Arg	Somatic		Capture	Illumina HiSeq	Phase_I	17664439	NM_178477	D3DW25|F5H3F6|Q7Z4M6	Missense_Mutation	SNP	ENST00000246090.5	37	CCDS13129.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.796845	0.70567	.	.	ENSG00000125888	ENST00000545418;ENST00000377805;ENST00000246090	T;T;T	0.59502	0.26;0.26;0.26	5.5	5.5	0.81552	.	0.165305	0.43919	D	0.000517	T	0.74861	0.3772	.	.	.	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.77004	0.982;0.989	T	0.78357	-0.2235	9	0.87932	D	0	.	11.9876	0.53157	0.0:0.0:0.0:1.0	.	93;86	F5H3F6;Q9H503	.;BAFL_HUMAN	R	93;86;86	ENSP00000439128:C93R;ENSP00000367036:C86R;ENSP00000246090:C86R	ENSP00000246090:C86R	C	+	1	0	BANF2	17664439	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.554000	0.45845	2.086000	0.62901	0.459000	0.35465	TGT		0.552	BANF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102261.2	NM_178477	
CRNKL1	51340	broad.mit.edu	37	20	20020253	20020253	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:20020253C>A	ENST00000377340.2	-	12	2059	c.2028G>T	c.(2026-2028)gaG>gaT	p.E676D	CRNKL1_ENST00000521379.1_5'Flank|CRNKL1_ENST00000536226.1_Splice_Site_p.E515D|CRNKL1_ENST00000377327.4_Splice_Site_p.E664D	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	676					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.E676D(1)		breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						AGATGCTCACCTCTGGCATGT	0.378																																					p.E676D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2028T	20						.						109.0	103.0	105.0					20																	20020253		2203	4300	6503	19968253	SO:0001630	splice_region_variant	51340	exon12			AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.2028+1G>T	20.37:g.20020253C>A		Somatic		Capture	Illumina HiSeq	Phase_I	19968253	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Missense_Mutation	SNP	ENST00000377340.2	37	CCDS33446.1	.	.	.	.	.	.	.	.	.	.	C	33	5.197819	0.94997	.	.	ENSG00000101343	ENST00000377327;ENST00000377340;ENST00000536226	T;T;T	0.42131	0.98;0.98;0.98	5.82	5.82	0.92795	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.68641	0.3023	M	0.89785	3.06	0.80722	D	1	P	0.45768	0.866	P	0.55011	0.766	T	0.72187	-0.4366	9	.	.	.	-30.1321	20.0979	0.97857	0.0:1.0:0.0:0.0	.	676	Q9BZJ0	CRNL1_HUMAN	D	664;676;515	ENSP00000366544:E664D;ENSP00000366557:E676D;ENSP00000440733:E515D	.	E	-	3	2	CRNKL1	19968253	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.818000	0.86416	2.761000	0.94854	0.591000	0.81541	GAG		0.378	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		Missense_Mutation
XRN2	22803	broad.mit.edu	37	20	21327098	21327098	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:21327098T>C	ENST00000377191.3	+	17	1670	c.1575T>C	c.(1573-1575)ttT>ttC	p.F525F	XRN2_ENST00000539513.1_Silent_p.F471F|XRN2_ENST00000430571.2_Silent_p.F449F	NM_012255.3	NP_036387.2	Q9H0D6	XRN2_HUMAN	5'-3' exoribonuclease 2	525					cell growth (GO:0016049)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA catabolic process (GO:0006401)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|RNA processing (GO:0006396)|spermatogenesis (GO:0007283)	aggresome (GO:0016235)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-3' exoribonuclease activity (GO:0004534)|nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.F525F(1)		endometrium(5)|kidney(6)|large_intestine(10)|lung(12)|ovary(1)|skin(5)	39						AGAACAAATTTGATGTGGATG	0.433																																					p.F525F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1575C	20						.						180.0	176.0	177.0					20																	21327098		2203	4300	6503	21275098	SO:0001819	synonymous_variant	22803	exon17			AF064257	CCDS13144.1	20p11.2-p11.1	2011-09-12			ENSG00000088930	ENSG00000088930	3.1.13.-		12836	protein-coding gene	gene with protein product		608851				10409438	Standard	NM_012255		Approved		uc002wsf.1	Q9H0D6	OTTHUMG00000032025	ENST00000377191.3:c.1575T>C	20.37:g.21327098T>C		Somatic		Capture	Illumina HiSeq	Phase_I	21275098	NM_012255	Q3L8N4|Q6KGZ9|Q9BQL1|Q9NTW0|Q9NXS6|Q9UL53	Silent	SNP	ENST00000377191.3	37	CCDS13144.1																																																																																				0.433	XRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078273.2	NM_012255	
NKX2-2	4821	broad.mit.edu	37	20	21494072	21494072	+	Missense_Mutation	SNP	C	C	T	rs143227190		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:21494072C>T	ENST00000377142.4	-	1	592	c.236G>A	c.(235-237)aGc>aAc	p.S79N	NKX2-2-AS1_ENST00000549659.1_RNA	NM_002509.3	NP_002500.1	O95096	NKX22_HUMAN	NK2 homeobox 2	79					astrocyte differentiation (GO:0048708)|brain development (GO:0007420)|digestive tract development (GO:0048565)|endocrine pancreas development (GO:0031018)|negative regulation of neuron differentiation (GO:0045665)|neuron fate specification (GO:0048665)|oligodendrocyte development (GO:0014003)|optic nerve development (GO:0021554)|pancreatic A cell fate commitment (GO:0003326)|pancreatic PP cell fate commitment (GO:0003329)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)|spinal cord oligodendrocyte cell fate specification (GO:0021530)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell fate commitment (GO:0003327)|ventral spinal cord interneuron fate determination (GO:0060580)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|core promoter proximal region DNA binding (GO:0001159)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.S79N(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	21						GCCCTCGGTGCTGGCCAGCCA	0.682																																					p.S79N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G236A	20						.	C	ASN/SER	0,4406		0,0,2203	35.0	33.0	34.0		236	4.7	1.0	20	dbSNP_134	34	1,8599	1.2+/-3.3	0,1,4299	no	missense	NKX2-2	NM_002509.3	46	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	79/274	21494072	1,13005	2203	4300	6503	21442072	SO:0001583	missense	4821	exon1			AF019415	CCDS13145.1	20p11.22	2012-03-09	2007-07-09	2002-10-04	ENSG00000125820	ENSG00000125820		"""Homeoboxes / ANTP class : NKL subclass"""	7835	protein-coding gene	gene with protein product		604612	"""NK-2 (Drosophila) homolog B"", ""NK2 transcription factor related, locus 2 (Drosophila)"""	NKX2B		9703340, 1346742	Standard	NM_002509		Approved	NKX2.2	uc002wsi.3	O95096	OTTHUMG00000170524	ENST00000377142.4:c.236G>A	20.37:g.21494072C>T	ENSP00000366347:p.Ser79Asn	Somatic		Capture	Illumina HiSeq	Phase_I	21442072	NM_002509		Missense_Mutation	SNP	ENST00000377142.4	37	CCDS13145.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858037	0.32791	0.0	1.16E-4	ENSG00000125820	ENST00000377142	D	0.90676	-2.71	4.73	4.73	0.59995	.	0.099447	0.64402	D	0.000002	D	0.85239	0.5651	L	0.42245	1.32	0.36983	D	0.894405	B	0.11235	0.004	B	0.09377	0.004	T	0.81665	-0.0830	10	0.14656	T	0.56	.	12.7929	0.57545	0.0:0.6997:0.3003:0.0	.	79	O95096	NKX22_HUMAN	N	79	ENSP00000366347:S79N	ENSP00000366347:S79N	S	-	2	0	NKX2-2	21442072	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.105000	0.50314	2.168000	0.68352	0.563000	0.77884	AGC		0.682	NKX2-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078278.9		
SSTR4	6754	broad.mit.edu	37	20	23016593	23016593	+	Missense_Mutation	SNP	G	G	A	rs377078024	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:23016593G>A	ENST00000255008.3	+	1	537	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	158					arachidonic acid metabolic process (GO:0019369)|cell migration (GO:0016477)|cellular response to glucocorticoid stimulus (GO:0071385)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|negative regulation of cell proliferation (GO:0008285)|positive regulation of MAPK cascade (GO:0043410)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)	p.R158Q(1)		breast(1)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)	32	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GCGACCTACCGGCGGCCCAGC	0.662													G|||	2	0.000399361	0.0008	0.0	5008	,	,		15406	0.001		0.0	False		,,,				2504	0.0				p.R158Q	Esophageal Squamous(15;850 1104 16640)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G473A	20						.	G	GLN/ARG	0,4396		0,0,2198	44.0	50.0	48.0		473	2.7	0.3	20		48	1,8585		0,1,4292	no	missense	SSTR4	NM_001052.2	43	0,1,6490	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	158/389	23016593	1,12981	2198	4293	6491	22964593	SO:0001583	missense	6754	exon1				CCDS42856.1	20p11.21	2014-07-11			ENSG00000132671	ENSG00000132671		"""GPCR / Class A : Somatostatin receptors"""	11333	protein-coding gene	gene with protein product		182454				8483934	Standard	NM_001052		Approved		uc002wsr.2	P31391	OTTHUMG00000032054	ENST00000255008.3:c.473G>A	20.37:g.23016593G>A	ENSP00000255008:p.Arg158Gln	Somatic		Capture	Illumina HiSeq	Phase_I	22964593	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.237184	0.39498	0.0	1.16E-4	ENSG00000132671	ENST00000255008	T	0.39229	1.09	3.72	2.65	0.31530	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000012	T	0.51500	0.1678	M	0.80332	2.49	0.43457	D	0.995658	P	0.43607	0.812	P	0.48677	0.586	T	0.54173	-0.8333	10	0.72032	D	0.01	.	8.682	0.34214	0.1343:0.0:0.8657:0.0	.	158	P31391	SSR4_HUMAN	Q	158	ENSP00000255008:R158Q	ENSP00000255008:R158Q	R	+	2	0	SSTR4	22964593	0.999000	0.42202	0.300000	0.25030	0.191000	0.23601	3.978000	0.56881	0.643000	0.30638	0.655000	0.94253	CGG		0.662	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1		
CD93	22918	broad.mit.edu	37	20	23066727	23066727	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:23066727C>T	ENST00000246006.4	-	1	250	c.103G>A	c.(103-105)Gcc>Acc	p.A35T		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	35	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				macrophage activation (GO:0042116)|phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|complement component C1q binding (GO:0001849)|receptor activity (GO:0004872)	p.A35T(1)		NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(10)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Colorectal(13;0.0352)|Lung NSC(19;0.0542)|all_lung(19;0.118)					GTGTAGCAGGCGGTCCCCACG	0.697																																					p.A35T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G103A	20						.						23.0	21.0	22.0					20																	23066727		2198	4292	6490	23014727	SO:0001583	missense	22918	exon1			U94333	CCDS13149.1	20p11.21	2009-01-29	2006-03-28	2006-02-22	ENSG00000125810	ENSG00000125810		"""CD molecules"""	15855	protein-coding gene	gene with protein product		120577	"""matrix-remodelling associated 4"", ""complement component 1, q subcomponent, receptor 1"", ""CD93 antigen"""	MXRA4, C1QR1		9047234, 10648005	Standard	NM_012072		Approved	C1qRP, C1qR(P), dJ737E23.1, CDw93, ECSM3	uc002wsv.3	Q9NPY3	OTTHUMG00000032058	ENST00000246006.4:c.103G>A	20.37:g.23066727C>T	ENSP00000246006:p.Ala35Thr	Somatic		Capture	Illumina HiSeq	Phase_I	23014727	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	37	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.451493	0.84209	.	.	ENSG00000125810	ENST00000246006;ENST00000413585	T	0.81415	-1.49	5.36	5.36	0.76844	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.000000	0.53938	D	0.000060	D	0.87826	0.6275	L	0.53617	1.68	0.54753	D	0.999981	D	0.89917	1.0	D	0.77557	0.99	D	0.88258	0.2921	10	0.72032	D	0.01	-42.5514	18.2557	0.90019	0.0:1.0:0.0:0.0	.	35	Q9NPY3	C1QR1_HUMAN	T	35	ENSP00000246006:A35T	ENSP00000246006:A35T	A	-	1	0	CD93	23014727	1.000000	0.71417	0.965000	0.40720	0.335000	0.28730	4.982000	0.63825	2.774000	0.95407	0.655000	0.94253	GCC		0.697	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072	
APMAP	57136	broad.mit.edu	37	20	24949640	24949640	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:24949640G>T	ENST00000217456.2	-	8	1219	c.929C>A	c.(928-930)cCc>cAc	p.P310H	APMAP_ENST00000447138.1_Intron	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	310					biosynthetic process (GO:0009058)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	arylesterase activity (GO:0004064)|strictosidine synthase activity (GO:0016844)	p.P310H(1)									AGAGCTGCTGGGCCGGATGTT	0.532																																					p.P310H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C929A	20						.						70.0	70.0	70.0					20																	24949640		2203	4300	6503	24897640	SO:0001583	missense	57136	exon8			AB033767	CCDS13166.1	20p11.2	2012-07-20	2012-07-20	2012-07-20	ENSG00000101474	ENSG00000101474			13238	protein-coding gene	gene with protein product		615884	"""chromosome 20 open reading frame 3"""	C20orf3		10945474, 11583587, 20552250	Standard	NM_020531		Approved	BSCv	uc002wty.3	Q9HDC9	OTTHUMG00000032107	ENST00000217456.2:c.929C>A	20.37:g.24949640G>T	ENSP00000217456:p.Pro310His	Somatic		Capture	Illumina HiSeq	Phase_I	24897640	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Missense_Mutation	SNP	ENST00000217456.2	37	CCDS13166.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.77|14.77	2.634849|2.634849	0.47049|0.47049	.|.	.|.	ENSG00000101474|ENSG00000101474	ENST00000217456|ENST00000451442	T|T	0.29397|0.28069	1.57|1.63	5.54|5.54	3.47|3.47	0.39725|0.39725	Six-bladed beta-propeller, TolB-like (1);|.	0.218667|0.218667	0.48767|0.48767	D|D	0.000174|0.000174	T|T	0.31575|0.31575	0.0801|0.0801	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	D;P|.	0.63046|.	0.992;0.913|.	P;P|.	0.53988|.	0.739;0.524|.	T|T	0.06250|0.06250	-1.0837|-1.0837	10|8	0.15499|0.22706	T|T	0.54|0.39	-10.1363|-10.1363	5.4878|5.4878	0.16759|0.16759	0.1742:0.1652:0.6607:0.0|0.1742:0.1652:0.6607:0.0	.|.	294;310|.	A2A2F9;Q9HDC9|.	.;APMAP_HUMAN|.	H|T	310|295	ENSP00000217456:P310H|ENSP00000395874:P295T	ENSP00000217456:P310H|ENSP00000395874:P295T	P|P	-|-	2|1	0|0	C20orf3|C20orf3	24897640|24897640	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.975000|0.975000	0.68041|0.68041	2.662000|2.662000	0.46766|0.46766	1.483000|1.483000	0.48342|0.48342	0.561000|0.561000	0.74099|0.74099	CCC|CCA		0.532	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	
ENTPD6	955	broad.mit.edu	37	20	25190505	25190505	+	Missense_Mutation	SNP	G	G	A	rs144718324	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:25190505G>A	ENST00000376652.4	+	4	560	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	ENTPD6_ENST00000433259.2_Missense_Mutation_p.E133K|ENTPD6_ENST00000360031.2_Missense_Mutation_p.E132K|ENTPD6_ENST00000354989.5_Missense_Mutation_p.E116K			O75354	ENTP6_HUMAN	ectonucleoside triphosphate diphosphohydrolase 6 (putative)	133					response to calcium ion (GO:0051592)|response to magnesium ion (GO:0032026)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity (GO:0008894)|nucleoside-triphosphatase activity (GO:0017111)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|prostate(1)|skin(1)	27						GTTAACCCACGAAACCTTCAA	0.443													G|||	3	0.000599042	0.0	0.0	5008	,	,		15389	0.003		0.0	False		,,,				2504	0.0				p.E116K												.	.	0			c.G346A	20						.						322.0	308.0	313.0					20																	25190505		2203	4300	6503	25138505	SO:0001583	missense	955	exon3			AF039916	CCDS13170.1, CCDS46586.1	20p11.21	2010-06-24	2010-06-24		ENSG00000197586	ENSG00000197586			3368	protein-coding gene	gene with protein product		603160	"""interleukin 6 signal transducer-2"""	CD39L2, IL6ST2		9676430	Standard	NM_001247		Approved	NTPDase-6, dJ738P15.3	uc002wuj.2	O75354	OTTHUMG00000032116	ENST00000376652.4:c.397G>A	20.37:g.25190505G>A	ENSP00000365840:p.Glu133Lys	None		Capture	Illumina HiSeq	Phase_I	25138505	NM_001114089	A6NCX6|D3DW49|Q5QPJ2|Q5QPJ5|Q7Z5B5|Q8N3H3|Q8TAS7|Q9UJD1	Missense_Mutation	SNP	ENST00000376652.4	37	CCDS13170.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	G	23.9	4.475540	0.84640	.	.	ENSG00000197586	ENST00000354989;ENST00000360031;ENST00000525986;ENST00000376641;ENST00000376652;ENST00000439162;ENST00000417467;ENST00000433259;ENST00000435520;ENST00000418890;ENST00000425813	T;T;T;T;T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7;2.7;2.7;2.7;2.7	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.26085	0.0636	L	0.58969	1.84	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.997;0.998;0.999;0.999	D;D;D;D;P;D;D;D	0.83275	0.993;0.996;0.995;0.99;0.875;0.924;0.955;0.955	T	0.01889	-1.1253	10	0.87932	D	0	-13.1082	15.203	0.73157	0.0:0.0:1.0:0.0	.	115;133;133;133;116;132;132;133	B4DDM7;B4DNK6;E7EP89;Q5QPI9;O75354-2;D3DW49;Q5QPJ2;O75354	.;.;.;.;.;.;.;ENTP6_HUMAN	K	116;132;53;29;133;115;115;133;132;116;133	ENSP00000347084:E116K;ENSP00000353131:E132K;ENSP00000365840:E133K;ENSP00000408098:E115K;ENSP00000395064:E115K;ENSP00000401895:E133K;ENSP00000398844:E132K;ENSP00000390511:E116K;ENSP00000390646:E133K	ENSP00000347084:E116K	E	+	1	0	ENTPD6	25138505	1.000000	0.71417	1.000000	0.80357	0.612000	0.37316	6.075000	0.71261	2.529000	0.85273	0.655000	0.94253	GAA		0.443	ENTPD6-020	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078414.2		
GINS1	9837	broad.mit.edu	37	20	25398741	25398741	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:25398741G>A	ENST00000262460.4	+	4	334	c.240G>A	c.(238-240)ctG>ctA	p.L80L	GINS1_ENST00000429262.2_Splice_Site_p.L80L|GINS1_ENST00000484893.1_3'UTR	NM_021067.3	NP_066545.3	Q14691	PSF1_HUMAN	GINS complex subunit 1 (Psf1 homolog)	80					DNA strand elongation involved in DNA replication (GO:0006271)|inner cell mass cell proliferation (GO:0001833)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.L80L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(1)	7						GATGTCCTAGGTATGACCGCT	0.478																																					p.L80L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G240A	20						.						226.0	194.0	205.0					20																	25398741		2203	4300	6503	25346741	SO:0001630	splice_region_variant	9837	exon4			BC012542	CCDS33451.1	20p11.21	2006-05-04			ENSG00000101003	ENSG00000101003			28980	protein-coding gene	gene with protein product		610608				8724849, 8786132	Standard	NM_021067		Approved	KIAA0186, PSF1	uc002wuv.1	Q14691	OTTHUMG00000032124	ENST00000262460.4:c.240-1G>A	20.37:g.25398741G>A		Somatic		Capture	Illumina HiSeq	Phase_I	25346741	NM_021067	Q9NQE2|Q9NQI7	Silent	SNP	ENST00000262460.4	37	CCDS33451.1																																																																																				0.478	GINS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078433.1	NM_021067	Silent
BPIFB2	80341	broad.mit.edu	37	20	31601617	31601617	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:31601617G>A	ENST00000170150.3	+	5	505	c.310G>A	c.(310-312)Gcc>Acc	p.A104T		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	104						extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)	p.A104T(1)									TCCCTACAGCGCCCCAGAGCC	0.637																																					p.A104T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G310A	20						.						42.0	44.0	43.0					20																	31601617		2203	4300	6503	31065278	SO:0001630	splice_region_variant	80341	exon5			AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.309-1G>A	20.37:g.31601617G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31065278	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Missense_Mutation	SNP	ENST00000170150.3	37	CCDS13210.1	.	.	.	.	.	.	.	.	.	.	G	5.357	0.251062	0.10130	.	.	ENSG00000078898	ENST00000170150	T	0.05925	3.37	3.7	1.75	0.24633	.	1.802660	0.03052	N	0.154671	T	0.03608	0.0103	N	0.14661	0.345	0.09310	N	1	P	0.34743	0.466	B	0.23716	0.048	T	0.37572	-0.9700	10	0.16420	T	0.52	-0.1137	5.6258	0.17482	0.2463:0.0:0.7537:0.0	.	104	Q8N4F0	BPIB2_HUMAN	T	104	ENSP00000170150:A104T	ENSP00000170150:A104T	A	+	1	0	BPIFB2	31065278	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	0.056000	0.14256	0.547000	0.28938	0.561000	0.74099	GCC		0.637	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	Missense_Mutation
AHCY	191	broad.mit.edu	37	20	32878409	32878409	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:32878409C>G	ENST00000217426.2	-	7	879	c.802G>C	c.(802-804)Gag>Cag	p.E268Q	AHCY_ENST00000468908.1_5'Flank|AHCY_ENST00000538132.1_Missense_Mutation_p.E240Q	NM_000687.2	NP_000678.1	P23526	SAHH_HUMAN	adenosylhomocysteinase	268					cellular nitrogen compound metabolic process (GO:0034641)|chronic inflammatory response to antigenic stimulus (GO:0002439)|circadian sleep/wake cycle (GO:0042745)|homocysteine biosynthetic process (GO:0071268)|methylation (GO:0032259)|one-carbon metabolic process (GO:0006730)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|S-adenosylhomocysteine catabolic process (GO:0019510)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|nucleus (GO:0005634)	adenosylhomocysteinase activity (GO:0004013)|adenyl nucleotide binding (GO:0030554)|NAD binding (GO:0051287)	p.E268Q(1)		endometrium(6)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ATGTTGCCCTCCTGACAGGCC	0.617																																					p.E268Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G802C	20						.						151.0	136.0	141.0					20																	32878409		2203	4300	6503	32342070	SO:0001583	missense	191	exon7			M61832	CCDS13233.1, CCDS54457.1	20q11.22	2009-06-12	2009-06-12		ENSG00000101444	ENSG00000101444	3.3.1.1		343	protein-coding gene	gene with protein product		180960	"""S-adenosylhomocysteine hydrolase"""			7079734, 6580258	Standard	NM_001161766		Approved	SAHH	uc002xai.3	P23526	OTTHUMG00000140098	ENST00000217426.2:c.802G>C	20.37:g.32878409C>G	ENSP00000217426:p.Glu268Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32342070	NM_000687	A8K307|B3KUN3|E1P5P2|F5H737|Q96A36	Missense_Mutation	SNP	ENST00000217426.2	37	CCDS13233.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.974965	0.53720	.	.	ENSG00000101444	ENST00000217426;ENST00000538132	T;T	0.76839	-1.05;-1.04	4.54	4.54	0.55810	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.000000	0.85682	D	0.000000	T	0.64000	0.2559	N	0.13168	0.305	0.80722	D	1	B	0.25521	0.128	B	0.26614	0.071	T	0.59658	-0.7413	10	0.20519	T	0.43	.	17.8243	0.88660	0.0:1.0:0.0:0.0	.	268	P23526	SAHH_HUMAN	Q	268;240	ENSP00000217426:E268Q;ENSP00000442820:E240Q	ENSP00000217426:E268Q	E	-	1	0	AHCY	32342070	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.529000	0.81952	2.529000	0.85273	0.561000	0.74099	GAG		0.617	AHCY-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078773.2	NM_000687	
GGT7	2686	broad.mit.edu	37	20	33440050	33440050	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:33440050C>T	ENST00000336431.5	-	12	1539	c.1495G>A	c.(1495-1497)Ggc>Agc	p.G499S	GGT7_ENST00000469018.1_5'UTR	NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	499					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)	p.G499S(1)		NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						GTGATAAGGCCGCTGCCAAAG	0.642																																					p.G499S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1495A	20						.						47.0	49.0	49.0					20																	33440050		2203	4300	6503	32903711	SO:0001583	missense	2686	exon12			AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.1495G>A	20.37:g.33440050C>T	ENSP00000338964:p.Gly499Ser	Somatic		Capture	Illumina HiSeq	Phase_I	32903711	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	37	CCDS13242.2	.	.	.	.	.	.	.	.	.	.	C	26.7	4.765860	0.90020	.	.	ENSG00000131067	ENST00000336431	T	0.07800	3.16	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.33933	0.0880	M	0.79343	2.45	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.949	T	0.00593	-1.1654	10	0.56958	D	0.05	-15.3958	20.6593	0.99626	0.0:1.0:0.0:0.0	.	499;499	A4FU32;Q9UJ14	.;GGT7_HUMAN	S	499	ENSP00000338964:G499S	ENSP00000338964:G499S	G	-	1	0	GGT7	32903711	0.996000	0.38824	0.994000	0.49952	0.577000	0.36160	3.430000	0.52807	2.885000	0.99019	0.655000	0.94253	GGC		0.642	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
MYH7B	57644	broad.mit.edu	37	20	33565798	33565798	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:33565798G>A	ENST00000262873.7	+	3	208	c.116G>A	c.(115-117)aGt>aAt	p.S39N		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	0						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.S39N(1)		NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CTTCACCCCAGTGCCACTGCC	0.602																																					p.S39N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G116A	20						.						108.0	117.0	114.0					20																	33565798		2163	4271	6434	33029459	SO:0001583	missense	57644	exon5			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.116G>A	20.37:g.33565798G>A	ENSP00000262873:p.Ser39Asn	Somatic		Capture	Illumina HiSeq	Phase_I	33029459	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	De_novo_Start_OutOfFrame	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582831	0.46006	.	.	ENSG00000078814	ENST00000262873	D	0.86230	-2.09	3.97	-2.87	0.05700	.	.	.	.	.	T	0.78886	0.4354	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.67039	-0.5771	6	0.33940	T	0.23	.	4.5737	0.12223	0.0803:0.3404:0.3699:0.2094	.	.	.	.	N	39	ENSP00000262873:S39N	ENSP00000262873:S39N	S	+	2	0	MYH7B	33029459	0.000000	0.05858	0.036000	0.18154	0.519000	0.34347	0.216000	0.17585	-0.285000	0.09089	-0.165000	0.13383	AGT		0.602	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
MYH7B	57644	broad.mit.edu	37	20	33575022	33575022	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:33575022T>C	ENST00000262873.7	+	14	1297	c.1205T>C	c.(1204-1206)cTg>cCg	p.L402P		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	360	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGCGCCCTCCTGCACTTTGGC	0.582																																					p.L402P												.	.	0			c.T1205C	20						.						95.0	99.0	98.0					20																	33575022		2203	4300	6503	33038683	SO:0001583	missense	57644	exon16			AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1205T>C	20.37:g.33575022T>C	ENSP00000262873:p.Leu402Pro	None		Capture	Illumina HiSeq	Phase_I	33038683	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.098360	0.76870	.	.	ENSG00000078814	ENST00000262873	D	0.95412	-3.7	3.53	3.53	0.40419	Myosin head, motor domain (2);	0.000000	0.28927	N	0.013700	D	0.97914	0.9314	H	0.97265	3.97	0.80722	D	1	D	0.61080	0.989	P	0.55303	0.773	D	0.98855	1.0760	10	0.87932	D	0	.	13.1334	0.59395	0.0:0.0:0.0:1.0	.	360	A7E2Y1	MYH7B_HUMAN	P	402	ENSP00000262873:L402P	ENSP00000262873:L402P	L	+	2	0	MYH7B	33038683	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.868000	0.87116	1.849000	0.53698	0.459000	0.35465	CTG		0.582	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
UQCC1	55245	broad.mit.edu	37	20	33891828	33891828	+	Silent	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:33891828T>G	ENST00000374385.5	-	10	987	c.810A>C	c.(808-810)acA>acC	p.T270T	UQCC1_ENST00000349714.5_Silent_p.T243T|UQCC1_ENST00000374384.2_Silent_p.T244T|UQCC1_ENST00000359226.2_Silent_p.T190T|UQCC1_ENST00000374380.2_Silent_p.T202T|UQCC1_ENST00000540457.1_Silent_p.T115T|UQCC1_ENST00000374377.5_Silent_p.T158T|UQCC1_ENST00000407996.2_Silent_p.T133T|UQCC1_ENST00000397556.3_Silent_p.T171T	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	270						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)		p.T270T(1)									TCACCTCCCCTGTCAGAAGCA	0.592											OREG0025888	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T270T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A810C	20						.						108.0	98.0	101.0					20																	33891828		2203	4300	6503	33355242	SO:0001819	synonymous_variant	55245	exon10			AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.810A>C	20.37:g.33891828T>G		Somatic	843	Capture	Illumina HiSeq	Phase_I	33355242	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Silent	SNP	ENST00000374385.5	37	CCDS13252.1																																																																																				0.592	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
CEP250	11190	broad.mit.edu	37	20	34099219	34099219	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:34099219T>C	ENST00000397527.1	+	35	7813	c.7093T>C	c.(7093-7095)Ttg>Ctg	p.L2365L	CEP250_ENST00000342580.4_Silent_p.L2309L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	2365					centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)	p.L2365L(1)		NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			TCAGCTGACTTTGGAGCGGAA	0.567																																					p.L2365L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T7093C	20						.						47.0	46.0	46.0					20																	34099219		2203	4300	6503	33562633	SO:0001819	synonymous_variant	11190	exon35			AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.7093T>C	20.37:g.34099219T>C		Somatic		Capture	Illumina HiSeq	Phase_I	33562633	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																				0.567	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
ATRN	8455	broad.mit.edu	37	20	3571903	3571903	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:3571903C>G	ENST00000262919.5	+	19	3340	c.3272C>G	c.(3271-3273)aCc>aGc	p.T1091S	ATRN_ENST00000446916.2_Missense_Mutation_p.T1091S	NM_139321.2	NP_647537.1	O75882	ATRN_HUMAN	attractin	1091	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cerebellum development (GO:0021549)|inflammatory response (GO:0006954)|myelination (GO:0042552)|pigmentation (GO:0043473)|regulation of multicellular organism growth (GO:0040014)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)	p.T1091S(1)		breast(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	59						CACTGCGAGACCTGCATATCT	0.488																																					p.T1091S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3272G	20						.						178.0	161.0	167.0					20																	3571903		2203	4300	6503	3519903	SO:0001583	missense	8455	exon19			AF034957	CCDS13053.1, CCDS13054.1	20p13	2008-07-02			ENSG00000088812	ENSG00000088812			885	protein-coding gene	gene with protein product	"""mahogany protein"""	603130				9736737, 8596018	Standard	NM_139321		Approved	DPPT-L, MGCA	uc002wim.2	O75882	OTTHUMG00000031746	ENST00000262919.5:c.3272C>G	20.37:g.3571903C>G	ENSP00000262919:p.Thr1091Ser	Somatic		Capture	Illumina HiSeq	Phase_I	3519903	NM_139322	A8KAE5|O60295|O95414|Q3MIT3|Q5TDA2|Q5TDA4|Q5VYW3|Q9NTQ3|Q9NTQ4|Q9NU01|Q9NZ57|Q9NZ58|Q9UC75|Q9UDF5	Missense_Mutation	SNP	ENST00000262919.5	37	CCDS13053.1	.	.	.	.	.	.	.	.	.	.	C	9.116	1.007770	0.19199	.	.	ENSG00000088812	ENST00000262919;ENST00000446916;ENST00000340500	T;T	0.62788	0.0;0.0	5.43	4.48	0.54585	EGF-like, laminin (3);	0.215995	0.47852	D	0.000217	T	0.36331	0.0963	N	0.04320	-0.23	0.39653	D	0.970492	B;B	0.16603	0.001;0.018	B;B	0.18561	0.002;0.022	T	0.29305	-1.0016	10	0.09338	T	0.73	-16.8602	13.2489	0.60039	0.0:0.9229:0.0:0.0771	.	1091;1091	O75882;O75882-2	ATRN_HUMAN;.	S	1091;1091;1017	ENSP00000262919:T1091S;ENSP00000416587:T1091S	ENSP00000262919:T1091S	T	+	2	0	ATRN	3519903	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.628000	0.46477	2.542000	0.85734	0.650000	0.86243	ACC		0.488	ATRN-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077740.2	NM_139321	
EPB41L1	2036	broad.mit.edu	37	20	34797635	34797635	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:34797635G>A	ENST00000338074.2	+	15	2055	c.1894G>A	c.(1894-1896)Gcc>Acc	p.A632T	EPB41L1_ENST00000479336.1_3'UTR|EPB41L1_ENST00000373950.2_Missense_Mutation_p.A523T|EPB41L1_ENST00000373941.1_Missense_Mutation_p.A632T|EPB41L1_ENST00000202028.5_Missense_Mutation_p.A558T|EPB41L1_ENST00000441639.1_Missense_Mutation_p.A558T|EPB41L1_ENST00000373946.3_Intron	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	632					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)	p.A632T(1)|p.A921T(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					CCATGGCAGCGCCTTCGAAGA	0.612																																					p.A632T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1894A	20						.						83.0	67.0	72.0					20																	34797635		2203	4300	6503	34261049	SO:0001583	missense	2036	exon15			AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1894G>A	20.37:g.34797635G>A	ENSP00000337168:p.Ala632Thr	Somatic		Capture	Illumina HiSeq	Phase_I	34261049	NM_012156	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	37	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.033471	0.75504	.	.	ENSG00000088367	ENST00000202028;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000344237;ENST00000338074;ENST00000373941	D;D;D;D;D	0.84800	-1.9;-1.78;-1.9;-1.83;-1.83	5.87	5.87	0.94306	.	0.165679	0.53938	D	0.000050	D	0.86847	0.6031	L	0.27053	0.805	0.30964	N	0.723274	D;D;D;D;P;P	0.89917	0.962;1.0;0.992;0.976;0.921;0.593	B;D;P;P;B;B	0.75020	0.173;0.985;0.642;0.599;0.149;0.09	T	0.78989	-0.1986	10	0.10111	T	0.7	-9.8903	19.5705	0.95413	0.0:0.0:1.0:0.0	.	632;921;632;523;523;558	B7Z653;E9PCJ3;Q9H4G0;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;.;E41L1_HUMAN;.;.;.	T	558;523;632;523;558;921;632;632	ENSP00000202028:A558T;ENSP00000363061:A523T;ENSP00000399214:A558T;ENSP00000337168:A632T;ENSP00000363052:A632T	ENSP00000202028:A558T	A	+	1	0	EPB41L1	34261049	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.154000	0.94694	2.941000	0.99782	0.655000	0.94253	GCC		0.612	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156	
TTI1	9675	broad.mit.edu	37	20	36641831	36641831	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:36641831A>G	ENST00000373448.2	-	3	626	c.388T>C	c.(388-390)Tta>Cta	p.L130L	TTI1_ENST00000487362.1_Intron|TTI1_ENST00000373447.3_Silent_p.L130L|TTI1_ENST00000449821.1_Silent_p.L130L	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	130					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)		p.L130L(1)		breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						GAGTGCATTAATGTGCTAAGT	0.463																																					p.L130L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T388C	20						.						104.0	104.0	104.0					20																	36641831		2203	4300	6503	36075245	SO:0001819	synonymous_variant	9675	exon3			BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.388T>C	20.37:g.36641831A>G		Somatic		Capture	Illumina HiSeq	Phase_I	36075245	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Silent	SNP	ENST00000373448.2	37	CCDS13300.1																																																																																				0.463	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
ADA	100	broad.mit.edu	37	20	43248963	43248963	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:43248963C>A	ENST00000372874.4	-	11	1189	c.1055G>T	c.(1054-1056)gGg>gTg	p.G352V	PKIG_ENST00000372887.1_Intron|ADA_ENST00000464097.1_5'UTR|PKIG_ENST00000372882.3_Intron|Z97053.1_ENST00000597250.1_5'Flank|ADA_ENST00000537820.1_Missense_Mutation_p.G328V	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	352					adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)	p.G352V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	AGGTGGCATCCCATAGGCTTT	0.537									Adenosine Deaminase Deficiency																												p.G352V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1055T	20						.						123.0	121.0	122.0					20																	43248963		2203	4300	6503	42682377	SO:0001583	missense	100	exon11	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.1055G>T	20.37:g.43248963C>A	ENSP00000361965:p.Gly352Val	Somatic		Capture	Illumina HiSeq	Phase_I	42682377	NM_000022	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.156258	0.78114	.	.	ENSG00000196839	ENST00000372874;ENST00000537820	D;D	0.95949	-3.68;-3.86	5.33	1.69	0.24217	.	0.282845	0.38720	N	0.001592	D	0.95516	0.8543	M	0.75447	2.3	0.48830	D	0.999714	P	0.47677	0.899	P	0.52309	0.695	D	0.93917	0.7202	10	0.59425	D	0.04	-14.7635	9.4489	0.38714	0.0:0.5909:0.0:0.4091	.	352	P00813	ADA_HUMAN	V	352;328	ENSP00000361965:G352V;ENSP00000441818:G328V	ENSP00000361965:G352V	G	-	2	0	ADA	42682377	0.023000	0.18921	0.023000	0.16930	0.799000	0.45148	0.480000	0.22244	0.530000	0.28619	-0.136000	0.14681	GGG		0.537	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
RIMS4	140730	broad.mit.edu	37	20	43379116	43379116	+	IGR	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:43379116C>T	ENST00000372851.3	-	0	5203				KCNK15_ENST00000372861.3_Silent_p.S210S	NM_001205317.1|NM_182970.3	NP_001192246.1|NP_892015.1	Q9H426	RIMS4_HUMAN	regulating synaptic membrane exocytosis 4						exocytosis (GO:0006887)|neurotransmitter transport (GO:0006836)|regulation of membrane potential (GO:0042391)	cell junction (GO:0030054)|presynaptic active zone (GO:0048786)|synaptic membrane (GO:0097060)		p.S210S(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(11)|ovary(5)|urinary_tract(1)	29		Myeloproliferative disorder(115;0.0122)				CACTGCAGAGCGGCGAGGCGC	0.617																																					p.S210S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C630T	20						.						72.0	65.0	67.0					20																	43379116		2203	4300	6503	42812530	SO:0001628	intergenic_variant	60598	exon2				CCDS13338.1, CCDS56191.1	20q13.12	2005-02-03	2003-06-18	2003-06-20	ENSG00000101098	ENSG00000101098			16183	protein-coding gene	gene with protein product		611601	"""chromosome 20 open reading frame 190"""	C20orf190		12620390	Standard	NM_182970		Approved	dJ781B1.3	uc010ggu.3	Q9H426	OTTHUMG00000032546		20.37:g.43379116C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42812530	NM_022358	A4FU94|E1P613|Q3MI44|Q5JWT7	Silent	SNP	ENST00000372851.3	37	CCDS13338.1																																																																																				0.617	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	
SEMG1	6406	broad.mit.edu	37	20	43836621	43836621	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:43836621A>C	ENST00000372781.3	+	2	740	c.683A>C	c.(682-684)gAg>gCg	p.E228A	SEMG1_ENST00000244069.6_Missense_Mutation_p.E228A	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	228	Interaction with EPPIN.|Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.E228A(1)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GAAGTGAGAGAGGAACATTCA	0.398																																					p.E228A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A683C	20						.						110.0	94.0	99.0					20																	43836621		2203	4300	6503	43270035	SO:0001583	missense	6406	exon2				CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.683A>C	20.37:g.43836621A>C	ENSP00000361867:p.Glu228Ala	Somatic		Capture	Illumina HiSeq	Phase_I	43270035	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	.	.	.	.	.	.	.	.	.	.	A	6.114	0.389291	0.11581	.	.	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.08634	3.07;3.07	1.43	-2.85	0.05734	.	.	.	.	.	T	0.09423	0.0232	L	0.51422	1.61	0.09310	N	1	P;P;P	0.48407	0.89;0.884;0.91	B;P;P	0.48704	0.419;0.587;0.554	T	0.09422	-1.0675	9	0.35671	T	0.21	.	3.0324	0.06111	0.366:0.2557:0.3783:0.0	.	228;228;228	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	A	228	ENSP00000244069:E228A;ENSP00000361867:E228A	ENSP00000244069:E228A	E	+	2	0	SEMG1	43270035	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.408000	0.07169	-1.102000	0.03023	-1.267000	0.01435	GAG		0.398	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
RBPJL	11317	broad.mit.edu	37	20	43943133	43943133	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:43943133G>A	ENST00000343694.3	+	9	1020	c.948G>A	c.(946-948)caG>caA	p.Q316Q	RBPJL_ENST00000372741.3_Silent_p.Q316Q|RBPJL_ENST00000372743.1_Silent_p.Q316Q|RBPJL_ENST00000464504.1_3'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	316					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q316Q(1)		NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GTGCATTCCAGTTTCCAGGCA	0.517																																					p.Q316Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G948A	20						.						126.0	110.0	115.0					20																	43943133		2203	4300	6503	43376547	SO:0001819	synonymous_variant	11317	exon9			AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.948G>A	20.37:g.43943133G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43376547	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	CCDS13349.1																																																																																				0.517	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
RBPJL	11317	broad.mit.edu	37	20	43945566	43945566	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:43945566G>A	ENST00000343694.3	+	12	1593	c.1521G>A	c.(1519-1521)acG>acA	p.T507T	RBPJL_ENST00000372741.3_3'UTR|RBPJL_ENST00000372743.1_Silent_p.T506T|RBPJL_ENST00000464504.1_3'UTR	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	507	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.T507T(1)		NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				AGGAGTTCACGCGCACCAACT	0.711																																					p.T507T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1521A	20						.						44.0	53.0	50.0					20																	43945566		2203	4298	6501	43378980	SO:0001819	synonymous_variant	11317	exon12			AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1521G>A	20.37:g.43945566G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43378980	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Silent	SNP	ENST00000343694.3	37	CCDS13349.1																																																																																				0.711	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
EPPIN	57119	broad.mit.edu	37	20	44171499	44171499	+	Silent	SNP	G	G	A	rs570448304		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:44171499G>A	ENST00000354280.4	-	3	297	c.231C>T	c.(229-231)tgC>tgT	p.C77C	EPPIN-WFDC6_ENST00000504988.1_Silent_p.C77C|EPPIN_ENST00000336443.3_Silent_p.C61C|EPPIN_ENST00000409554.1_Intron|EPPIN_ENST00000555685.1_Silent_p.C77C	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor	77	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.C61C(2)									TTGGCATTTCGCATACATCTG	0.433													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19018	0.0		0.0	False		,,,				2504	0.0				p.C61C												.	.	2	Substitution - coding silent(2)	prostate(2)	c.C183T	20						.						80.0	79.0	79.0					20																	44171499		2203	4300	6503	43604913	SO:0001819	synonymous_variant	57119	exon2			AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"""WAP four-disulfide core domain containing"""	15932	protein-coding gene	gene with protein product	"""epididymal protease inhibitor"", ""cancer/testis antigen 72"""	609031	"""serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)"", ""serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"""	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588	ENST00000354280.4:c.231C>T	20.37:g.44171499G>A		None		Capture	Illumina HiSeq	Phase_I	43604913	NM_181502	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	37	CCDS13359.1																																																																																				0.433	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4		
MMP9	4318	broad.mit.edu	37	20	44640341	44640341	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:44640341G>A	ENST00000372330.3	+	6	971	c.952G>A	c.(952-954)Gcc>Acc	p.A318T	RP11-465L10.10_ENST00000535913.1_RNA	NM_004994.2	NP_004985.2	P14780	MMP9_HUMAN	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	318	Fibronectin type-II 2. {ECO:0000255|PROSITE-ProRule:PRU00479}.				collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|macrophage differentiation (GO:0030225)|negative regulation of cation channel activity (GO:2001258)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of receptor binding (GO:1900122)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)|identical protein binding (GO:0042802)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.A318T(1)		breast(2)|endometrium(4)|large_intestine(14)|liver(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	46		Myeloproliferative disorder(115;0.0122)			Captopril(DB01197)|Glucosamine(DB01296)|Marimastat(DB00786)|Minocycline(DB01017)	CGCCACCACCGCCAACTACGA	0.627											OREG0025989	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A318T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G952A	20						.						59.0	53.0	55.0					20																	44640341		2203	4300	6503	44073748	SO:0001583	missense	4318	exon6				CCDS13390.1	20q12-q13	2008-01-07	2005-08-08		ENSG00000100985	ENSG00000100985	3.4.24.35		7176	protein-coding gene	gene with protein product		120361	"""matrix metalloproteinase 9 (gelatinase B, 92kD gelatinase, 92kD type IV collagenase)"", ""matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)"""	CLG4B		2158484	Standard	NM_004994		Approved		uc002xqz.3	P14780	OTTHUMG00000033044	ENST00000372330.3:c.952G>A	20.37:g.44640341G>A	ENSP00000361405:p.Ala318Thr	Somatic	925	Capture	Illumina HiSeq	Phase_I	44073748	NM_004994	B2R7V9|Q3LR70|Q8N725|Q9H4Z1|Q9UCJ9|Q9UCL1|Q9UDK2	Missense_Mutation	SNP	ENST00000372330.3	37	CCDS13390.1	.	.	.	.	.	.	.	.	.	.	G	14.89	2.669274	0.47677	.	.	ENSG00000100985	ENST00000372330	T	0.49720	0.77	4.3	3.34	0.38264	Peptidase M10, metallopeptidase (1);Fibronectin, type II, collagen-binding (5);Kringle-like fold (1);Peptidase, metallopeptidase (1);	0.403117	0.26887	N	0.021994	T	0.40956	0.1138	M	0.74881	2.28	0.49582	D	0.999804	P	0.41624	0.757	B	0.27076	0.076	T	0.46414	-0.9193	10	0.38643	T	0.18	.	12.4551	0.55700	0.0:0.0:0.6988:0.3012	.	318	P14780	MMP9_HUMAN	T	318	ENSP00000361405:A318T	ENSP00000361405:A318T	A	+	1	0	MMP9	44073748	0.615000	0.27026	0.956000	0.39512	0.666000	0.39218	2.532000	0.45659	1.161000	0.42604	-0.268000	0.10319	GCC		0.627	MMP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080337.1		
NCOA5	57727	broad.mit.edu	37	20	44692031	44692031	+	Missense_Mutation	SNP	C	C	A	rs201177001		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:44692031C>A	ENST00000290231.6	-	7	1282	c.1118G>T	c.(1117-1119)cGg>cTg	p.R373L		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	373					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R373L(1)		central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				CCTCATCAGCCGCTCCTTCCG	0.567																																					p.R373L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1118T	20						.						63.0	57.0	59.0					20																	44692031		2203	4300	6503	44125438	SO:0001583	missense	57727	exon7				CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"""coactivator independent of AF-2"""					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.1118G>T	20.37:g.44692031C>A	ENSP00000290231:p.Arg373Leu	Somatic		Capture	Illumina HiSeq	Phase_I	44125438	NM_020967	B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	C	18.89	3.719356	0.68844	.	.	ENSG00000124160	ENST00000290231	T	0.50813	0.73	5.41	5.41	0.78517	.	0.099940	0.64402	D	0.000001	T	0.58235	0.2108	L	0.27053	0.805	0.58432	D	0.999994	D	0.89917	1.0	D	0.87578	0.998	T	0.58781	-0.7576	10	0.52906	T	0.07	-14.4572	18.3708	0.90406	0.0:1.0:0.0:0.0	.	373	Q9HCD5	NCOA5_HUMAN	L	373	ENSP00000290231:R373L	ENSP00000290231:R373L	R	-	2	0	NCOA5	44125438	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	3.529000	0.53532	2.816000	0.96949	0.561000	0.74099	CGG		0.567	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967	
ZNF334	55713	broad.mit.edu	37	20	45129973	45129973	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:45129973A>C	ENST00000347606.4	-	5	2187	c.2005T>G	c.(2005-2007)Tca>Gca	p.S669A	ZNF334_ENST00000457685.2_Missense_Mutation_p.S631A|ZNF334_ENST00000593880.1_Missense_Mutation_p.S692A	NM_018102.4	NP_060572.3	Q9HCZ1	ZN334_HUMAN	zinc finger protein 334	669					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S669A(1)		NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	32		Myeloproliferative disorder(115;0.0122)				AGAAAGTTTGATTTGTGGCGA	0.353																																					p.S669A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2005G	20						.						142.0	138.0	140.0					20																	45129973		2203	4300	6503	44563380	SO:0001583	missense	55713	exon5			AK001331	CCDS33480.1, CCDS74736.1	20q13.12	2013-09-20			ENSG00000198185	ENSG00000198185		"""Zinc fingers, C2H2-type"", ""-"""	15806	protein-coding gene	gene with protein product							Standard	NM_018102		Approved	bA179N14.1	uc002xsc.4	Q9HCZ1	OTTHUMG00000032654	ENST00000347606.4:c.2005T>G	20.37:g.45129973A>C	ENSP00000255129:p.Ser669Ala	Somatic		Capture	Illumina HiSeq	Phase_I	44563380	NM_018102	Q5T6U2|Q9NVW4	Missense_Mutation	SNP	ENST00000347606.4	37	CCDS33480.1	.	.	.	.	.	.	.	.	.	.	A	9.951	1.220251	0.22457	.	.	ENSG00000198185	ENST00000457685;ENST00000347606	T;T	0.61859	0.07;0.07	3.23	0.656	0.17844	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40791	0.1131	L	0.37466	1.105	0.09310	N	1	P;P;P	0.38504	0.634;0.634;0.634	B;B;B	0.35607	0.206;0.206;0.206	T	0.28776	-1.0033	9	0.51188	T	0.08	.	3.8475	0.08940	0.6925:0.0:0.1193:0.1882	.	631;669;692	B3KQ93;Q9HCZ1;Q8N3P8	.;ZN334_HUMAN;.	A	631;669	ENSP00000402582:S631A;ENSP00000255129:S669A	ENSP00000255129:S669A	S	-	1	0	ZNF334	44563380	0.001000	0.12720	0.640000	0.29408	0.575000	0.36095	1.576000	0.36504	0.429000	0.26202	0.482000	0.46254	TCA		0.353	ZNF334-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079575.1		
ZNFX1	57169	broad.mit.edu	37	20	47864336	47864336	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:47864336G>C	ENST00000396105.1	-	14	5471	c.5225C>G	c.(5224-5226)gCc>gGc	p.A1742G	ZNFX1_ENST00000371752.1_Missense_Mutation_p.A1742G|ZNFX1_ENST00000371754.4_Intron	NM_021035.2	NP_066363.1	Q9P2E3	ZNFX1_HUMAN	zinc finger, NFX1-type containing 1	1742							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(8)|kidney(7)|large_intestine(15)|liver(1)|lung(17)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	60			BRCA - Breast invasive adenocarcinoma(12;0.00173)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GCGCTTCTTGGCCAGCCACTC	0.502																																					p.A1742G												.	.	0			c.C5225G	20						.						102.0	99.0	100.0					20																	47864336		2203	4300	6503	47297743	SO:0001583	missense	57169	exon14			AK022641	CCDS13417.1	20q13.13	2014-02-12			ENSG00000124201	ENSG00000124201			29271	protein-coding gene	gene with protein product						10718198	Standard	NM_021035		Approved	KIAA1404, FLJ11277	uc002xui.3	Q9P2E3	OTTHUMG00000032696	ENST00000396105.1:c.5225C>G	20.37:g.47864336G>C	ENSP00000379412:p.Ala1742Gly	None		Capture	Illumina HiSeq	Phase_I	47297743	NM_021035	Q9BQM7|Q9BQM8|Q9H8C1|Q9H9S2|Q9NUM1|Q9NWW1	Missense_Mutation	SNP	ENST00000396105.1	37	CCDS13417.1	.	.	.	.	.	.	.	.	.	.	G	3.235	-0.156598	0.06544	.	.	ENSG00000124201	ENST00000371752;ENST00000396105	D;D	0.86562	-2.14;-2.14	6.17	0.241	0.15494	.	0.877466	0.10363	N	0.683755	T	0.79452	0.4448	L	0.41236	1.265	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60224	-0.7305	10	0.16896	T	0.51	-0.1907	10.0364	0.42131	0.0:0.2139:0.2556:0.5305	.	1742	Q9P2E3	ZNFX1_HUMAN	G	1742	ENSP00000360817:A1742G;ENSP00000379412:A1742G	ENSP00000360817:A1742G	A	-	2	0	ZNFX1	47297743	0.000000	0.05858	0.006000	0.13384	0.852000	0.48524	-0.054000	0.11826	0.109000	0.17891	0.655000	0.94253	GCC		0.502	ZNFX1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079647.2	NM_021035	
NFATC2	4773	broad.mit.edu	37	20	50048660	50048660	+	Missense_Mutation	SNP	G	G	T	rs6067777	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:50048660G>T	ENST00000396009.3	-	9	2885	c.2666C>A	c.(2665-2667)cCt>cAt	p.P889H	NFATC2_ENST00000371564.3_Missense_Mutation_p.P889H|NFATC2_ENST00000609507.1_Missense_Mutation_p.P670H|NFATC2_ENST00000414705.1_Missense_Mutation_p.P869H|NFATC2_ENST00000610033.1_Missense_Mutation_p.P670H|NFATC2_ENST00000609943.1_Missense_Mutation_p.P869H	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	889					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|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 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)|sequence-specific DNA binding transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CACCCCCGCAGGTAATACTTC	0.537																																					p.P889H												.	.	0			c.C2666A	20						.						165.0	150.0	155.0					20																	50048660		2203	4300	6503	49482067	SO:0001583	missense	4773	exon9			U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.2666C>A	20.37:g.50048660G>T	ENSP00000379330:p.Pro889His	None		Capture	Illumina HiSeq	Phase_I	49482067	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	16.29	3.081054	0.55753	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.17528	2.28;2.27;2.3	5.42	5.42	0.78866	.	0.086985	0.50627	D	0.000107	T	0.39835	0.1093	M	0.62723	1.935	0.43647	D	0.996057	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	P;P;P;D	0.63033	0.903;0.87;0.885;0.91	T	0.16689	-1.0394	10	0.87932	D	0	-15.3632	19.2321	0.93843	0.0:0.0:1.0:0.0	.	869;869;889;889	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	H	889;889;869	ENSP00000360619:P889H;ENSP00000379330:P889H;ENSP00000396471:P869H	ENSP00000360619:P889H	P	-	2	0	NFATC2	49482067	1.000000	0.71417	0.338000	0.25549	0.573000	0.36030	7.842000	0.86851	2.533000	0.85409	0.591000	0.81541	CCT		0.537	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
ZFP64	55734	broad.mit.edu	37	20	50701516	50701516	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:50701516G>A	ENST00000361387.2	-	9	1578	c.1518C>T	c.(1516-1518)agC>agT	p.S506S	ZFP64_ENST00000371523.4_Silent_p.S287S|ZFP64_ENST00000371518.2_Intron	NM_199427.2	NP_955459.2	Q9NPA5	ZF64A_HUMAN	ZFP64 zinc finger protein	354					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S506S(1)		breast(2)|endometrium(5)|large_intestine(8)|lung(11)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	33						GGGCGGCCGCGCTGGAGCAGG	0.672																																					p.S506S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1518T	20						.						55.0	56.0	56.0					20																	50701516		2203	4300	6503	50134923	SO:0001819	synonymous_variant	55734	exon9			AK001596	CCDS13439.1, CCDS13440.1, CCDS13441.1, CCDS13442.1	20q13.11-q13.13	2013-01-08	2012-11-27		ENSG00000020256	ENSG00000020256		"""Zinc fingers, C2H2-type"""	15940	protein-coding gene	gene with protein product			"""zinc finger protein 338"", ""zinc finger protein 64 homolog (mouse)"", ""zinc finger protein 64"""	ZNF338		9034307	Standard	NM_199427		Approved	FLJ10734, dJ831D17.1, FLJ12628, dJ548G19.1	uc002xwl.3	Q9NPA5	OTTHUMG00000032756	ENST00000361387.2:c.1518C>T	20.37:g.50701516G>A		Somatic		Capture	Illumina HiSeq	Phase_I	50134923	NM_199427	Q9NTS7|Q9NVH4	Silent	SNP	ENST00000361387.2	37	CCDS13439.1																																																																																				0.672	ZFP64-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079743.2	NM_018197	
ZNF831	128611	broad.mit.edu	37	20	57769115	57769115	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:57769115A>T	ENST00000371030.2	+	1	3041	c.3041A>T	c.(3040-3042)cAg>cTg	p.Q1014L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1014							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.Q1014L(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)					TCCAGGCCACAGGATGGGAGA	0.667																																					p.Q1014L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3041T	20						.						25.0	28.0	27.0					20																	57769115		1955	4146	6101	57202510	SO:0001583	missense	128611	exon1			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.3041A>T	20.37:g.57769115A>T	ENSP00000360069:p.Gln1014Leu	Somatic		Capture	Illumina HiSeq	Phase_I	57202510	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	a	9.593	1.126644	0.20959	.	.	ENSG00000124203	ENST00000371030	T	0.04406	3.63	4.56	1.49	0.22878	.	1.663470	0.03269	N	0.184423	T	0.03220	0.0094	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.40001	-0.9586	10	0.28530	T	0.3	0.6038	6.2235	0.20695	0.3927:0.0:0.6073:0.0	.	1014	Q5JPB2	ZN831_HUMAN	L	1014	ENSP00000360069:Q1014L	ENSP00000360069:Q1014L	Q	+	2	0	ZNF831	57202510	0.002000	0.14202	0.002000	0.10522	0.005000	0.04900	-0.158000	0.10070	0.473000	0.27368	-0.394000	0.06481	CAG		0.667	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
CDH4	1002	broad.mit.edu	37	20	60348222	60348222	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:60348222C>T	ENST00000360469.5	+	4	648	c.560C>T	c.(559-561)cCg>cTg	p.P187L	CDH4_ENST00000543233.1_Missense_Mutation_p.P113L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	187	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P187L(1)		NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			GGGCCCTTCCCGCAGCAGCTC	0.701																																					p.P187L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C560T	20						.						14.0	13.0	13.0					20																	60348222		2189	4284	6473	59781617	SO:0001583	missense	1002	exon4			L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.560C>T	20.37:g.60348222C>T	ENSP00000353656:p.Pro187Leu	Somatic		Capture	Illumina HiSeq	Phase_I	59781617	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.715221	0.89112	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.49432	0.78;0.78	4.84	4.84	0.62591	Cadherin (3);Cadherin-like (2);	0.000000	0.85682	D	0.000000	T	0.64692	0.2621	M	0.80028	2.48	0.80722	D	1	D	0.71674	0.998	P	0.54238	0.746	T	0.69928	-0.5012	9	.	.	.	.	17.9449	0.89036	0.0:1.0:0.0:0.0	.	187	P55283	CADH4_HUMAN	L	187;95;113	ENSP00000353656:P187L;ENSP00000443301:P113L	.	P	+	2	0	CDH4	59781617	1.000000	0.71417	0.929000	0.37066	0.830000	0.47004	7.257000	0.78362	2.221000	0.72209	0.655000	0.94253	CCG		0.701	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794	
GMEB2	26205	broad.mit.edu	37	20	62227004	62227004	+	Missense_Mutation	SNP	G	G	A	rs148884295		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:62227004G>A	ENST00000266068.1	-	5	1056	c.578C>T	c.(577-579)aCg>aTg	p.T193M	GMEB2_ENST00000370077.1_Missense_Mutation_p.T193M|GMEB2_ENST00000370069.1_Missense_Mutation_p.T142M			Q9UKD1	GMEB2_HUMAN	glucocorticoid modulatory element binding protein 2	193					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription coactivator activity (GO:0003713)	p.T193M(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	18	all_cancers(38;2.51e-11)|all_epithelial(29;8.27e-13)		Epithelial(9;4.79e-09)|all cancers(9;2.76e-08)|BRCA - Breast invasive adenocarcinoma(10;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.0114)			CTCGGCCGACGTGGGGCTGCT	0.652																																					p.T193M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C578T	20						.	G	MET/THR	0,4406		0,0,2203	67.0	56.0	60.0		578	4.5	0.0	20	dbSNP_134	60	1,8599	1.2+/-3.3	0,1,4299	no	missense	GMEB2	NM_012384.3	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	193/531	62227004	1,13005	2203	4300	6503	61697448	SO:0001583	missense	26205	exon6			AF173867	CCDS13528.1	20q13.33	2008-07-02			ENSG00000101216	ENSG00000101216			4371	protein-coding gene	gene with protein product		607451				10523663, 11743720	Standard	NM_012384		Approved	P79PIF, KIAA1269, PIF79	uc002yfq.1	Q9UKD1	OTTHUMG00000032988	ENST00000266068.1:c.578C>T	20.37:g.62227004G>A	ENSP00000266068:p.Thr193Met	Somatic		Capture	Illumina HiSeq	Phase_I	61697448	NM_012384	E1P5J3|Q5TDS0|Q9H431|Q9H4X7|Q9H4X8|Q9UF78|Q9ULF1	Missense_Mutation	SNP	ENST00000266068.1	37	CCDS13528.1	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295661	0.23564	0.0	1.16E-4	ENSG00000101216	ENST00000370069;ENST00000370077;ENST00000266068	T;T;T	0.66995	-0.24;0.35;0.35	4.49	4.49	0.54785	.	0.421964	0.25607	N	0.029514	T	0.54287	0.1849	N	0.22421	0.69	0.09310	N	1	P	0.42123	0.771	B	0.39531	0.302	T	0.55673	-0.8104	10	0.52906	T	0.07	0.0293	15.7236	0.77736	0.0:0.0:1.0:0.0	.	193	Q9UKD1	GMEB2_HUMAN	M	142;193;193	ENSP00000359086:T142M;ENSP00000359094:T193M;ENSP00000266068:T193M	ENSP00000266068:T193M	T	-	2	0	GMEB2	61697448	0.978000	0.34361	0.012000	0.15200	0.222000	0.24845	3.104000	0.50306	2.218000	0.71995	0.563000	0.77884	ACG		0.652	GMEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080166.1	NM_012384	
LAMP5	24141	broad.mit.edu	37	20	9498833	9498833	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:9498833A>C	ENST00000246070.2	+	5	1114	c.622A>C	c.(622-624)Atc>Ctc	p.I208L	LAMP5_ENST00000427562.2_Missense_Mutation_p.I164L	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	208						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)		p.I208L(1)									TGCGGTCCACATCCAACCTTT	0.483																																					p.I164L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A490C	20						.						133.0	111.0	119.0					20																	9498833		2203	4300	6503	9446833	SO:0001583	missense	24141	exon4			AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"""brain and dendritic cell associated LAMP"""	614641	"""chromosome 20 open reading frame 103"""	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.622A>C	20.37:g.9498833A>C	ENSP00000246070:p.Ile208Leu	Somatic		Capture	Illumina HiSeq	Phase_I	9446833	NM_001199897	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	A	11.25	1.582081	0.28180	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.25250	1.81;1.81	5.84	5.84	0.93424	.	0.206174	0.49916	D	0.000128	T	0.13243	0.0321	N	0.08118	0	0.46298	D	0.998974	B;B	0.12013	0.001;0.005	B;B	0.12156	0.004;0.007	T	0.19160	-1.0314	9	.	.	.	-24.9164	12.0623	0.53568	0.7356:0.2643:0.0:0.0	.	164;208	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	L	208;164	ENSP00000246070:I208L;ENSP00000406360:I164L	.	I	+	1	0	C20orf103	9446833	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.747000	0.55134	2.243000	0.73865	0.533000	0.62120	ATC		0.483	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261	
LPIN3	64900	broad.mit.edu	37	20	39986621	39986621	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:39986621delC	ENST00000373257.3	+	17	2230	c.2139delC	c.(2137-2139)ctcfs	p.L713fs	LPIN3_ENST00000491528.1_3'UTR	NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	713	C-LIP.				fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.K715fs*19(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				GCTGTAGCCTCCCCAAGGGCC	0.632																																					p.L713fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2139delC	20						.						56.0	56.0	56.0					20																	39986621		2203	4299	6502	39420035	SO:0001589	frameshift_variant	64900	exon17			AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.2139delC	20.37:g.39986621delC	ENSP00000362354:p.Leu713fs	Somatic		Capture	Illumina HiSeq	Phase_I	39420035	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Frame_Shift_Del	DEL	ENST00000373257.3	37	CCDS33469.1																																																																																				0.632	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
NEURL2	140825	broad.mit.edu	37	20	44519048	44519048	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:44519048delA	ENST00000372518.4	-	1	878	c.583delT	c.(583-585)tgcfs	p.C195fs	RP3-337O18.9_ENST00000607703.1_RNA|CTSA_ENST00000372459.2_5'Flank|CTSA_ENST00000354880.5_5'Flank|CTSA_ENST00000372484.3_5'Flank|CTSA_ENST00000191018.5_5'Flank|SPATA25_ENST00000372519.3_5'Flank	NM_001278535.1|NM_080749.2	NP_001265464.1|NP_542787.1	Q9BR09	NEUL2_HUMAN	neuralized E3 ubiquitin protein ligase 2	195	NHR. {ECO:0000255|PROSITE- ProRule:PRU00400}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|sarcomere organization (GO:0045214)	muscle tendon junction (GO:0005927)|VCB complex (GO:0030891)		p.C195fs*63(1)		large_intestine(1)|lung(2)	3		Myeloproliferative disorder(115;0.0122)				GGGCGCGGGCAAAAGAGGACA	0.687											OREG0025985	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C195fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.583delT	20						.						28.0	31.0	30.0					20																	44519048		2200	4291	6491	43952455	SO:0001589	frameshift_variant	140825	exon1			AL008726	CCDS13384.1	20q13.12	2013-10-24	2013-10-24	2004-02-27	ENSG00000124257	ENSG00000124257			16156	protein-coding gene	gene with protein product		608597	"""chromosome 20 open reading frame 163"", ""neuralized-like 2 (Drosophila)"", ""neuralized homolog 2 (Drosophila)"""	C20orf163		12076535, 19723503	Standard	NM_001278535		Approved	dJ337O18.6, FLJ30259, Ozz, Ozz-E3	uc002xqg.2	Q9BR09	OTTHUMG00000032626	ENST00000372518.4:c.583delT	20.37:g.44519048delA	ENSP00000361596:p.Cys195fs	Somatic	924	Capture	Illumina HiSeq	Phase_I	43952455	NM_080749	Q3KR34	Frame_Shift_Del	DEL	ENST00000372518.4	37	CCDS13384.1																																																																																				0.687	NEURL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079539.2		
STX16	8675	broad.mit.edu	37	20	57245599	57245599	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:57245599delT	ENST00000371141.4	+	6	1312	c.588delT	c.(586-588)catfs	p.H196fs	STX16_ENST00000371132.4_Frame_Shift_Del_p.H175fs|STX16_ENST00000358029.4_Frame_Shift_Del_p.H192fs|STX16_ENST00000361830.3_Frame_Shift_Del_p.H196fs|STX16-NPEPL1_ENST00000530122.1_Frame_Shift_Del_p.H196fs|STX16_ENST00000359617.4_Frame_Shift_Del_p.H143fs|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000361770.5_Frame_Shift_Del_p.H179fs|STX16_ENST00000355957.5_Frame_Shift_Del_p.H179fs	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	196					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)	p.F177fs*7(1)		breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			GATCCCAGCATTTTTTCGACA	0.413																																					p.H175fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.525delT	20						.						192.0	156.0	168.0					20																	57245599		2203	4300	6503	56679005	SO:0001589	frameshift_variant	8675	exon5			AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.588delT	20.37:g.57245599delT	ENSP00000360183:p.His196fs	Somatic		Capture	Illumina HiSeq	Phase_I	56679005	NM_003763	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Frame_Shift_Del	DEL	ENST00000371141.4	37	CCDS13468.1																																																																																				0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
ZBTB46	140685	broad.mit.edu	37	20	62421650	62421650	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr20:62421650G>A	ENST00000245663.4	-	2	611	c.461C>T	c.(460-462)aCg>aTg	p.T154M	ZBTB46_ENST00000302995.2_Missense_Mutation_p.T154M|ZBTB46_ENST00000395104.1_Missense_Mutation_p.T154M|ZBTB46_ENST00000480766.1_5'Flank	NM_025224.3	NP_079500.2	Q86UZ6	ZBT46_HUMAN	zinc finger and BTB domain containing 46	154					negative regulation of dendritic cell differentiation (GO:2001199)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of dendritic cell differentiation (GO:2001200)|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.T154M(1)		endometrium(2)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(38;2.09e-12)|all_epithelial(29;3.8e-14)|Lung NSC(23;7.61e-10)|all_lung(23;2.64e-09)					GAGAGCTTCCGTGCTGCTGCT	0.632																																					p.T154M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C461T	20						.						32.0	29.0	30.0					20																	62421650		2203	4300	6503	61892094	SO:0001583	missense	140685	exon2			AK131482	CCDS13538.1	20q13.33	2013-01-08	2006-09-19	2006-09-19	ENSG00000130584	ENSG00000130584		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16094	protein-coding gene	gene with protein product	"""BTB-ZF protein expressed in effector lymphocytes"""	614639	"""BTB (POZ) domain containing 4"""	ZNF340, BTBD4			Standard	NM_025224		Approved	FLJ13502, RINZF, BZEL	uc002ygv.2	Q86UZ6	OTTHUMG00000033001	ENST00000245663.4:c.461C>T	20.37:g.62421650G>A	ENSP00000245663:p.Thr154Met	Somatic		Capture	Illumina HiSeq	Phase_I	61892094	NM_025224	E1P5K9|Q5JWJ3|Q6GMV4|Q9BQK3|Q9H3Z8|Q9H3Z9	Missense_Mutation	SNP	ENST00000245663.4	37	CCDS13538.1	.	.	.	.	.	.	.	.	.	.	G	7.494	0.651249	0.14516	.	.	ENSG00000130584	ENST00000245663;ENST00000302995;ENST00000395104	T;T;T	0.10668	2.85;2.85;2.85	5.64	4.69	0.59074	.	0.362958	0.30969	N	0.008517	T	0.10766	0.0263	L	0.50333	1.59	0.09310	N	1	P	0.47604	0.898	B	0.34138	0.176	T	0.11665	-1.0578	10	0.48119	T	0.1	.	15.7828	0.78275	0.0:0.1364:0.8636:0.0	.	154	Q86UZ6	ZBT46_HUMAN	M	154	ENSP00000245663:T154M;ENSP00000303102:T154M;ENSP00000378536:T154M	ENSP00000245663:T154M	T	-	2	0	ZBTB46	61892094	0.989000	0.36119	0.005000	0.12908	0.007000	0.05969	6.923000	0.75817	1.388000	0.46506	-0.172000	0.13284	ACG		0.632	ZBTB46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080232.2	NM_025224	
KRTAP13-1	140258	broad.mit.edu	37	21	31768612	31768612	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:31768612T>C	ENST00000355459.2	+	1	221	c.208T>C	c.(208-210)Tat>Cat	p.Y70H		NM_181599.2	NP_853630.2	Q8IUC0	KR131_HUMAN	keratin associated protein 13-1	70	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)		p.Y70H(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CCAGACATCCTATGTGGAGTC	0.607																																					p.Y70H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T208C	21						.						59.0	60.0	60.0					21																	31768612		2203	4300	6503	30690483	SO:0001583	missense	140258	exon1			AJ457066	CCDS13590.2	21q22.11	2013-06-20			ENSG00000198390	ENSG00000198390		"""Keratin associated proteins"""	18924	protein-coding gene	gene with protein product		608718				12359730	Standard	NM_181599		Approved	KAP13.1	uc002yoa.3	Q8IUC0	OTTHUMG00000057800	ENST00000355459.2:c.208T>C	21.37:g.31768612T>C	ENSP00000347635:p.Tyr70His	Somatic		Capture	Illumina HiSeq	Phase_I	30690483	NM_181599	Q14D20|Q3LI79	Missense_Mutation	SNP	ENST00000355459.2	37	CCDS13590.2	.	.	.	.	.	.	.	.	.	.	T	8.776	0.927187	0.18056	.	.	ENSG00000198390	ENST00000355459	T	0.02837	4.14	4.39	1.98	0.26296	.	1.160920	0.06677	N	0.767303	T	0.02230	0.0069	N	0.14661	0.345	0.09310	N	1	B	0.29835	0.258	B	0.34452	0.183	T	0.49504	-0.8933	10	0.27785	T	0.31	.	2.583	0.04823	0.1974:0.2137:0.0:0.5889	.	70	Q8IUC0	KR131_HUMAN	H	70	ENSP00000347635:Y70H	ENSP00000347635:Y70H	Y	+	1	0	KRTAP13-1	30690483	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.233000	0.09041	0.431000	0.26258	0.455000	0.32223	TAT		0.607	KRTAP13-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128252.3		
TIAM1	7074	broad.mit.edu	37	21	32493120	32493120	+	Silent	SNP	G	G	T	rs142900370	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:32493120G>T	ENST00000286827.3	-	29	4813	c.4342C>A	c.(4342-4344)Cgg>Agg	p.R1448R	TIAM1_ENST00000541036.1_Silent_p.R1388R	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1448	Poly-Arg.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1448R(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						GCCAGCCGCCGCCTCCTCCTC	0.537																																					p.R1448R												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C4342A	21						.						21.0	24.0	23.0					21																	32493120		2191	4289	6480	31414991	SO:0001819	synonymous_variant	7074	exon29				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.4342C>A	21.37:g.32493120G>T		Somatic		Capture	Illumina HiSeq	Phase_I	31414991	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Silent	SNP	ENST00000286827.3	37	CCDS13609.1																																																																																				0.537	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
TIAM1	7074	broad.mit.edu	37	21	32508317	32508317	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:32508317C>T	ENST00000286827.3	-	24	4288	c.3817G>A	c.(3817-3819)Gtg>Atg	p.V1273M	TIAM1_ENST00000541036.1_Missense_Mutation_p.V1213M	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	1273	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V1273M(2)		autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						AGCCAGATCACGGTAGTGTGC	0.507																																					p.V1273M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3817A	21						.						88.0	84.0	86.0					21																	32508317		2203	4300	6503	31430188	SO:0001583	missense	7074	exon24				CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.3817G>A	21.37:g.32508317C>T	ENSP00000286827:p.Val1273Met	Somatic		Capture	Illumina HiSeq	Phase_I	31430188	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	33	5.268596	0.95429	.	.	ENSG00000156299	ENST00000286827;ENST00000541036	T;T	0.52754	0.65;0.67	5.49	5.49	0.81192	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.69477	0.3115	M	0.70275	2.135	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.994;0.986;0.986	T	0.70117	-0.4960	10	0.52906	T	0.07	.	19.3968	0.94610	0.0:1.0:0.0:0.0	.	1213;1213;1273	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	M	1273;1213	ENSP00000286827:V1273M;ENSP00000441570:V1213M	ENSP00000286827:V1273M	V	-	1	0	TIAM1	31430188	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	7.773000	0.85462	2.565000	0.86533	0.655000	0.94253	GTG		0.507	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
ITSN1	6453	broad.mit.edu	37	21	35257409	35257409	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:35257409C>T	ENST00000381318.3	+	37	5029	c.4741C>T	c.(4741-4743)Cgc>Tgc	p.R1581C	ITSN1_ENST00000399367.3_Missense_Mutation_p.R1576C|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399326.3_3'UTR|ITSN1_ENST00000437442.2_Missense_Mutation_p.R1520C|ITSN1_ENST00000381285.4_Missense_Mutation_p.R1581C	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1581					apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.R1581C(1)		breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GAAAAAGAAGCGCGAGAAAGC	0.517																																					p.R1581C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4741T	21						.						77.0	74.0	75.0					21																	35257409		2203	4300	6503	34179279	SO:0001583	missense	6453	exon37			AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.4741C>T	21.37:g.35257409C>T	ENSP00000370719:p.Arg1581Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34179279	NM_003024	A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	CCDS33545.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.4|23.4	4.410174|4.410174	0.83340|0.83340	.|.	.|.	ENSG00000205726|ENSG00000205726	ENST00000381284|ENST00000381318;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000437442;ENST00000415023	.|T;T;T;T;T	.|0.51817	.|0.71;0.71;0.82;0.84;0.69	5.58|5.58	4.58|4.58	0.56647|0.56647	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63462|0.63462	0.2513|0.2513	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.85130	.|0.997;0.98;0.98	T|T	0.64968|0.64968	-0.6282|-0.6282	5|10	.|0.87932	.|D	.|0	.|.	11.3515|11.3515	0.49589|0.49589	0.3655:0.6345:0.0:0.0|0.3655:0.6345:0.0:0.0	.|.	.|1520;1576;1581	.|A8CTY3;A8CTX8;Q15811	.|.;.;ITSN1_HUMAN	V|C	260|1581;1581;1510;1576;1520;117	.|ENSP00000370719:R1581C;ENSP00000370685:R1581C;ENSP00000382301:R1576C;ENSP00000387377:R1520C;ENSP00000409800:R117C	.|ENSP00000370685:R1581C	A|R	+|+	2|1	0|0	ITSN1|ITSN1	34179279|34179279	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.276000|4.276000	0.58933|0.58933	2.782000|2.782000	0.95742|0.95742	0.655000|0.655000	0.94253|0.94253	GCG|CGC		0.517	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
CHAF1B	8208	broad.mit.edu	37	21	37788591	37788591	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:37788591A>G	ENST00000314103.5	+	14	1758	c.1607A>G	c.(1606-1608)cAg>cGg	p.Q536R		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	536					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)	p.Q536R(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						GGAGACGCTCAGGGCAGTCCC	0.512																																					p.Q536R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1607G	21						.						51.0	52.0	52.0					21																	37788591		2203	4300	6503	36710461	SO:0001583	missense	8208	exon14			U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259		"""WD repeat domain containing"""	1911	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 7"", ""Chromatin assembly factor I, p60 subunit"", ""human chromatin assembly factor-I p60 subunit"""	601245				7600578, 8792829	Standard	NM_005441		Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.1607A>G	21.37:g.37788591A>G	ENSP00000315700:p.Gln536Arg	Somatic		Capture	Illumina HiSeq	Phase_I	36710461	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	37	CCDS13644.1	.	.	.	.	.	.	.	.	.	.	A	5.508	0.278786	0.10458	.	.	ENSG00000159259	ENST00000314103	T	0.45276	0.9	5.29	0.873	0.19118	.	1.566800	0.03042	N	0.153498	T	0.25232	0.0613	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10428	-1.0630	10	0.15499	T	0.54	-4.8868	2.6074	0.04881	0.6159:0.1405:0.0897:0.1539	.	536	Q13112	CAF1B_HUMAN	R	536	ENSP00000315700:Q536R	ENSP00000315700:Q536R	Q	+	2	0	CHAF1B	36710461	0.014000	0.17966	0.007000	0.13788	0.107000	0.19398	0.191000	0.17076	0.298000	0.22638	0.460000	0.39030	CAG		0.512	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441	
KCNJ15	3772	broad.mit.edu	37	21	39671475	39671475	+	Missense_Mutation	SNP	G	G	A	rs140719548	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:39671475G>A	ENST00000328656.4	+	4	595	c.292G>A	c.(292-294)Ggt>Agt	p.G98S	KCNJ15_ENST00000398932.1_Missense_Mutation_p.G98S|KCNJ15_ENST00000398934.1_Missense_Mutation_p.G98S|KCNJ15_ENST00000398930.1_Missense_Mutation_p.G98S|KCNJ15_ENST00000398938.2_Missense_Mutation_p.G98S	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	98			G -> D (in dbSNP:rs2230033). {ECO:0000269|PubMed:8995301, ECO:0000269|Ref.3}.		potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.G98S(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CTTAGAACCCGGTGAGCCCAT	0.483																																					p.G98S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G292A	21						.						118.0	117.0	117.0					21																	39671475		2203	4300	6503	38593345	SO:0001583	missense	3772	exon3			Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.292G>A	21.37:g.39671475G>A	ENSP00000331698:p.Gly98Ser	Somatic		Capture	Illumina HiSeq	Phase_I	38593345	NM_170736	D3DSH5|O00564|Q96L28|Q99446	Missense_Mutation	SNP	ENST00000328656.4	37	CCDS13656.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.029029	0.00410	.	.	ENSG00000157551	ENST00000328656;ENST00000398928;ENST00000398938;ENST00000398932;ENST00000438657;ENST00000398930;ENST00000398934;ENST00000398927;ENST00000419868	D;D;D;D;D;D;D;D;D	0.93189	-3.18;-3.18;-3.18;-3.18;-3.18;-3.18;-3.18;-3.18;-3.18	5.13	-3.11	0.05299	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.593826	0.15252	N	0.272284	T	0.79930	0.4531	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.66300	-0.5958	9	.	.	.	.	11.3189	0.49410	0.6557:0.0:0.3443:0.0	.	98	Q99712	IRK15_HUMAN	S	98	ENSP00000331698:G98S;ENSP00000381902:G98S;ENSP00000381911:G98S;ENSP00000381905:G98S;ENSP00000414487:G98S;ENSP00000381904:G98S;ENSP00000381907:G98S;ENSP00000381901:G98S;ENSP00000400849:G98S	.	G	+	1	0	KCNJ15	38593345	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.104000	0.31074	-0.781000	0.04548	-1.623000	0.00790	GGT		0.483	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
DSCAM	1826	broad.mit.edu	37	21	41516640	41516640	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:41516640G>A	ENST00000400454.1	-	17	3514	c.3037C>T	c.(3037-3039)Caa>Taa	p.Q1013*		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1013	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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.Q1013*(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)				ATCCCATTTTGCAAATGTTTC	0.468																																					p.Q1013X	Melanoma(134;970 1778 1785 21664 32388)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3037T	21						.						74.0	69.0	70.0					21																	41516640		1954	4147	6101	40438510	SO:0001587	stop_gained	1826	exon17			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.3037C>T	21.37:g.41516640G>A	ENSP00000383303:p.Gln1013*	Somatic		Capture	Illumina HiSeq	Phase_I	40438510	NM_001389	O60468	Nonsense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	G	40	8.241038	0.98722	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	.	.	.	5.0	4.08	0.47627	.	0.056968	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	15.0042	0.71498	0.0:0.1435:0.8565:0.0	.	.	.	.	X	1013;765	.	ENSP00000383303:Q1013X	Q	-	1	0	DSCAM	40438510	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.605000	0.98321	1.032000	0.39892	0.558000	0.71614	CAA		0.468	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
RIPK4	54101	broad.mit.edu	37	21	43166793	43166793	+	Missense_Mutation	SNP	C	C	T	rs144179743		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:43166793C>T	ENST00000352483.2	-	5	876	c.812G>A	c.(811-813)cGa>cAa	p.R271Q	RIPK4_ENST00000542057.1_Missense_Mutation_p.R208Q|RIPK4_ENST00000544709.1_Missense_Mutation_p.R208Q|RIPK4_ENST00000332512.3_Missense_Mutation_p.R271Q			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	271	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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.R271Q(2)		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						GGGCCTAACTCGCGGATCCCC	0.687													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15019	0.0		0.0	False		,,,				2504	0.0				p.R271Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G812A	21						.	C	GLN/ARG	3,4401	6.2+/-15.9	0,3,2199	30.0	32.0	31.0		812	1.3	0.0	21	dbSNP_134	31	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RIPK4	NM_020639.2	43	0,4,6498	TT,TC,CC		0.0116,0.0681,0.0308	benign	271/785	43166793	4,13000	2202	4300	6502	42039862	SO:0001583	missense	54101	exon5			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.812G>A	21.37:g.43166793C>T	ENSP00000330161:p.Arg271Gln	Somatic		Capture	Illumina HiSeq	Phase_I	42039862	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		.	.	.	.	.	.	.	.	.	.	C	7.616	0.675846	0.14841	6.81E-4	1.16E-4	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057;ENST00000330470	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.28	1.33	0.21861	.	0.549745	0.16012	N	0.233752	T	0.41627	0.1167	N	0.17723	0.515	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20240	-1.0281	10	0.21014	T	0.42	-10.2104	9.0428	0.36327	0.0:0.5868:0.0:0.4132	.	271	P57078-2	.	Q	271;271;208;208;10	ENSP00000332454:R271Q;ENSP00000330161:R271Q;ENSP00000441754:R208Q;ENSP00000442901:R208Q	ENSP00000330975:R10Q	R	-	2	0	RIPK4	42039862	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.396000	0.20867	0.381000	0.24851	0.561000	0.74099	CGA		0.687	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639	
SLC37A1	54020	broad.mit.edu	37	21	43979129	43979129	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:43979129T>C	ENST00000352133.2	+	11	1893	c.911T>C	c.(910-912)gTc>gCc	p.V304A	AP001625.6_ENST00000442605.1_RNA|SLC37A1_ENST00000398341.3_Missense_Mutation_p.V304A			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	304					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)	p.V304A(1)		breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						CCGAACCACGTCGTCATTCTC	0.567																																					p.V304A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T911C	21						.						62.0	51.0	55.0					21																	43979129		2203	4300	6503	42852198	SO:0001583	missense	54020	exon12			AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.911T>C	21.37:g.43979129T>C	ENSP00000344648:p.Val304Ala	Somatic		Capture	Illumina HiSeq	Phase_I	42852198	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	.	.	.	.	.	.	.	.	.	.	T	0.017	-1.490901	0.01018	.	.	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.23147	1.92;1.92	5.7	2.06	0.26882	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.273270	0.05216	N	0.507771	T	0.15869	0.0382	L	0.28776	0.89	0.09310	N	1	B	0.13594	0.008	B	0.19946	0.027	T	0.27123	-1.0083	10	0.02654	T	1	-14.2039	4.0599	0.09834	0.1422:0.235:0.0:0.6228	.	304	P57057	GLPT_HUMAN	A	304	ENSP00000381383:V304A;ENSP00000344648:V304A	ENSP00000344648:V304A	V	+	2	0	SLC37A1	42852198	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	1.369000	0.34227	0.112000	0.17975	-0.912000	0.02778	GTC		0.567	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
PWP2	5822	broad.mit.edu	37	21	45544508	45544508	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:45544508C>T	ENST00000291576.7	+	15	1992	c.1865C>T	c.(1864-1866)gCg>gTg	p.A622V		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	622					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)	p.A622V(1)		cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		AGCATCCTGGCGGGAGGCATG	0.582																																					p.A622V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1865T	21						.						120.0	89.0	100.0					21																	45544508		2203	4300	6503	44368936	SO:0001583	missense	5822	exon15				CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1865C>T	21.37:g.45544508C>T	ENSP00000291576:p.Ala622Val	Somatic		Capture	Illumina HiSeq	Phase_I	44368936	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	.	.	.	.	.	.	.	.	.	.	C	34	5.376763	0.95945	.	.	ENSG00000241945	ENST00000291576	T	0.58210	0.35	4.63	4.63	0.57726	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.055437	0.64402	D	0.000001	T	0.67401	0.2889	M	0.89163	3.01	0.80722	D	1	D	0.60575	0.988	P	0.47827	0.558	T	0.78342	-0.2241	10	0.87932	D	0	-13.8983	17.8694	0.88807	0.0:1.0:0.0:0.0	.	622	Q15269	PWP2_HUMAN	V	622	ENSP00000291576:A622V	ENSP00000291576:A622V	A	+	2	0	PWP2	44368936	1.000000	0.71417	0.962000	0.40283	0.984000	0.73092	5.594000	0.67557	2.270000	0.75569	0.655000	0.94253	GCG		0.582	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
BACH1	571	broad.mit.edu	37	21	30698571	30698571	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:30698571delA	ENST00000399921.1	+	3	669	c.426delA	c.(424-426)agafs	p.R142fs	BACH1_ENST00000286800.3_Frame_Shift_Del_p.R142fs	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K144fs*22(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						AATGCCCAAGAAAAAAATGCT	0.378																																					p.R142fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.426delA	21						.		,	1,4261		0,1,2130	78.0	81.0	80.0		,	2.8	0.3	21		80	8,8246		3,2,4122	no	frameshift,frameshift	BACH1	NM_206866.1,NM_001186.2	,	3,3,6252	A1A1,A1R,RR		0.0969,0.0235,0.0719	,	,	30698571	9,12507	2203	4300	6503	29620442	SO:0001589	frameshift_variant	571	exon3			AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.426delA	21.37:g.30698571delA	ENSP00000382805:p.Arg142fs	Somatic		Capture	Illumina HiSeq	Phase_I	29620442	NM_206866	Q3MJE2|Q8NCI5	Frame_Shift_Del	DEL	ENST00000399921.1	37	CCDS13585.1																																																																																				0.378	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866	
ADARB1	104	broad.mit.edu	37	21	46596173	46596173	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:46596173C>T	ENST00000360697.3	+	2	572	c.557C>T	c.(556-558)gCg>gTg	p.A186V	ADARB1_ENST00000539173.1_Missense_Mutation_p.A186V|ADARB1_ENST00000437626.1_Intron|ADARB1_ENST00000348831.4_Missense_Mutation_p.A186V|ADARB1_ENST00000389863.4_Missense_Mutation_p.A186V			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	186					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A186V(2)		endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		CCTGACAAGGCGGAGCCTCCC	0.592																																					p.A186V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C557T	21						.						47.0	47.0	47.0					21																	46596173		2203	4300	6503	45420601	SO:0001583	missense	104	exon4			U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"""RED1 homolog (rat)"""	601218	"""adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"""			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.557C>T	21.37:g.46596173C>T	ENSP00000353920:p.Ala186Val	Somatic		Capture	Illumina HiSeq	Phase_I	45420601	NM_015834	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Missense_Mutation	SNP	ENST00000360697.3	37	CCDS33589.1	.	.	.	.	.	.	.	.	.	.	C	8.196	0.797153	0.16327	.	.	ENSG00000197381	ENST00000539173;ENST00000539917;ENST00000389863;ENST00000348831;ENST00000360697	T;T;T;T	0.29655	1.56;1.56;1.57;1.56	5.21	2.16	0.27623	.	0.879247	0.10266	N	0.695396	T	0.13798	0.0334	N	0.04203	-0.255	0.29884	N	0.825759	B;B;B;B;B	0.10296	0.001;0.001;0.0;0.001;0.003	B;B;B;B;B	0.08055	0.003;0.002;0.001;0.002;0.003	T	0.30909	-0.9962	10	0.25106	T	0.35	0.3541	7.4802	0.27400	0.0:0.6718:0.0:0.3282	.	213;186;186;214;186	P78563-4;P78563;Q4AE77;G5E9B4;P78563-3	.;RED1_HUMAN;.;.;.	V	186	ENSP00000441897:A186V;ENSP00000374513:A186V;ENSP00000015877:A186V;ENSP00000353920:A186V	ENSP00000015877:A186V	A	+	2	0	ADARB1	45420601	0.000000	0.05858	0.001000	0.08648	0.380000	0.30137	1.105000	0.31086	0.201000	0.20466	0.655000	0.94253	GCG		0.592	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833	
COL18A1	80781	broad.mit.edu	37	21	46842371	46842371	+	Intron	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr21:46842371T>A	ENST00000400337.2	+	2	200				COL18A1-AS1_ENST00000397787.1_RNA|COL18A1-AS1_ENST00000485206.1_RNA	NM_130445.2	NP_569712	P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1						angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)	p.T37S(1)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CAGGATAGAGTTGCAGGACAG	0.652																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	21						.						28.0	32.0	31.0					21																	46842371		2201	4299	6500	45666799	SO:0001627	intron_variant	378832	.				CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000400337.2:c.106+16983T>A	21.37:g.46842371T>A		Somatic		Capture	Illumina HiSeq	Phase_I	45666799	.	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000400337.2	37	CCDS42971.1																																																																																				0.652	COL18A1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206828.1		
PI4KA	5297	broad.mit.edu	37	22	21150562	21150562	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:21150562C>T	ENST00000572273.1	-	18	2205	c.1975G>A	c.(1975-1977)Gcg>Acg	p.A659T	PI4KA_ENST00000255882.6_Missense_Mutation_p.A717T|PI4KA_ENST00000466162.1_5'Flank			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	659					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.A659T(2)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			ATGTTGGCCGCGATGTTGGCC	0.582																																					p.A659T	GBM(136;1332 1831 3115 23601 50806)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1975A	22						.						78.0	55.0	63.0					22																	21150562		2203	4300	6503	19480562	SO:0001583	missense	5297	exon18			L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.1975G>A	22.37:g.21150562C>T	ENSP00000458238:p.Ala659Thr	Somatic		Capture	Illumina HiSeq	Phase_I	19480562	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	C	28.1	4.888757	0.91814	.	.	ENSG00000241973	ENST00000255882	.	.	.	4.62	4.62	0.57501	.	0.057574	0.64402	D	0.000002	T	0.77644	0.4161	M	0.79475	2.455	0.80722	D	1	D	0.76494	0.999	P	0.60886	0.88	T	0.81848	-0.0744	9	0.87932	D	0	-14.0797	17.6482	0.88154	0.0:1.0:0.0:0.0	.	659	P42356	PI4KA_HUMAN	T	659	.	ENSP00000255882:A659T	A	-	1	0	PI4KA	19480562	1.000000	0.71417	0.906000	0.35671	0.692000	0.40212	7.597000	0.82733	2.402000	0.81655	0.591000	0.81541	GCG		0.582	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
LZTR1	8216	broad.mit.edu	37	22	21345925	21345925	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:21345925G>A	ENST00000215739.8	+	9	1159	c.800G>A	c.(799-801)cGc>cAc	p.R267H	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Missense_Mutation_p.R248H	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	267					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R267H(2)		breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			AGGTGGACACGCATCCCAACT	0.652																																					p.R267H												.	.	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.G800A	22						.						35.0	26.0	29.0					22																	21345925		2202	4292	6494	19675925	SO:0001583	missense	8216	exon9			D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"""BTB/POZ domain containing"""	6742	protein-coding gene	gene with protein product		600574	"""leucine-zipper-like transcriptional regulator 1"""			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.800G>A	22.37:g.21345925G>A	ENSP00000215739:p.Arg267His	Somatic		Capture	Illumina HiSeq	Phase_I	19675925	NM_006767	Q14776|Q20WK0	Missense_Mutation	SNP	ENST00000215739.8	37	CCDS33606.1	.	.	.	.	.	.	.	.	.	.	G	32	5.136480	0.94517	.	.	ENSG00000099949	ENST00000539817;ENST00000215739;ENST00000389355	T;T	0.67698	-0.28;-0.28	5.18	5.18	0.71444	Kelch-type beta propeller (1);	0.053822	0.85682	D	0.000000	T	0.81230	0.4779	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;0.999	D;D;D;P	0.74023	0.957;0.982;0.947;0.904	D	0.83501	0.0075	10	0.72032	D	0.01	-35.8024	16.1666	0.81759	0.0:0.0:1.0:0.0	.	248;226;267;226	B7Z3T9;Q6ZSY0;Q8N653;F5GXU8	.;.;LZTR1_HUMAN;.	H	226;267;248	ENSP00000215739:R267H;ENSP00000374006:R248H	ENSP00000215739:R267H	R	+	2	0	LZTR1	19675925	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.621000	0.83083	2.409000	0.81822	0.407000	0.27541	CGC		0.652	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
TOP3B	8940	broad.mit.edu	37	22	22326264	22326264	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:22326264C>A	ENST00000398793.2	-	5	803	c.369G>T	c.(367-369)gaG>gaT	p.E123D	TOP3B_ENST00000357179.5_Missense_Mutation_p.E123D|TOP3B_ENST00000413067.2_Intron	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	123	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)	p.E123D(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		AGCAGATGTTCTCCCCCTCCT	0.567																																					p.E123D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G369T	22						.						272.0	149.0	190.0					22																	22326264		2203	4300	6503	20656264	SO:0001583	missense	8940	exon5			AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.369G>T	22.37:g.22326264C>A	ENSP00000381773:p.Glu123Asp	Somatic		Capture	Illumina HiSeq	Phase_I	20656264	NM_003935	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	ENST00000398793.2	37	CCDS13797.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.788905	0.90367	.	.	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000424393	T;T;T	0.37411	1.2;1.2;1.2	5.36	5.36	0.76844	DNA topoisomerase, type IA, core domain (1);Toprim domain (2);	0.000000	0.85682	D	0.000000	T	0.69097	0.3073	H	0.97240	3.965	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76187	-0.3051	10	0.87932	D	0	-1.1773	6.433	0.21807	0.0:0.7938:0.0:0.2062	.	123	O95985	TOP3B_HUMAN	D	123	ENSP00000349705:E123D;ENSP00000381773:E123D;ENSP00000390977:E123D	ENSP00000349705:E123D	E	-	3	2	TOP3B	20656264	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.072000	0.50049	2.782000	0.95742	0.655000	0.94253	GAG		0.567	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935	
ZNF280B	140883	broad.mit.edu	37	22	22842637	22842637	+	Missense_Mutation	SNP	C	C	T	rs201645345		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:22842637C>T	ENST00000406426.1	-	4	1829	c.1087G>A	c.(1087-1089)Gaa>Aaa	p.E363K	ZNF280B_ENST00000360412.2_Missense_Mutation_p.E363K			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	363					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E363K(2)		autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TGGACATTTTCGATGTGACAC	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		16761	0.0		0.001	False		,,,				2504	0.0				p.E363K												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1087A	22						.						137.0	126.0	130.0					22																	22842637		2203	4300	6503	21172637	SO:0001583	missense	140883	exon4			AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1087G>A	22.37:g.22842637C>T	ENSP00000385998:p.Glu363Lys	Somatic		Capture	Illumina HiSeq	Phase_I	21172637	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.08	3.296773	0.60086	.	.	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.03468	3.92;3.92	4.85	4.85	0.62838	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	.	.	.	.	T	0.03178	0.0093	N	0.17631	0.505	0.40237	D	0.977919	P	0.50066	0.931	B	0.36504	0.226	T	0.54938	-0.8218	9	0.87932	D	0	-6.6835	15.8711	0.79119	0.0:1.0:0.0:0.0	.	363	Q86YH2	Z280B_HUMAN	K	363	ENSP00000385998:E363K;ENSP00000353586:E363K	ENSP00000353586:E363K	E	-	1	0	ZNF280B	21172637	1.000000	0.71417	0.981000	0.43875	0.251000	0.25915	5.134000	0.64770	2.689000	0.91719	0.655000	0.94253	GAA		0.498	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
CABIN1	23523	broad.mit.edu	37	22	24572103	24572103	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:24572103C>T	ENST00000398319.2	+	35	6450	c.6065C>T	c.(6064-6066)gCa>gTa	p.A2022V	CABIN1_ENST00000405822.2_Missense_Mutation_p.A1943V|CABIN1_ENST00000263119.5_Missense_Mutation_p.A2022V|CABIN1_ENST00000337989.7_Intron	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	2022					cell surface receptor signaling pathway (GO:0007166)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|negative regulation of catalytic activity (GO:0043086)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase inhibitor activity (GO:0004864)	p.A2022V(1)		breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(13)|liver(1)|lung(18)|ovary(5)|pancreas(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						GCGAGAGTGGCAGAGGGCACC	0.637																																					p.A2022V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6065T	22						.						24.0	24.0	24.0					22																	24572103		2201	4295	6496	22902103	SO:0001583	missense	23523	exon35			AF072441	CCDS13823.1, CCDS74830.1	22q11.23	2008-09-16			ENSG00000099991	ENSG00000099991			24187	protein-coding gene	gene with protein product		604251				9655484, 9205841	Standard	NM_001199281		Approved	KIAA0330, PPP3IN	uc002zzi.1	Q9Y6J0	OTTHUMG00000150797	ENST00000398319.2:c.6065C>T	22.37:g.24572103C>T	ENSP00000381364:p.Ala2022Val	Somatic		Capture	Illumina HiSeq	Phase_I	22902103	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.652577	0.29336	.	.	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.21031	2.03;2.03;2.03	4.64	3.62	0.41486	.	0.501458	0.19774	N	0.106365	T	0.09686	0.0238	N	0.08118	0	0.58432	D	0.999994	B;B	0.22683	0.073;0.044	B;B	0.24394	0.053;0.014	T	0.13098	-1.0522	10	0.40728	T	0.16	.	5.7107	0.17933	0.0:0.8142:0.0:0.1858	.	1943;2022	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	V	2022;1943;2022	ENSP00000263119:A2022V;ENSP00000384694:A1943V;ENSP00000381364:A2022V	ENSP00000263119:A2022V	A	+	2	0	CABIN1	22902103	0.995000	0.38212	0.997000	0.53966	0.165000	0.22458	1.340000	0.33896	2.543000	0.85770	0.650000	0.86243	GCA		0.637	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295	
SEZ6L	23544	broad.mit.edu	37	22	26743798	26743798	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:26743798G>A	ENST00000248933.6	+	11	2421	c.2326G>A	c.(2326-2328)Ggc>Agc	p.G776S	SEZ6L_ENST00000343706.4_Missense_Mutation_p.G776S|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G776S|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G776S|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G776S|SEZ6L_ENST00000402979.1_Missense_Mutation_p.G549S|SEZ6L_ENST00000411842.2_5'UTR|SEZ6L_ENST00000403121.1_Missense_Mutation_p.G549S			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	776	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)		p.G776S(1)		breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						GTGTGACCCCGGCTATGACAT	0.557																																					p.G776S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2326A	22						.						87.0	83.0	84.0					22																	26743798		2203	4300	6503	25073798	SO:0001583	missense	23544	exon11			AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.2326G>A	22.37:g.26743798G>A	ENSP00000248933:p.Gly776Ser	Somatic		Capture	Illumina HiSeq	Phase_I	25073798	NM_001184776	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	35	5.486368	0.96323	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.76448	-1.02;-1.02;-1.02;-1.02;-1.02;-1.02;-1.02	4.99	4.99	0.66335	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.56097	D	0.000021	D	0.89938	0.6860	M	0.89095	3.005	0.80722	D	1	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	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.91728	0.5394	10	0.87932	D	0	.	17.4431	0.87570	0.0:0.0:1.0:0.0	.	776;776;549;776;776;776;776	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	S	776;776;776;776;776;549;549	ENSP00000384772:G776S;ENSP00000437037:G776S;ENSP00000354185:G776S;ENSP00000248933:G776S;ENSP00000342661:G776S;ENSP00000384838:G549S;ENSP00000384733:G549S	ENSP00000248933:G776S	G	+	1	0	SEZ6L	25073798	1.000000	0.71417	0.977000	0.42913	0.988000	0.76386	9.089000	0.94137	2.600000	0.87896	0.655000	0.94253	GGC		0.557	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
PITPNB	23760	broad.mit.edu	37	22	28254426	28254426	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:28254426C>T	ENST00000335272.5	-	10	793	c.717G>A	c.(715-717)acG>acA	p.T239T	PITPNB_ENST00000320996.10_Silent_p.T239T|PITPNB_ENST00000455418.3_Silent_p.T241T	NM_012399.3	NP_036531.1	P48739	PIPNB_HUMAN	phosphatidylinositol transfer protein, beta	239					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|lipid metabolic process (GO:0006629)|phospholipid metabolic process (GO:0006644)|phospholipid transport (GO:0015914)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)	lipid binding (GO:0008289)	p.T239T(1)		large_intestine(4)|lung(3)|skin(1)	8						TGTCTTCCATCGTGAGATCGA	0.363																																					p.T239T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G717A	22						.																																			26584426	SO:0001819	synonymous_variant	23760	exon10			D30037	CCDS13842.1, CCDS63433.1	22q12.1	2006-12-15			ENSG00000180957	ENSG00000180957			9002	protein-coding gene	gene with protein product		606876				10591208	Standard	NM_012399		Approved	VIB1B	uc003adk.3	P48739	OTTHUMG00000150976	ENST00000335272.5:c.717G>A	22.37:g.28254426C>T		Somatic		Capture	Illumina HiSeq	Phase_I	26584426	NM_012399	B3KYB8|B7Z7Q0|Q8N5W1	Silent	SNP	ENST00000335272.5	37	CCDS13842.1																																																																																				0.363	PITPNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320740.1		
NEFH	4744	broad.mit.edu	37	22	29886319	29886319	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:29886319C>A	ENST00000310624.6	+	4	2723	c.2690C>A	c.(2689-2691)gCt>gAt	p.A897D		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	903	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.A897D(1)		cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAGGAAGAGGCTGAAGATAAG	0.512																																					p.A897D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2690A	22						.						56.0	61.0	59.0					22																	29886319		2203	4300	6503	28216319	SO:0001583	missense	4744	exon4				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2690C>A	22.37:g.29886319C>A	ENSP00000311997:p.Ala897Asp	Somatic		Capture	Illumina HiSeq	Phase_I	28216319	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067157	0.36470	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.85013	-1.93	5.92	2.66	0.31614	.	0.388925	0.22246	N	0.062605	T	0.77605	0.4155	L	0.50333	1.59	0.31633	N	0.648819	P	0.39216	0.664	B	0.33042	0.157	T	0.77191	-0.2678	10	0.87932	D	0	.	8.2934	0.31971	0.0:0.5641:0.2954:0.1405	.	903	P12036	NFH_HUMAN	D	848;897	ENSP00000311997:A897D	ENSP00000311997:A897D	A	+	2	0	NEFH	28216319	0.000000	0.05858	0.660000	0.29694	0.945000	0.59286	0.522000	0.22909	0.387000	0.25024	0.655000	0.94253	GCT		0.512	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
TBC1D10A	83874	broad.mit.edu	37	22	30690043	30690043	+	Silent	SNP	C	C	T	rs375538912		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:30690043C>T	ENST00000215790.7	-	7	926	c.762G>A	c.(760-762)ccG>ccA	p.P254P	TBC1D10A_ENST00000403362.1_Silent_p.P166P|TBC1D10A_ENST00000403477.3_Silent_p.P261P|RP1-130H16.18_ENST00000447976.1_Silent_p.P128P	NM_031937.2	NP_114143.1	Q9BXI6	TB10A_HUMAN	TBC1 domain family, member 10A	254	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				activation of cysteine-type endopeptidase activity (GO:0097202)|positive regulation of proteolysis (GO:0045862)|retrograde transport, endosome to Golgi (GO:0042147)	extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rab GTPase activator activity (GO:0005097)	p.P254P(1)		cervix(2)|endometrium(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	23						TGTGGGCCACCGGCGACACCT	0.607																																					p.P254P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G762A	22						.	C	,	1,4405	2.1+/-5.4	0,1,2202	146.0	132.0	137.0		783,762	-9.6	0.0	22		137	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TBC1D10A	NM_001204240.1,NM_031937.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	261/516,254/509	30690043	1,13005	2203	4300	6503	29020043	SO:0001819	synonymous_variant	83874	exon7			AF331038	CCDS13874.1, CCDS56227.1	22q12.2	2013-07-09	2005-03-10	2005-03-10	ENSG00000099992	ENSG00000099992			23609	protein-coding gene	gene with protein product	"""EBP50-PDZ interactor of 64 kD"""	610020	"""TBC1 domain family, member 10"""	TBC1D10		11285285, 20404108	Standard	NM_001204240		Approved	EPI64, AC004997.C22.2	uc010gvu.3	Q9BXI6	OTTHUMG00000150924	ENST00000215790.7:c.762G>A	22.37:g.30690043C>T		Somatic		Capture	Illumina HiSeq	Phase_I	29020043	NM_031937	B3KXT8|O76053|Q20WK7|Q543A2	Silent	SNP	ENST00000215790.7	37	CCDS13874.1																																																																																				0.607	TBC1D10A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320550.1	NM_031937	
GAL3ST1	9514	broad.mit.edu	37	22	30951873	30951873	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:30951873A>G	ENST00000402321.1	-	3	656	c.339T>C	c.(337-339)aaT>aaC	p.N113N	GAL3ST1_ENST00000406361.1_Silent_p.N113N|GAL3ST1_ENST00000401975.1_Silent_p.N113N|GAL3ST1_ENST00000406955.1_Silent_p.N113N|GAL3ST1_ENST00000402369.1_Silent_p.N113N|GAL3ST1_ENST00000338911.5_Silent_p.N113N|GAL3ST1_ENST00000443111.2_Silent_p.N113N			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	113					galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)	p.N113N(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						AGTCGAAGTCATTGCGGCCGT	0.602																																					p.N113N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T339C	22						.						98.0	83.0	88.0					22																	30951873		2203	4300	6503	29281873	SO:0001819	synonymous_variant	9514	exon4			D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"""Sulfotransferases, membrane-bound"""	24240	protein-coding gene	gene with protein product	"""cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"""	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.339T>C	22.37:g.30951873A>G		Somatic		Capture	Illumina HiSeq	Phase_I	29281873	NM_004861	Q96C63	Silent	SNP	ENST00000402321.1	37	CCDS13879.1																																																																																				0.602	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861	
DEPDC5	9681	broad.mit.edu	37	22	32270298	32270298	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:32270298A>G	ENST00000382112.3	+	35	3646	c.3576A>G	c.(3574-3576)tcA>tcG	p.S1192S	DEPDC5_ENST00000400249.2_Silent_p.S1170S|DEPDC5_ENST00000400248.2_Silent_p.S1170S|DEPDC5_ENST00000382105.2_Silent_p.S1123S|DEPDC5_ENST00000539165.1_Silent_p.S18S|DEPDC5_ENST00000535622.1_Silent_p.S1101S|DEPDC5_ENST00000494060.1_3'UTR|DEPDC5_ENST00000382111.2_Silent_p.S1201S|DEPDC5_ENST00000400246.1_Silent_p.S1201S|DEPDC5_ENST00000266091.3_Silent_p.S1179S	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1201	DEP. {ECO:0000255|PROSITE- ProRule:PRU00066}.				intracellular signal transduction (GO:0035556)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(24)|ovary(5)|pancreas(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGGGCCTCTCACCGTACTGCT	0.587																																					p.S1170S												.	.	0			c.A3510G	22						.						45.0	48.0	47.0					22																	32270298		2064	4190	6254	30600298	SO:0001819	synonymous_variant	9681	exon35			AB014545	CCDS43006.1, CCDS43007.1, CCDS46692.1, CCDS56229.1, CCDS74849.1	22q12.3	2013-04-29			ENSG00000100150	ENSG00000100150			18423	protein-coding gene	gene with protein product		614191				23542697, 23542701	Standard	NM_001242896		Approved	KIAA0645, DEP.5	uc011alu.2	O75140	OTTHUMG00000030926	ENST00000382112.3:c.3576A>G	22.37:g.32270298A>G		None		Capture	Illumina HiSeq	Phase_I	30600298	NM_014662	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Silent	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	A	7.578	0.668197	0.14710	.	.	ENSG00000100150	ENST00000433147	.	.	.	4.92	-9.85	0.00476	.	.	.	.	.	T	0.32941	0.0846	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39078	-0.9631	4	.	.	.	.	1.6609	0.02792	0.443:0.2047:0.1933:0.159	.	.	.	.	A	577	.	.	T	+	1	0	DEPDC5	30600298	0.000000	0.05858	0.078000	0.20375	0.813000	0.45954	-3.939000	0.00330	-2.310000	0.00650	-1.251000	0.01509	ACC		0.587	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662	
SLC5A1	6523	broad.mit.edu	37	22	32480499	32480499	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:32480499T>C	ENST00000266088.4	+	8	988	c.738T>C	c.(736-738)gaT>gaC	p.D246D	SLC5A1_ENST00000543737.1_Silent_p.D119D	NM_000343.3	NP_000334.1	P13866	SC5A1_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 1	246					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intestinal absorption (GO:0050892)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glucose:sodium symporter activity (GO:0005412)	p.D246D(1)		NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	37					Canagliflozin(DB08907)	TAGTGTCTGATGGCAACACCA	0.502																																					p.D246D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T738C	22						.						146.0	108.0	121.0					22																	32480499		2203	4300	6503	30810499	SO:0001819	synonymous_variant	6523	exon8				CCDS13902.1, CCDS58805.1	22q12.3	2013-05-22			ENSG00000100170	ENSG00000100170		"""Solute carriers"""	11036	protein-coding gene	gene with protein product	"""sodium/glucose cotransporter 1"""	182380		SGLT1		8195156	Standard	NM_000343		Approved	D22S675, NAGT	uc003amc.3	P13866	OTTHUMG00000030768	ENST00000266088.4:c.738T>C	22.37:g.32480499T>C		Somatic		Capture	Illumina HiSeq	Phase_I	30810499	NM_000343	B2R7E2|B7Z4Q9|B7ZA69	Silent	SNP	ENST00000266088.4	37	CCDS13902.1																																																																																				0.502	SLC5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075656.3	NM_000343	
SYN3	8224	broad.mit.edu	37	22	33402393	33402393	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:33402393C>T	ENST00000358763.2	-	2	497	c.255G>A	c.(253-255)acG>acA	p.T85T	SYN3_ENST00000332840.5_Silent_p.T85T	NM_001135774.1	NP_001129246.1	O14994	SYN3_HUMAN	synapsin III	85	B; linker.				neurotransmitter secretion (GO:0007269)|regulation of synaptic transmission, GABAergic (GO:0032228)	cell junction (GO:0030054)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)	p.T85T(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33						GAACAATGGGCGTGGAGGGAC	0.552																																					p.T85T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G255A	22						.						108.0	106.0	107.0					22																	33402393		2203	4300	6503	31732393	SO:0001819	synonymous_variant	8224	exon2			AF046873	CCDS13908.1	22q12.3	2008-05-14			ENSG00000185666	ENSG00000185666			11496	protein-coding gene	gene with protein product		602705				9539796	Standard	NM_003490		Approved		uc003amx.3	O14994	OTTHUMG00000031004	ENST00000358763.2:c.255G>A	22.37:g.33402393C>T		Somatic		Capture	Illumina HiSeq	Phase_I	31732393	NM_001135774	B1B1F9	Silent	SNP	ENST00000358763.2	37	CCDS13908.1																																																																																				0.552	SYN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075892.4		
HMGXB4	10042	broad.mit.edu	37	22	35689038	35689038	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:35689038T>C	ENST00000216106.5	+	10	1820	c.1692T>C	c.(1690-1692)tgT>tgC	p.C564C	HMGXB4_ENST00000444518.2_Silent_p.C455C	NM_001003681.2	NP_001003681.1	Q9UGU5	HMGX4_HUMAN	HMG box domain containing 4	564					endosome to lysosome transport (GO:0008333)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	NURF complex (GO:0016589)	DNA binding (GO:0003677)	p.C564C(1)		breast(1)|endometrium(1)|large_intestine(6)|liver(1)|lung(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCATTATCTGTGCCCTTGGCC	0.488																																					p.C564C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1692C	22						.						248.0	194.0	212.0					22																	35689038		2203	4300	6503	34019038	SO:0001819	synonymous_variant	10042	exon10			AJ010069	CCDS33641.1	22q13	2011-07-01	2009-01-05	2009-01-05	ENSG00000100281	ENSG00000100281		"""High mobility group / Non-canonical"""	5003	protein-coding gene	gene with protein product		604702	"""high-mobility group protein 2-like 1"""	HMG2L1		10329004, 10591208, 20511232	Standard	NM_001003681		Approved	THC211630	uc003anl.3	Q9UGU5	OTTHUMG00000150439	ENST00000216106.5:c.1692T>C	22.37:g.35689038T>C		Somatic		Capture	Illumina HiSeq	Phase_I	34019038	NM_001003681	O75672|O75673|Q9UMT5	Silent	SNP	ENST00000216106.5	37	CCDS33641.1																																																																																				0.488	HMGXB4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318104.2	NM_005487	
RBFOX2	23543	broad.mit.edu	37	22	36164391	36164391	+	Silent	SNP	G	G	A	rs577472929		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:36164391G>A	ENST00000438146.2	-	6	668	c.669C>T	c.(667-669)ttC>ttT	p.F223F	RBFOX2_ENST00000416721.2_Silent_p.F152F|RBFOX2_ENST00000397303.2_Silent_p.F133F|RBFOX2_ENST00000449924.2_Silent_p.F152F|RBFOX2_ENST00000262829.7_Silent_p.F134F|RBFOX2_ENST00000359369.4_Silent_p.F132F|RBFOX2_ENST00000414461.2_Silent_p.F152F|RBFOX2_ENST00000405409.2_Silent_p.F153F	NM_001082578.1|NM_001082579.1	NP_001076047|NP_001076048.1	O43251	RFOX2_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 2	162					dendrite morphogenesis (GO:0048813)|intracellular estrogen receptor signaling pathway (GO:0030520)|mRNA processing (GO:0006397)|negative regulation of transcription, DNA-templated (GO:0045892)|neuromuscular process controlling balance (GO:0050885)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of cell proliferation (GO:0042127)|regulation of definitive erythrocyte differentiation (GO:0010724)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.F153F(1)		endometrium(4)|large_intestine(7)|lung(7)	18						TTACGAACCCGAATCCCTGCA	0.448																																					p.F222F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C666T	22						.						127.0	112.0	117.0					22																	36164391		2203	4300	6503	34494337	SO:0001819	synonymous_variant	23543	exon6			AL009266	CCDS13921.1, CCDS43013.1, CCDS46699.1, CCDS46700.1, CCDS46701.1	22q12-q13	2013-02-12	2010-09-10	2010-09-10	ENSG00000100320	ENSG00000100320		"""RNA binding motif (RRM) containing"""	9906	protein-coding gene	gene with protein product	"""hexaribonucleotide binding protein 2"""	612149	"""RNA binding motif protein 9"""	RBM9			Standard	NM_014309		Approved	HNRBP2, FOX-2, HRNBP2	uc003aon.4	O43251	OTTHUMG00000150585	ENST00000438146.2:c.669C>T	22.37:g.36164391G>A		Somatic		Capture	Illumina HiSeq	Phase_I	34494337	NM_001082579	A4F5G8|A8K5Z5|B0QYY8|B0QYY9|Q0PRL5|Q0VH35|Q5TF71|Q6IC09|Q8TD00|Q8WYB1|Q96DZ6|Q96NL7|Q9UGW4|Q9UH33	Silent	SNP	ENST00000438146.2	37	CCDS43013.1																																																																																				0.448	RBFOX2-005	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319299.3		
CSF2RB	1439	broad.mit.edu	37	22	37333573	37333573	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:37333573G>T	ENST00000403662.3	+	14	1945	c.1723G>T	c.(1723-1725)Gcc>Tcc	p.A575S	CSF2RB_ENST00000262825.5_Missense_Mutation_p.A581S|CSF2RB_ENST00000406230.1_Missense_Mutation_p.A581S|CSF2RB_ENST00000536485.1_Missense_Mutation_p.A522S			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	575					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.A575S(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	AGGCCCGCCTGCCGCCTCCCA	0.652																																					p.A575S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1723T	22						.						20.0	23.0	22.0					22																	37333573		2202	4297	6499	35663519	SO:0001583	missense	1439	exon14			M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1723G>T	22.37:g.37333573G>T	ENSP00000384053:p.Ala575Ser	Somatic		Capture	Illumina HiSeq	Phase_I	35663519	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	37	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612405	0.28712	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.92048	-2.45;-2.96;-2.96;-2.96	5.36	-0.505	0.11993	.	1.557160	0.04046	N	0.304007	D	0.88145	0.6358	L	0.57536	1.79	0.09310	N	1	P;P	0.39424	0.673;0.544	B;B	0.37144	0.242;0.077	T	0.74006	-0.3803	10	0.19147	T	0.46	.	4.7778	0.13187	0.3496:0.1479:0.5025:0.0	.	581;575	P32927-2;P32927	.;IL3RB_HUMAN	S	575;575;581;581;522	ENSP00000384053:A575S;ENSP00000262825:A581S;ENSP00000385271:A581S;ENSP00000440003:A522S	ENSP00000262825:A581S	A	+	1	0	CSF2RB	35663519	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.331000	0.07914	-0.230000	0.09840	0.557000	0.71058	GCC		0.652	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
RAC2	5880	broad.mit.edu	37	22	37628841	37628841	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:37628841C>T	ENST00000249071.6	-	3	346	c.225G>A	c.(223-225)acG>acA	p.T75T	RAC2_ENST00000406508.1_Splice_Site_p.T31T|RAC2_ENST00000405484.1_Splice_Site_p.T68T	NM_002872.3	NP_002863.1	P15153	RAC2_HUMAN	ras-related C3 botulinum toxin substrate 2 (rho family, small GTP binding protein Rac2)	75					actin filament organization (GO:0007015)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|bone resorption (GO:0045453)|cell projection assembly (GO:0030031)|G-protein coupled receptor signaling pathway (GO:0007186)|lymphocyte aggregation (GO:0071593)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neutrophil chemotaxis (GO:0090023)|regulation of cell-substrate adhesion (GO:0010810)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of neutrophil migration (GO:1902622)|regulation of respiratory burst (GO:0060263)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.T75T(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)	12					Dextromethorphan(DB00514)	agcAGCACACCGTCTGTGGAT	0.612																																					p.T75T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G225A	22						.						80.0	56.0	64.0					22																	37628841		2203	4300	6503	35958787	SO:0001630	splice_region_variant	5880	exon3			M64595	CCDS13945.1	22q13.1	2014-09-17			ENSG00000128340	ENSG00000128340		"""Endogenous ligands"""	9802	protein-coding gene	gene with protein product		602049				2674130	Standard	NM_002872		Approved	EN-7	uc003arc.3	P15153	OTTHUMG00000150540	ENST00000249071.6:c.225+1G>A	22.37:g.37628841C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35958787	NM_002872	Q9UDJ4	Silent	SNP	ENST00000249071.6	37	CCDS13945.1																																																																																				0.612	RAC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318812.1		Silent
CARD10	29775	broad.mit.edu	37	22	37900667	37900667	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:37900667A>G	ENST00000403299.1	-	9	1709	c.1493T>C	c.(1492-1494)aTg>aCg	p.M498T	CARD10_ENST00000406271.3_Missense_Mutation_p.M212T|CARD10_ENST00000251973.5_Missense_Mutation_p.M498T			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	498					activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein complex assembly (GO:0006461)|regulation of apoptotic process (GO:0042981)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)	receptor signaling complex scaffold activity (GO:0030159)	p.M498T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	Melanoma(58;0.0574)					AGGTCCCCCCATGACAGCTGC	0.567																																					p.M498T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1493C	22						.						52.0	48.0	49.0					22																	37900667		2203	4300	6503	36230613	SO:0001583	missense	29775	exon8			AF086324	CCDS13948.1	22q13.1	2008-05-22			ENSG00000100065	ENSG00000100065			16422	protein-coding gene	gene with protein product		607209				11259443, 11356195	Standard	NM_014550		Approved	CARMA3, BIMP1	uc003asu.1	Q9BWT7	OTTHUMG00000150592	ENST00000403299.1:c.1493T>C	22.37:g.37900667A>G	ENSP00000384570:p.Met498Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36230613	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Missense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	A	3.433	-0.115791	0.06881	.	.	ENSG00000100065	ENST00000403299;ENST00000406271;ENST00000251973;ENST00000437756	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.49	-9.1	0.00714	.	5.281270	0.00166	N	0.000000	T	0.27027	0.0662	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16482	-1.0401	10	0.13108	T	0.6	14.0392	14.8546	0.70326	0.1732:0.0868:0.74:0.0	.	498;212	Q9BWT7;Q8NC81	CAR10_HUMAN;.	T	498;212;498;139	ENSP00000384570:M498T;ENSP00000385799:M212T;ENSP00000251973:M498T;ENSP00000416239:M139T	ENSP00000251973:M498T	M	-	2	0	CARD10	36230613	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.219000	0.02973	-1.803000	0.01242	-0.411000	0.06167	ATG		0.567	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550	
C22orf23	84645	broad.mit.edu	37	22	38340193	38340193	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:38340193C>T	ENST00000249079.2	-	7	899	c.643G>A	c.(643-645)Gcc>Acc	p.A215T	C22orf23_ENST00000403305.1_Missense_Mutation_p.A215T|C22orf23_ENST00000403026.1_Missense_Mutation_p.A215T			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	215								p.A215T(1)		endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					TAAGTGGTGGCAAGACCCTTC	0.567																																					p.A215T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G643A	22						.						156.0	126.0	136.0					22																	38340193		2203	4300	6503	36670139	SO:0001583	missense	84645	exon7			AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.643G>A	22.37:g.38340193C>T	ENSP00000249079:p.Ala215Thr	Somatic		Capture	Illumina HiSeq	Phase_I	36670139	NM_032561	Q5JYU9|Q96M68	Missense_Mutation	SNP	ENST00000249079.2	37	CCDS13962.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.283157	0.59867	.	.	ENSG00000128346	ENST00000403305;ENST00000249079;ENST00000403026	T;T;T	0.44881	0.91;0.91;0.91	5.41	1.92	0.25849	.	0.909102	0.09444	N	0.801286	T	0.33614	0.0869	L	0.50333	1.59	0.09310	N	1	B	0.20052	0.041	B	0.24541	0.054	T	0.35001	-0.9806	10	0.11182	T	0.66	-0.1024	7.363	0.26758	0.0:0.7071:0.1359:0.157	.	215	Q9BZE7	EVG1_HUMAN	T	215	ENSP00000384667:A215T;ENSP00000249079:A215T;ENSP00000384618:A215T	ENSP00000249079:A215T	A	-	1	0	C22orf23	36670139	0.049000	0.20398	0.065000	0.19835	0.666000	0.39218	0.736000	0.26130	0.626000	0.30322	0.650000	0.86243	GCC		0.567	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561	
SOX10	6663	broad.mit.edu	37	22	38370168	38370168	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:38370168C>T	ENST00000396884.2	-	4	1017	c.735G>A	c.(733-735)ccG>ccA	p.P245P	POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000360880.2_Silent_p.P245P|POLR2F_ENST00000407936.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	245					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)	p.P245P(1)		NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					GCTCTGTCTTCGGGGTGGTTG	0.657																																					p.P245P	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G735A	22						.						79.0	85.0	83.0					22																	38370168		2193	4286	6479	36700114	SO:0001819	synonymous_variant	6663	exon4				CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"""SRY (sex determining region Y)-boxes"""	11190	protein-coding gene	gene with protein product	"""dominant megacolon, mouse, human homolog of"""	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.735G>A	22.37:g.38370168C>T		Somatic		Capture	Illumina HiSeq	Phase_I	36700114	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	37	CCDS13964.1	.	.	.	.	.	.	.	.	.	.	C	7.526	0.657641	0.14645	.	.	ENSG00000100146	ENST00000446929	.	.	.	4.73	0.0287	0.14159	.	.	.	.	.	T	0.41766	0.1173	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22871	-1.0204	4	.	.	.	.	1.5635	0.02599	0.1344:0.2327:0.1236:0.5093	.	.	.	.	Q	122	.	.	R	-	2	0	SOX10	36700114	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	1.589000	0.36644	-0.095000	0.12351	-0.505000	0.04504	CGA		0.657	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941	
RPS19BP1	91582	broad.mit.edu	37	22	39925602	39925602	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:39925602C>A	ENST00000334678.3	-	4	422	c.306G>T	c.(304-306)aaG>aaT	p.K102N		NM_194326.2	NP_919307.1	Q86WX3	AROS_HUMAN	ribosomal protein S19 binding protein 1	102						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)	p.K102N(1)		endometrium(1)|kidney(1)|large_intestine(1)	3	Melanoma(58;0.04)					GGTCACAGGCCTTGCGGCCCC	0.607											OREG0026578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K102N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G306T	22						.						62.0	62.0	62.0					22																	39925602		2203	4300	6503	38255548	SO:0001583	missense	91582	exon4			BC037573	CCDS13997.1	22q13.1	2006-03-17			ENSG00000187051	ENSG00000187051			28749	protein-coding gene	gene with protein product		610225				16289379	Standard	NM_194326		Approved	MGC52010, FLJ21770	uc003ayb.3	Q86WX3	OTTHUMG00000151101	ENST00000334678.3:c.306G>T	22.37:g.39925602C>A	ENSP00000333948:p.Lys102Asn	Somatic	889	Capture	Illumina HiSeq	Phase_I	38255548	NM_194326	B0QY96|Q5JZA1	Missense_Mutation	SNP	ENST00000334678.3	37	CCDS13997.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.518817	0.64634	.	.	ENSG00000187051	ENST00000334678	T	0.52526	0.66	4.92	1.33	0.21861	.	0.052485	0.85682	D	0.000000	T	0.60741	0.2292	M	0.72118	2.19	0.42518	D	0.992999	D	0.76494	0.999	D	0.76575	0.988	T	0.59731	-0.7399	10	0.62326	D	0.03	-37.4363	6.9052	0.24305	0.0:0.532:0.0:0.468	.	102	Q86WX3	AROS_HUMAN	N	102	ENSP00000333948:K102N	ENSP00000333948:K102N	K	-	3	2	RPS19BP1	38255548	1.000000	0.71417	1.000000	0.80357	0.639000	0.38242	0.993000	0.29680	0.463000	0.27118	0.561000	0.74099	AAG		0.607	RPS19BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321307.1	NM_194326	
CACNA1I	8911	broad.mit.edu	37	22	40069988	40069989	+	Missense_Mutation	DNP	GC	GC	CT			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:40069988_40069989GC>CT	ENST00000402142.3	+	29	4804_4805	c.4804_4805GC>CT	c.(4804-4806)GCc>CTc	p.A1602L	CACNA1I_ENST00000404898.1_Missense_Mutation_p.A1567L|CACNA1I_ENST00000336649.4_Missense_Mutation_p.A1608L|CACNA1I_ENST00000401624.1_Missense_Mutation_p.A1602L|CACNA1I_ENST00000400164.3_Missense_Mutation_p.A1567L|CACNA1I_ENST00000407673.1_Missense_Mutation_p.A1567L	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	1602					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.A1567>?(1)		breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	GTTGAAGATGGCCACAGGAATG	0.629																																					.												.	.	1	Complex(1)	large_intestine(1)	c.4804_4805CT	22						.																																			38399935	SO:0001583	missense	8911	exon29			AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	Exception_encountered	22.37:g.40069988_40069989delinsCT	ENSP00000385019:p.Ala1602Leu	Somatic		Capture	Illumina HiSeq	Phase_I	38399934	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	DNP	ENST00000402142.3	37	CCDS46710.1																																																																																				0.629	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
GRAP2	9402	broad.mit.edu	37	22	40364136	40364136	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:40364136C>T	ENST00000344138.4	+	6	813	c.550C>T	c.(550-552)Cgg>Tgg	p.R184W	GRAP2_ENST00000407075.3_Missense_Mutation_p.R184W|GRAP2_ENST00000399090.2_Missense_Mutation_p.R71W|GRAP2_ENST00000544756.1_Missense_Mutation_p.R112W|GRAP2_ENST00000540310.1_Missense_Mutation_p.R118W|GRAP2_ENST00000543252.1_Missense_Mutation_p.R144W	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	184					cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)	p.R184W(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						TTCGATGAACCGGAAGCTGTC	0.662																																					p.R184W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C550T	22						.						39.0	33.0	35.0					22																	40364136		2203	4299	6502	38694082	SO:0001583	missense	9402	exon6			AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"""SH2 domain containing"""	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.550C>T	22.37:g.40364136C>T	ENSP00000339186:p.Arg184Trp	Somatic		Capture	Illumina HiSeq	Phase_I	38694082	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	17.00	3.277728	0.59758	.	.	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.75477	-0.44;-0.94;1.44;0.85;0.5;-0.44	5.44	1.95	0.26073	.	1.564180	0.03434	N	0.208200	T	0.80226	0.4584	L	0.27053	0.805	0.31937	N	0.611366	D;D;D;D;D	0.89917	0.997;1.0;1.0;1.0;1.0	P;D;D;D;D	0.74674	0.635;0.913;0.984;0.965;0.913	T	0.70132	-0.4956	10	0.72032	D	0.01	-20.8468	11.5403	0.50663	0.6209:0.3791:0.0:0.0	.	71;184;118;158;184	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	W	184;144;158;118;112;71;184	ENSP00000339186:R184W;ENSP00000446350:R144W;ENSP00000444734:R118W;ENSP00000442195:R112W;ENSP00000382040:R71W;ENSP00000385607:R184W	ENSP00000339186:R184W	R	+	1	2	GRAP2	38694082	0.999000	0.42202	1.000000	0.80357	0.545000	0.35147	0.917000	0.28665	0.632000	0.30432	0.514000	0.50259	CGG		0.662	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810	
ADSL	158	broad.mit.edu	37	22	40757501	40757501	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:40757501C>T	ENST00000216194.7	+	9	928	c.872C>T	c.(871-873)gCg>gTg	p.A291V	ADSL_ENST00000454266.2_Missense_Mutation_p.A305V|ADSL_ENST00000342312.6_Missense_Mutation_p.A291V|ADSL_ENST00000480775.1_3'UTR	NM_000026.2	NP_000017.1	P30566	PUR8_HUMAN	adenylosuccinate lyase	291					'de novo' AMP biosynthetic process (GO:0044208)|'de novo' IMP biosynthetic process (GO:0006189)|aerobic respiration (GO:0009060)|AMP biosynthetic process (GO:0006167)|metabolic process (GO:0008152)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to hypoxia (GO:0001666)|response to muscle activity (GO:0014850)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	(S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido)succinate AMP-lyase (fumarate-forming) activity (GO:0070626)|N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity (GO:0004018)	p.A291V(2)		breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(2)|ovary(1)|prostate(1)	19						GGCTCAAGTGCGATGCCATAT	0.527																																					p.A291V	Colon(4;65 130 1097 1516)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C872T	22						.						151.0	128.0	135.0					22																	40757501		2203	4300	6503	39087447	SO:0001583	missense	158	exon9			X65867	CCDS14001.1, CCDS46714.1	22q13.1	2011-02-17			ENSG00000239900	ENSG00000239900	4.3.2.2		291	protein-coding gene	gene with protein product		608222				8404037	Standard	NM_000026		Approved		uc003ayp.4	P30566	OTTHUMG00000166425	ENST00000216194.7:c.872C>T	22.37:g.40757501C>T	ENSP00000216194:p.Ala291Val	Somatic		Capture	Illumina HiSeq	Phase_I	39087447	NM_000026	B0QY76|O75495|Q5TI34	Missense_Mutation	SNP	ENST00000216194.7	37	CCDS14001.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.605570	0.87157	.	.	ENSG00000239900	ENST00000216194;ENST00000454266;ENST00000537028;ENST00000342312	D;D;D	0.99287	-5.69;-5.69;-5.69	5.91	4.88	0.63580	Lyase 1, N-terminal (1);L-Aspartase-like (1);Fumarate lyase, conserved site (1);	0.047070	0.85682	D	0.000000	D	0.99654	0.9872	H	0.98466	4.24	0.80722	D	1	P;D;P;B	0.76494	0.788;0.999;0.507;0.355	P;D;B;B	0.64237	0.449;0.923;0.327;0.327	D	0.97249	0.9896	10	0.87932	D	0	-23.0649	16.9988	0.86376	0.0:0.8725:0.1275:0.0	.	305;291;291;291	E7ERF4;P30566-2;Q71UA4;P30566	.;.;.;PUR8_HUMAN	V	291;305;111;291	ENSP00000216194:A291V;ENSP00000390107:A305V;ENSP00000341429:A291V	ENSP00000216194:A291V	A	+	2	0	ADSL	39087447	1.000000	0.71417	0.996000	0.52242	0.789000	0.44602	7.140000	0.77322	1.466000	0.48025	0.655000	0.94253	GCG		0.527	ADSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321386.1	NM_000026	
MCHR1	2847	broad.mit.edu	37	22	41077724	41077724	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:41077724C>T	ENST00000249016.4	+	2	1757	c.1061C>T	c.(1060-1062)cCg>cTg	p.P354L	MCHR1_ENST00000498400.1_3'UTR|MCHR1_ENST00000381433.2_Missense_Mutation_p.P228L	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	354					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cytosolic calcium ion concentration (GO:0007204)	integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|melanin-concentrating hormone receptor activity (GO:0030273)|neuropeptide receptor activity (GO:0008188)	p.P354L(1)		endometrium(5)|large_intestine(7)|lung(6)|pancreas(1)|urinary_tract(1)	20						ATCAGCCGCCCGACCCTCACC	0.552																																					p.P354L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1061T	22						.						116.0	90.0	99.0					22																	41077724		2203	4300	6503	39407670	SO:0001583	missense	2847	exon2				CCDS14004.1	22q13.3	2014-06-05	2006-02-15	2006-02-15	ENSG00000128285	ENSG00000128285		"""GPCR / Class A : MCH receptors"""	4479	protein-coding gene	gene with protein product		601751	"""G protein-coupled receptor 24"""	GPR24			Standard	XM_005261581		Approved	SLC1, MCH1R	uc003ayz.3	Q99705	OTTHUMG00000150256	ENST00000249016.4:c.1061C>T	22.37:g.41077724C>T	ENSP00000249016:p.Pro354Leu	Somatic		Capture	Illumina HiSeq	Phase_I	39407670	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.734913	0.69189	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.71341	-0.56;-0.56	5.51	5.51	0.81932	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.83649	0.5300	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84875	0.0827	10	0.87932	D	0	.	17.2757	0.87114	0.0:1.0:0.0:0.0	.	354	Q99705	MCHR1_HUMAN	L	354;228	ENSP00000249016:P354L;ENSP00000370841:P228L	ENSP00000249016:P354L	P	+	2	0	MCHR1	39407670	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.772000	0.85439	2.756000	0.94617	0.655000	0.94253	CCG		0.552	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297	
EFCAB6	64800	broad.mit.edu	37	22	44022463	44022463	+	Missense_Mutation	SNP	G	G	T	rs146319951		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:44022463G>T	ENST00000262726.7	-	20	2582	c.2329C>A	c.(2329-2331)Ctc>Atc	p.L777I	EFCAB6_ENST00000396231.2_Missense_Mutation_p.L625I	NM_022785.3	NP_073622.2	Q5THR3	EFCB6_HUMAN	EF-hand calcium binding domain 6	777					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(16)|lung(25)|ovary(4)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	68		Ovarian(80;0.0247)|all_neural(38;0.025)				TCGTCTTTGAGATTAAGCAGT	0.438																																					p.L625I												.	.	0			c.C1873A	22						.						98.0	94.0	95.0					22																	44022463		2203	4300	6503	42353796	SO:0001583	missense	64800	exon18			Z82201	CCDS14049.1, CCDS14050.1	22q13.2	2013-01-10			ENSG00000186976	ENSG00000186976		"""EF-hand domain containing"""	24204	protein-coding gene	gene with protein product						11258795, 12612053	Standard	NM_022785		Approved	FLJ23588, DJBP, HSCBCIP1, KIAA1672, dJ185D5.1	uc003bdy.2	Q5THR3	OTTHUMG00000150522	ENST00000262726.7:c.2329C>A	22.37:g.44022463G>T	ENSP00000262726:p.Leu777Ile	None		Capture	Illumina HiSeq	Phase_I	42353796	NM_198856	A8K8P6|A8K8Y3|B0QYI4|B0QYI6|Q5U5T6|Q9BY88|Q9H5C4|Q9NSF5	Missense_Mutation	SNP	ENST00000262726.7	37	CCDS14049.1	.	.	.	.	.	.	.	.	.	.	G	3.093	-0.186354	0.06340	.	.	ENSG00000186976	ENST00000396231;ENST00000262726	T;T	0.09255	3.0;3.0	4.74	3.64	0.41730	EF-hand-like domain (1);	0.324205	0.24671	N	0.036546	T	0.10551	0.0258	L	0.38175	1.15	0.80722	D	1	P;P	0.45957	0.869;0.552	P;B	0.45276	0.475;0.1	T	0.21999	-1.0229	10	0.23891	T	0.37	-20.8431	9.9326	0.41532	0.0:0.0:0.5234:0.4766	.	625;777	Q5THR3-2;Q5THR3	.;EFCB6_HUMAN	I	625;777	ENSP00000379533:L625I;ENSP00000262726:L777I	ENSP00000262726:L777I	L	-	1	0	EFCAB6	42353796	0.992000	0.36948	0.853000	0.33588	0.011000	0.07611	1.389000	0.34453	0.982000	0.38575	0.563000	0.77884	CTC		0.438	EFCAB6-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353176.1	NM_022785	
NUP50	10762	broad.mit.edu	37	22	45574147	45574147	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:45574147C>A	ENST00000347635.4	+	5	835	c.369C>A	c.(367-369)acC>acA	p.T123T	NUP50_ENST00000396096.2_Silent_p.T95T|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000486184.1_3'UTR|NUP50_ENST00000425733.2_De_novo_Start_InFrame|NUP50_ENST00000407019.2_Silent_p.T95T	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	123	5 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|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)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T123T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GCCCTACCACCTTGGTTGATA	0.403																																					p.T123T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C369A	22						.						71.0	70.0	70.0					22																	45574147		2203	4300	6503	43952811	SO:0001819	synonymous_variant	10762	exon5			AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"""nucleoporin 50kD"""	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.369C>A	22.37:g.45574147C>A		Somatic		Capture	Illumina HiSeq	Phase_I	43952811	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Silent	SNP	ENST00000347635.4	37	CCDS14062.1	.	.	.	.	.	.	.	.	.	.	C	1.311	-0.602202	0.03744	.	.	ENSG00000093000	ENST00000430547	.	.	.	5.25	-2.53	0.06326	.	.	.	.	.	T	0.26195	0.0639	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.36672	-0.9738	5	0.87932	D	0	-0.2565	0.382	0.00396	0.2877:0.2857:0.1877:0.2388	.	.	.	.	H	61	.	ENSP00000397960:P61H	P	+	2	0	NUP50	43952811	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	-0.602000	0.05680	-0.492000	0.06687	-0.176000	0.13171	CCT		0.403	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2		
WNT7B	7477	broad.mit.edu	37	22	46345824	46345824	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:46345824C>T	ENST00000339464.4	-	2	648	c.274G>A	c.(274-276)Gtc>Atc	p.V92I	WNT7B_ENST00000409496.3_Missense_Mutation_p.V96I|WNT7B_ENST00000410058.1_Missense_Mutation_p.V92I|WNT7B_ENST00000410089.1_Missense_Mutation_p.V76I	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	92					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.V92I(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		TGCCCGAAGACGGTCTTCTCG	0.637																																					p.V92I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G274A	22						.						38.0	36.0	37.0					22																	46345824		2203	4300	6503	44724488	SO:0001583	missense	7477	exon2			AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.274G>A	22.37:g.46345824C>T	ENSP00000341032:p.Val92Ile	Somatic		Capture	Illumina HiSeq	Phase_I	44724488	NM_058238	B8A596|Q96Q12	Missense_Mutation	SNP	ENST00000339464.4	37	CCDS33667.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949779	0.53186	.	.	ENSG00000188064	ENST00000339464;ENST00000410089;ENST00000409496;ENST00000410058;ENST00000428540	T;T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01;-1.01	3.82	3.82	0.43975	.	0.149604	0.44097	U	0.000487	T	0.67221	0.2870	L	0.37561	1.115	0.80722	D	1	B;P	0.41102	0.4;0.738	B;B	0.36567	0.136;0.228	T	0.68554	-0.5378	10	0.32370	T	0.25	.	14.8554	0.70332	0.0:1.0:0.0:0.0	.	96;92	A8K0G1;P56706	.;WNT7B_HUMAN	I	92;76;96;92;25	ENSP00000341032:V92I;ENSP00000386781:V76I;ENSP00000386546:V96I;ENSP00000387217:V92I;ENSP00000392750:V25I	ENSP00000341032:V92I	V	-	1	0	WNT7B	44724488	1.000000	0.71417	0.972000	0.41901	0.594000	0.36715	5.587000	0.67510	1.961000	0.56991	0.561000	0.74099	GTC		0.637	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238	
CELSR1	9620	broad.mit.edu	37	22	46835284	46835284	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:46835284C>T	ENST00000262738.3	-	3	4207	c.4208G>A	c.(4207-4209)cGc>cAc	p.R1403H		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1403	EGF-like 3; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)	p.R1403H(1)		breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCGGCCTGAGCGGGCATCCAC	0.642																																					p.R1403H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4208A	22						.						44.0	36.0	39.0					22																	46835284		2203	4300	6503	45213948	SO:0001583	missense	9620	exon3			AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4208G>A	22.37:g.46835284C>T	ENSP00000262738:p.Arg1403His	Somatic		Capture	Illumina HiSeq	Phase_I	45213948	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	15.72	2.915666	0.52546	.	.	ENSG00000075275	ENST00000262738	D	0.87491	-2.26	5.1	4.08	0.47627	Epidermal growth factor-like, type 3 (1);	0.189148	0.33753	U	0.004581	T	0.81847	0.4909	L	0.58101	1.795	0.80722	D	1	P	0.37525	0.598	B	0.28232	0.087	T	0.79741	-0.1676	10	0.34782	T	0.22	.	12.9399	0.58337	0.0:0.9206:0.0:0.0794	.	1403	Q9NYQ6	CELR1_HUMAN	H	1403	ENSP00000262738:R1403H	ENSP00000262738:R1403H	R	-	2	0	CELSR1	45213948	1.000000	0.71417	0.976000	0.42696	0.810000	0.45777	3.837000	0.55820	1.150000	0.42419	0.561000	0.74099	CGC		0.642	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
TTLL8	164714	broad.mit.edu	37	22	50471725	50471725	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:50471725G>A	ENST00000266182.6	-	10	1188	c.1189C>T	c.(1189-1191)Ctc>Ttc	p.L397F	TTLL8_ENST00000440475.1_Missense_Mutation_p.L377F			A6PVC2	TTLL8_HUMAN	tubulin tyrosine ligase-like family, member 8	413	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(4)	12		all_cancers(38;3.44e-07)|all_epithelial(38;2.44e-06)|all_lung(38;0.00141)|Breast(42;0.00519)|Lung NSC(38;0.0199)|Ovarian(80;0.142)|Lung SC(80;0.162)		READ - Rectum adenocarcinoma(2;0.000882)|Colorectal(2;0.00311)|BRCA - Breast invasive adenocarcinoma(115;0.226)		TCCGTGACGAGGAACCACTGT	0.547																																					p.L397F												.	.	0			c.C1189T	22						.						44.0	51.0	49.0					22																	50471725		2145	4257	6402	48813852	SO:0001583	missense	164714	exon10					22q13.33	2013-02-14			ENSG00000138892	ENSG00000138892		"""Tubulin tyrosine ligase-like family"""	34000	protein-coding gene	gene with protein product						15890843	Standard	XM_003403745		Approved			A6PVC2	OTTHUMG00000150241	ENST00000266182.6:c.1189C>T	22.37:g.50471725G>A	ENSP00000266182:p.Leu397Phe	None		Capture	Illumina HiSeq	Phase_I	48813852	NM_001080447	B5MDV0	Missense_Mutation	SNP	ENST00000266182.6	37		.	.	.	.	.	.	.	.	.	.	G	24.9	4.582518	0.86748	.	.	ENSG00000138892	ENST00000266182;ENST00000440475;ENST00000433387	T;T;T	0.10477	2.87;2.87;2.87	4.44	4.44	0.53790	.	0.000000	0.64402	D	0.000003	T	0.39963	0.1098	M	0.89030	3	0.47994	D	0.999561	D	0.89917	1.0	D	0.91635	0.999	T	0.50491	-0.8822	10	0.87932	D	0	.	15.9944	0.80230	0.0:0.0:1.0:0.0	.	397	B5MDV0	.	F	397;377;413	ENSP00000266182:L397F;ENSP00000387509:L377F;ENSP00000392252:L413F	ENSP00000266182:L397F	L	-	1	0	TTLL8	48813852	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.045000	0.71020	2.300000	0.77407	0.561000	0.74099	CTC		0.547	TTLL8-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001080447	
MOV10L1	54456	broad.mit.edu	37	22	50589273	50589273	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:50589273C>T	ENST00000262794.5	+	21	2920	c.2837C>T	c.(2836-2838)gCg>gTg	p.A946V	MOV10L1_ENST00000540615.1_Missense_Mutation_p.A926V|MOV10L1_ENST00000545383.1_Missense_Mutation_p.A946V|MOV10L1_ENST00000395843.1_Intron|MOV10L1_ENST00000395852.1_Missense_Mutation_p.A73V|MOV10L1_ENST00000354853.2_Intron|MOV10L1_ENST00000395858.3_Missense_Mutation_p.A946V	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	946					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.A946V(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		TCTCGACCCGCGTACCAGAGG	0.577																																					p.A946V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2837T	22						.						147.0	115.0	126.0					22																	50589273		2203	4300	6503	48931400	SO:0001583	missense	54456	exon21			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.2837C>T	22.37:g.50589273C>T	ENSP00000262794:p.Ala946Val	Somatic		Capture	Illumina HiSeq	Phase_I	48931400	NM_001164104	A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	ENST00000262794.5	37	CCDS14084.1	.	.	.	.	.	.	.	.	.	.	.	0.021	-1.426267	0.01117	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615;ENST00000395852	D;D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6;-1.6	5.62	-0.702	0.11265	.	0.500084	0.21843	N	0.068287	T	0.58836	0.2150	N	0.11064	0.09	0.09310	N	1	B;B;B;B	0.18166	0.009;0.0;0.026;0.026	B;B;B;B	0.14578	0.006;0.002;0.011;0.011	T	0.49360	-0.8948	10	0.02654	T	1	-10.4762	9.3639	0.38212	0.0:0.4155:0.0:0.5845	.	926;73;946;946	F5H403;Q9BXT6-2;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	V	946;946;946;926;73	ENSP00000438978:A946V;ENSP00000262794:A946V;ENSP00000379199:A946V;ENSP00000438542:A926V;ENSP00000379193:A73V	ENSP00000262794:A946V	A	+	2	0	MOV10L1	48931400	0.000000	0.05858	0.003000	0.11579	0.038000	0.13279	-0.192000	0.09587	0.067000	0.16545	-0.150000	0.13652	GCG		0.577	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075009.2	NM_018995	
CECR5	27440	broad.mit.edu	37	22	17619152	17619152	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:17619152delC	ENST00000336737.4	-	8	1056	c.1031delG	c.(1030-1032)ggcfs	p.G344fs	CECR5_ENST00000155674.5_Frame_Shift_Del_p.G314fs|CECR5_ENST00000399852.3_Frame_Shift_Del_p.G144fs	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	344						mitochondrion (GO:0005739)		p.G344fs*61(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				CTGCCGTGTGCCCCCGGCCCC	0.602																																					p.G344fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1031delG	22						.						74.0	68.0	70.0					22																	17619152		2203	4300	6503	15999152	SO:0001589	frameshift_variant	27440	exon8			AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.1031delG	22.37:g.17619152delC	ENSP00000337358:p.Gly344fs	Somatic		Capture	Illumina HiSeq	Phase_I	15999152	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Frame_Shift_Del	DEL	ENST00000336737.4	37	CCDS33595.1																																																																																				0.602	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829	
CSF2RB	1439	broad.mit.edu	37	22	37333632	37333632	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:37333632delG	ENST00000403662.3	+	14	2004	c.1782delG	c.(1780-1782)ctgfs	p.L594fs	CSF2RB_ENST00000262825.5_Frame_Shift_Del_p.L600fs|CSF2RB_ENST00000406230.1_Frame_Shift_Del_p.L600fs|CSF2RB_ENST00000536485.1_Frame_Shift_Del_p.L541fs			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	594					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)	p.P596fs*102(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GGCCCTACCTGGGGCCGCCCC	0.687																																					p.L594fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1782delG	22						.						9.0	10.0	10.0					22																	37333632		2188	4271	6459	35663578	SO:0001589	frameshift_variant	1439	exon14			M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.1782delG	22.37:g.37333632delG	ENSP00000384053:p.Leu594fs	Somatic		Capture	Illumina HiSeq	Phase_I	35663578	NM_000395	Q5JZI1|Q6ICE0	Frame_Shift_Del	DEL	ENST00000403662.3	37	CCDS13936.1																																																																																				0.687	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
PLXNB2	23654	broad.mit.edu	37	22	50718980	50718980	+	Silent	SNP	C	C	T	rs534787648		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr22:50718980C>T	ENST00000449103.1	-	25	4253	c.4113G>A	c.(4111-4113)acG>acA	p.T1371T	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Silent_p.T1371T			O15031	PLXB2_HUMAN	plexin B2	1371					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)	p.T1414T(1)		breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		CCAGGAAGAGCGTGTGCATGA	0.662																																					p.T1371T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4113A	22						.						90.0	97.0	94.0					22																	50718980		2194	4295	6489	49061107	SO:0001819	synonymous_variant	23654	exon24				CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.4113G>A	22.37:g.50718980C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49061107	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																				0.662	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TTN	7273	broad.mit.edu	37	2	179635157	179635158	+	Frame_Shift_Ins	INS	-	-	CT	rs577337149		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179635157_179635158insCT	ENST00000591111.1	-	35	8585_8586	c.8361_8362insAG	c.(8359-8364)agtgccfs	p.A2788fs	TTN-AS1_ENST00000584485.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Ins_p.A2742fs|TTN_ENST00000460472.2_Frame_Shift_Ins_p.A2742fs|TTN_ENST00000342175.6_Frame_Shift_Ins_p.A2742fs|TTN_ENST00000342992.6_Frame_Shift_Ins_p.A2788fs|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000360870.5_Frame_Shift_Ins_p.A2788fs|TTN_ENST00000589042.1_Frame_Shift_Ins_p.A2788fs|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13114					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A2742fs*18(3)|p.A2788fs*18(2)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGCAGTCTGGCACTGGCTCCAA	0.431																																					p.A2742fs												.	.	5	Insertion - Frameshift(5)	large_intestine(5)	c.8224_8225insAG	2						.																																			179343403	SO:0001589	frameshift_variant	7273	exon34			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8361_8362insAG	2.37:g.179635157_179635158insCT	ENSP00000465570:p.Ala2788fs	Somatic		Capture	Illumina HiSeq	Phase_I	179343402	NM_133432	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Ins	INS	ENST00000591111.1	37																																																																																					0.431	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CASP8	841	broad.mit.edu	37	2	202151253	202151254	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:202151253_202151254insG	ENST00000432109.2	+	10	1565_1566	c.1376_1377insG	c.(1375-1380)atggggfs	p.MG459fs	CASP8_ENST00000264275.5_Frame_Shift_Ins_p.MG476fs|CASP8_ENST00000392266.3_3'UTR|CASP8_ENST00000358485.4_Frame_Shift_Ins_p.MG518fs|CASP8_ENST00000264274.9_Frame_Shift_Ins_p.MG375fs|CASP8_ENST00000392259.2_3'UTR|CASP8_ENST00000323492.7_Frame_Shift_Ins_p.MG444fs	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	459					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|heart development (GO:0007507)|hepatocyte apoptotic process (GO:0097284)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|macrophage differentiation (GO:0030225)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|natural killer cell activation (GO:0030101)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of necroptotic process (GO:0060546)|neural tube formation (GO:0001841)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|protein heterooligomerization (GO:0051291)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of thymocyte apoptotic process (GO:0070243)|response to antibiotic (GO:0046677)|response to cobalt ion (GO:0032025)|response to cold (GO:0009409)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|syncytiotrophoblast cell differentiation involved in labyrinthine layer development (GO:0060715)|T cell activation (GO:0042110)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|Noc1p-Noc2p complex (GO:0030690)|nucleus (GO:0005634)|ripoptosome (GO:0097342)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097199)|cysteine-type peptidase activity (GO:0008234)|death effector domain binding (GO:0035877)|peptidase activity (GO:0008233)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)	p.K520fs*19(1)|p.K478fs*19(1)		breast(5)|cervix(2)|endometrium(6)|large_intestine(11)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(9)|urinary_tract(3)	52						AAGAAAAACATGGGGAAACAGA	0.361										HNSCC(4;0.00038)																											p.M518fs	Melanoma(82;831 1348 20716 36952 40159)											.	.	2	Insertion - Frameshift(2)	large_intestine(2)	c.1553_1554insG	2						.																																			201859499	SO:0001589	frameshift_variant	841	exon9			U60520	CCDS2342.1, CCDS2343.1, CCDS2345.1, CCDS42798.1, CCDS42799.1	2q33-q34	2014-09-17	2005-08-17		ENSG00000064012	ENSG00000064012		"""Caspases"""	1509	protein-coding gene	gene with protein product		601763	"""caspase 8, apoptosis-related cysteine protease"""			8681376, 8681377	Standard	NM_033355		Approved	MCH5, MACH, FLICE, Casp-8	uc002uxt.1	Q14790	OTTHUMG00000132821	ENST00000432109.2:c.1380dupG	2.37:g.202151257_202151257dupG	ENSP00000412523:p.Met459fs	Somatic		Capture	Illumina HiSeq	Phase_I	201859498	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Frame_Shift_Ins	INS	ENST00000432109.2	37	CCDS2342.1																																																																																				0.361	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228	
ITSN2	50618	broad.mit.edu	37	2	24484598	24484599	+	Frame_Shift_Ins	INS	-	-	T	rs546355561		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:24484598_24484599insT	ENST00000355123.4	-	21	2811_2812	c.2368_2369insA	c.(2368-2370)accfs	p.T790fs	ITSN2_ENST00000406921.3_Frame_Shift_Ins_p.T790fs|ITSN2_ENST00000361999.3_Frame_Shift_Ins_p.T763fs	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	790	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)	p.T789fs*11(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCTCCTACGGTTTTTTCATCA	0.327																																					p.T790fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2369_2370insA	2						.																																			24338103	SO:0001589	frameshift_variant	50618	exon21			AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.2369dupA	2.37:g.24484604_24484604dupT	ENSP00000347244:p.Thr790fs	Somatic		Capture	Illumina HiSeq	Phase_I	24338102	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Frame_Shift_Ins	INS	ENST00000355123.4	37	CCDS1710.2																																																																																				0.327	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
OXER1	165140	broad.mit.edu	37	2	42991088	42991089	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:42991088_42991089insC	ENST00000378661.2	-	1	312_313	c.231_232insG	c.(229-234)gggtccfs	p.S78fs		NM_148962.4	NP_683765.1	Q8TDS5	OXER1_HUMAN	oxoeicosanoid (OXE) receptor 1	78	Ser-rich.				G-protein coupled receptor signaling pathway (GO:0007186)|regulation of cAMP biosynthetic process (GO:0030817)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	5(S)-hydroxyperoxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050648)|5-hydroxy-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050647)|5-oxo-6E,8Z,11Z,14Z-icosatetraenoic acid binding (GO:0050646)|G-protein coupled receptor activity (GO:0004930)	p.S78fs*61(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	10						CCTCCAGAGGACCCCCCCACAG	0.634																																					p.S78fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.232_233insG	2						.																																			42844593	SO:0001589	frameshift_variant	165140	exon1			AB083055	CCDS1810.1	2p22.1	2012-08-10			ENSG00000162881	ENSG00000162881		"""GPCR / Class A : Leukotriene receptors"""	24884	protein-coding gene	gene with protein product	"""5-oxo-ETE acid G-protein-coupled receptor 1"""					12065583, 15001665	Standard	NM_148962		Approved	GPCR, TG1019, GPR170	uc002rss.3	Q8TDS5	OTTHUMG00000128643	ENST00000378661.2:c.232dupG	2.37:g.42991095_42991095dupC	ENSP00000367930:p.Ser78fs	Somatic		Capture	Illumina HiSeq	Phase_I	42844592	NM_148962	Q86WP7|Q8NGW4	Frame_Shift_Ins	INS	ENST00000378661.2	37	CCDS1810.1																																																																																				0.634	OXER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250514.1	NM_148962	
KIAA1211L	343990	broad.mit.edu	37	2	99448968	99448969	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:99448968_99448969insT	ENST00000397899.2	-	5	713_714	c.382_383insA	c.(382-384)atafs	p.I128fs	KIAA1211L_ENST00000462314.1_5'UTR	NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	128								p.I128fs*4(1)									ATTACACTGTATTTTTAACTAG	0.47																																					p.I128fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.383_384insA	2						.																																			98815401	SO:0001589	frameshift_variant	343990	exon5			BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.383dupA	2.37:g.99448973_99448973dupT	ENSP00000380996:p.Ile128fs	Somatic		Capture	Illumina HiSeq	Phase_I	98815400	NM_207362		Frame_Shift_Ins	INS	ENST00000397899.2	37	CCDS42720.1																																																																																				0.470	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362	
TBC1D8	11138	broad.mit.edu	37	2	101655075	101655075	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:101655075G>A	ENST00000376840.4	-	7	1077	c.1078C>T	c.(1078-1080)Cat>Tat	p.H360Y	TBC1D8_ENST00000409318.1_Missense_Mutation_p.H375Y			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	360					blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.H360Y(1)		breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						ATGATGGGATGCGGCAGCAGG	0.577																																					p.H360Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1078T	2						.						124.0	132.0	130.0					2																	101655075		2154	4234	6388	101021507	SO:0001583	missense	11138	exon7			AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1078C>T	2.37:g.101655075G>A	ENSP00000366036:p.His360Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	101021507	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Missense_Mutation	SNP	ENST00000376840.4	37	CCDS46375.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.597478	0.46318	.	.	ENSG00000204634	ENST00000376840;ENST00000409318	T;T	0.03152	4.03;4.03	5.09	1.33	0.21861	.	0.091376	0.47455	D	0.000240	T	0.01835	0.0058	N	0.08118	0	0.28412	N	0.918151	B;B	0.25850	0.13;0.136	B;B	0.23150	0.018;0.044	T	0.46400	-0.9194	10	0.02654	T	1	-19.0211	13.2441	0.60014	0.0:0.0:0.2794:0.7206	.	375;360	B7Z6L4;O95759	.;TBCD8_HUMAN	Y	360;375	ENSP00000366036:H360Y;ENSP00000386856:H375Y	ENSP00000366036:H360Y	H	-	1	0	TBC1D8	101021507	1.000000	0.71417	0.285000	0.24819	0.983000	0.72400	3.316000	0.51960	-0.017000	0.14103	-0.152000	0.13540	CAT		0.577	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
PDIA6	10130	broad.mit.edu	37	2	10929027	10929027	+	Silent	SNP	A	A	G	rs143264920		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:10929027A>G	ENST00000272227.3	-	9	1068	c.921T>C	c.(919-921)gaT>gaC	p.D307D	PDIA6_ENST00000404371.2_Silent_p.D359D|PDIA6_ENST00000404824.2_Silent_p.D355D|PDIA6_ENST00000381611.4_Silent_p.D312D|PDIA6_ENST00000540494.1_Silent_p.D304D	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	307					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)	p.D307D(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		TCTTACCAGTATCAAGGATAT	0.433													A|||	1	0.000199681	0.0	0.0014	5008	,	,		18735	0.0		0.0	False		,,,				2504	0.0				p.D307D	GBM(73;509 1219 34219 41343 41551)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T921C	2						.	A		0,4406		0,0,2203	140.0	135.0	137.0		921	-3.6	0.1	2	dbSNP_134	137	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDIA6	NM_005742.2		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		307/441	10929027	1,13005	2203	4300	6503	10846478	SO:0001819	synonymous_variant	10130	exon9			BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.921T>C	2.37:g.10929027A>G		Somatic		Capture	Illumina HiSeq	Phase_I	10846478	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																				0.433	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
SLC5A7	60482	broad.mit.edu	37	2	108604639	108604639	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:108604639G>A	ENST00000264047.2	+	2	304	c.28G>A	c.(28-30)Gct>Act	p.A10T	SLC5A7_ENST00000409059.1_Missense_Mutation_p.A10T|SLC5A7_ENST00000540517.1_Intron	NM_021815.2	NP_068587.1	Q9GZV3	SC5A7_HUMAN	solute carrier family 5 (sodium/choline cotransporter), member 7	10					acetylcholine biosynthetic process (GO:0008292)|cell death (GO:0008219)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	choline binding (GO:0033265)|choline transmembrane transporter activity (GO:0015220)|choline:sodium symporter activity (GO:0005307)	p.A10T(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(23)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	49					Choline(DB00122)	AGGACTGATAGCTATCATCGT	0.443																																					p.A10T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G28A	2						.						152.0	142.0	145.0					2																	108604639		2203	4300	6503	107971071	SO:0001583	missense	60482	exon2			AF276871	CCDS2074.1	2q12	2013-07-19	2013-07-19		ENSG00000115665	ENSG00000115665		"""Solute carriers"""	14025	protein-coding gene	gene with protein product		608761	"""solute carrier family 5 (choline transporter), member 7"""			11027560	Standard	NM_021815		Approved	hCHT, CHT1	uc002tdv.3	Q9GZV3	OTTHUMG00000130959	ENST00000264047.2:c.28G>A	2.37:g.108604639G>A	ENSP00000264047:p.Ala10Thr	Somatic		Capture	Illumina HiSeq	Phase_I	107971071	NM_021815	Q53TF2	Missense_Mutation	SNP	ENST00000264047.2	37	CCDS2074.1	.	.	.	.	.	.	.	.	.	.	G	36	5.641548	0.96704	.	.	ENSG00000115665	ENST00000409059;ENST00000264047	D;D	0.91631	-2.88;-2.88	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.95211	0.8447	M	0.86178	2.8	0.80722	D	1	D	0.59357	0.985	P	0.56751	0.805	D	0.92705	0.6178	10	0.10377	T	0.69	-3.4075	20.0887	0.97806	0.0:0.0:1.0:0.0	.	10	Q9GZV3	SC5A7_HUMAN	T	10	ENSP00000387346:A10T;ENSP00000264047:A10T	ENSP00000264047:A10T	A	+	1	0	SLC5A7	107971071	1.000000	0.71417	0.999000	0.59377	0.944000	0.59088	9.420000	0.97426	2.825000	0.97269	0.655000	0.94253	GCT		0.443	SLC5A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253562.1		
PSD4	23550	broad.mit.edu	37	2	113956444	113956444	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:113956444C>A	ENST00000245796.6	+	15	2947	c.2752C>A	c.(2752-2754)Ccc>Acc	p.P918T	PSD4_ENST00000441564.3_Missense_Mutation_p.P889T	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	918					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)	p.P918T(1)		cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GCCCGTGGGCCCCGCCCAGAG	0.726																																					p.P918T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2752A	2						.						7.0	8.0	8.0					2																	113956444		2158	4181	6339	113672915	SO:0001583	missense	23550	exon15			U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.2752C>A	2.37:g.113956444C>A	ENSP00000245796:p.Pro918Thr	Somatic		Capture	Illumina HiSeq	Phase_I	113672915	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.785443	0.31593	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.09630	2.96;2.99	5.4	5.4	0.78164	.	0.118698	0.64402	D	0.000019	T	0.08313	0.0207	N	0.17723	0.515	0.80722	D	1	B;B;B;B	0.21520	0.034;0.057;0.018;0.006	B;B;B;B	0.33196	0.014;0.053;0.159;0.076	T	0.06144	-1.0843	10	0.02654	T	1	.	14.6799	0.69009	0.0:1.0:0.0:0.0	.	148;575;889;918	B4DFU9;Q59HG0;Q8NDX1-2;Q8NDX1	.;.;.;PSD4_HUMAN	T	918;889	ENSP00000245796:P918T;ENSP00000413997:P889T	ENSP00000245796:P918T	P	+	1	0	PSD4	113672915	0.172000	0.23043	0.912000	0.35992	0.292000	0.27327	1.067000	0.30616	2.537000	0.85549	0.561000	0.74099	CCC		0.726	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
NTSR2	23620	broad.mit.edu	37	2	11800178	11800178	+	Missense_Mutation	SNP	G	G	A	rs377014236		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:11800178G>A	ENST00000306928.5	-	3	1014	c.980C>T	c.(979-981)gCg>gTg	p.A327V		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	327					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)	p.A327V(1)		breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CTCAGTCCACGCGTCATCAGG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		21195	0.0		0.0	False		,,,				2504	0.001				p.A327V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C980T	2						.	G	VAL/ALA	0,4406		0,0,2203	103.0	87.0	93.0		980	-6.0	0.0	2		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	NTSR2	NM_012344.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	327/411	11800178	1,13005	2203	4300	6503	11717629	SO:0001583	missense	23620	exon3			Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.980C>T	2.37:g.11800178G>A	ENSP00000303686:p.Ala327Val	Somatic		Capture	Illumina HiSeq	Phase_I	11717629	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Missense_Mutation	SNP	ENST00000306928.5	37	CCDS1681.1	.	.	.	.	.	.	.	.	.	.	G	7.480	0.648529	0.14516	0.0	1.16E-4	ENSG00000169006	ENST00000306928	T	0.74315	-0.83	3.33	-6.04	0.02178	GPCR, rhodopsin-like superfamily (1);	3.522020	0.00649	N	0.000556	T	0.50497	0.1619	N	0.14661	0.345	0.09310	N	1	B	0.31290	0.318	B	0.24269	0.052	T	0.44787	-0.9305	10	0.15952	T	0.53	0.7382	6.8186	0.23845	0.0:0.1572:0.3673:0.4755	.	327	O95665	NTR2_HUMAN	V	327	ENSP00000303686:A327V	ENSP00000303686:A327V	A	-	2	0	NTSR2	11717629	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.071000	0.14594	-1.535000	0.01740	-1.313000	0.01306	GCG		0.597	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1		
LPIN1	23175	broad.mit.edu	37	2	11905777	11905777	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:11905777G>A	ENST00000256720.2	+	2	203	c.110G>A	c.(109-111)cGc>cAc	p.R37H	MIR548S_ENST00000581352.1_RNA|LPIN1_ENST00000449576.2_Missense_Mutation_p.R86H|LPIN1_ENST00000396098.1_Missense_Mutation_p.R43H|LPIN1_ENST00000396099.1_Missense_Mutation_p.R43H|LPIN1_ENST00000425416.2_Missense_Mutation_p.R43H	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	37	N-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.R37H(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		ATTGTCATCCGCCAGCCCAAT	0.592																																					p.R37H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G110A	2						.						146.0	135.0	139.0					2																	11905777		2203	4300	6503	11823228	SO:0001583	missense	23175	exon2			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.110G>A	2.37:g.11905777G>A	ENSP00000256720:p.Arg37His	Somatic		Capture	Illumina HiSeq	Phase_I	11823228	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.804010	0.90623	.	.	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000441684	T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12	5.37	5.37	0.77165	Lipin, N-terminal (1);	0.105471	0.64402	D	0.000006	D	0.87633	0.6226	M	0.73372	2.23	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.75484	0.982;0.986;0.955	D	0.87026	0.2132	9	.	.	.	-25.5188	19.1172	0.93346	0.0:0.0:1.0:0.0	.	86;37;43	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	H	86;43;43;43;37;37	ENSP00000397908:R86H;ENSP00000379405:R43H;ENSP00000379406:R43H;ENSP00000401522:R43H;ENSP00000256720:R37H;ENSP00000412578:R37H	.	R	+	2	0	LPIN1	11823228	1.000000	0.71417	0.981000	0.43875	0.582000	0.36321	5.172000	0.65003	2.528000	0.85240	0.655000	0.94253	CGC		0.592	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
LPIN1	23175	broad.mit.edu	37	2	11905843	11905843	+	Missense_Mutation	SNP	G	G	A	rs140179571		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:11905843G>A	ENST00000256720.2	+	2	269	c.176G>A	c.(175-177)cGc>cAc	p.R59H	MIR548S_ENST00000581352.1_RNA|LPIN1_ENST00000449576.2_Missense_Mutation_p.R108H|LPIN1_ENST00000396098.1_Missense_Mutation_p.R65H|LPIN1_ENST00000396099.1_Missense_Mutation_p.R65H|LPIN1_ENST00000425416.2_Missense_Mutation_p.R65H	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	59	N-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)	p.R59H(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GGGGTCCTGCGCTCCCGAGAG	0.572																																					p.R59H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G176A	2						.	G	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	80.0	74.0	76.0		176	4.9	1.0	2	dbSNP_134	76	2,8598	2.2+/-6.3	0,2,4298	yes	missense	LPIN1	NM_145693.1	29	0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308	probably-damaging	59/891	11905843	4,13002	2203	4300	6503	11823294	SO:0001583	missense	23175	exon2			D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.176G>A	2.37:g.11905843G>A	ENSP00000256720:p.Arg59His	Somatic		Capture	Illumina HiSeq	Phase_I	11823294	NM_145693	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.899858	0.91962	4.54E-4	2.33E-4	ENSG00000134324	ENST00000449576;ENST00000396098;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000441684	T;T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16;-1.16	4.92	4.92	0.64577	Lipin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88610	0.6483	M	0.80183	2.485	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.97110	0.985;1.0;0.971	D	0.89260	0.3597	9	.	.	.	-24.7433	18.149	0.89668	0.0:0.0:1.0:0.0	.	108;59;65	F5GY24;Q14693;A8MU38	.;LPIN1_HUMAN;.	H	108;65;65;65;59;59	ENSP00000397908:R108H;ENSP00000379405:R65H;ENSP00000379406:R65H;ENSP00000401522:R65H;ENSP00000256720:R59H;ENSP00000412578:R59H	.	R	+	2	0	LPIN1	11823294	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	9.251000	0.95483	2.284000	0.76573	0.563000	0.77884	CGC		0.572	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
FOXD4L1	200350	broad.mit.edu	37	2	114257020	114257020	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:114257020C>T	ENST00000306507.5	+	1	360	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	63					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R63W(1)		NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(10)|prostate(1)|skin(2)	26						GCAGGTGGCCCGGTGGGGCGG	0.677																																					p.R63W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C187T	2						.						26.0	45.0	38.0					2																	114257020		2144	4202	6346	113973490	SO:0001583	missense	200350	exon1			AF452723	CCDS2117.1	2q14.1	2008-02-05			ENSG00000184492	ENSG00000184492			18521	protein-coding gene	gene with protein product		611084				12421752, 15233989	Standard	NM_012184		Approved	FOXD5	uc002tjw.4	Q9NU39	OTTHUMG00000131359	ENST00000306507.5:c.187C>T	2.37:g.114257020C>T	ENSP00000302756:p.Arg63Trp	Somatic		Capture	Illumina HiSeq	Phase_I	113973490	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.698586	0.48307	.	.	ENSG00000184492	ENST00000306507	D	0.94687	-3.49	1.58	1.58	0.23477	.	1.140370	0.07238	U	0.863748	D	0.89884	0.6844	L	0.27053	0.805	0.09310	N	1	D	0.63880	0.993	B	0.44315	0.446	T	0.82432	-0.0460	10	0.54805	T	0.06	.	6.5367	0.22357	0.0:1.0:0.0:0.0	.	63	Q9NU39	FX4L1_HUMAN	W	63	ENSP00000302756:R63W	ENSP00000302756:R63W	R	+	1	2	FOXD4L1	113973490	0.000000	0.05858	0.005000	0.12908	0.204000	0.24138	-0.324000	0.07986	0.850000	0.35239	0.184000	0.17185	CGG		0.677	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
CLASP1	23332	broad.mit.edu	37	2	122125291	122125291	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:122125291C>T	ENST00000263710.4	-	35	4148	c.3759G>A	c.(3757-3759)ccG>ccA	p.P1253P	CLASP1_ENST00000455322.2_Silent_p.P1209P|CLASP1_ENST00000409078.3_Silent_p.P1186P|CLASP1_ENST00000545861.1_Silent_p.P960P|CLASP1_ENST00000397587.3_Silent_p.P1193P|CLASP1_ENST00000541377.1_Silent_p.P1192P|CLASP1_ENST00000541859.1_Silent_p.P970P	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1253					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)	p.P1253P(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					GGAAGGCGCGCGGAGGCTGGG	0.637																																					p.P1186P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G3558A	2						.						106.0	109.0	108.0					2																	122125291		1987	4143	6130	121841761	SO:0001819	synonymous_variant	23332	exon33			AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.3759G>A	2.37:g.122125291C>T		Somatic		Capture	Illumina HiSeq	Phase_I	121841761	NM_001142274	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	37																																																																																					0.637	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
CNTNAP5	129684	broad.mit.edu	37	2	125521670	125521670	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:125521670G>A	ENST00000431078.1	+	16	2840	c.2476G>A	c.(2476-2478)Gga>Aga	p.G826R		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	826	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)		p.G826R(1)		NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		AGCATTATCCGGAGTTTTCCT	0.373																																					p.G826R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2476A	2						.						129.0	123.0	125.0					2																	125521670		1824	4071	5895	125238140	SO:0001583	missense	129684	exon16			AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.2476G>A	2.37:g.125521670G>A	ENSP00000399013:p.Gly826Arg	Somatic		Capture	Illumina HiSeq	Phase_I	125238140	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.008353	0.93346	.	.	ENSG00000155052	ENST00000431078	D	0.90563	-2.69	5.9	5.9	0.94986	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.000000	0.49916	D	0.000137	D	0.97757	0.9264	H	0.99104	4.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98903	1.0777	10	0.87932	D	0	.	19.2581	0.93955	0.0:0.0:1.0:0.0	.	826	Q8WYK1	CNTP5_HUMAN	R	826	ENSP00000399013:G826R	ENSP00000399013:G826R	G	+	1	0	CNTNAP5	125238140	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	9.726000	0.98782	2.804000	0.96469	0.655000	0.94253	GGA		0.373	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
GYPC	2995	broad.mit.edu	37	2	127413872	127413872	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:127413872G>A	ENST00000259254.4	+	1	364	c.33G>A	c.(31-33)gcG>gcA	p.A11A	GYPC_ENST00000409836.3_Silent_p.A11A|GYPC_ENST00000356887.7_5'UTR|GYPC_ENST00000464053.1_3'UTR	NM_002101.4	NP_002092.1	P04921	GLPC_HUMAN	glycophorin C (Gerbich blood group)	11						cortical cytoskeleton (GO:0030863)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)		p.A11A(1)		central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|prostate(2)|urinary_tract(1)	13	Colorectal(110;0.0533)			BRCA - Breast invasive adenocarcinoma(221;0.075)		ACAGCACGGCGTGGCCTCTCA	0.761																																					p.A11A	Melanoma(110;806 1600 6704 9981 33404)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G33A	2						.						8.0	11.0	10.0					2																	127413872		2122	4206	6328	127130342	SO:0001819	synonymous_variant	2995	exon1				CCDS2136.1, CCDS46402.1, CCDS58724.1	2q14-q21	2014-07-19			ENSG00000136732	ENSG00000136732		"""CD molecules"", ""Blood group antigens"""	4704	protein-coding gene	gene with protein product		110750					Standard	NM_016815		Approved	GPC, GYPD, Ge, CD236, CD236R	uc002tnq.4	P04921	OTTHUMG00000131464	ENST00000259254.4:c.33G>A	2.37:g.127413872G>A		Somatic		Capture	Illumina HiSeq	Phase_I	127130342	NM_016815	B2R522|Q53SV9|Q92642	Silent	SNP	ENST00000259254.4	37	CCDS2136.1																																																																																				0.761	GYPC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254297.1	NM_002101	
BIN1	274	broad.mit.edu	37	2	127808053	127808053	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:127808053G>T	ENST00000316724.5	-	18	2029	c.1618C>A	c.(1618-1620)Cag>Aag	p.Q540K	BIN1_ENST00000259238.4_Missense_Mutation_p.Q444K|BIN1_ENST00000409400.1_Missense_Mutation_p.Q386K|BIN1_ENST00000351659.3_Missense_Mutation_p.Q453K|BIN1_ENST00000393040.3_Missense_Mutation_p.Q429K|BIN1_ENST00000352848.3_Missense_Mutation_p.Q401K|BIN1_ENST00000376113.2_Missense_Mutation_p.Q371K|BIN1_ENST00000393041.3_Missense_Mutation_p.Q422K|BIN1_ENST00000357970.3_Missense_Mutation_p.Q497K|BIN1_ENST00000346226.3_Missense_Mutation_p.Q465K|BIN1_ENST00000466111.1_5'UTR|BIN1_ENST00000348750.4_Missense_Mutation_p.Q356K	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	540	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)	p.Q540K(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GCCTTGAGCTGCAGCTCGTCT	0.647											OREG0014962	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q429K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1285A	2						.						134.0	104.0	114.0					2																	127808053		2203	4300	6503	127524523	SO:0001583	missense	274	exon14			U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1618C>A	2.37:g.127808053G>T	ENSP00000316779:p.Gln540Lys	Somatic	1560	Capture	Illumina HiSeq	Phase_I	127524523	NM_139348	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Missense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.147263	0.57151	.	.	ENSG00000136717	ENST00000376113;ENST00000357970;ENST00000393040;ENST00000348750;ENST00000259238;ENST00000346226;ENST00000393041;ENST00000351659;ENST00000352848;ENST00000316724;ENST00000409400	T;T;T;T;T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92;0.92	4.58	3.67	0.42095	Src homology-3 domain (4);Variant SH3 (1);	0.174660	0.51477	D	0.000100	T	0.39358	0.1075	N	0.12182	0.205	0.30608	N	0.759843	B;B;B;B;B;B;B;B;B;B;B;B;D	0.54207	0.202;0.021;0.129;0.317;0.129;0.321;0.11;0.452;0.213;0.412;0.05;0.05;0.965	B;B;B;B;B;B;B;B;B;B;B;B;D	0.74348	0.171;0.056;0.17;0.228;0.134;0.205;0.077;0.228;0.134;0.337;0.059;0.037;0.983	T	0.22103	-1.0226	10	0.30854	T	0.27	-24.3381	7.4105	0.27016	0.0901:0.0:0.745:0.1649	.	417;332;422;386;429;465;453;401;444;497;371;356;540	B7Z2Z2;B7Z6Y2;O00499-4;O00499-7;O00499-6;O00499-2;O00499-3;O00499-8;O00499-11;O00499-5;O00499-10;O00499-9;O00499	.;.;.;.;.;.;.;.;.;.;.;.;BIN1_HUMAN	K	371;497;429;356;444;465;422;453;401;540;386	ENSP00000365281:Q371K;ENSP00000350654:Q497K;ENSP00000376760:Q429K;ENSP00000259237:Q356K;ENSP00000259238:Q444K;ENSP00000315411:Q465K;ENSP00000376761:Q422K;ENSP00000315388:Q453K;ENSP00000315284:Q401K;ENSP00000316779:Q540K;ENSP00000386797:Q386K	ENSP00000259238:Q444K	Q	-	1	0	BIN1	127524523	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.595000	0.36708	2.397000	0.81536	0.555000	0.69702	CAG		0.647	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
CCNT2	905	broad.mit.edu	37	2	135711242	135711242	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:135711242T>A	ENST00000264157.5	+	9	1247	c.1217T>A	c.(1216-1218)gTt>gAt	p.V406D	CCNT2_ENST00000537343.1_Missense_Mutation_p.V231D|CCNT2_ENST00000295238.6_Missense_Mutation_p.V406D	NM_001241.3|NM_058241.2	NP_001232.1|NP_490595.1	O60583	CCNT2_HUMAN	cyclin T2	406					cell cycle (GO:0007049)|cell division (GO:0051301)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.V406D(1)		endometrium(2)|kidney(3)|large_intestine(10)|lung(6)|ovary(2)|prostate(1)|skin(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.107)		CATTCTTCTGTTAAGCAAGAA	0.388																																					p.V406D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1217A	2						.						68.0	70.0	69.0					2																	135711242		2203	4300	6503	135427712	SO:0001583	missense	905	exon9			AF048731	CCDS2174.1, CCDS2175.1	2q21.3	2010-11-15			ENSG00000082258	ENSG00000082258			1600	protein-coding gene	gene with protein product		603862				9499409, 10465067	Standard	NM_001241		Approved		uc002tuc.2	O60583	OTTHUMG00000131712	ENST00000264157.5:c.1217T>A	2.37:g.135711242T>A	ENSP00000264157:p.Val406Asp	Somatic		Capture	Illumina HiSeq	Phase_I	135427712	NM_058241	A8KA48|D3DP73|D3DP74|O60582|Q29R66|Q53SR4|Q5I1Y0	Missense_Mutation	SNP	ENST00000264157.5	37	CCDS2174.1	.	.	.	.	.	.	.	.	.	.	T	7.115	0.576778	0.13686	.	.	ENSG00000082258	ENST00000537343;ENST00000295238;ENST00000264157	T;T	0.28069	1.69;1.63	5.65	0.637	0.17735	.	1.053330	0.07273	N	0.869502	T	0.23766	0.0575	L	0.40543	1.245	0.40499	D	0.980625	B;B;B	0.29590	0.06;0.203;0.25	B;B;B	0.34590	0.134;0.068;0.186	T	0.20538	-1.0272	10	0.12430	T	0.62	.	5.265	0.15593	0.0:0.2288:0.1408:0.6304	.	231;406;406	B4DH21;O60583;O60583-2	.;CCNT2_HUMAN;.	D	231;406;406	ENSP00000295238:V406D;ENSP00000264157:V406D	ENSP00000264157:V406D	V	+	2	0	CCNT2	135427712	0.864000	0.29904	0.280000	0.24747	0.896000	0.52359	0.857000	0.27831	0.094000	0.17404	-0.323000	0.08544	GTT		0.388	CCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254629.1	NM_058241	
ZRANB3	84083	broad.mit.edu	37	2	136073066	136073066	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:136073066C>T	ENST00000264159.6	-	7	828	c.712G>A	c.(712-714)Ggg>Agg	p.G238R	ZRANB3_ENST00000401392.1_Missense_Mutation_p.G238R|ZRANB3_ENST00000536680.1_Missense_Mutation_p.G238R	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	238	DNA annealing helicase activity.				cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)	p.G238R(1)		NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		TTTGATGCCCCTCTACAATCC	0.338																																					p.G238R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G712A	2						.						64.0	61.0	62.0					2																	136073066		1827	4077	5904	135789536	SO:0001583	missense	84083	exon7			AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.712G>A	2.37:g.136073066C>T	ENSP00000264159:p.Gly238Arg	Somatic		Capture	Illumina HiSeq	Phase_I	135789536	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Missense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.934004	0.92458	.	.	ENSG00000121988	ENST00000401392;ENST00000264159;ENST00000536680;ENST00000397448	D;D;D	0.93019	-3.15;-3.15;-3.15	5.67	5.67	0.87782	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97062	0.9040	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.97286	0.9921	10	0.87932	D	0	-22.4515	19.7627	0.96329	0.0:1.0:0.0:0.0	.	178;238;238	E9PBP0;Q5FWF4;Q5FWF4-3	.;ZRAB3_HUMAN;.	R	238;238;238;178	ENSP00000383979:G238R;ENSP00000264159:G238R;ENSP00000441320:G238R	ENSP00000264159:G238R	G	-	1	0	ZRANB3	135789536	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.079000	0.76829	2.661000	0.90470	0.460000	0.39030	GGG		0.338	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
THSD7B	80731	broad.mit.edu	37	2	138000091	138000091	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:138000091A>T	ENST00000409968.1	+	10	2393	c.2215A>T	c.(2215-2217)Att>Ttt	p.I739F	THSD7B_ENST00000543459.1_Intron|THSD7B_ENST00000413152.2_Missense_Mutation_p.I708F|THSD7B_ENST00000272643.3_Missense_Mutation_p.I739F			Q9C0I4	THS7B_HUMAN	thrombospondin, type I, domain containing 7B	739	TSP type-1 9. {ECO:0000255|PROSITE- ProRule:PRU00210}.					integral component of membrane (GO:0016021)		p.I739F(1)		NS(3)|breast(3)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(14)|lung(57)|ovary(4)|pancreas(3)|prostate(11)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	134				BRCA - Breast invasive adenocarcinoma(221;0.19)		AAAAGACTGTATTGTGACTGC	0.463																																					p.I708F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2122T	2						.						134.0	131.0	132.0					2																	138000091		1996	4171	6167	137716561	SO:0001583	missense	80731	exon9					2q22.1	2006-11-24			ENSG00000144229	ENSG00000144229			29348	protein-coding gene	gene with protein product						11214970	Standard	NM_001080427		Approved	KIAA1679	uc002tva.1	Q9C0I4	OTTHUMG00000153590	ENST00000409968.1:c.2215A>T	2.37:g.138000091A>T	ENSP00000387145:p.Ile739Phe	Somatic		Capture	Illumina HiSeq	Phase_I	137716561	NM_001080427		Missense_Mutation	SNP	ENST00000409968.1	37		.	.	.	.	.	.	.	.	.	.	A	16.00	2.998215	0.54147	.	.	ENSG00000144229	ENST00000409968;ENST00000272643;ENST00000413152	T;T;T	0.18338	2.22;2.22;2.22	5.78	-8.14	0.01069	.	0.770609	0.12726	N	0.444285	T	0.15696	0.0378	M	0.74881	2.28	0.09310	N	1	B;B	0.32781	0.384;0.384	B;B	0.35182	0.197;0.197	T	0.13072	-1.0523	10	0.16896	T	0.51	.	10.8858	0.46965	0.2855:0.2636:0.4509:0.0	.	739;708	Q9C0I4;C9JKN6	THS7B_HUMAN;.	F	739;739;708	ENSP00000387145:I739F;ENSP00000272643:I739F;ENSP00000413841:I708F	ENSP00000272643:I739F	I	+	1	0	THSD7B	137716561	0.000000	0.05858	0.005000	0.12908	0.827000	0.46813	-0.460000	0.06720	-1.409000	0.02038	0.533000	0.62120	ATT		0.463	THSD7B-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000331769.2	XM_046570.9	
NEB	4703	broad.mit.edu	37	2	152483635	152483635	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:152483635C>A	ENST00000172853.10	-	66	9646	c.9499G>T	c.(9499-9501)Gct>Tct	p.A3167S	NEB_ENST00000603639.1_Missense_Mutation_p.A3410S|NEB_ENST00000604864.1_Missense_Mutation_p.A3410S|NEB_ENST00000409198.1_Missense_Mutation_p.A3167S|NEB_ENST00000427231.2_Missense_Mutation_p.A3410S|NEB_ENST00000397345.3_Missense_Mutation_p.A3410S			P20929	NEBU_HUMAN	nebulin	3167					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.A3167S(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)		ATTTCAGCAGCTCTCTTGCAC	0.483																																					p.A3410S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G10228T	2						.						129.0	127.0	128.0					2																	152483635		2063	4219	6282	152191881	SO:0001583	missense	4703	exon70			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.9499G>T	2.37:g.152483635C>A	ENSP00000172853:p.Ala3167Ser	Somatic		Capture	Illumina HiSeq	Phase_I	152191881	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	21.5	4.155814	0.78114	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.09538	2.99;3.04;3.0;2.97	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.38161	0.1030	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	T	0.14671	-1.0464	10	0.62326	D	0.03	.	19.5244	0.95197	0.0:1.0:0.0:0.0	.	3167	P20929	NEBU_HUMAN	S	3167;3410;3410;3167	ENSP00000386259:A3167S;ENSP00000380505:A3410S;ENSP00000416578:A3410S;ENSP00000172853:A3167S	ENSP00000172853:A3167S	A	-	1	0	NEB	152191881	1.000000	0.71417	0.995000	0.50966	0.222000	0.24845	7.641000	0.83368	2.687000	0.91594	0.655000	0.94253	GCT		0.483	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152536488	152536488	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:152536488G>A	ENST00000172853.10	-	31	3238	c.3091C>T	c.(3091-3093)Cca>Tca	p.P1031S	NEB_ENST00000603639.1_Missense_Mutation_p.P1031S|NEB_ENST00000604864.1_Missense_Mutation_p.P1031S|NEB_ENST00000409198.1_Missense_Mutation_p.P1031S|NEB_ENST00000427231.2_Missense_Mutation_p.P1031S|NEB_ENST00000397345.3_Missense_Mutation_p.P1031S			P20929	NEBU_HUMAN	nebulin	1031					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.P1031S(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)		AGGTCTGGTGGCAGGTTGTAT	0.408																																					p.P1031S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3091T	2						.						156.0	153.0	154.0					2																	152536488		1966	4138	6104	152244734	SO:0001583	missense	4703	exon31			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.3091C>T	2.37:g.152536488G>A	ENSP00000172853:p.Pro1031Ser	Somatic		Capture	Illumina HiSeq	Phase_I	152244734	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	8.862	0.947213	0.18356	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.05025	3.53;3.54;3.51;3.52	5.17	5.17	0.71159	.	0.196582	0.43919	D	0.000504	T	0.05777	0.0151	N	0.17379	0.485	0.80722	D	1	B	0.31485	0.325	B	0.36335	0.222	T	0.45963	-0.9225	10	0.09843	T	0.71	.	17.8255	0.88664	0.0:0.0:1.0:0.0	.	1031	P20929	NEBU_HUMAN	S	1031	ENSP00000386259:P1031S;ENSP00000380505:P1031S;ENSP00000416578:P1031S;ENSP00000172853:P1031S	ENSP00000172853:P1031S	P	-	1	0	NEB	152244734	1.000000	0.71417	0.708000	0.30435	0.458000	0.32498	7.435000	0.80391	2.571000	0.86741	0.650000	0.86243	CCA		0.408	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
NEB	4703	broad.mit.edu	37	2	152580800	152580800	+	Missense_Mutation	SNP	C	C	T	rs201433028		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:152580800C>T	ENST00000172853.10	-	8	733	c.586G>A	c.(586-588)Gtt>Att	p.V196I	NEB_ENST00000603639.1_Missense_Mutation_p.V196I|NEB_ENST00000604864.1_Missense_Mutation_p.V196I|NEB_ENST00000409198.1_Missense_Mutation_p.V196I|NEB_ENST00000427231.2_Missense_Mutation_p.V196I|NEB_ENST00000397345.3_Missense_Mutation_p.V196I			P20929	NEBU_HUMAN	nebulin	196					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.V196I(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)		GTGTTCTTAACGGCCTGGACA	0.463													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.V196I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G586A	2						.						130.0	142.0	138.0					2																	152580800		1985	4154	6139	152289046	SO:0001583	missense	4703	exon8			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.586G>A	2.37:g.152580800C>T	ENSP00000172853:p.Val196Ile	Somatic		Capture	Illumina HiSeq	Phase_I	152289046	NM_001164507	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.22	2.469593	0.43839	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853;ENST00000439291	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	6.02	-6.14	0.02111	.	0.412580	0.25695	N	0.028914	T	0.35885	0.0947	L	0.51422	1.61	0.80722	D	1	B	0.17268	0.021	B	0.24006	0.05	T	0.11084	-1.0602	10	0.22109	T	0.4	.	14.6035	0.68460	0.0:0.2009:0.0:0.7991	.	196	P20929	NEBU_HUMAN	I	196	ENSP00000386259:V196I;ENSP00000380505:V196I;ENSP00000416578:V196I;ENSP00000172853:V196I	ENSP00000172853:V196I	V	-	1	0	NEB	152289046	0.886000	0.30341	0.177000	0.23020	0.873000	0.50193	0.557000	0.23454	-1.053000	0.03218	0.650000	0.86243	GTT		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
GALNT5	11227	broad.mit.edu	37	2	158115519	158115519	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:158115519G>T	ENST00000259056.4	+	1	1410	c.925G>T	c.(925-927)Ggg>Tgg	p.G309W		NM_014568.1	NP_055383.1	Q7Z7M9	GALT5_HUMAN	polypeptide N-acetylgalactosaminyltransferase 5	309					cellular protein metabolic process (GO:0044267)|glycosaminoglycan biosynthetic process (GO:0006024)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.G309W(1)		breast(4)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	56						TGGAGCTAGAGGGGCTCATGG	0.403																																					p.G309W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G925T	2						.						66.0	71.0	70.0					2																	158115519		2203	4299	6502	157823765	SO:0001583	missense	11227	exon1			AJ245539	CCDS2203.1	2q24.1	2014-03-13	2014-03-13		ENSG00000136542	ENSG00000136542	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4127	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 5"""	615129	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 5 (GalNAc-T5)"""			10545594	Standard	NM_014568		Approved	GalNAc-T5	uc002tzg.3	Q7Z7M9	OTTHUMG00000131965	ENST00000259056.4:c.925G>T	2.37:g.158115519G>T	ENSP00000259056:p.Gly309Trp	Somatic		Capture	Illumina HiSeq	Phase_I	157823765	NM_014568	A5PKZ1|Q9UGK7|Q9UHL6	Missense_Mutation	SNP	ENST00000259056.4	37	CCDS2203.1	.	.	.	.	.	.	.	.	.	.	G	8.535	0.871879	0.17322	.	.	ENSG00000136542	ENST00000259056	T	0.57107	0.42	5.43	3.63	0.41609	.	3.283110	0.00702	N	0.000796	T	0.37945	0.1022	N	0.14661	0.345	0.09310	N	1	P	0.44006	0.824	B	0.37047	0.24	T	0.38351	-0.9665	10	0.66056	D	0.02	.	6.9903	0.24751	0.1512:0.0:0.7065:0.1423	.	309	Q7Z7M9	GALT5_HUMAN	W	309	ENSP00000259056:G309W	ENSP00000259056:G309W	G	+	1	0	GALNT5	157823765	0.994000	0.37717	0.040000	0.18447	0.104000	0.19210	0.806000	0.27126	0.778000	0.33520	0.655000	0.94253	GGG		0.403	GALNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254925.2	NM_014568	
PLA2R1	22925	broad.mit.edu	37	2	160843841	160843841	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:160843841T>C	ENST00000283243.7	-	12	2069	c.1863A>G	c.(1861-1863)cgA>cgG	p.R621R	PLA2R1_ENST00000392771.1_Silent_p.R621R	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	621	C-type lectin 3. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)	p.R621R(1)	PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						GATGCCTTCCTCGCATGGCAA	0.463																																					p.R621R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1863G	2						.						51.0	43.0	46.0					2																	160843841		2203	4300	6503	160552087	SO:0001819	synonymous_variant	22925	exon12			U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.1863A>G	2.37:g.160843841T>C		Somatic		Capture	Illumina HiSeq	Phase_I	160552087	NM_007366	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																				0.463	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
SCN3A	6328	broad.mit.edu	37	2	165986674	165986674	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:165986674C>T	ENST00000360093.3	-	17	3189	c.2698G>A	c.(2698-2700)Ggc>Agc	p.G900S	SCN3A_ENST00000409101.3_Missense_Mutation_p.G851S|SCN3A_ENST00000283254.7_Missense_Mutation_p.G900S	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	900					membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.G900S(1)		NS(1)|breast(7)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(19)|liver(2)|lung(47)|ovary(6)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(3)	120					Lacosamide(DB06218)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGCTGCATGCCGACCACAGCA	0.463																																					p.G900S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2698A	2						.						143.0	141.0	142.0					2																	165986674		2203	4300	6503	165694920	SO:0001583	missense	6328	exon17			AF035685	CCDS33312.1, CCDS46440.1	2q24	2012-02-26	2007-01-23		ENSG00000153253	ENSG00000153253		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10590	protein-coding gene	gene with protein product		182391	"""sodium channel, voltage-gated, type III, alpha polypeptide"""			9589372, 16382098	Standard	NM_001081676		Approved	Nav1.3	uc002ucx.3	Q9NY46	OTTHUMG00000044171	ENST00000360093.3:c.2698G>A	2.37:g.165986674C>T	ENSP00000353206:p.Gly900Ser	Somatic		Capture	Illumina HiSeq	Phase_I	165694920	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	C	35	5.558512	0.96514	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000440431	D;D;D;D	0.97642	-4.47;-4.47;-4.47;-4.47	5.49	5.49	0.81192	Ion transport (1);	0.000000	0.64402	D	0.000014	D	0.99017	0.9664	H	0.95043	3.615	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;1.0	D	0.99391	1.0925	10	0.87932	D	0	.	19.353	0.94398	0.0:1.0:0.0:0.0	.	900;851;851;851;900	Q9NY46;E7EUE6;Q9NY46-2;Q9NY46-4;Q9NY46-3	SCN3A_HUMAN;.;.;.;.	S	900;900;851;851	ENSP00000353206:G900S;ENSP00000283254:G900S;ENSP00000386726:G851S;ENSP00000403348:G851S	ENSP00000283254:G900S	G	-	1	0	SCN3A	165694920	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.776000	0.85560	2.571000	0.86741	0.563000	0.77884	GGC		0.463	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922	
SCN2A	6326	broad.mit.edu	37	2	166245864	166245864	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:166245864G>A	ENST00000375437.2	+	27	5838	c.5548G>A	c.(5548-5550)Gac>Aac	p.D1850N	SCN2A_ENST00000283256.6_Missense_Mutation_p.D1850N|SCN2A_ENST00000357398.3_Missense_Mutation_p.D1850N|SCN2A_ENST00000375427.2_Missense_Mutation_p.D1850N	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	1850					intrinsic apoptotic signaling pathway in response to osmotic stress (GO:0008627)|membrane depolarization during action potential (GO:0086010)|myelination (GO:0042552)|neuron apoptotic process (GO:0051402)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intrinsic component of plasma membrane (GO:0031226)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.D1850N(1)		NS(1)|breast(7)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|liver(2)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	118					Lamotrigine(DB00555)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGTGAGTGGTGACCGGATCCA	0.468																																					p.D1850N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G5548A	2						.						127.0	116.0	120.0					2																	166245864		2203	4300	6503	165954110	SO:0001583	missense	6326	exon26			AB208888	CCDS33313.1, CCDS33314.1	2q24.3	2012-02-26	2007-01-23	2007-01-23	ENSG00000136531	ENSG00000136531		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10588	protein-coding gene	gene with protein product		182390	"""sodium channel, voltage-gated, type II, alpha 2 polypeptide"", ""sodium channel, voltage-gated, type II, alpha 1 polypeptide"""	SCN2A1, SCN2A2		1317301, 16382098	Standard	XM_005246753		Approved	Nav1.2, HBSCII, HBSCI	uc002ude.3	Q99250	OTTHUMG00000044172	ENST00000375437.2:c.5548G>A	2.37:g.166245864G>A	ENSP00000364586:p.Asp1850Asn	Somatic		Capture	Illumina HiSeq	Phase_I	165954110	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Missense_Mutation	SNP	ENST00000375437.2	37	CCDS33314.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.238200	0.79800	.	.	ENSG00000136531	ENST00000375437;ENST00000357398;ENST00000283256;ENST00000375427	D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.98147	0.9388	M	0.77103	2.36	0.80722	D	1	P;P	0.52316	0.911;0.952	P;D	0.79784	0.863;0.993	D	0.98645	1.0677	10	0.87932	D	0	.	19.8849	0.96909	0.0:0.0:1.0:0.0	.	1850;1850	Q99250-2;Q99250	.;SCN2A_HUMAN	N	1850	ENSP00000364586:D1850N;ENSP00000349973:D1850N;ENSP00000283256:D1850N;ENSP00000364576:D1850N	ENSP00000283256:D1850N	D	+	1	0	SCN2A	165954110	1.000000	0.71417	0.977000	0.42913	0.964000	0.63967	9.734000	0.98822	2.781000	0.95711	0.580000	0.79431	GAC		0.468	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007	
SCN7A	6332	broad.mit.edu	37	2	167298159	167298159	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:167298159A>G	ENST00000409855.1	-	14	2030	c.1904T>C	c.(1903-1905)tTc>tCc	p.F635S		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	635					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.F635S(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GATGAATGTGAACAACAACAG	0.418																																					p.F635S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1904C	2						.						121.0	126.0	124.0					2																	167298159		2191	4298	6489	167006405	SO:0001583	missense	6332	exon14			M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.1904T>C	2.37:g.167298159A>G	ENSP00000386796:p.Phe635Ser	Somatic		Capture	Illumina HiSeq	Phase_I	167006405	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	A	12.23	1.874337	0.33069	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.97665	-4.48;-4.48	4.78	0.933	0.19471	Ion transport (1);	0.878865	0.09908	N	0.740144	D	0.93900	0.8048	L	0.56769	1.78	0.21184	N	0.999763	B	0.18461	0.028	B	0.18263	0.021	D	0.86053	0.1527	10	0.62326	D	0.03	.	0.7627	0.01009	0.4867:0.1704:0.1794:0.1635	.	635	Q01118	SCN7A_HUMAN	S	635	ENSP00000386796:F635S;ENSP00000413699:F635S	ENSP00000259060:F635S	F	-	2	0	SCN7A	167006405	0.997000	0.39634	0.000000	0.03702	0.015000	0.08874	1.311000	0.33562	0.066000	0.16515	0.477000	0.44152	TTC		0.418	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
LRP2	4036	broad.mit.edu	37	2	170112696	170112696	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:170112696C>A	ENST00000263816.3	-	19	2975	c.2690G>T	c.(2689-2691)aGc>aTc	p.S897I	LRP2_ENST00000443831.1_Missense_Mutation_p.S760I	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	897					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S897I(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	ATCAAAGGTGCTGTGCTCAAT	0.358																																					p.S897I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2690T	2						.						109.0	106.0	107.0					2																	170112696		2203	4300	6503	169820942	SO:0001583	missense	4036	exon19				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.2690G>T	2.37:g.170112696C>A	ENSP00000263816:p.Ser897Ile	Somatic		Capture	Illumina HiSeq	Phase_I	169820942	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.861303	0.32884	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.89939	-2.59;-2.59	5.48	5.48	0.80851	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.91119	0.7204	L	0.45051	1.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.996	D	0.85716	0.1322	10	0.02654	T	1	.	19.4077	0.94655	0.0:1.0:0.0:0.0	.	760;897	E9PC35;P98164	.;LRP2_HUMAN	I	897;760	ENSP00000263816:S897I;ENSP00000409813:S760I	ENSP00000263816:S897I	S	-	2	0	LRP2	169820942	1.000000	0.71417	0.996000	0.52242	0.673000	0.39480	7.551000	0.82182	2.589000	0.87451	0.586000	0.80456	AGC		0.358	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CDCA7	83879	broad.mit.edu	37	2	174228118	174228118	+	Silent	SNP	C	C	T	rs35285795	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:174228118C>T	ENST00000347703.3	+	3	456	c.312C>T	c.(310-312)tcC>tcT	p.S104S	CDCA7_ENST00000410101.3_Silent_p.S139S|CDCA7_ENST00000410019.3_Silent_p.S62S|CDCA7_ENST00000392567.2_Silent_p.S104S|CDCA7_ENST00000306721.3_Silent_p.S183S	NM_145810.2	NP_665809.1	Q9BWT1	CDCA7_HUMAN	cell division cycle associated 7	104					apoptotic process (GO:0006915)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S183S(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			ATTCCAACTCCGATTCAGAAG	0.433													C|||	5	0.000998403	0.0038	0.0	5008	,	,		18636	0.0		0.0	False		,,,				2504	0.0				p.S183S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C549T	2						.	C	,	8,4398	14.3+/-33.2	0,8,2195	61.0	68.0	66.0		549,312	-11.9	0.0	2	dbSNP_126	66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CDCA7	NM_031942.4,NM_145810.2	,	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	,	183/451,104/372	174228118	8,12998	2203	4300	6503	173936364	SO:0001819	synonymous_variant	83879	exon4			BG354580	CCDS2252.1, CCDS2253.1	2q31.1	2008-02-05			ENSG00000144354	ENSG00000144354			14628	protein-coding gene	gene with protein product		609937				11598121, 12188893	Standard	NM_145810		Approved	FLJ14736, JPO1	uc002uic.1	Q9BWT1	OTTHUMG00000132296	ENST00000347703.3:c.312C>T	2.37:g.174228118C>T		Somatic		Capture	Illumina HiSeq	Phase_I	173936364	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Silent	SNP	ENST00000347703.3	37	CCDS2253.1																																																																																				0.433	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942	
AGPS	8540	broad.mit.edu	37	2	178326734	178326734	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:178326734T>C	ENST00000264167.4	+	9	1130	c.984T>C	c.(982-984)aaT>aaC	p.N328N	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	328	FAD-binding PCMH-type. {ECO:0000255|PROSITE-ProRule:PRU00718}.				cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)	p.N328N(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			TCTATGGCAATATCGAGGACC	0.328																																					p.N328N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T984C	2						.						79.0	76.0	77.0					2																	178326734		2203	4300	6503	178034980	SO:0001819	synonymous_variant	8540	exon9			Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.984T>C	2.37:g.178326734T>C		Somatic		Capture	Illumina HiSeq	Phase_I	178034980	NM_003659	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																				0.328	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2		
TTN	7273	broad.mit.edu	37	2	179433591	179433591	+	Silent	SNP	T	T	C	rs376372388		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179433591T>C	ENST00000591111.1	-	276	72569	c.72345A>G	c.(72343-72345)gcA>gcG	p.A24115A	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN_ENST00000359218.5_Silent_p.A16816A|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Silent_p.A16691A|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000342175.6_Silent_p.A16883A|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000342992.6_Silent_p.A23188A|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000589042.1_Silent_p.A25756A|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24115	Fibronectin type-III 75. {ECO:0000255|PROSITE-ProRule:PRU00316}.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A23186A(1)|p.A16691A(1)|p.A16883A(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGGTAATTACTGCCTGAAGAG	0.408																																					p.Q16691R												.	.	3	Substitution - coding silent(3)	large_intestine(3)	c.A50072G	2						.	T	,,,	3,3843		0,3,1920	115.0	114.0	114.0		50073,69564,50448,50649	-5.1	0.8	2		114	0,8246		0,0,4123	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,3,6043	CC,CT,TT		0.0,0.078,0.0248	,,,	16691/26927,23188/33424,16816/27052,16883/27119	179433591	3,12089	1923	4123	6046	179141837	SO:0001819	synonymous_variant	7273	exon154			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72345A>G	2.37:g.179433591T>C		Somatic		Capture	Illumina HiSeq	Phase_I	179141837	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179545033	179545033	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179545033G>A	ENST00000591111.1	-	137	32639	c.32415C>T	c.(32413-32415)gtC>gtT	p.V10805V	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Silent_p.V9878V|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000589042.1_Silent_p.V11122V|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000589830.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.V9878V(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TTTCTTCTGCGACAACCCTCT	0.403																																					p.V9878V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C29634T	2						.						202.0	193.0	196.0					2																	179545033		1860	4100	5960	179253278	SO:0001819	synonymous_variant	7273	exon136			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.32415C>T	2.37:g.179545033G>A		Somatic		Capture	Illumina HiSeq	Phase_I	179253278	NM_133378	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179604833	179604833	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179604833T>C	ENST00000591111.1	-	46	12400	c.12176A>G	c.(12175-12177)gAc>gGc	p.D4059G	TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D4138G|TTN_ENST00000460472.2_Missense_Mutation_p.D4013G|TTN_ENST00000342175.6_Missense_Mutation_p.D4205G|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.D4376G|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	0					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.D4205G(1)|p.D4013G(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AGAAAGAAGGTCCCTTCCCTG	0.483																																					p.D4013G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A12038G	2						.						62.0	61.0	61.0					2																	179604833		1851	4097	5948	179313078	SO:0001583	missense	7273	exon45			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.12176A>G	2.37:g.179604833T>C	ENSP00000465570:p.Asp4059Gly	Somatic		Capture	Illumina HiSeq	Phase_I	179313078	NM_003319	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	1.835	-0.468785	0.04445	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.60424	0.24;0.2;0.19	5.92	1.03	0.20045	.	.	.	.	.	T	0.42787	0.1218	L	0.27053	0.805	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.38542	-0.9656	9	0.87932	D	0	.	9.3102	0.37900	0.0:0.2682:0.0:0.7318	.	4013;4138;4205	D3DPF9;E7EQE6;E7ET18	.;.;.	G	4013;4205;4138;4013	ENSP00000434586:D4013G;ENSP00000340554:D4205G;ENSP00000352154:D4138G	ENSP00000340554:D4205G	D	-	2	0	TTN	179313078	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	0.653000	0.24902	0.158000	0.19367	-0.290000	0.09829	GAC		0.483	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179614865	179614865	+	Intron	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179614865G>T	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.P4088T|TTN_ENST00000589042.1_Intron|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.P4088T(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GGAACTGGTGGGTTAGTTTTT	0.433																																					p.P4088T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C12262A	2						.						87.0	81.0	83.0					2																	179614865		2203	4299	6502	179323110	SO:0001627	intron_variant	7273	exon46			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+2985C>A	2.37:g.179614865G>T		Somatic		Capture	Illumina HiSeq	Phase_I	179323110	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	5.747	0.322262	0.10900	.	.	ENSG00000155657	ENST00000360870	T	0.56444	0.46	5.76	2.76	0.32466	.	.	.	.	.	T	0.31263	0.0791	N	0.12182	0.205	0.09310	N	0.999993	B	0.15473	0.013	B	0.09377	0.004	T	0.15752	-1.0426	9	0.15066	T	0.55	.	10.5162	0.44892	0.0:0.2704:0.59:0.1396	.	4088	Q8WZ42-6	.	T	4088	ENSP00000354117:P4088T	ENSP00000354117:P4088T	P	-	1	0	TTN	179323110	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.084000	0.14891	0.869000	0.35703	0.655000	0.94253	CCA		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	broad.mit.edu	37	2	179622346	179622346	+	Intron	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:179622346G>T	ENST00000591111.1	-	44	10528				TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A3488D|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000360870.5_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.A3534D|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.A3488D(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTACTGCCCAGCATGCTCTGA	0.458																																					p.A3488D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C10463A	2						.						103.0	104.0	104.0					2																	179622346		1973	4152	6125	179330591	SO:0001627	intron_variant	7273	exon44			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10303+1364C>A	2.37:g.179622346G>T		Somatic		Capture	Illumina HiSeq	Phase_I	179330591	NM_133432	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	G	14.25	2.479840	0.44044	.	.	ENSG00000155657	ENST00000359218	T	0.68331	-0.32	6.16	5.12	0.69794	.	.	.	.	.	T	0.80292	0.4596	.	.	.	0.33785	D	0.624726	D	0.55800	0.973	P	0.62089	0.898	D	0.85484	0.1181	8	0.87932	D	0	.	16.4524	0.83996	0.072:0.0:0.928:0.0	.	3488	E7EQE6	.	D	3488	ENSP00000352154:A3488D	ENSP00000352154:A3488D	A	-	2	0	TTN	179330591	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.678000	0.74508	2.937000	0.99478	0.650000	0.86243	GCT		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CWC22	57703	broad.mit.edu	37	2	180838480	180838480	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:180838480A>C	ENST00000410053.3	-	7	930	c.631T>G	c.(631-633)Ttc>Gtc	p.F211V	CWC22_ENST00000295749.6_Missense_Mutation_p.F211V	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	211	MIF4G. {ECO:0000255|PROSITE- ProRule:PRU00698}.				mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)	p.F211V(1)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						ACATGGGTGAAGATTGGAGAA	0.338																																					p.F211V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T631G	2						.						70.0	65.0	66.0					2																	180838480		1833	4096	5929	180546725	SO:0001583	missense	57703	exon7				CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.631T>G	2.37:g.180838480A>C	ENSP00000387006:p.Phe211Val	Somatic		Capture	Illumina HiSeq	Phase_I	180546725	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	37	CCDS46465.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.663059	0.88251	.	.	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.26957	1.7;1.7;1.7	5.52	5.52	0.82312	MIF4G-like, type 3 (2);Armadillo-type fold (1);MIF4-like, type 1/2/3 (1);	0.000000	0.85682	D	0.000000	T	0.63733	0.2536	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.75863	-0.3167	10	0.87932	D	0	-23.3881	14.8114	0.69996	1.0:0.0:0.0:0.0	.	211	Q9HCG8	CWC22_HUMAN	V	211	ENSP00000387006:F211V;ENSP00000295749:F211V;ENSP00000384159:F211V	ENSP00000295749:F211V	F	-	1	0	CWC22	180546725	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.133000	0.94460	2.092000	0.63282	0.528000	0.53228	TTC		0.338	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
RDH14	57665	broad.mit.edu	37	2	18736570	18736570	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:18736570C>A	ENST00000381249.3	-	2	1005	c.898G>T	c.(898-900)Gga>Tga	p.G300*	RDH14_ENST00000468071.1_5'UTR	NM_020905.3	NP_065956.1	Q9HBH5	RDH14_HUMAN	retinol dehydrogenase 14 (all-trans/9-cis/11-cis)	300					osteoblast differentiation (GO:0001649)	endoplasmic reticulum (GO:0005783)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	oxidoreductase activity (GO:0016491)	p.G300*(1)		breast(2)|endometrium(1)|large_intestine(2)|lung(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.177)				Vitamin A(DB00162)	AAGTATCTTCCTGACACTCCT	0.433																																					p.G300X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G898T	2						.						140.0	137.0	138.0					2																	18736570		2203	4300	6503	18600051	SO:0001587	stop_gained	93034	exon2			AF237952	CCDS1693.1	2p24.2	2011-09-14	2006-05-09		ENSG00000240857	ENSG00000240857	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19979	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 4"""		"""retinol dehydrogenase 14 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_020905		Approved	PAN2, SDR7C4		Q9HBH5	OTTHUMG00000090705	ENST00000381249.3:c.898G>T	2.37:g.18736570C>A	ENSP00000370648:p.Gly300*	Somatic		Capture	Illumina HiSeq	Phase_I	18600051	NM_020905		Nonsense_Mutation	SNP	ENST00000381249.3	37	CCDS1693.1	.	.	.	.	.	.	.	.	.	.	C	37	6.198198	0.97367	.	.	ENSG00000240857	ENST00000381249	.	.	.	5.67	5.67	0.87782	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.7728	0.96373	0.0:1.0:0.0:0.0	.	.	.	.	X	300	.	ENSP00000370648:G300X	G	-	1	0	RDH14	18600051	1.000000	0.71417	0.996000	0.52242	0.981000	0.71138	7.818000	0.86416	2.687000	0.91594	0.655000	0.94253	GGA		0.433	RDH14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207394.1		
SSFA2	6744	broad.mit.edu	37	2	182786689	182786689	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:182786689G>A	ENST00000431877.2	+	16	3404	c.3225G>A	c.(3223-3225)atG>atA	p.M1075I	SSFA2_ENST00000409136.1_Missense_Mutation_p.M584I|SSFA2_ENST00000467172.2_3'UTR|SSFA2_ENST00000409001.1_Missense_Mutation_p.M1053I|SSFA2_ENST00000320370.7_Missense_Mutation_p.M1075I|SSFA2_ENST00000428267.2_Missense_Mutation_p.M900I	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	1075						cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.M1075I(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CTGAACTGATGCAGGAGCAGT	0.403																																					p.M1075I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3225A	2						.						60.0	61.0	61.0					2																	182786689		2203	4299	6502	182494934	SO:0001583	missense	6744	exon16			M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.3225G>A	2.37:g.182786689G>A	ENSP00000388731:p.Met1075Ile	Somatic		Capture	Illumina HiSeq	Phase_I	182494934	NM_006751	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	.	.	.	.	.	.	.	.	.	.	G	4.007	-0.001388	0.07819	.	.	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136;ENST00000451836	T;T;T;T;T	0.13657	2.81;2.57;2.81;2.82;2.6	5.81	-1.51	0.08664	.	0.235802	0.51477	N	0.000092	T	0.06735	0.0172	L	0.38838	1.175	0.19775	N	0.999959	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.35351	-0.9792	10	0.15499	T	0.54	-3.7423	1.3386	0.02150	0.287:0.0842:0.3213:0.3076	.	900;584;1053;1075;1075	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	I	1075;1075;1053;900;584;20	ENSP00000388731:M1075I;ENSP00000314669:M1075I;ENSP00000387319:M1053I;ENSP00000409867:M900I;ENSP00000386916:M584I	ENSP00000314669:M1075I	M	+	3	0	SSFA2	182494934	0.301000	0.24444	0.005000	0.12908	0.875000	0.50365	-0.235000	0.09016	-0.673000	0.05259	-1.987000	0.00451	ATG		0.403	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
GULP1	51454	broad.mit.edu	37	2	189449015	189449015	+	Silent	SNP	G	G	A	rs376024527		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:189449015G>A	ENST00000409580.1	+	11	1347	c.633G>A	c.(631-633)tcG>tcA	p.S211S	GULP1_ENST00000359135.3_Silent_p.S211S|GULP1_ENST00000409843.1_Silent_p.S211S|GULP1_ENST00000409805.1_Silent_p.S108S|GULP1_ENST00000409830.1_Silent_p.S211S|GULP1_ENST00000409609.1_Silent_p.S211S			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	211					apoptotic process (GO:0006915)|lipid transport (GO:0006869)|phagocytosis, engulfment (GO:0006911)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)			endometrium(3)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	13			OV - Ovarian serous cystadenocarcinoma(117;0.0423)|Epithelial(96;0.158)			CACCTAAGTCGCCCTCCACTG	0.388																																					p.S211S	Pancreas(178;563 2065 20199 42378 52815)											.	.	0			c.G633A	2						.	G		1,4405	2.1+/-5.4	0,1,2202	241.0	208.0	219.0		633	-7.8	0.7	2		219	0,8600		0,0,4300	no	coding-synonymous	GULP1	NM_016315.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		211/305	189449015	1,13005	2203	4300	6503	189157260	SO:0001819	synonymous_variant	51454	exon10			AF191771	CCDS2295.1, CCDS58742.1, CCDS58743.1	2q32.3-q33	2008-02-05			ENSG00000144366	ENSG00000144366			18649	protein-coding gene	gene with protein product		608165				11729193	Standard	NM_001252668		Approved	CED6, CED-6, GULP	uc010fru.3	Q9UBP9	OTTHUMG00000132647	ENST00000409580.1:c.633G>A	2.37:g.189449015G>A		None		Capture	Illumina HiSeq	Phase_I	189157260	NM_016315	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Silent	SNP	ENST00000409580.1	37	CCDS2295.1	.	.	.	.	.	.	.	.	.	.	G	8.987	0.976766	0.18812	2.27E-4	0.0	ENSG00000144366	ENST00000451191;ENST00000433052	.	.	.	5.62	-7.83	0.01201	.	.	.	.	.	T	0.44456	0.1294	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48864	-0.8997	4	.	.	.	-6.3303	6.1143	0.20117	0.351:0.0:0.3961:0.2529	.	.	.	.	H	36;96	.	.	R	+	2	0	GULP1	189157260	0.420000	0.25457	0.670000	0.29842	0.748000	0.42578	-0.251000	0.08818	-1.500000	0.01819	-0.781000	0.03364	CGC		0.388	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315	
COL3A1	1281	broad.mit.edu	37	2	189866308	189866308	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:189866308G>A	ENST00000304636.3	+	34	2554	c.2384G>A	c.(2383-2385)gGt>gAt	p.G795D	COL3A1_ENST00000317840.5_Missense_Mutation_p.G795D	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	795	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.G795D(1)		NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GGACCTCGTGGTAGCCCTGTA	0.463																																					p.G795D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2384A	2						.						103.0	108.0	107.0					2																	189866308		2203	4300	6503	189574553	SO:0001583	missense	1281	exon34			X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2384G>A	2.37:g.189866308G>A	ENSP00000304408:p.Gly795Asp	Somatic		Capture	Illumina HiSeq	Phase_I	189574553	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.313593	0.81358	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99619	-6.28;-6.28	5.28	5.28	0.74379	.	0.000000	0.50627	D	0.000108	D	0.99775	0.9907	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97208	0.9869	10	0.87932	D	0	.	19.2744	0.94026	0.0:0.0:1.0:0.0	.	795	P02461	CO3A1_HUMAN	D	795	ENSP00000304408:G795D;ENSP00000315243:G795D	ENSP00000304408:G795D	G	+	2	0	COL3A1	189574553	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.549000	0.98106	2.637000	0.89404	0.557000	0.71058	GGT		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
MYO1B	4430	broad.mit.edu	37	2	192234334	192234334	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:192234334C>T	ENST00000392318.3	+	12	1346	c.1099C>T	c.(1099-1101)Cga>Tga	p.R367*	MYO1B_ENST00000304164.4_Nonsense_Mutation_p.R367*|MYO1B_ENST00000339514.4_Nonsense_Mutation_p.R367*|MYO1B_ENST00000392316.1_Nonsense_Mutation_p.R367*|RNU6-1045P_ENST00000516321.1_RNA	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	367	Myosin motor.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.R367*(2)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			GTTGGTAAATCGAATCAATGA	0.318																																					p.R367X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1099T	2						.						73.0	73.0	73.0					2																	192234334		2203	4300	6503	191942579	SO:0001587	stop_gained	4430	exon12			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.1099C>T	2.37:g.192234334C>T	ENSP00000376132:p.Arg367*	Somatic		Capture	Illumina HiSeq	Phase_I	191942579	NM_012223	O43794|Q7Z6L5	Nonsense_Mutation	SNP	ENST00000392318.3	37	CCDS46477.1	.	.	.	.	.	.	.	.	.	.	C	37	6.255787	0.97417	.	.	ENSG00000128641	ENST00000339514;ENST00000392318;ENST00000304164;ENST00000392316	.	.	.	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2594	0.54642	0.2139:0.7861:0.0:0.0	.	.	.	.	X	367	.	ENSP00000306382:R367X	R	+	1	2	MYO1B	191942579	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.934000	0.48956	2.565000	0.86533	0.655000	0.94253	CGA		0.318	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
ANKRD44	91526	broad.mit.edu	37	2	197878289	197878289	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:197878289C>T	ENST00000328737.2	-	18	1871	c.1795G>A	c.(1795-1797)Gca>Aca	p.A599T	ANKRD44_ENST00000450567.1_Missense_Mutation_p.A599T|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A616T|ANKRD44_ENST00000337207.5_Missense_Mutation_p.A599T			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	624								p.A599T(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(20)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.246)			AAGATGGATGCGCCCTGATTG	0.498																																					p.A624T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1870A	2						.						211.0	198.0	203.0					2																	197878289		2203	4300	6503	197586534	SO:0001583	missense	91526	exon18			AK097086	CCDS33355.1, CCDS33355.2, CCDS74619.1	2q33.1	2013-01-10			ENSG00000065413	ENSG00000065413		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	25259	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit B"""						Standard	NM_153697		Approved	PP6-ARS-B	uc021vuj.1	Q8N8A2	OTTHUMG00000154411	ENST00000328737.2:c.1795G>A	2.37:g.197878289C>T	ENSP00000331516:p.Ala599Thr	Somatic		Capture	Illumina HiSeq	Phase_I	197586534	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		.	.	.	.	.	.	.	.	.	.	C	25.0	4.596475	0.86953	.	.	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886	T;T;T;T;T;T	0.77358	1.77;-1.09;1.65;1.65;1.65;0.87	4.43	4.43	0.53597	.	0.122533	0.56097	D	0.000036	D	0.88822	0.6541	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.90891	0.4761	10	0.87932	D	0	.	17.2648	0.87083	0.0:1.0:0.0:0.0	.	642	Q8N8A2-2	.	T	439;616;599;599;599;299	ENSP00000403415:A439T;ENSP00000282272:A616T;ENSP00000331516:A599T;ENSP00000402420:A599T;ENSP00000338794:A599T;ENSP00000416319:A299T	ENSP00000282272:A616T	A	-	1	0	ANKRD44	197586534	1.000000	0.71417	0.731000	0.30826	0.519000	0.34347	7.651000	0.83577	2.294000	0.77228	0.655000	0.94253	GCA		0.498	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697	
SATB2	23314	broad.mit.edu	37	2	200298197	200298197	+	Silent	SNP	G	G	A	rs34311963	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:200298197G>A	ENST00000417098.1	-	3	1026	c.210C>T	c.(208-210)gaC>gaT	p.D70D	SATB2_ENST00000457245.1_Silent_p.D70D|SATB2_ENST00000260926.5_Silent_p.D70D|SATB2_ENST00000443023.1_Intron|SATB2_ENST00000428695.1_Silent_p.D70D	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	70					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)	p.D70D(1)		breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CAAGAGAGCCGTCCAACTGCT	0.473													G|||	8	0.00159744	0.0061	0.0	5008	,	,		18365	0.0		0.0	False		,,,				2504	0.0				p.D70D	Colon(30;262 767 11040 24421 36230)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C210T	2						.	G	,,	9,4397	15.5+/-35.6	0,9,2194	109.0	109.0	109.0		210,210,210	-4.5	0.5	2	dbSNP_126	109	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous,coding-synonymous	SATB2	NM_001172509.1,NM_001172517.1,NM_015265.3	,,	0,9,6494	AA,AG,GG		0.0,0.2043,0.0692	,,	70/734,70/734,70/734	200298197	9,12997	2203	4300	6503	200006442	SO:0001819	synonymous_variant	23314	exon3			AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"""Homeoboxes / CUT class"""	21637	protein-coding gene	gene with protein product		608148	"""SATB family member 2"""				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.210C>T	2.37:g.200298197G>A		Somatic		Capture	Illumina HiSeq	Phase_I	200006442	NM_001172509	A8K5Z8|Q3ZB87|Q4V763	Silent	SNP	ENST00000417098.1	37	CCDS2327.1																																																																																				0.473	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265	
AOX1	316	broad.mit.edu	37	2	201507487	201507487	+	Missense_Mutation	SNP	C	C	T	rs373608049		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:201507487C>T	ENST00000374700.2	+	25	3051	c.2810C>T	c.(2809-2811)aCg>aTg	p.T937M	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	937					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.T937M(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TCTTGTATCACGGAAGTTGCA	0.512																																					p.T937M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2810T	2						.						85.0	78.0	80.0					2																	201507487		2203	4300	6503	201215732	SO:0001583	missense	316	exon25			AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.2810C>T	2.37:g.201507487C>T	ENSP00000363832:p.Thr937Met	Somatic		Capture	Illumina HiSeq	Phase_I	201215732	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Missense_Mutation	SNP	ENST00000374700.2	37	CCDS33360.1	.	.	.	.	.	.	.	.	.	.	C	2.838	-0.241020	0.05906	.	.	ENSG00000138356	ENST00000374700	T	0.43294	0.95	5.17	1.43	0.22495	Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding (3);	0.697862	0.14980	N	0.287297	T	0.45296	0.1335	M	0.81802	2.56	0.09310	N	1	B	0.20164	0.042	B	0.28849	0.095	T	0.45101	-0.9284	10	0.46703	T	0.11	-11.0766	8.6083	0.33786	0.0:0.6998:0.1155:0.1847	.	937	Q06278	ADO_HUMAN	M	937	ENSP00000363832:T937M	ENSP00000363832:T937M	T	+	2	0	AOX1	201215732	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.270000	0.08584	0.086000	0.17137	-1.197000	0.01672	ACG		0.512	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
CLK1	1195	broad.mit.edu	37	2	201724903	201724903	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:201724903C>A	ENST00000321356.4	-	4	561	c.426G>T	c.(424-426)gaG>gaT	p.E142D	CLK1_ENST00000409769.2_5'Flank|CLK1_ENST00000434813.2_Missense_Mutation_p.E184D|Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000492793.1_5'Flank	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	142					cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)	p.E142D(1)		NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						CCTCATCATCCTCTACACTCC	0.428																																					p.E184D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G552T	2						.						202.0	173.0	183.0					2																	201724903		2203	4300	6503	201433148	SO:0001583	missense	1195	exon4			L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.426G>T	2.37:g.201724903C>A	ENSP00000326830:p.Glu142Asp	Somatic		Capture	Illumina HiSeq	Phase_I	201433148	NM_001162407	B4DFW7|Q0P694|Q8N5V8	De_novo_Start_OutOfFrame	SNP	ENST00000321356.4	37	CCDS2331.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.763332	0.49574	.	.	ENSG00000013441	ENST00000321356;ENST00000434813	T;T	0.68765	-0.32;-0.35	5.5	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.69424	0.3109	M	0.75615	2.305	0.54753	D	0.999988	B;B	0.29552	0.248;0.248	B;B	0.32805	0.153;0.153	T	0.71241	-0.4651	10	0.56958	D	0.05	.	16.2495	0.82475	0.0:0.8667:0.1333:0.0	.	184;142	B4DFW7;P49759	.;CLK1_HUMAN	D	142;184	ENSP00000326830:E142D;ENSP00000394734:E184D	ENSP00000326830:E142D	E	-	3	2	CLK1	201433148	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.089000	0.71384	1.425000	0.47237	0.650000	0.86243	GAG		0.428	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2		
ALS2	57679	broad.mit.edu	37	2	202619229	202619229	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:202619229G>T	ENST00000264276.6	-	6	2009	c.1637C>A	c.(1636-1638)cCt>cAt	p.P546H		NM_020919.3	NP_065970.2	Q96Q42	ALS2_HUMAN	amyotrophic lateral sclerosis 2 (juvenile)	546					behavioral fear response (GO:0001662)|cell death (GO:0008219)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|locomotory behavior (GO:0007626)|neuromuscular junction development (GO:0007528)|neuron projection morphogenesis (GO:0048812)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Rab GTPase activity (GO:0032851)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of Ran GTPase activity (GO:0032853)|protein localization (GO:0008104)|receptor recycling (GO:0001881)|regulation of endosome size (GO:0051036)|response to oxidative stress (GO:0006979)|synaptic transmission, glutamatergic (GO:0035249)|vesicle organization (GO:0016050)	centrosome (GO:0005813)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|early endosome (GO:0005769)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|ruffle (GO:0001726)|vesicle (GO:0031982)	protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activator activity (GO:0043539)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Ran guanyl-nucleotide exchange factor activity (GO:0005087)	p.P546H(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(22)|ovary(1)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	72						CGCTTACCTAGGCAGAACATC	0.498																																					p.P546H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1637A	2						.						114.0	117.0	116.0					2																	202619229		1959	4144	6103	202327474	SO:0001583	missense	57679	exon6			AB053305	CCDS42800.1, CCDS46492.1	2q33-q35	2014-09-17	2004-06-23		ENSG00000003393	ENSG00000003393		"""Rho guanine nucleotide exchange factors"""	443	protein-coding gene	gene with protein product	"""alsin"""	606352	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 6"""	ALS2CR6		11586298	Standard	NM_020919		Approved		uc002uyo.3	Q96Q42	OTTHUMG00000154507	ENST00000264276.6:c.1637C>A	2.37:g.202619229G>T	ENSP00000264276:p.Pro546His	Somatic		Capture	Illumina HiSeq	Phase_I	202327474	NM_020919	Q53TT1|Q53TV2|Q8N1E0|Q96PC4|Q96Q41|Q9H973|Q9HCK9	Missense_Mutation	SNP	ENST00000264276.6	37	CCDS42800.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735011	0.69189	.	.	ENSG00000003393	ENST00000264276	T	0.80480	-1.38	5.92	5.03	0.67393	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.227334	0.39210	N	0.001431	D	0.83899	0.5354	N	0.25890	0.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.986;0.982	D	0.85442	0.1155	10	0.52906	T	0.07	.	16.3448	0.83120	0.0:0.0:0.867:0.133	.	546;546;546	Q96Q42-3;Q6IQ41;Q96Q42	.;.;ALS2_HUMAN	H	546	ENSP00000264276:P546H	ENSP00000264276:P546H	P	-	2	0	ALS2	202327474	1.000000	0.71417	0.894000	0.35097	0.710000	0.40934	4.775000	0.62346	1.461000	0.47929	0.655000	0.94253	CCT		0.498	ALS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335562.3	NM_020919	
BMPR2	659	broad.mit.edu	37	2	203383560	203383560	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:203383560C>T	ENST00000374580.4	+	6	1176	c.637C>T	c.(637-639)Cga>Tga	p.R213*	BMPR2_ENST00000374574.2_Nonsense_Mutation_p.R213*	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	213	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.R213*(1)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						TGGCCGAGGTCGATATGGAGC	0.343																																					p.R213X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C637T	2	GRCh37	CM041256	BMPR2	M		.						83.0	76.0	78.0					2																	203383560		2203	4300	6503	203091805	SO:0001587	stop_gained	659	exon6			Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.637C>T	2.37:g.203383560C>T	ENSP00000363708:p.Arg213*	None		Capture	Illumina HiSeq	Phase_I	203091805	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Nonsense_Mutation	SNP	ENST00000374580.4	37	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	34	5.380854	0.95945	.	.	ENSG00000204217	ENST00000374580;ENST00000374574	.	.	.	6.05	4.19	0.49359	.	0.115223	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3342	0.74238	0.2713:0.7287:0.0:0.0	.	.	.	.	X	213	.	ENSP00000363702:R213X	R	+	1	2	BMPR2	203091805	0.988000	0.35896	1.000000	0.80357	0.992000	0.81027	1.460000	0.35244	0.813000	0.34350	-0.284000	0.09977	CGA		0.343	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
FAM117B	150864	broad.mit.edu	37	2	203620336	203620336	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:203620336G>A	ENST00000392238.2	+	5	1036	c.1036G>A	c.(1036-1038)Gtg>Atg	p.V346M	FAM117B_ENST00000303116.6_Missense_Mutation_p.V102M			Q6P1L5	F117B_HUMAN	family with sequence similarity 117, member B	346								p.V102M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)	17						CCGGAATAGCGTGGAAGGATT	0.398																																					p.V346M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1036A	2						.						113.0	113.0	113.0					2																	203620336		2203	4300	6503	203328581	SO:0001583	missense	150864	exon5			AB053315	CCDS33362.1, CCDS33362.2	2q33	2008-08-18	2008-08-18	2008-08-18	ENSG00000138439	ENSG00000138439			14440	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 13"""	ALS2CR13		11586298	Standard	NM_173511		Approved	FLJ38771	uc010zhx.2	Q6P1L5	OTTHUMG00000154550	ENST00000392238.2:c.1036G>A	2.37:g.203620336G>A	ENSP00000376071:p.Val346Met	Somatic		Capture	Illumina HiSeq	Phase_I	203328581	NM_173511	Q53QZ5|Q585T9|Q8N8W1|Q96Q34	Missense_Mutation	SNP	ENST00000392238.2	37	CCDS33362.2	.	.	.	.	.	.	.	.	.	.	G	18.70	3.680634	0.68042	.	.	ENSG00000138439	ENST00000303116;ENST00000392238	.	.	.	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.64371	0.2592	L	0.48362	1.52	0.52099	D	0.999947	D	0.67145	0.996	P	0.59288	0.855	T	0.63152	-0.6701	9	0.45353	T	0.12	-2.2527	12.4211	0.55520	0.1214:0.0:0.8786:0.0	.	346	Q6P1L5	F117B_HUMAN	M	102;346	.	ENSP00000306299:V102M	V	+	1	0	FAM117B	203328581	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.613000	0.61176	2.703000	0.92315	0.655000	0.94253	GTG		0.398	FAM117B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335888.3	NM_173511	
NBEAL1	65065	broad.mit.edu	37	2	204053285	204053285	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:204053285A>G	ENST00000449802.1	+	44	7042	c.6709A>G	c.(6709-6711)Aac>Gac	p.N2237D		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2237	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.							p.N947D(1)|p.N2237D(1)		NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						AGAGGCACTCAACGTTTTCTA	0.338																																					p.N2237D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A6709G	2						.						137.0	134.0	135.0					2																	204053285		1842	4091	5933	203761530	SO:0001583	missense	65065	exon44			AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6709A>G	2.37:g.204053285A>G	ENSP00000399903:p.Asn2237Asp	Somatic		Capture	Illumina HiSeq	Phase_I	203761530	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	29.8	5.040348	0.93630	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	D;D	0.87029	-2.2;-2.2	5.85	5.85	0.93711	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.96178	0.8754	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	D	0.97734	1.0204	10	0.87932	D	0	.	15.8979	0.79350	1.0:0.0:0.0:0.0	.	2237;2226	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	D	2237;2237;252	ENSP00000399903:N2237D;ENSP00000388466:N252D	ENSP00000344985:N2237D	N	+	1	0	NBEAL1	203761530	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.229000	0.95273	2.238000	0.73509	0.477000	0.44152	AAC		0.338	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
ADAM23	8745	broad.mit.edu	37	2	207431995	207431995	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:207431995A>T	ENST00000264377.3	+	15	1771	c.1443A>T	c.(1441-1443)agA>agT	p.R481S	ADAM23_ENST00000374416.1_Missense_Mutation_p.R481S|ADAM23_ENST00000374415.3_Missense_Mutation_p.R481S	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	481	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.R481S(1)		NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		TGGAGTATAGAGACTTTTTAC	0.363																																					p.R481S	Melanoma(194;1127 2130 19620 24042 27855)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1443T	2						.						79.0	84.0	82.0					2																	207431995		2203	4300	6503	207140240	SO:0001583	missense	8745	exon15			AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.1443A>T	2.37:g.207431995A>T	ENSP00000264377:p.Arg481Ser	Somatic		Capture	Illumina HiSeq	Phase_I	207140240	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	37	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	A	13.12	2.141353	0.37825	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.62941	-0.01;-0.01;-0.01	5.94	4.77	0.60923	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.081789	0.51477	D	0.000081	T	0.46983	0.1421	L	0.31476	0.935	0.47214	D	0.999359	B	0.15473	0.013	B	0.17098	0.017	T	0.38693	-0.9649	10	0.25751	T	0.34	.	9.5351	0.39218	0.864:0.0:0.136:0.0	.	481	O75077	ADA23_HUMAN	S	481;481;375;481	ENSP00000264377:R481S;ENSP00000363537:R481S;ENSP00000363536:R481S	ENSP00000264377:R481S	R	+	3	2	ADAM23	207140240	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.984000	0.40658	2.272000	0.75746	0.459000	0.35465	AGA		0.363	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
ADAM23	8745	broad.mit.edu	37	2	207459518	207459518	+	Silent	SNP	G	G	A	rs540645451		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:207459518G>A	ENST00000264377.3	+	23	2464	c.2136G>A	c.(2134-2136)acG>acA	p.T712T	ADAM23_ENST00000374416.1_Silent_p.T712T|ADAM23_ENST00000374415.3_Silent_p.T712T	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	712					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(6)|kidney(3)|large_intestine(5)|liver(2)|lung(22)|ovary(2)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	51				LUSC - Lung squamous cell carcinoma(261;0.0961)|Lung(261;0.182)|Epithelial(149;0.205)		AAGATGGAACGCCATGTGGCC	0.428													G|||	1	0.000199681	0.0	0.0	5008	,	,		21482	0.0		0.0	False		,,,				2504	0.001				p.T712T	Melanoma(194;1127 2130 19620 24042 27855)											.	.	0			c.G2136A	2						.						223.0	210.0	214.0					2																	207459518		2203	4300	6503	207167763	SO:0001819	synonymous_variant	8745	exon23			AB009672	CCDS2369.1	2q33	2008-06-12	2005-08-18		ENSG00000114948	ENSG00000114948		"""ADAM metallopeptidase domain containing"""	202	protein-coding gene	gene with protein product		603710	"""a disintegrin and metalloproteinase domain 23"""			9693107	Standard	NM_003812		Approved	MDC3	uc002vbq.4	O75077	OTTHUMG00000132919	ENST00000264377.3:c.2136G>A	2.37:g.207459518G>A		None		Capture	Illumina HiSeq	Phase_I	207167763	NM_003812	A2RU59	Silent	SNP	ENST00000264377.3	37	CCDS2369.1																																																																																				0.428	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812	
IDH1	3417	broad.mit.edu	37	2	209108305	209108305	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:209108305T>A	ENST00000415913.1	-	6	925	c.544A>T	c.(544-546)Atg>Ttg	p.M182L	IDH1_ENST00000446179.1_Missense_Mutation_p.M182L|IDH1_ENST00000345146.2_Missense_Mutation_p.M182L	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	182					2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.M182L(1)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		TGATTATACATCCCCATGGCA	0.403			Mis		gliobastoma																																p.M182L	Pancreas(158;264 1958 3300 35450 36047)		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A544T	2						.						86.0	80.0	82.0					2																	209108305		2203	4300	6503	208816550	SO:0001583	missense	3417	exon6				CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.544A>T	2.37:g.209108305T>A	ENSP00000390265:p.Met182Leu	Somatic		Capture	Illumina HiSeq	Phase_I	208816550	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.732413	0.89482	.	.	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.76578	-1.03;-1.03;-1.03	5.52	4.34	0.51931	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.84502	0.5486	H	0.94808	3.585	0.80722	D	1	P	0.35527	0.507	B	0.38616	0.277	D	0.86045	0.1522	10	0.87932	D	0	-9.3529	12.895	0.58093	0.0:0.0:0.136:0.864	.	182	O75874	IDHC_HUMAN	L	182	ENSP00000260985:M182L;ENSP00000410513:M182L;ENSP00000390265:M182L	ENSP00000260985:M182L	M	-	1	0	IDH1	208816550	1.000000	0.71417	0.994000	0.49952	0.965000	0.64279	6.299000	0.72770	1.012000	0.39366	0.397000	0.26171	ATG		0.403	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
MYL1	4632	broad.mit.edu	37	2	211158509	211158509	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:211158509T>C	ENST00000352451.3	-	5	641	c.494A>G	c.(493-495)gAg>gGg	p.E165G	MYL1_ENST00000341685.4_Missense_Mutation_p.E121G|MYL1_ENST00000496436.1_5'UTR	NM_079420.2	NP_524144.1	P05976	MYL1_HUMAN	myosin, light chain 1, alkali; skeletal, fast	165	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				cardiac muscle contraction (GO:0060048)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|sarcomere (GO:0030017)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)	16				Epithelial(149;0.00573)|Lung(261;0.0422)|LUSC - Lung squamous cell carcinoma(261;0.0444)|all cancers(144;0.057)		CACTTCTTCCTCTTTCATCTT	0.438																																					p.E121G												.	.	0			c.A362G	2						.						213.0	194.0	200.0					2																	211158509		2203	4300	6503	210866754	SO:0001583	missense	4632	exon5				CCDS2390.1, CCDS2391.1	2q33-q34	2013-01-10	2006-09-29		ENSG00000168530	ENSG00000168530		"""Myosins / Light chain"", ""EF-hand domain containing"""	7582	protein-coding gene	gene with protein product		160780	"""myosin, light polypeptide 1, alkali; skeletal, fast"""			2304459, 3422212	Standard	NM_079422		Approved		uc002vec.3	P05976	OTTHUMG00000132992	ENST00000352451.3:c.494A>G	2.37:g.211158509T>C	ENSP00000307280:p.Glu165Gly	None		Capture	Illumina HiSeq	Phase_I	210866754	NM_079422	B2R4N6|B2R4T6|P06741|Q6IBD5	Missense_Mutation	SNP	ENST00000352451.3	37	CCDS2390.1	.	.	.	.	.	.	.	.	.	.	T	21.9	4.209909	0.79240	.	.	ENSG00000168530	ENST00000341685;ENST00000352451	D;D	0.86030	-2.06;-2.06	5.91	5.91	0.95273	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92021	0.7472	H	0.94385	3.53	0.80722	D	1	B;B	0.31581	0.329;0.295	B;B	0.41813	0.32;0.367	D	0.92439	0.5960	10	0.87932	D	0	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	165;121	P05976;P05976-2	MYL1_HUMAN;.	G	121;165	ENSP00000343321:E121G;ENSP00000307280:E165G	ENSP00000343321:E121G	E	-	2	0	MYL1	210866754	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	GAG		0.438	MYL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256566.2	NM_079420	
CPS1	1373	broad.mit.edu	37	2	211441123	211441123	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:211441123C>A	ENST00000233072.5	+	3	486	c.290C>A	c.(289-291)gCc>gAc	p.A97D	CPS1_ENST00000430249.2_Missense_Mutation_p.A103D	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	97	Anthranilate phosphoribosyltransferase homolog.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)	p.A97D(1)		breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	CTCACAATGGCCAACCCTATT	0.413																																					p.A97D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C290A	2						.						184.0	168.0	174.0					2																	211441123		2203	4300	6503	211149368	SO:0001583	missense	1373	exon3			AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.290C>A	2.37:g.211441123C>A	ENSP00000233072:p.Ala97Asp	Somatic		Capture	Illumina HiSeq	Phase_I	211149368	NM_001875	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.952425	0.53293	.	.	ENSG00000021826	ENST00000417946;ENST00000518043;ENST00000523702;ENST00000430249;ENST00000539150;ENST00000233072;ENST00000536125	D;D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38;-3.38	5.96	2.27	0.28462	Carbamoyl-phosphate synthase, small subunit, N-terminal (3);	0.162024	0.56097	D	0.000024	D	0.90721	0.7088	L	0.41492	1.28	0.80722	D	1	P;P	0.36392	0.551;0.551	B;B	0.43413	0.419;0.419	D	0.87404	0.2371	10	0.87932	D	0	-0.1181	10.0664	0.42306	0.0:0.6817:0.0:0.3183	.	107;97	Q59HF8;P31327	.;CPSM_HUMAN	D	97;97;103;103;105;97;97	ENSP00000388496:A97D;ENSP00000430697:A97D;ENSP00000430644:A103D;ENSP00000402608:A103D;ENSP00000233072:A97D	ENSP00000233072:A97D	A	+	2	0	CPS1	211149368	0.781000	0.28676	0.997000	0.53966	0.848000	0.48234	1.328000	0.33758	0.149000	0.19098	-0.808000	0.03180	GCC		0.413	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		
ERBB4	2066	broad.mit.edu	37	2	212570072	212570072	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:212570072T>A	ENST00000342788.4	-	10	1479	c.1169A>T	c.(1168-1170)aAc>aTc	p.N390I	ERBB4_ENST00000436443.1_Missense_Mutation_p.N390I|ERBB4_ENST00000402597.1_Missense_Mutation_p.N390I	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	390					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.N390I(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CCGAAAGACGTTCAGTTTCTC	0.328										TSP Lung(8;0.080)																											p.N390I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1169T	2						.						131.0	132.0	132.0					2																	212570072		2203	4300	6503	212278317	SO:0001583	missense	2066	exon10			L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.1169A>T	2.37:g.212570072T>A	ENSP00000342235:p.Asn390Ile	Somatic		Capture	Illumina HiSeq	Phase_I	212278317	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.5|20.5	4.008118|4.008118	0.75046|0.75046	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.80214|.	-1.35;-1.35;-1.35|.	5.33|5.33	4.17|4.17	0.49024|0.49024	EGF receptor, L domain (1);|.	0.040925|.	0.85682|.	D|.	0.000000|.	T|T	0.63698|0.63698	0.2533|0.2533	M|M	0.64170|0.64170	1.965|1.965	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.89917|.	1.0;0.976;0.999;1.0;1.0|.	D;P;D;D;D|.	0.97110|.	1.0;0.81;0.99;1.0;1.0|.	T|T	0.61387|0.61387	-0.7073|-0.7073	10|5	0.72032|.	D|.	0.01|.	.|.	11.079|11.079	0.48049|0.48049	0.0:0.0733:0.0:0.9267|0.0:0.0733:0.0:0.9267	.|.	390;390;249;390;390|.	Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303|.	.;.;.;.;ERBB4_HUMAN|.	I|S	390|390	ENSP00000342235:N390I;ENSP00000403204:N390I;ENSP00000385565:N390I|.	ENSP00000342235:N390I|.	N|T	-|-	2|1	0|0	ERBB4|ERBB4	212278317|212278317	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.961000|0.961000	0.63080|0.63080	5.112000|5.112000	0.64634|0.64634	0.969000|0.969000	0.38237|0.38237	0.477000|0.477000	0.44152|0.44152	AAC|ACG		0.328	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
MARCH4	57574	broad.mit.edu	37	2	217142429	217142429	+	Silent	SNP	G	G	A	rs138565372		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:217142429G>A	ENST00000273067.4	-	3	2597	c.831C>T	c.(829-831)taC>taT	p.Y277Y		NM_020814.2	NP_065865.1	Q9P2E8	MARH4_HUMAN	membrane-associated ring finger (C3HC4) 4, E3 ubiquitin protein ligase	277						Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.Y277Y(1)		breast(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(1)	20		Renal(323;0.0854)		Epithelial(149;2.19e-05)|all cancers(144;0.00121)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(261;0.0125)		CATACATCCCGTAGCAGATCT	0.557																																					p.Y277Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C831T	2						.						207.0	174.0	185.0					2																	217142429		2203	4300	6503	216850674	SO:0001819	synonymous_variant	57574	exon3			AB037820	CCDS33376.1	2q35	2013-01-09	2012-02-23		ENSG00000144583	ENSG00000144583		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	29269	protein-coding gene	gene with protein product		608208	"""membrane-associated ring finger (C3HC4) 4"""			10718198, 14722266	Standard	NM_020814		Approved	KIAA1399, MARCH-IV, RNF174	uc002vgb.3	Q9P2E8	OTTHUMG00000154824	ENST00000273067.4:c.831C>T	2.37:g.217142429G>A		Somatic		Capture	Illumina HiSeq	Phase_I	216850674	NM_020814	Q4KMN7|Q86WR8	Silent	SNP	ENST00000273067.4	37	CCDS33376.1																																																																																				0.557	MARCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337272.2	NM_020814	
STK11IP	114790	broad.mit.edu	37	2	220466108	220466108	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:220466108T>C	ENST00000456909.1	+	3	303	c.213T>C	c.(211-213)gtT>gtC	p.V71V	STK11IP_ENST00000459692.1_3'UTR|STK11IP_ENST00000295641.10_Silent_p.V82V			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	82					protein localization (GO:0008104)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)	protein kinase binding (GO:0019901)	p.V71V(1)|p.V82V(1)		breast(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|urinary_tract(1)	23		Renal(207;0.0183)		Epithelial(149;2.69e-07)|all cancers(144;5.91e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ACTCCCCTGTTATTCTTCAGC	0.557																																					p.V82V												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T246C	2						.						63.0	66.0	65.0					2																	220466108		2072	4216	6288	220174352	SO:0001819	synonymous_variant	114790	exon3			AF450267	CCDS46521.1	2q35	2008-06-03			ENSG00000144589	ENSG00000144589			19184	protein-coding gene	gene with protein product	"""LKB1 interacting protein"""	607172				11741830	Standard	NM_052902		Approved	LIP1, KIAA1898, LKB1IP, STK11IP1	uc002vml.3	Q8N1F8	OTTHUMG00000059239	ENST00000456909.1:c.213T>C	2.37:g.220466108T>C		Somatic		Capture	Illumina HiSeq	Phase_I	220174352	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	37																																																																																					0.557	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902	
FARSB	10056	broad.mit.edu	37	2	223505628	223505628	+	Missense_Mutation	SNP	G	G	A	rs141167193		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:223505628G>A	ENST00000281828.6	-	4	555	c.292C>T	c.(292-294)Cgg>Tgg	p.R98W	FARSB_ENST00000536361.1_De_novo_Start_OutOfFrame	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	98					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)	p.R98W(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GGCATTACCCGTTTATACACT	0.249													G|||	1	0.000199681	0.0	0.0	5008	,	,		15209	0.0		0.001	False		,,,				2504	0.0				p.R98W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C292T	2						.	G	TRP/ARG	1,4399	2.1+/-5.4	0,1,2199	35.0	37.0	36.0		292	3.7	1.0	2	dbSNP_134	36	7,8585	5.0+/-18.6	0,7,4289	yes	missense	FARSB	NM_005687.3	101	0,8,6488	AA,AG,GG		0.0815,0.0227,0.0616	possibly-damaging	98/590	223505628	8,12984	2200	4296	6496	223213872	SO:0001583	missense	10056	exon4			AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	17800	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, beta, cytoplasmic"""	609690	"""phenylalanyl-tRNA synthetase-like, beta subunit"""	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.292C>T	2.37:g.223505628G>A	ENSP00000281828:p.Arg98Trp	Somatic		Capture	Illumina HiSeq	Phase_I	223213872	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	De_novo_Start_OutOfFrame	SNP	ENST00000281828.6	37	CCDS2454.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.70	2.612957	0.46631	2.27E-4	8.15E-4	ENSG00000116120	ENST00000281828	.	.	.	5.61	3.71	0.42584	.	0.104568	0.64402	D	0.000007	T	0.47040	0.1424	M	0.64997	1.995	0.80722	D	1	P;D	0.53745	0.956;0.962	B;B	0.38428	0.273;0.273	T	0.55412	-0.8145	9	0.52906	T	0.07	-4.3997	13.0634	0.59020	0.0:0.0:0.5418:0.4582	.	98;98	A8K666;Q9NSD9	.;SYFB_HUMAN	W	98	.	ENSP00000281828:R98W	R	-	1	2	FARSB	223213872	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.521000	0.45563	1.361000	0.45981	0.555000	0.69702	CGG		0.249	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687	
FARSB	10056	broad.mit.edu	37	2	223520749	223520749	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:223520749A>G	ENST00000281828.6	-	1	307	c.44T>C	c.(43-45)cTg>cCg	p.L15P	FARSB_ENST00000536361.1_5'UTR	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	15					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|RNA binding (GO:0003723)	p.L15P(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	24		Renal(207;0.0183)		Epithelial(121;3.47e-10)|all cancers(144;1.86e-07)|LUSC - Lung squamous cell carcinoma(224;0.00871)|Lung(261;0.011)	L-Phenylalanine(DB00120)	GGTGCGGCCCAGGGCTTGGAA	0.627																																					p.L15P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T44C	2						.						47.0	35.0	39.0					2																	223520749		2203	4300	6503	223228993	SO:0001583	missense	10056	exon1			AF042346	CCDS2454.1	2q36.2	2011-07-01	2007-02-23	2007-02-23	ENSG00000116120	ENSG00000116120	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	17800	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 1, beta, cytoplasmic"""	609690	"""phenylalanyl-tRNA synthetase-like, beta subunit"""	FARSLB		10049785	Standard	NM_005687		Approved	PheHB, FRSB	uc002vne.1	Q9NSD9	OTTHUMG00000133155	ENST00000281828.6:c.44T>C	2.37:g.223520749A>G	ENSP00000281828:p.Leu15Pro	Somatic		Capture	Illumina HiSeq	Phase_I	223228993	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Missense_Mutation	SNP	ENST00000281828.6	37	CCDS2454.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204003	0.79127	.	.	ENSG00000116120	ENST00000281828	.	.	.	5.79	5.79	0.91817	DNA binding domain, putative (1);	0.136010	0.50627	D	0.000106	D	0.84692	0.5528	M	0.93898	3.47	0.80722	D	1	D;D	0.69078	0.997;0.978	D;D	0.65443	0.935;0.935	D	0.88356	0.2984	9	0.87932	D	0	-7.3197	12.5221	0.56065	1.0:0.0:0.0:0.0	.	15;15	A8K666;Q9NSD9	.;SYFB_HUMAN	P	15	.	ENSP00000281828:L15P	L	-	2	0	FARSB	223228993	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.661000	0.68025	2.218000	0.71995	0.533000	0.62120	CTG		0.627	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687	
IRS1	3667	broad.mit.edu	37	2	227662972	227662972	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:227662972T>G	ENST00000305123.5	-	1	1503	c.483A>C	c.(481-483)aaA>aaC	p.K161N	RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	161	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid catabolic process (GO:0016042)|mammary gland development (GO:0030879)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|protein kinase B signaling (GO:0043491)|protein localization to nucleus (GO:0034504)|regulation of gene expression (GO:0010468)|response to insulin (GO:0032868)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)	caveola (GO:0005901)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|insulin receptor complex (GO:0005899)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein kinase C binding (GO:0005080)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.K161N(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(10)|lung(33)|ovary(6)|pancreas(1)|prostate(1)|urinary_tract(2)	69		Renal(207;0.023)|all_lung(227;0.0994)|all_hematologic(139;0.118)|Esophageal squamous(248;0.23)		Epithelial(121;3.03e-11)|all cancers(144;2.42e-08)|Lung(261;0.00712)|LUSC - Lung squamous cell carcinoma(224;0.0137)		GCCAGACCTCTTTGAATGCGG	0.622											OREG0015248	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K161N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A483C	2						.						52.0	52.0	52.0					2																	227662972		2203	4300	6503	227371216	SO:0001583	missense	3667	exon1				CCDS2463.1	2q36	2013-01-10			ENSG00000169047	ENSG00000169047		"""Pleckstrin homology (PH) domain containing"""	6125	protein-coding gene	gene with protein product		147545				1648180	Standard	NM_005544		Approved	HIRS-1	uc002voh.4	P35568	OTTHUMG00000133179	ENST00000305123.5:c.483A>C	2.37:g.227662972T>G	ENSP00000304895:p.Lys161Asn	Somatic	2321	Capture	Illumina HiSeq	Phase_I	227371216	NM_005544		Missense_Mutation	SNP	ENST00000305123.5	37	CCDS2463.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.049217	0.55110	.	.	ENSG00000169047	ENST00000305123	T	0.42513	0.97	5.79	1.6	0.23607	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.000000	0.64402	D	0.000001	T	0.57917	0.2086	M	0.70595	2.14	0.44728	D	0.997724	D	0.89917	1.0	D	0.81914	0.995	T	0.56823	-0.7915	10	0.72032	D	0.01	-34.2072	8.8161	0.34996	0.0:0.475:0.0:0.525	.	161	P35568	IRS1_HUMAN	N	161	ENSP00000304895:K161N	ENSP00000304895:K161N	K	-	3	2	IRS1	227371216	0.998000	0.40836	1.000000	0.80357	0.911000	0.54048	0.838000	0.27572	0.249000	0.21456	0.459000	0.35465	AAA		0.622	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544	
COL4A4	1286	broad.mit.edu	37	2	227979359	227979359	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:227979359G>T	ENST00000396625.3	-	8	750	c.543C>A	c.(541-543)gcC>gcA	p.A181A	COL4A4_ENST00000329662.7_Silent_p.A181A	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	181	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)	p.A181A(1)		breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TACCTTTAACGGCACCTAAAA	0.348																																					p.A181A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C543A	2						.						124.0	113.0	116.0					2																	227979359		1815	4074	5889	227687603	SO:0001819	synonymous_variant	1286	exon8				CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.543C>A	2.37:g.227979359G>T		Somatic		Capture	Illumina HiSeq	Phase_I	227687603	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																				0.348	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
SLC19A3	80704	broad.mit.edu	37	2	228552263	228552263	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:228552263T>A	ENST00000258403.3	-	6	1412	c.1341A>T	c.(1339-1341)gcA>gcT	p.A447A	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Silent_p.A443A	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	447					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)	p.A447A(1)		breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	CAGCAATTACTGCAAAATAGC	0.353																																					p.A447A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1341T	2						.						96.0	96.0	96.0					2																	228552263		2203	4300	6503	228260507	SO:0001819	synonymous_variant	80704	exon6			AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.1341A>T	2.37:g.228552263T>A		Somatic		Capture	Illumina HiSeq	Phase_I	228260507	NM_025243		Silent	SNP	ENST00000258403.3	37	CCDS2468.1																																																																																				0.353	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
B3GNT7	93010	broad.mit.edu	37	2	232262452	232262452	+	Missense_Mutation	SNP	G	G	A	rs367701147		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:232262452G>A	ENST00000287590.5	+	2	283	c.22G>A	c.(22-24)Gtc>Atc	p.V8I	B3GNT7_ENST00000479618.1_3'UTR|AC017104.6_ENST00000415129.1_RNA	NM_145236.2	NP_660279.1	Q8NFL0	B3GN7_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7	8					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)	p.V8I(1)		endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(1)	17		Renal(207;0.025)|all_hematologic(139;0.094)|Acute lymphoblastic leukemia(138;0.164)|Medulloblastoma(418;0.232)		Epithelial(121;3.22e-11)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0139)		GAAGAAAACCGTCTACCGGAG	0.647																																					p.V8I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G22A	2						.	G	ILE/VAL	0,4208		0,0,2104	39.0	49.0	46.0		22	-8.0	0.0	2		46	1,8453		0,1,4226	no	missense	B3GNT7	NM_145236.2	29	0,1,6330	AA,AG,GG		0.0118,0.0,0.0079	benign	8/402	232262452	1,12661	2104	4227	6331	231970696	SO:0001583	missense	93010	exon2			AK000770	CCDS46540.1	2q36.1	2013-02-21			ENSG00000156966	ENSG00000156966		"""Beta 3-glycosyltransferases"""	18811	protein-coding gene	gene with protein product		615313				12061784	Standard	NM_145236		Approved	beta3GnT7	uc002vrs.3	Q8NFL0	OTTHUMG00000153880	ENST00000287590.5:c.22G>A	2.37:g.232262452G>A	ENSP00000287590:p.Val8Ile	Somatic		Capture	Illumina HiSeq	Phase_I	231970696	NM_145236	B3KWY4|B7WNP0	Missense_Mutation	SNP	ENST00000287590.5	37	CCDS46540.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-2.005437	0.00426	0.0	1.18E-4	ENSG00000156966	ENST00000287590	T	0.32988	1.43	5.82	-8.0	0.01126	.	4.088830	0.00166	N	0.000003	T	0.12902	0.0313	N	0.17474	0.49	0.09310	N	0.999999	B	0.09022	0.002	B	0.04013	0.001	T	0.32079	-0.9920	10	0.02654	T	1	.	5.1334	0.14922	0.4899:0.3232:0.1036:0.0832	.	8	Q8NFL0	B3GN7_HUMAN	I	8	ENSP00000287590:V8I	ENSP00000287590:V8I	V	+	1	0	B3GNT7	231970696	0.010000	0.17322	0.004000	0.12327	0.029000	0.11900	0.054000	0.14205	-1.557000	0.01692	-1.779000	0.00650	GTC		0.647	B3GNT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332827.1	NM_145236	
DIS3L2	129563	broad.mit.edu	37	2	232952410	232952410	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:232952410T>C	ENST00000409307.1	+	5	580	c.580T>C	c.(580-582)Tca>Cca	p.S194P	DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000273009.6_Missense_Mutation_p.S194P|DIS3L2_ENST00000360410.4_Missense_Mutation_p.S194P|DIS3L2_ENST00000409401.3_Missense_Mutation_p.S194P|DIS3L2_ENST00000325385.7_Missense_Mutation_p.S194P					DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		TAAGAAACTCTCAGTTTGTGT	0.403																																					p.S194P												.	.	0			c.T580C	2						.						60.0	61.0	60.0					2																	232952410		1971	4167	6138	232660654	SO:0001583	missense	129563	exon6			BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409307.1:c.580T>C	2.37:g.232952410T>C	ENSP00000386799:p.Ser194Pro	None		Capture	Illumina HiSeq	Phase_I	232660654	NM_152383		Missense_Mutation	SNP	ENST00000409307.1	37	CCDS42834.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.945309	0.73672	.	.	ENSG00000144535	ENST00000273009;ENST00000542873;ENST00000325385;ENST00000360410;ENST00000409401;ENST00000431466;ENST00000409307	T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78	4.92	4.92	0.64577	.	0.567917	0.17217	N	0.182495	T	0.57755	0.2075	L	0.44542	1.39	0.37156	D	0.902377	B;D	0.76494	0.004;0.999	B;D	0.64776	0.007;0.929	T	0.58880	-0.7558	10	0.32370	T	0.25	-9.4123	13.844	0.63457	0.0:0.0:0.0:1.0	.	194;194	Q8IYB7;Q8IYB7-4	DI3L2_HUMAN;.	P	194	ENSP00000273009:S194P;ENSP00000315569:S194P;ENSP00000353584:S194P;ENSP00000386594:S194P;ENSP00000386799:S194P	ENSP00000273009:S194P	S	+	1	0	DIS3L2	232660654	0.954000	0.32549	0.832000	0.32986	0.819000	0.46315	1.175000	0.31944	2.161000	0.67846	0.533000	0.62120	TCA		0.403	DIS3L2-015	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330988.1	NM_152383	
GIGYF2	26058	broad.mit.edu	37	2	233697779	233697779	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:233697779G>A	ENST00000409547.1	+	24	3053	c.2742G>A	c.(2740-2742)caG>caA	p.Q914Q	GIGYF2_ENST00000373566.3_Silent_p.Q936Q|GIGYF2_ENST00000409480.1_Silent_p.Q936Q|GIGYF2_ENST00000409451.3_Silent_p.Q935Q|GIGYF2_ENST00000409196.3_Silent_p.Q908Q|GIGYF2_ENST00000452341.2_Silent_p.Q745Q|GIGYF2_ENST00000373563.4_Silent_p.Q914Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	914	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.Q914Q(2)		NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		agcagcagcagcaacaacagc	0.547																																					p.Q908Q												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2724A	2						.						7.0	9.0	8.0					2																	233697779		2147	4200	6347	233406023	SO:0001819	synonymous_variant	26058	exon21			U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.2742G>A	2.37:g.233697779G>A		Somatic		Capture	Illumina HiSeq	Phase_I	233406023	NM_001103148	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Silent	SNP	ENST00000409547.1	37	CCDS33401.1																																																																																				0.547	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
INPP5D	3635	broad.mit.edu	37	2	234072469	234072469	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:234072469G>A	ENST00000359570.5	+	14	1321	c.1321G>A	c.(1321-1323)Gag>Aag	p.E441K	INPP5D_ENST00000455936.2_Missense_Mutation_p.E205K|INPP5D_ENST00000450745.1_Missense_Mutation_p.E205K|INPP5D_ENST00000538935.1_Missense_Mutation_p.E440K			Q92835	SHIP1_HUMAN	inositol polyphosphate-5-phosphatase, 145kDa	453					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|determination of adult lifespan (GO:0008340)|immunoglobulin mediated immune response (GO:0016064)|inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of bone resorption (GO:0045779)|negative regulation of immune response (GO:0050777)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of neutrophil differentiation (GO:0045659)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of signal transduction (GO:0009968)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of erythrocyte differentiation (GO:0045648)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	cytosol (GO:0005829)|membrane (GO:0016020)	inositol-polyphosphate 5-phosphatase activity (GO:0004445)|phosphatidylinositol trisphosphate phosphatase activity (GO:0034594)	p.E453K(1)		central_nervous_system(1)|ovary(1)	2		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0273)|Acute lymphoblastic leukemia(138;0.0328)|Lung NSC(271;0.0843)		Epithelial(121;1.16e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000479)|LUSC - Lung squamous cell carcinoma(224;0.00655)|Lung(119;0.00802)|GBM - Glioblastoma multiforme(43;0.0185)		CGGCACCCAAGAGGACCCCCT	0.547																																					p.K294K	NSCLC(82;1215 1426 16163 20348 41018)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G882A	2						.						98.0	101.0	100.0					2																	234072469		2017	4176	6193	233736541	SO:0001583	missense	3635	exon7			U57650	CCDS74672.1	2q37.1	2013-02-14	2002-08-29		ENSG00000168918	ENSG00000168918		"""SH2 domain containing"""	6079	protein-coding gene	gene with protein product		601582	"""inositol polyphosphate-5-phosphatase, 145kD"""			8643691, 8874179	Standard	NM_001017915		Approved	SHIP, hp51CN	uc010zmp.2	Q92835	OTTHUMG00000133688	ENST00000359570.5:c.1321G>A	2.37:g.234072469G>A	ENSP00000352575:p.Glu441Lys	Somatic		Capture	Illumina HiSeq	Phase_I	233736541	NM_005541	O00145|Q13544|Q13545|Q6P5A4|Q92656|Q9UE80	Missense_Mutation	SNP	ENST00000359570.5	37		.	.	.	.	.	.	.	.	.	.	G	35	5.431845	0.96150	.	.	ENSG00000168918	ENST00000359570;ENST00000538935;ENST00000450745;ENST00000455936;ENST00000435188;ENST00000415617;ENST00000445964	D;D;D;D;D;D;D	0.99760	-6.66;-6.66;-6.66;-6.66;-6.66;-6.66;-6.66	5.08	5.08	0.68730	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	D	0.99680	0.9880	.	.	.	0.58432	D	0.999999	D;D	0.63046	0.992;0.983	P;P	0.58820	0.837;0.846	D	0.97729	1.0201	9	0.87932	D	0	.	18.6649	0.91486	0.0:0.0:1.0:0.0	.	452;453	Q92835-2;Q92835	.;SHIP1_HUMAN	K	441;440;205;205;74;74;74	ENSP00000352575:E441K;ENSP00000441010:E440K;ENSP00000407916:E205K;ENSP00000404610:E205K;ENSP00000400151:E74K;ENSP00000397421:E74K;ENSP00000405338:E74K	ENSP00000352575:E441K	E	+	1	0	INPP5D	233736541	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.203000	0.95033	2.652000	0.90054	0.655000	0.94253	GAG		0.547	INPP5D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001017915	
UGT1A1	54658	broad.mit.edu	37	2	234669123	234669123	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:234669123G>A	ENST00000608383.1	+	1	190	c.190G>A	c.(190-192)Gcc>Acc	p.A64T	UGT1A6_ENST00000305139.6_Intron|UGT1A6_ENST00000373424.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A3_ENST00000482026.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A1_ENST00000360418.3_Missense_Mutation_p.A64T|UGT1A10_ENST00000373445.1_Intron|UGT1A8_ENST00000305208.5_Missense_Mutation_p.A64T|UGT1A5_ENST00000373414.3_Intron			P22309	UD11_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A1	64					acute-phase response (GO:0006953)|bilirubin conjugation (GO:0006789)|biphenyl catabolic process (GO:0070980)|cellular glucuronidation (GO:0052695)|cellular response to ethanol (GO:0071361)|cellular response to glucocorticoid stimulus (GO:0071385)|digestion (GO:0007586)|drug metabolic process (GO:0017144)|estrogen metabolic process (GO:0008210)|flavone metabolic process (GO:0051552)|flavonoid glucuronidation (GO:0052696)|heme catabolic process (GO:0042167)|heterocycle metabolic process (GO:0046483)|liver development (GO:0001889)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cellular glucuronidation (GO:2001030)|negative regulation of steroid metabolic process (GO:0045939)|organ regeneration (GO:0031100)|porphyrin-containing compound metabolic process (GO:0006778)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|retinoic acid metabolic process (GO:0042573)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic glucuronidation (GO:0052697)|xenobiotic metabolic process (GO:0006805)	cytochrome complex (GO:0070069)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|steroid binding (GO:0005496)	p.A64T(1)		breast(1)|central_nervous_system(2)|endometrium(7)|large_intestine(5)|lung(9)|skin(4)|urinary_tract(2)	30		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;4.1e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000435)|Lung(119;0.00211)|LUSC - Lung squamous cell carcinoma(224;0.0054)	Abacavir(DB01048)|Acetaminophen(DB00316)|Adenine(DB00173)|Atorvastatin(DB01076)|Axitinib(DB06626)|Diclofenac(DB00586)|Dolutegravir(DB08930)|Eltrombopag(DB06210)|Erlotinib(DB00530)|Estradiol(DB00783)|Etoposide(DB00773)|Ezetimibe(DB00973)|Ezogabine(DB04953)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indacaterol(DB05039)|Indomethacin(DB00328)|Irinotecan(DB00762)|Losartan(DB00678)|Lovastatin(DB00227)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naltrexone(DB00704)|Naproxen(DB00788)|Nilotinib(DB04868)|Pazopanib(DB06589)|Propofol(DB00818)|Raltegravir(DB06817)|Regorafenib(DB08896)|Rifampicin(DB01045)|Simvastatin(DB00641)|Sorafenib(DB00398)|Suprofen(DB00870)|Testosterone Propionate(DB01420)	AGCACCTGACGCCTCGTTGTA	0.527																																					p.A64T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G190A	2						.						169.0	141.0	150.0					2																	234669123		2203	4300	6503	234333862	SO:0001583	missense	54658	exon1			M57899	CCDS2510.1	2q37.1	2014-09-17	2005-07-20		ENSG00000242366	ENSG00000242366	2.4.1.17	"""UDP glucuronosyltransferases"""	12530	other	complex locus constituent		191740	"""UDP glycosyltransferase 1 family, polypeptide A1"""	UGT1, GNT1		9295054, 9535849	Standard	NM_000463		Approved	UGT1A		P22309	OTTHUMG00000059117	ENST00000608383.1:c.190G>A	2.37:g.234669123G>A	ENSP00000476741:p.Ala64Thr	Somatic		Capture	Illumina HiSeq	Phase_I	234333862	NM_000463	A6NJC3|B8K286	Missense_Mutation	SNP	ENST00000608383.1	37	CCDS2510.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.367108	0.24771	.	.	ENSG00000241635	ENST00000305208;ENST00000360418	T;T	0.63096	-0.02;-0.02	6.07	4.22	0.49857	.	.	.	.	.	T	0.56834	0.2012	L	0.39326	1.205	0.09310	N	1	P;B	0.43094	0.799;0.381	P;B	0.45428	0.48;0.044	T	0.43669	-0.9377	9	0.37606	T	0.19	.	9.3752	0.38278	0.1272:0.0:0.7473:0.1255	.	64;64	A6NJC3;P22309	.;UD11_HUMAN	T	64	ENSP00000304845:A64T;ENSP00000353593:A64T	ENSP00000304845:A64T	A	+	1	0	UGT1A1	234333862	0.000000	0.05858	0.003000	0.11579	0.150000	0.21749	0.198000	0.17217	0.834000	0.34852	0.650000	0.86243	GCC		0.527	UGT1A1-203	KNOWN	basic|CCDS	protein_coding	protein_coding			
UBXN2A	165324	broad.mit.edu	37	2	24199878	24199878	+	Missense_Mutation	SNP	G	G	A	rs13386425	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:24199878G>A	ENST00000309033.4	+	4	464	c.220G>A	c.(220-222)Gtc>Atc	p.V74I	UBXN2A_ENST00000446425.2_3'UTR|UBXN2A_ENST00000535786.1_Missense_Mutation_p.V74I|UBXN2A_ENST00000404924.1_Missense_Mutation_p.V74I	NM_181713.3	NP_859064.2	P68543	UBX2A_HUMAN	UBX domain protein 2A	74	SEP. {ECO:0000255|PROSITE- ProRule:PRU00732}.				regulation of gene expression (GO:0010468)|regulation of protein catabolic process (GO:0042176)|regulation of protein ubiquitination (GO:0031396)	cis-Golgi network (GO:0005801)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)		p.V74I(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(6)	11						CGGATTCACCGTCAACGACGA	0.398													G|||	2	0.000399361	0.0	0.0	5008	,	,		15616	0.0		0.0	False		,,,				2504	0.002				p.V74I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G220A	2						.						81.0	79.0	80.0					2																	24199878		2203	4300	6503	24053382	SO:0001583	missense	165324	exon4			BC037901	CCDS1704.1	2p24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000173960	ENSG00000173960		"""UBX domain containing"""	27265	protein-coding gene	gene with protein product			"""UBX domain containing 4"""	UBXD4		12477932	Standard	NM_181713		Approved		uc002ren.3	P68543	OTTHUMG00000125497	ENST00000309033.4:c.220G>A	2.37:g.24199878G>A	ENSP00000312107:p.Val74Ile	Somatic		Capture	Illumina HiSeq	Phase_I	24053382	NM_181713	A8K577|B7ZKP8|Q569G8	Missense_Mutation	SNP	ENST00000309033.4	37	CCDS1704.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466836	0.43839	.	.	ENSG00000173960	ENST00000404924;ENST00000309033;ENST00000535786	T;T;T	0.55234	0.68;0.68;0.53	4.81	3.94	0.45596	SEP domain (4);	0.123988	0.53938	D	0.000043	T	0.48447	0.1500	L	0.39147	1.195	0.35115	D	0.766487	D;D	0.63046	0.992;0.986	P;P	0.51135	0.636;0.66	T	0.55921	-0.8064	10	0.23891	T	0.37	2.5641	9.1992	0.37246	0.174:0.0:0.826:0.0	rs13386425;rs13386425	74;74	B7ZKP8;P68543	.;UBX2A_HUMAN	I	74	ENSP00000385525:V74I;ENSP00000312107:V74I;ENSP00000440533:V74I	ENSP00000312107:V74I	V	+	1	0	UBXN2A	24053382	1.000000	0.71417	0.942000	0.38095	0.428000	0.31595	4.855000	0.62925	1.348000	0.45733	0.561000	0.74099	GTC		0.398	UBXN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246824.2	NM_181713	
ILKAP	80895	broad.mit.edu	37	2	239079587	239079587	+	Silent	SNP	G	G	A	rs372551657	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:239079587G>A	ENST00000254654.3	-	11	1210	c.1035C>T	c.(1033-1035)ctC>ctT	p.L345L		NM_030768.2	NP_110395.1	Q9H0C8	ILKAP_HUMAN	integrin-linked kinase-associated serine/threonine phosphatase	345	PP2C-like.				protein dephosphorylation (GO:0006470)|regulation of nuclear cell cycle DNA replication (GO:0033262)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)	p.L345L(1)		endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_lung(227;0.152)|all_hematologic(139;0.158)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;5.49e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.93e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.82e-08)|BRCA - Breast invasive adenocarcinoma(100;0.00012)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0163)		TTCTCACCTCGAGACAGGACA	0.478													G|||	2	0.000399361	0.0015	0.0	5008	,	,		14587	0.0		0.0	False		,,,				2504	0.0				p.L345L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1035T	2						.	G		1,4405	2.1+/-5.4	0,1,2202	132.0	148.0	142.0		1035	-11.3	0.0	2		142	0,8600		0,0,4300	no	coding-synonymous	ILKAP	NM_030768.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		345/393	239079587	1,13005	2203	4300	6503	238744326	SO:0001819	synonymous_variant	80895	exon11			AY024365	CCDS2526.1	2q37.3	2012-04-17	2010-10-25		ENSG00000132323	ENSG00000132323	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	15566	protein-coding gene	gene with protein product			"""integrin-linked kinase-associated serine/threonine phosphatase 2C"""				Standard	NM_030768		Approved	DKFZP434J2031, FLJ10181	uc002vxv.3	Q9H0C8	OTTHUMG00000133334	ENST00000254654.3:c.1035C>T	2.37:g.239079587G>A		Somatic		Capture	Illumina HiSeq	Phase_I	238744326	NM_030768	B3KM39	Silent	SNP	ENST00000254654.3	37	CCDS2526.1																																																																																				0.478	ILKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257163.2	NM_030768	
NCOA1	8648	broad.mit.edu	37	2	24951187	24951187	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:24951187A>G	ENST00000406961.1	+	16	3380	c.2728A>G	c.(2728-2730)Agc>Ggc	p.S910G	NCOA1_ENST00000395856.3_Missense_Mutation_p.S910G|NCOA1_ENST00000288599.5_Missense_Mutation_p.S910G|NCOA1_ENST00000348332.3_Missense_Mutation_p.S910G|NCOA1_ENST00000405141.1_Missense_Mutation_p.S910G|NCOA1_ENST00000407230.1_Missense_Mutation_p.S759G|NCOA1_ENST00000538539.1_Missense_Mutation_p.S910G			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	910	Interaction with CREBBP.				androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)	p.S910G(2)	PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCAGTGTATTAGCTCACAATT	0.368			T	PAX3	alveolar rhadomyosarcoma																																p.S910G			Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A2728G	2						.						68.0	63.0	64.0					2																	24951187		2203	4300	6503	24804691	SO:0001583	missense	8648	exon14			U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.2728A>G	2.37:g.24951187A>G	ENSP00000385216:p.Ser910Gly	Somatic		Capture	Illumina HiSeq	Phase_I	24804691	NM_003743	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	.	.	.	.	.	.	.	.	.	.	A	9.428	1.084884	0.20309	.	.	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.01804	4.76;4.77;4.63;4.77;4.76;4.77;4.76	5.62	4.47	0.54385	.	0.284672	0.40908	D	0.000988	T	0.00666	0.0022	N	0.00483	-1.445	0.29292	N	0.869315	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.43376	-0.9395	10	0.13853	T	0.58	.	9.7032	0.40200	0.9207:0.0:0.0793:0.0	.	910;910;910;759	Q15788-3;Q15788;Q15788-2;B5MCN7	.;NCOA1_HUMAN;.;.	G	910;910;759;910;910;910;910	ENSP00000385216:S910G;ENSP00000385097:S910G;ENSP00000385195:S759G;ENSP00000444039:S910G;ENSP00000320940:S910G;ENSP00000288599:S910G;ENSP00000379197:S910G	ENSP00000288599:S910G	S	+	1	0	NCOA1	24804691	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.165000	0.58196	2.268000	0.75426	0.533000	0.62120	AGC		0.368	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
OTOF	9381	broad.mit.edu	37	2	26686955	26686955	+	Silent	SNP	G	G	A	rs149549554	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:26686955G>A	ENST00000272371.2	-	40	5106	c.4980C>T	c.(4978-4980)gaC>gaT	p.D1660D	OTOF_ENST00000402415.3_Silent_p.D970D|OTOF_ENST00000403946.3_Silent_p.D1660D|OTOF_ENST00000339598.3_Silent_p.D893D|OTOF_ENST00000338581.6_Silent_p.D893D	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1660					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)	p.D893D(1)|p.D1660D(1)		NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCACATGCTCGTCTGTGGGCT	0.647													G|||	5	0.000998403	0.003	0.0	5008	,	,		19362	0.0		0.0	False		,,,				2504	0.001				p.D893D	GBM(102;732 1451 20652 24062 31372)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2679T	2						.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	56.0	59.0	58.0		2679,4980,2910,2679	-8.8	0.1	2	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	,,,	893/1231,1660/1998,970/1308,893/1231	26686955	26,12980	2203	4300	6503	26540459	SO:0001819	synonymous_variant	9381	exon23			AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.4980C>T	2.37:g.26686955G>A		Somatic		Capture	Illumina HiSeq	Phase_I	26540459	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																				0.647	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
IFT172	26160	broad.mit.edu	37	2	27683894	27683894	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:27683894C>T	ENST00000260570.3	-	23	2612	c.2509G>A	c.(2509-2511)Gca>Aca	p.A837T		NM_015662.1	NP_056477.1	Q9UG01	IF172_HUMAN	intraflagellar transport 172	837					bone development (GO:0060348)|brain development (GO:0007420)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|epidermis development (GO:0008544)|heart looping (GO:0001947)|hindgut development (GO:0061525)|left/right axis specification (GO:0070986)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|neural tube closure (GO:0001843)|Notch signaling pathway (GO:0007219)|palate development (GO:0060021)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|smoothened signaling pathway (GO:0007224)|spinal cord motor neuron differentiation (GO:0021522)	axoneme (GO:0005930)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)|vesicle (GO:0031982)		p.A837T(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(17)|lung(17)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	43	Acute lymphoblastic leukemia(172;0.155)					TTCATGAATGCGTTGCCTTTA	0.493																																					p.A837T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2509A	2						.						207.0	168.0	181.0					2																	27683894		2203	4300	6503	27537398	SO:0001583	missense	26160	exon23			AB033005	CCDS1755.1	2p23.3	2014-07-03	2014-07-03		ENSG00000138002	ENSG00000138002		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	30391	protein-coding gene	gene with protein product	"""wimple homolog"""	607386	"""intraflagellar transport 172 homolog (Chlamydomonas)"""			10788441, 10574461, 24140113	Standard	XM_005264254		Approved	SLB, wim, osm-1, NPHP17	uc002rku.3	Q9UG01	OTTHUMG00000128425	ENST00000260570.3:c.2509G>A	2.37:g.27683894C>T	ENSP00000260570:p.Ala837Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27537398	NM_015662	A5PKZ0|B2RNU5|Q86X44|Q96HW4|Q9UFJ9|Q9ULP1	Missense_Mutation	SNP	ENST00000260570.3	37	CCDS1755.1	.	.	.	.	.	.	.	.	.	.	C	33	5.208191	0.95033	.	.	ENSG00000138002	ENST00000260570	T	0.71341	-0.56	5.99	5.99	0.97316	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.81894	0.4919	M	0.78049	2.395	0.80722	D	1	D	0.64830	0.994	P	0.55545	0.778	T	0.82043	-0.0653	10	0.51188	T	0.08	-12.8806	19.0212	0.92916	0.0:1.0:0.0:0.0	.	837	Q9UG01	IF172_HUMAN	T	837	ENSP00000260570:A837T	ENSP00000260570:A837T	A	-	1	0	IFT172	27537398	0.972000	0.33761	0.951000	0.38953	0.873000	0.50193	2.376000	0.44292	2.843000	0.97960	0.591000	0.81541	GCA		0.493	IFT172-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250213.2	NM_015662	
ALK	238	broad.mit.edu	37	2	29462663	29462663	+	Silent	SNP	G	G	A	rs142109683	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:29462663G>A	ENST00000389048.3	-	13	3144	c.2238C>T	c.(2236-2238)ggC>ggT	p.G746G	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	746					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.G746G(1)	ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TGTTCTTCCCGCCTTTCCCGC	0.592			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.G746G		yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2238T	2						.	G		10,4396	16.8+/-37.8	0,10,2193	87.0	67.0	74.0		2238	1.4	1.0	2	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	ALK	NM_004304.4		0,10,6493	AA,AG,GG		0.0,0.227,0.0769		746/1621	29462663	10,12996	2203	4300	6503	29316167	SO:0001819	synonymous_variant	238	exon13	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.2238C>T	2.37:g.29462663G>A		Somatic		Capture	Illumina HiSeq	Phase_I	29316167	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																				0.592	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
LBH	81606	broad.mit.edu	37	2	30480348	30480348	+	Missense_Mutation	SNP	G	G	A	rs201301340		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:30480348G>A	ENST00000395323.3	+	3	387	c.179G>A	c.(178-180)cGt>cAt	p.R60H	LBH_ENST00000404397.1_Intron|LBH_ENST00000407930.2_Missense_Mutation_p.R43H|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000406087.1_3'UTR|LBH_ENST00000401506.1_Missense_Mutation_p.R66H	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	60					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.R60H(1)		endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					CTGAAGGACCGTCTGCCCTCC	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		16794	0.0		0.001	False		,,,				2504	0.0				p.R60H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G179A	2						.						60.0	66.0	64.0					2																	30480348		2203	4300	6503	30333852	SO:0001583	missense	81606	exon3			AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"""limb bud and heart development homolog (mouse)"""			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.179G>A	2.37:g.30480348G>A	ENSP00000378733:p.Arg60His	Somatic		Capture	Illumina HiSeq	Phase_I	30333852	NM_030915	B2RBC2|Q9H0Q1	Missense_Mutation	SNP	ENST00000395323.3	37	CCDS33173.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	31	5.066342	0.93898	.	.	ENSG00000213626	ENST00000395323;ENST00000401506;ENST00000407930	.	.	.	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.78553	0.4301	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.81716	-0.0806	9	0.87932	D	0	-25.004	16.8734	0.86045	0.0:0.0:1.0:0.0	.	60	Q53QV2	LBH_HUMAN	H	60;66;43	.	ENSP00000378733:R60H	R	+	2	0	LBH	30333852	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.462000	0.97649	2.220000	0.72140	0.561000	0.74099	CGT		0.557	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915	
GALNT14	79623	broad.mit.edu	37	2	31215864	31215864	+	Missense_Mutation	SNP	C	C	T	rs142757379		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:31215864C>T	ENST00000349752.5	-	2	778	c.139G>A	c.(139-141)Gct>Act	p.A47T	GALNT14_ENST00000420311.2_Missense_Mutation_p.A12T|GALNT14_ENST00000406653.1_Missense_Mutation_p.A27T|GALNT14_ENST00000356174.3_Missense_Mutation_p.A47T|GALNT14_ENST00000324589.5_Intron|AC009305.1_ENST00000449780.1_RNA	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14	47					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A47T(1)		cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					TCCCAGTCAGCGTCCGAAGGC	0.572													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18759	0.0		0.0	False		,,,				2504	0.0				p.A47T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G139A	2						.	C	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	73.0	61.0	65.0		139	1.8	0.1	2	dbSNP_134	65	0,8600		0,0,4300	yes	missense	GALNT14	NM_024572.2	58	0,6,6497	TT,TC,CC		0.0,0.1362,0.0461	benign	47/553	31215864	6,13000	2203	4300	6503	31069368	SO:0001583	missense	79623	exon2			AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.139G>A	2.37:g.31215864C>T	ENSP00000288988:p.Ala47Thr	Somatic		Capture	Illumina HiSeq	Phase_I	31069368	NM_024572	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	.	.	.	.	.	.	.	.	.	.	C	11.03	1.519739	0.27211	0.001362	0.0	ENSG00000158089	ENST00000349752;ENST00000406653;ENST00000356174;ENST00000420311;ENST00000430167	T;T;T;T;T	0.62788	0.46;0.44;0.25;0.45;-0.0	4.8	1.76	0.24704	.	.	.	.	.	T	0.35537	0.0935	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.12013	0.003;0.001;0.005;0.002;0.002	B;B;B;B;B	0.08055	0.003;0.001;0.003;0.002;0.001	T	0.19712	-1.0297	9	0.13853	T	0.58	.	7.3657	0.26772	0.0:0.6447:0.1371:0.2181	.	12;12;47;47;27	F5H263;B7Z5C5;Q96FL9-2;Q96FL9;B3KV89	.;.;.;GLT14_HUMAN;.	T	47;27;47;12;47	ENSP00000288988:A47T;ENSP00000385435:A27T;ENSP00000348497:A47T;ENSP00000415514:A12T;ENSP00000406399:A47T	ENSP00000288988:A47T	A	-	1	0	GALNT14	31069368	0.000000	0.05858	0.086000	0.20670	0.151000	0.21798	0.733000	0.26087	0.612000	0.30071	0.555000	0.69702	GCT		0.572	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
SPAST	6683	broad.mit.edu	37	2	32352080	32352080	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:32352080A>G	ENST00000315285.3	+	8	1287	c.1162A>G	c.(1162-1164)Aag>Gag	p.K388E	SPAST_ENST00000345662.1_Missense_Mutation_p.K356E	NM_014946.3	NP_055761.2			spastin									p.K388E(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(8)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					TGGGAATGGGAAGACAATGCT	0.363																																					p.K356E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1066G	2						.						81.0	85.0	84.0					2																	32352080		2203	4300	6503	32205584	SO:0001583	missense	6683	exon7			AJ246001	CCDS1778.1, CCDS1779.1	2p24-p21	2014-09-17	2005-03-15	2005-03-17	ENSG00000021574	ENSG00000021574		"""ATPases / AAA-type"""	11233	protein-coding gene	gene with protein product		604277	"""spastic paraplegia 4 (autosomal dominant; spastin)"""	SPG4		10493830, 10610178	Standard	NM_014946		Approved	FSP2, ADPSP, KIAA1083	uc002roc.3	Q9UBP0	OTTHUMG00000128455	ENST00000315285.3:c.1162A>G	2.37:g.32352080A>G	ENSP00000320885:p.Lys388Glu	Somatic		Capture	Illumina HiSeq	Phase_I	32205584	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885206	0.91814	.	.	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.99771	-6.71;-6.71	5.69	5.69	0.88448	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	H	0.98466	4.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96259	0.9189	10	0.87932	D	0	-36.1504	15.6109	0.76716	1.0:0.0:0.0:0.0	.	356;388	E5KRP6;Q9UBP0	.;SPAST_HUMAN	E	356;388	ENSP00000340817:K356E;ENSP00000320885:K388E	ENSP00000320885:K388E	K	+	1	0	SPAST	32205584	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.392000	0.90180	2.164000	0.68074	0.460000	0.39030	AAG		0.363	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436	
BIRC6	57448	broad.mit.edu	37	2	32750663	32750663	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:32750663C>A	ENST00000421745.2	+	59	12022	c.11888C>A	c.(11887-11889)cCa>cAa	p.P3963Q		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	3963					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.P3935Q(1)|p.P3963Q(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATTACTGTCCCAGTGTTTCAC	0.423																																					p.P3963Q	Pancreas(94;175 1509 16028 18060 45422)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C11888A	2						.						75.0	74.0	75.0					2																	32750663		2203	4300	6503	32604167	SO:0001583	missense	57448	exon59			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.11888C>A	2.37:g.32750663C>A	ENSP00000393596:p.Pro3963Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32604167	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872538	0.91587	.	.	ENSG00000115760	ENST00000421745	T	0.76060	-0.99	5.61	5.61	0.85477	.	0.115412	0.64402	D	0.000015	T	0.80571	0.4648	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.81961	-0.0693	10	0.59425	D	0.04	.	19.6295	0.95694	0.0:1.0:0.0:0.0	.	3963	Q9NR09	BIRC6_HUMAN	Q	3963	ENSP00000393596:P3963Q	ENSP00000393596:P3963Q	P	+	2	0	BIRC6	32604167	1.000000	0.71417	0.969000	0.41365	0.984000	0.73092	7.274000	0.78538	2.647000	0.89833	0.655000	0.94253	CCA		0.423	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
BIRC6	57448	broad.mit.edu	37	2	32800304	32800304	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:32800304T>C	ENST00000421745.2	+	66	13360	c.13226T>C	c.(13225-13227)gTg>gCg	p.V4409A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4409					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)	p.V4409A(1)|p.V4381A(1)		NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					GCTGCCATGGTGCCCCTATTG	0.468																																					p.V4409A	Pancreas(94;175 1509 16028 18060 45422)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T13226C	2						.						192.0	187.0	189.0					2																	32800304		2203	4300	6503	32653808	SO:0001583	missense	57448	exon66			AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13226T>C	2.37:g.32800304T>C	ENSP00000393596:p.Val4409Ala	Somatic		Capture	Illumina HiSeq	Phase_I	32653808	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	T	16.55	3.155480	0.57259	.	.	ENSG00000115760	ENST00000421745	T	0.75704	-0.96	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.80358	0.4608	L	0.46157	1.445	0.80722	D	1	D	0.58970	0.984	D	0.68192	0.956	T	0.75451	-0.3313	10	0.13108	T	0.6	.	15.9677	0.79987	0.0:0.0:0.0:1.0	.	4409	Q9NR09	BIRC6_HUMAN	A	4409	ENSP00000393596:V4409A	ENSP00000393596:V4409A	V	+	2	0	BIRC6	32653808	1.000000	0.71417	1.000000	0.80357	0.840000	0.47671	8.040000	0.89188	2.181000	0.69327	0.533000	0.62120	GTG		0.468	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LTBP1	4052	broad.mit.edu	37	2	33246030	33246030	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:33246030G>C	ENST00000404816.2	+	3	973	c.620G>C	c.(619-621)tGt>tCt	p.C207S	LTBP1_ENST00000354476.3_Missense_Mutation_p.C207S			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	207	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)	p.C207S(1)		breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CCACAACTCTGTGTGTGTAAA	0.527																																					p.C207S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G620C	2						.						188.0	191.0	190.0					2																	33246030		2203	4299	6502	33099534	SO:0001583	missense	4052	exon3				CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.620G>C	2.37:g.33246030G>C	ENSP00000386043:p.Cys207Ser	Somatic		Capture	Illumina HiSeq	Phase_I	33099534	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	G	17.98	3.521904	0.64747	.	.	ENSG00000049323	ENST00000404816;ENST00000354476	D;D	0.99773	-6.72;-6.72	4.8	4.8	0.61643	.	.	.	.	.	D	0.99857	0.9933	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.96505	0.9374	9	0.87932	D	0	.	18.2483	0.89995	0.0:0.0:1.0:0.0	.	207	Q14766-4	.	S	207	ENSP00000386043:C207S;ENSP00000346467:C207S	ENSP00000346467:C207S	C	+	2	0	LTBP1	33099534	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.628000	0.90979	2.359000	0.80004	0.637000	0.83480	TGT		0.527	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
CEBPZ	10153	broad.mit.edu	37	2	37455760	37455760	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:37455760A>G	ENST00000234170.5	-	2	721	c.576T>C	c.(574-576)taT>taC	p.Y192Y		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	192					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|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)	p.Y192Y(1)		breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GTTTCAAAGAATATTCATTGC	0.363																																					p.Y192Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T576C	2						.						124.0	126.0	125.0					2																	37455760		2203	4300	6503	37309264	SO:0001819	synonymous_variant	10153	exon2			M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.576T>C	2.37:g.37455760A>G		Somatic		Capture	Illumina HiSeq	Phase_I	37309264	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																				0.363	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
SOS1	6654	broad.mit.edu	37	2	39250359	39250359	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:39250359C>T	ENST00000426016.1	-	11	1296	c.1210G>A	c.(1210-1212)Gca>Aca	p.A404T	SOS1_ENST00000402219.2_Missense_Mutation_p.A404T|SOS1_ENST00000472480.1_5'UTR|SOS1_ENST00000395038.2_Missense_Mutation_p.A404T|SOS1_ENST00000428721.2_3'UTR			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	404					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A404T(1)		autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				AACCGACATGCAGATTCACTG	0.348									Noonan syndrome																												p.A404T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1210A	2						.						50.0	46.0	48.0					2																	39250359		2200	4294	6494	39103863	SO:0001583	missense	6654	exon10	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.1210G>A	2.37:g.39250359C>T	ENSP00000387784:p.Ala404Thr	Somatic		Capture	Illumina HiSeq	Phase_I	39103863	NM_005633	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393584	0.42410	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.78003	-1.01;-1.01;-1.14	5.52	5.52	0.82312	Dbl homology (DH) domain (2);	0.000000	0.85682	D	0.000000	T	0.58337	0.2115	N	0.02539	-0.55	0.80722	D	1	B;B	0.26809	0.16;0.1	B;B	0.27500	0.08;0.021	T	0.56780	-0.7922	10	0.22706	T	0.39	.	19.8	0.96502	0.0:1.0:0.0:0.0	.	136;404	F5GX06;Q07889	.;SOS1_HUMAN	T	404;404;136;404;404	ENSP00000387784:A404T;ENSP00000384675:A404T;ENSP00000378479:A404T	ENSP00000263879:A404T	A	-	1	0	SOS1	39103863	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	2.567000	0.45956	2.753000	0.94483	0.557000	0.71058	GCA		0.348	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219948.3	NM_005633	
MAP4K3	8491	broad.mit.edu	37	2	39526917	39526917	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:39526917C>T	ENST00000263881.3	-	16	1469	c.1145G>A	c.(1144-1146)gGa>gAa	p.G382E	MAP4K3_ENST00000536018.1_5'UTR|MAP4K3_ENST00000437545.1_Missense_Mutation_p.G298E|MAP4K3_ENST00000341681.5_Missense_Mutation_p.G361E	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	382					intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.G382E(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				ACCTTGGTGTCCTTGTCCATA	0.259																																					p.G382E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1145A	2						.						38.0	41.0	40.0					2																	39526917		2201	4284	6485	39380421	SO:0001583	missense	8491	exon16			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.1145G>A	2.37:g.39526917C>T	ENSP00000263881:p.Gly382Glu	Somatic		Capture	Illumina HiSeq	Phase_I	39380421	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.045391	0.36085	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	T;T;T	0.15139	2.45;2.45;2.45	5.49	5.49	0.81192	Protein kinase-like domain (1);	0.179126	0.48767	D	0.000178	T	0.18425	0.0442	L	0.44542	1.39	0.80722	D	1	B;B	0.15141	0.012;0.004	B;B	0.13407	0.009;0.003	T	0.04723	-1.0931	9	.	.	.	.	19.3536	0.94401	0.0:1.0:0.0:0.0	.	361;382	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	E	382;298;361	ENSP00000263881:G382E;ENSP00000416958:G298E;ENSP00000345434:G361E	.	G	-	2	0	MAP4K3	39380421	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	4.513000	0.60476	2.578000	0.87016	0.313000	0.20887	GGA		0.259	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
MAP4K3	8491	broad.mit.edu	37	2	39570590	39570590	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:39570590T>A	ENST00000263881.3	-	4	573	c.249A>T	c.(247-249)cgA>cgT	p.R83R	MAP4K3_ENST00000437545.1_Silent_p.R20R|MAP4K3_ENST00000341681.5_Silent_p.R83R	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	83	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|protein phosphorylation (GO:0006468)|response to tumor necrosis factor (GO:0034612)|response to UV (GO:0009411)		ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)	p.R83R(1)		NS(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_hematologic(82;0.211)				AAAGCTTATCTCGCCTATAAA	0.343																																					p.R83R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A249T	2						.						80.0	82.0	81.0					2																	39570590		2203	4298	6501	39424094	SO:0001819	synonymous_variant	8491	exon4			AF000145	CCDS1803.1, CCDS58707.1	2p22.3	2011-06-09			ENSG00000011566	ENSG00000011566		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6865	protein-coding gene	gene with protein product		604921		RAB8IPL1		9275185	Standard	NM_003618		Approved	GLK, MAPKKKK3	uc002rro.4	Q8IVH8	OTTHUMG00000102127	ENST00000263881.3:c.249A>T	2.37:g.39570590T>A		Somatic		Capture	Illumina HiSeq	Phase_I	39424094	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Silent	SNP	ENST00000263881.3	37	CCDS1803.1																																																																																				0.343	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618	
ZFP36L2	678	broad.mit.edu	37	2	43452622	43452622	+	Silent	SNP	G	G	C	rs200743741		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:43452622G>C	ENST00000282388.3	-	2	614	c.321C>G	c.(319-321)ggC>ggG	p.G107G	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	107	Poly-Gly.				cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G107G(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				CTGTGCCGCCGCCCCCCGACG	0.697																																					p.G107G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C321G	2						.						16.0	20.0	19.0					2																	43452622		2190	4297	6487	43306126	SO:0001819	synonymous_variant	678	exon2			X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.321C>G	2.37:g.43452622G>C		Somatic		Capture	Illumina HiSeq	Phase_I	43306126	NM_006887	Q53TB4|Q9BSJ3	Silent	SNP	ENST00000282388.3	37	CCDS1811.1																																																																																				0.697	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887	
LRPPRC	10128	broad.mit.edu	37	2	44201298	44201298	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:44201298A>G	ENST00000260665.7	-	9	1203	c.1146T>C	c.(1144-1146)acT>acC	p.T382T	LRPPRC_ENST00000409946.1_Silent_p.T382T|LRPPRC_ENST00000409659.1_Silent_p.T382T	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	382					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.T382T(1)		breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				CCGTATTCATAGTCACACAGT	0.358																																					p.T382T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1146C	2						.						92.0	90.0	91.0					2																	44201298		2203	4300	6503	44054802	SO:0001819	synonymous_variant	10128	exon9			M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1146T>C	2.37:g.44201298A>G		Somatic		Capture	Illumina HiSeq	Phase_I	44054802	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																				0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
STON1	11037	broad.mit.edu	37	2	48809199	48809199	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:48809199delA	ENST00000406226.1	+	3	1622	c.1427delA	c.(1426-1428)gaafs	p.E476fs	STON1-GTF2A1L_ENST00000394754.1_Frame_Shift_Del_p.E476fs|STON1-GTF2A1L_ENST00000309827.2_Frame_Shift_Del_p.E476fs|STON1_ENST00000309835.3_Frame_Shift_Del_p.E476fs|STON1-GTF2A1L_ENST00000402114.2_Frame_Shift_Del_p.E476fs|STON1-GTF2A1L_ENST00000405008.1_Frame_Shift_Del_p.E476fs|STON1-GTF2A1L_ENST00000394751.3_Frame_Shift_Del_p.E476fs|STON1_ENST00000404752.1_Frame_Shift_Del_p.E476fs	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	476	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.K478fs*14(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AAGGACTCAGAAAAAAAGGGG	0.383																																					p.E476fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1427delA	2						.						111.0	115.0	114.0					2																	48809199		2203	4300	6503	48662703	SO:0001589	frameshift_variant	286749	exon1			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1427delA	2.37:g.48809199delA	ENSP00000384615:p.Glu476fs	Somatic		Capture	Illumina HiSeq	Phase_I	48662703	NM_001198594	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Frame_Shift_Del	DEL	ENST00000406226.1	37	CCDS1841.1																																																																																				0.383	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
STON1	11037	broad.mit.edu	37	2	48809431	48809431	+	Silent	SNP	G	G	C	rs370458736		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:48809431G>C	ENST00000406226.1	+	3	1854	c.1659G>C	c.(1657-1659)gcG>gcC	p.A553A	STON1-GTF2A1L_ENST00000394754.1_Silent_p.A553A|STON1-GTF2A1L_ENST00000309827.2_Silent_p.A553A|STON1_ENST00000309835.3_Silent_p.A553A|STON1-GTF2A1L_ENST00000402114.2_Silent_p.A553A|STON1-GTF2A1L_ENST00000405008.1_Silent_p.A553A|STON1-GTF2A1L_ENST00000394751.3_Silent_p.A553A|STON1_ENST00000404752.1_Silent_p.A553A	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	553	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)		p.A553A(2)		NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CCTCATTGGCGCAGAGGTCAT	0.478																																					p.A553A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G1659C	2						.						148.0	146.0	146.0					2																	48809431		2203	4300	6503	48662935	SO:0001819	synonymous_variant	286749	exon1			AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1659G>C	2.37:g.48809431G>C		Somatic		Capture	Illumina HiSeq	Phase_I	48662935	NM_001198594	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	CCDS1841.1																																																																																				0.478	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
TSPYL6	388951	broad.mit.edu	37	2	54483109	54483109	+	Silent	SNP	C	C	T	rs570502084		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:54483109C>T	ENST00000317802.7	-	1	300	c.180G>A	c.(178-180)gcG>gcA	p.A60A	ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000607452.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	60			A -> V (in dbSNP:rs6743719).		nucleosome assembly (GO:0006334)	nucleus (GO:0005634)		p.A60A(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						GATCCTGGGGCGCGACCCCCT	0.597													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16726	0.0		0.0	False		,,,				2504	0.0				p.A60A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G180A	2						.						61.0	70.0	67.0					2																	54483109		1944	4138	6082	54336613	SO:0001819	synonymous_variant	388951	exon1			AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.180G>A	2.37:g.54483109C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54336613	NM_001003937	Q6NUJ3	Silent	SNP	ENST00000317802.7	37	CCDS42682.1																																																																																				0.597	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
VRK2	7444	broad.mit.edu	37	2	58362286	58362286	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:58362286G>A	ENST00000435505.2	+	13	1553	c.808G>A	c.(808-810)Gag>Aag	p.E270K	VRK2_ENST00000440705.2_Missense_Mutation_p.E247K|VRK2_ENST00000417641.2_Missense_Mutation_p.E270K|VRK2_ENST00000412104.2_Missense_Mutation_p.E270K|VRK2_ENST00000340157.4_Missense_Mutation_p.E270K			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	270	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						TCTGTTGGACGAGCTCCCCCA	0.393																																					p.E270K												.	.	0			c.G808A	2						.						208.0	194.0	199.0					2																	58362286		2203	4300	6503	58215790	SO:0001583	missense	7444	exon10			AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.808G>A	2.37:g.58362286G>A	ENSP00000408002:p.Glu270Lys	None		Capture	Illumina HiSeq	Phase_I	58215790	NM_001130483	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Missense_Mutation	SNP	ENST00000435505.2	37	CCDS1859.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725064	0.68959	.	.	ENSG00000028116	ENST00000435505;ENST00000417641;ENST00000412104;ENST00000340157;ENST00000394539;ENST00000440705	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	5.73	5.73	0.89815	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.199236	0.53938	D	0.000056	T	0.59528	0.2200	L	0.46947	1.48	0.44447	D	0.997375	D;B;P	0.54964	0.969;0.278;0.497	B;B;B	0.42882	0.401;0.031;0.135	T	0.63786	-0.6558	10	0.56958	D	0.05	-20.4498	17.4149	0.87497	0.0:0.0:1.0:0.0	.	270;270;270	Q86Y07-2;Q86Y07-5;Q86Y07	.;.;VRK2_HUMAN	K	270;270;270;270;270;247	ENSP00000408002:E270K;ENSP00000402375:E270K;ENSP00000404156:E270K;ENSP00000342381:E270K;ENSP00000398323:E247K	ENSP00000342381:E270K	E	+	1	0	VRK2	58215790	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	5.613000	0.67688	2.861000	0.98227	0.655000	0.94253	GAG		0.393	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
USP34	9736	broad.mit.edu	37	2	61493208	61493208	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:61493208G>A	ENST00000398571.2	-	42	5604	c.5528C>T	c.(5527-5529)gCc>gTc	p.A1843V		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1843					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A1843V(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ATCGTAAGCGGCAGCTCTTGA	0.428																																					p.A1843V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5528T	2						.						134.0	123.0	126.0					2																	61493208		1857	4106	5963	61346712	SO:0001583	missense	9736	exon42			AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.5528C>T	2.37:g.61493208G>A	ENSP00000381577:p.Ala1843Val	Somatic		Capture	Illumina HiSeq	Phase_I	61346712	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960615	0.74016	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571;ENST00000453734	T;T	0.05717	3.54;3.4	5.48	5.48	0.80851	Armadillo-type fold (1);	0.054226	0.64402	D	0.000001	T	0.12475	0.0303	M	0.70595	2.14	0.80722	D	1	B	0.12630	0.006	B	0.16722	0.016	T	0.01781	-1.1275	10	0.87932	D	0	.	17.5436	0.87855	0.0:0.0:1.0:0.0	.	1843	Q70CQ2	UBP34_HUMAN	V	1691;1691;1843;121	ENSP00000381577:A1843V;ENSP00000410559:A121V	ENSP00000263989:A1691V	A	-	2	0	USP34	61346712	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.869000	0.99810	2.584000	0.87258	0.563000	0.77884	GCC		0.428	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
XPO1	7514	broad.mit.edu	37	2	61709556	61709556	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:61709556A>G	ENST00000401558.2	-	23	3658	c.2931T>C	c.(2929-2931)taT>taC	p.Y977Y	RP11-355B11.2_ENST00000603028.1_RNA|RP11-355B11.2_ENST00000603199.1_RNA|XPO1_ENST00000404992.2_Silent_p.Y977Y|RP11-355B11.2_ENST00000578974.2_RNA|RP11-355B11.2_ENST00000605437.1_RNA|RP11-355B11.2_ENST00000603652.1_RNA|XPO1_ENST00000406957.1_Silent_p.Y977Y	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	977					gene expression (GO:0010467)|intracellular transport of virus (GO:0075733)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein export from nucleus (GO:0006611)|protein localization to nucleus (GO:0034504)|regulation of centrosome duplication (GO:0010824)|regulation of protein catabolic process (GO:0042176)|regulation of protein export from nucleus (GO:0046825)|response to drug (GO:0042493)|ribosomal large subunit export from nucleus (GO:0000055)|ribosomal small subunit export from nucleus (GO:0000056)|RNA metabolic process (GO:0016070)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)	annulate lamellae (GO:0005642)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleocytoplasmic transporter activity (GO:0005487)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|transporter activity (GO:0005215)	p.Y977Y(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	39			LUSC - Lung squamous cell carcinoma(7;5.71e-05)|Epithelial(17;0.0662)|all cancers(80;0.226)			GATTAGCCACATATTCCTGAA	0.373			Mis		CLL																																p.Y977Y		-'	Dom	yes		2	2p15	7514	"""exportin 1 (CRM1 homolog, yeast)"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2931C	2						.						137.0	138.0	138.0					2																	61709556		2203	4300	6503	61563060	SO:0001819	synonymous_variant	7514	exon23			Y08614	CCDS33205.1	2p15	2014-02-19	2014-02-19		ENSG00000082898	ENSG00000082898		"""Exportins"""	12825	protein-coding gene	gene with protein product	"""chromosome region maintenance 1 homolog (yeast)"""	602559	"""exportin 1 (CRM1, yeast, homolog)"", ""exportin 1 (CRM1 homolog, yeast)"""			9205132, 9368044	Standard	XM_005264544		Approved	CRM1, emb	uc002sbj.3	O14980	OTTHUMG00000152316	ENST00000401558.2:c.2931T>C	2.37:g.61709556A>G		Somatic		Capture	Illumina HiSeq	Phase_I	61563060	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Silent	SNP	ENST00000401558.2	37	CCDS33205.1																																																																																				0.373	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400	
WDPCP	51057	broad.mit.edu	37	2	63660967	63660967	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:63660967T>C	ENST00000272321.7	-	9	1264	c.737A>G	c.(736-738)aAc>aGc	p.N246S	WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000398544.3_Missense_Mutation_p.N87S|WDPCP_ENST00000409199.1_Missense_Mutation_p.N54S|WDPCP_ENST00000409120.1_Missense_Mutation_p.N54S|WDPCP_ENST00000409562.3_Missense_Mutation_p.N246S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	246					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.N246S(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						AGCATCATCGTTGACCAGTGG	0.453																																					p.N246S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A737G	2						.						71.0	71.0	71.0					2																	63660967		1912	4119	6031	63514471	SO:0001583	missense	51057	exon9				CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.737A>G	2.37:g.63660967T>C	ENSP00000272321:p.Asn246Ser	Somatic		Capture	Illumina HiSeq	Phase_I	63514471	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.719241	0.00700	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.43	1.51	0.23008	.	0.431594	0.27130	N	0.020787	T	0.07954	0.0199	N	0.00465	-1.465	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.001	T	0.30765	-0.9967	10	0.02654	T	1	-1.2846	1.7278	0.02925	0.1434:0.4802:0.1393:0.2371	.	54;246;246;87	E9PFG9;O95876-2;O95876;O95876-3	.;.;FRITZ_HUMAN;.	S	246;54;54;87;246	ENSP00000272321:N246S;ENSP00000386592:N54S;ENSP00000386769:N54S;ENSP00000381552:N87S;ENSP00000387222:N246S	ENSP00000272321:N246S	N	-	2	0	WDPCP	63514471	0.999000	0.42202	0.739000	0.30968	0.877000	0.50540	0.503000	0.22610	-0.004000	0.14419	-0.468000	0.05107	AAC		0.453	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
SPRED2	200734	broad.mit.edu	37	2	65572014	65572014	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:65572014G>A	ENST00000356388.4	-	2	232	c.43C>T	c.(43-45)Cgt>Tgt	p.R15C	SPRED2_ENST00000474228.1_5'UTR|SPRED2_ENST00000443619.2_Missense_Mutation_p.R12C	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	15	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)	p.R15C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						GCCTTGACACGCACAATATAG	0.512																																					p.R15C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C43T	2						.						66.0	54.0	58.0					2																	65572014		2203	4300	6503	65425518	SO:0001583	missense	200734	exon2			AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.43C>T	2.37:g.65572014G>A	ENSP00000348753:p.Arg15Cys	Somatic		Capture	Illumina HiSeq	Phase_I	65425518	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.326518	0.81690	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315;ENST00000440972	D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05	4.98	4.98	0.66077	EVH1 (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.99165	0.9711	M	0.88031	2.925	0.80722	D	1	D;D	0.89917	0.995;1.0	D;D	0.97110	0.964;1.0	D	0.99260	1.0890	10	0.66056	D	0.02	-11.1309	14.0272	0.64592	0.0:0.0:0.8482:0.1518	.	12;15	E9PEP0;Q7Z698	.;SPRE2_HUMAN	C	15;12;30;15	ENSP00000348753:R15C;ENSP00000393697:R12C;ENSP00000390595:R30C;ENSP00000406481:R15C	ENSP00000348753:R15C	R	-	1	0	SPRED2	65425518	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.917000	0.87498	2.281000	0.76405	0.305000	0.20034	CGT		0.512	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1		
ARHGAP25	9938	broad.mit.edu	37	2	69049547	69049547	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:69049547C>T	ENST00000295381.3	+	10	1692	c.1273C>T	c.(1273-1275)Ccc>Tcc	p.P425S	ARHGAP25_ENST00000409030.3_Missense_Mutation_p.P418S|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.P426S|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.P419S|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.P386S|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.P119S	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	425					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.P419S(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CAGCAAAGTACCCAGGGAAAA	0.502																																					p.P419S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1255T	2						.						98.0	102.0	101.0					2																	69049547		2203	4300	6503	68903051	SO:0001583	missense	9938	exon9			D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1273C>T	2.37:g.69049547C>T	ENSP00000295381:p.Pro425Ser	Somatic		Capture	Illumina HiSeq	Phase_I	68903051	NM_001166276	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		.	.	.	.	.	.	.	.	.	.	C	10.12	1.262907	0.23051	.	.	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.17370	2.84;2.84;2.57;2.85;2.85;2.28	5.38	-1.85	0.07784	.	1.108850	0.06705	N	0.772192	T	0.06872	0.0175	N	0.05124	-0.11	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.0	T	0.41502	-0.9505	10	0.10636	T	0.68	.	6.9227	0.24397	0.0:0.3289:0.1251:0.546	.	386;426;419;418;425	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	S	425;426;386;418;419;419;410;119	ENSP00000295381:P425S;ENSP00000386911:P426S;ENSP00000420583:P386S;ENSP00000386863:P418S;ENSP00000386241:P419S;ENSP00000417467:P119S	ENSP00000295381:P425S	P	+	1	0	ARHGAP25	68903051	0.000000	0.05858	0.002000	0.10522	0.058000	0.15608	-0.144000	0.10280	-0.193000	0.10415	-0.259000	0.10710	CCC		0.502	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
C2orf42	54980	broad.mit.edu	37	2	70408586	70408586	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:70408586C>A	ENST00000264434.2	-	3	911	c.532G>T	c.(532-534)Ggt>Tgt	p.G178C	C2orf42_ENST00000470096.1_5'Flank|C2orf42_ENST00000420306.1_Missense_Mutation_p.G178C	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	178								p.G178C(1)		endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						ACCAGAGGACCTGTGGGTTCC	0.517																																					p.G178C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G532T	2						.						89.0	88.0	88.0					2																	70408586		2203	4300	6503	70262090	SO:0001583	missense	54980	exon3			AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.532G>T	2.37:g.70408586C>A	ENSP00000264434:p.Gly178Cys	Somatic		Capture	Illumina HiSeq	Phase_I	70262090	NM_017880	D6W5G3|Q9H629	Missense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227237	0.79576	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	T;T	0.47177	0.85;0.85	4.96	4.96	0.65561	.	0.000000	0.85682	D	0.000000	T	0.66036	0.2749	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68762	-0.5323	10	0.87932	D	0	-10.2156	16.994	0.86361	0.0:1.0:0.0:0.0	.	178	Q9NWW7	CB042_HUMAN	C	178	ENSP00000264434:G178C;ENSP00000404515:G178C	ENSP00000264434:G178C	G	-	1	0	C2orf42	70262090	1.000000	0.71417	0.986000	0.45419	0.905000	0.53344	7.205000	0.77881	2.576000	0.86940	0.485000	0.47835	GGT		0.517	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
DYSF	8291	broad.mit.edu	37	2	71909755	71909755	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:71909755T>C	ENST00000258104.3	+	54	6429	c.6152T>C	c.(6151-6153)aTc>aCc	p.I2051T	DYSF_ENST00000409651.1_Missense_Mutation_p.I2083T|DYSF_ENST00000394120.2_Missense_Mutation_p.I2052T|DYSF_ENST00000409582.3_Missense_Mutation_p.I2089T|DYSF_ENST00000409744.1_Missense_Mutation_p.I2059T|DYSF_ENST00000413539.2_Missense_Mutation_p.I2082T|DYSF_ENST00000410020.3_Missense_Mutation_p.I2090T|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000410041.1_Missense_Mutation_p.I2069T|DYSF_ENST00000429174.2_Missense_Mutation_p.I2072T|DYSF_ENST00000409366.1_Missense_Mutation_p.I2073T|DYSF_ENST00000409762.1_Missense_Mutation_p.I2068T	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	2051					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)	p.I2051T(1)		autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						atcctcttcatcatcctcttc	0.577																																					p.I2083T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T6248C	2						.						182.0	124.0	144.0					2																	71909755		2203	4300	6503	71763263	SO:0001583	missense	8291	exon55			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.6152T>C	2.37:g.71909755T>C	ENSP00000258104:p.Ile2051Thr	Somatic		Capture	Illumina HiSeq	Phase_I	71763263	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.481749	0.63849	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.84442	-1.83;-1.83;-1.84;-1.85;-1.84;-1.83;-1.83;-1.85;-1.85;-1.84;-1.83	5.1	5.1	0.69264	.	0.434933	0.26612	N	0.023403	D	0.83105	0.5182	L	0.55213	1.73	0.45354	D	0.998342	P;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.40660	0.726;0.078;0.078;0.078;0.043;0.039;0.039;0.039;0.039;0.078;0.039;0.036;0.043;0.078;0.026	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.40864	0.342;0.127;0.127;0.127;0.127;0.237;0.237;0.237;0.127;0.127;0.237;0.127;0.127;0.127;0.06	D	0.85259	0.1049	10	0.87932	D	0	-17.922	13.1302	0.59377	0.0:0.0:0.0:1.0	.	815;2083;2090;2073;2038;2069;2059;2068;2058;2082;2089;2072;2037;2052;2051	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	T	2082;2068;2089;2072;2051;2083;2052;2059;2073;2090;2069	ENSP00000407046:I2082T;ENSP00000387137:I2068T;ENSP00000386547:I2089T;ENSP00000398305:I2072T;ENSP00000258104:I2051T;ENSP00000386683:I2083T;ENSP00000377678:I2052T;ENSP00000386285:I2059T;ENSP00000386512:I2073T;ENSP00000386881:I2090T;ENSP00000386617:I2069T	ENSP00000258104:I2051T	I	+	2	0	DYSF	71763263	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	7.950000	0.87804	2.034000	0.60081	0.533000	0.62120	ATC		0.577	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
DCTN1	1639	broad.mit.edu	37	2	74592215	74592215	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:74592215A>G	ENST00000361874.3	-	26	3500	c.3183T>C	c.(3181-3183)tcT>tcC	p.S1061S	DCTN1_ENST00000409868.1_Silent_p.S1044S|DCTN1_ENST00000409567.3_Silent_p.S1041S|RP11-287D1.3_ENST00000451608.2_5'Flank|DCTN1_ENST00000407639.2_Silent_p.S927S|DCTN1_ENST00000409240.1_Silent_p.S1024S|DCTN1_ENST00000394003.3_Silent_p.S1054S|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409438.1_Silent_p.S927S	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1061					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)	p.S1061S(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CAGCAATGCCAGAGACCAGAG	0.557																																					p.S927S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T2781C	2						.						139.0	120.0	127.0					2																	74592215		2203	4300	6503	74445723	SO:0001819	synonymous_variant	1639	exon21				CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.3183T>C	2.37:g.74592215A>G		Somatic		Capture	Illumina HiSeq	Phase_I	74445723	NM_023019	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																				0.557	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
HK2	3099	broad.mit.edu	37	2	75108866	75108866	+	Silent	SNP	T	T	G	rs139170126		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:75108866T>G	ENST00000290573.2	+	11	2199	c.1599T>G	c.(1597-1599)ctT>ctG	p.L533L	HK2_ENST00000409174.1_Silent_p.L505L	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	533	Catalytic.|Glucose-6-phosphate 2 binding.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.L533L(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CCTTGGACCTTGGAGGAACAA	0.522																																					p.L533L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1599G	2						.						84.0	83.0	83.0					2																	75108866		2203	4300	6503	74962374	SO:0001819	synonymous_variant	3099	exon11				CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1599T>G	2.37:g.75108866T>G		Somatic		Capture	Illumina HiSeq	Phase_I	74962374	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																				0.522	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
HK2	3099	broad.mit.edu	37	2	75113788	75113788	+	Missense_Mutation	SNP	C	C	A	rs146476722	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:75113788C>A	ENST00000290573.2	+	15	2807	c.2207C>A	c.(2206-2208)cCc>cAc	p.P736H	HK2_ENST00000409174.1_Missense_Mutation_p.P708H	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	736	Catalytic.|Hexokinase type-2 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.P736H(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TCACTCAACCCCGGCAAGCAG	0.537																																					p.P736H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2207A	2						.						66.0	69.0	68.0					2																	75113788		2203	4300	6503	74967296	SO:0001583	missense	3099	exon15				CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.2207C>A	2.37:g.75113788C>A	ENSP00000290573:p.Pro736His	Somatic		Capture	Illumina HiSeq	Phase_I	74967296	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	C	19.69	3.874029	0.72180	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98968	-5.28;-5.28	5.49	4.62	0.57501	Hexokinase, C-terminal (1);	0.185614	0.64402	D	0.000013	D	0.99190	0.9719	H	0.94306	3.52	0.53688	D	0.999971	D	0.76494	0.999	P	0.61658	0.892	D	0.99136	1.0854	10	0.87932	D	0	-0.9867	12.1976	0.54307	0.0:0.9183:0.0:0.0817	.	736	P52789	HXK2_HUMAN	H	736;736;708	ENSP00000290573:P736H;ENSP00000387140:P708H	ENSP00000290573:P736H	P	+	2	0	HK2	74967296	0.639000	0.27234	0.839000	0.33178	0.992000	0.81027	3.102000	0.50291	1.559000	0.49555	0.655000	0.94253	CCC		0.537	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
GCFC2	6936	broad.mit.edu	37	2	75891900	75891900	+	Silent	SNP	G	G	A	rs373336103		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:75891900G>A	ENST00000321027.3	-	17	2371	c.2238C>T	c.(2236-2238)gtC>gtT	p.V746V	GCFC2_ENST00000541687.1_3'UTR|MRPL19_ENST00000409374.1_Intron|MRPL19_ENST00000358788.6_Intron|RP11-342K6.1_ENST00000604845.1_RNA|GCFC2_ENST00000409857.3_Silent_p.V708V	NM_001201334.1|NM_003203.4	NP_001188263.1|NP_003194.3	P16383	GCFC2_HUMAN	GC-rich sequence DNA-binding factor 2	746					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	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 negative regulation of transcription (GO:0001078)	p.V746V(1)									TTATTTCTTCGACTTCATCCC	0.333																																					p.V746V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2238T	2						.	G	,	1,4403	2.1+/-5.4	0,1,2201	67.0	70.0	69.0		1731,2238	-3.5	0.9	2		69	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	C2orf3	NM_001201334.1,NM_003203.4	,	0,1,6500	AA,AG,GG		0.0,0.0227,0.0077	,	577/613,746/782	75891900	1,13001	2202	4299	6501	75745408	SO:0001819	synonymous_variant	6936	exon17			AB026911	CCDS1961.1, CCDS62943.1	2p12	2014-01-17	2011-11-24	2011-11-24	ENSG00000005436	ENSG00000005436			1317	protein-coding gene	gene with protein product	"""GC binding factor"""	189901	"""transcription factor 9 (binds GC-rich sequences)"", ""chromosome 2 open reading frame 3"""	TCF9, C2orf3		1370479, 2556218, 17309879, 24304693	Standard	NM_003203		Approved	DNABF, GCF	uc002sno.3	P16383	OTTHUMG00000129989	ENST00000321027.3:c.2238C>T	2.37:g.75891900G>A		Somatic		Capture	Illumina HiSeq	Phase_I	75745408	NM_003203	A4UHQ8|O95032|Q53TY0|Q6P2F2	Silent	SNP	ENST00000321027.3	37	CCDS1961.1																																																																																				0.333	GCFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252255.2	NM_003203	
POLR1A	25885	broad.mit.edu	37	2	86269012	86269012	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:86269012C>A	ENST00000263857.6	-	24	3950	c.3572G>T	c.(3571-3573)aGg>aTg	p.R1191M	POLR1A_ENST00000409681.1_Splice_Site_p.R1191M			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	1191					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)	p.R1191M(1)		NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						CTGTCAATACCTGTCGAGAGA	0.493																																					p.R1191M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3572T	2						.						107.0	106.0	106.0					2																	86269012		1980	4179	6159	86122523	SO:0001630	splice_region_variant	25885	exon24			AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.3572+1G>T	2.37:g.86269012C>A		Somatic		Capture	Illumina HiSeq	Phase_I	86122523	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.257791	0.59321	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.68624	-0.34;-0.34	5.28	5.28	0.74379	RNA polymerase Rpb1, domain 5 (1);	0.342375	0.35739	N	0.003009	T	0.77405	0.4125	M	0.65320	2	0.54753	D	0.999985	P;P	0.46457	0.878;0.878	P;P	0.56343	0.744;0.796	T	0.75814	-0.3185	9	.	.	.	-13.7226	18.8998	0.92437	0.0:1.0:0.0:0.0	.	557;1191	B7Z8X7;O95602	.;RPA1_HUMAN	M	1191	ENSP00000263857:R1191M;ENSP00000386300:R1191M	.	R	-	2	0	POLR1A	86122523	1.000000	0.71417	1.000000	0.80357	0.829000	0.46940	5.359000	0.66074	2.486000	0.83907	0.655000	0.94253	AGG		0.493	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	Missense_Mutation
RNF103	7844	broad.mit.edu	37	2	86831408	86831408	+	Missense_Mutation	SNP	G	G	A	rs143477816		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:86831408G>A	ENST00000237455.4	-	4	2584	c.1616C>T	c.(1615-1617)tCg>tTg	p.S539L	RNF103-CHMP3_ENST00000604011.1_Intron|CHMP3_ENST00000439940.2_Intron|AC015971.2_ENST00000426549.1_RNA|RNF103_ENST00000477307.1_5'Flank|AC015971.2_ENST00000424788.1_RNA|AC015971.2_ENST00000439077.1_RNA|AC015971.2_ENST00000597638.1_RNA	NM_001198951.1|NM_005667.3	NP_001185880.1|NP_005658.1	O00237	RN103_HUMAN	ring finger protein 103	539					central nervous system development (GO:0007417)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S539L(1)		central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(7)|skin(2)	25						CTCACTTTCCGAGTCATTTTC	0.398																																					p.S535L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1604T	2						.						160.0	167.0	165.0					2																	86831408		2203	4300	6503	86684919	SO:0001583	missense	7844	exon5			D76444	CCDS33237.1	2p11.2	2013-01-09	2003-05-14	2003-05-16	ENSG00000239305	ENSG00000239305		"""RING-type (C3HC4) zinc fingers"""	12859	protein-coding gene	gene with protein product		602507	"""zinc finger protein 103 homolog (mouse)"""	ZFP103		9070305	Standard	NM_005667		Approved	hkf-1, KF1	uc021vkg.1	O00237	OTTHUMG00000153197	ENST00000237455.4:c.1616C>T	2.37:g.86831408G>A	ENSP00000237455:p.Ser539Leu	Somatic		Capture	Illumina HiSeq	Phase_I	86684919	NM_001198951	A6NFV6|B2RAG4|Q53SU6|Q8IVB9	Missense_Mutation	SNP	ENST00000237455.4	37	CCDS33237.1	.	.	.	.	.	.	.	.	.	.	G	9.333	1.061095	0.19987	.	.	ENSG00000239305	ENST00000237455	T	0.44482	0.92	5.73	5.73	0.89815	.	0.259165	0.39083	N	0.001469	T	0.36110	0.0955	L	0.54323	1.7	0.54753	D	0.999987	P	0.44659	0.84	B	0.25614	0.062	T	0.41484	-0.9506	10	0.49607	T	0.09	-9.226	19.8992	0.96978	0.0:0.0:1.0:0.0	.	539	O00237	RN103_HUMAN	L	539	ENSP00000237455:S539L	ENSP00000237455:S539L	S	-	2	0	RNF103	86684919	1.000000	0.71417	0.993000	0.49108	0.307000	0.27823	3.616000	0.54174	2.699000	0.92147	0.460000	0.39030	TCG		0.398	RNF103-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330041.2	NM_005667	
PROM2	150696	broad.mit.edu	37	2	95940475	95940475	+	Silent	SNP	C	C	A	rs138718796		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:95940475C>A	ENST00000317620.9	+	1	275	c.142C>A	c.(142-144)Cgg>Agg	p.R48R	PROM2_ENST00000542147.1_Silent_p.R48R|PROM2_ENST00000463580.1_3'UTR|PROM2_ENST00000317668.4_Silent_p.R48R|PROM2_ENST00000403131.2_Silent_p.R48R	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	48					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)	p.R48R(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						AGCCAGGGCCCGGTGGCTGGC	0.672																																					p.R48R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C142A	2						.						62.0	74.0	70.0					2																	95940475		2203	4299	6502	95304202	SO:0001819	synonymous_variant	150696	exon1			AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.142C>A	2.37:g.95940475C>A		Somatic		Capture	Illumina HiSeq	Phase_I	95304202	NM_144707	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Silent	SNP	ENST00000317620.9	37	CCDS2012.1																																																																																				0.672	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
PROM2	150696	broad.mit.edu	37	2	95943724	95943724	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:95943724A>C	ENST00000317620.9	+	8	1155	c.1022A>C	c.(1021-1023)gAg>gCg	p.E341A	PROM2_ENST00000542147.1_Missense_Mutation_p.E341A|PROM2_ENST00000463580.1_3'UTR|PROM2_ENST00000317668.4_Missense_Mutation_p.E341A|PROM2_ENST00000403131.2_Missense_Mutation_p.E341A	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	341					negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of pinocytosis (GO:0048550)|positive regulation of cell projection organization (GO:0031346)|positive regulation of protein phosphorylation (GO:0001934)|regulation of Cdc42 GTPase activity (GO:0043088)	cell projection (GO:0042995)|cell surface (GO:0009986)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|microspike (GO:0044393)|microvillus (GO:0005902)|prominosome (GO:0071914)	cholesterol binding (GO:0015485)	p.E341A(1)		breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	32						GGTGTCCCCGAGGCCAACTTC	0.577																																					p.E341A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1022C	2						.						82.0	64.0	70.0					2																	95943724		2202	4300	6502	95307451	SO:0001583	missense	150696	exon8			AF245303	CCDS2012.1	2q11.1	2008-02-05			ENSG00000155066	ENSG00000155066			20685	protein-coding gene	gene with protein product						12514187	Standard	NM_001165978		Approved		uc002sui.3	Q8N271	OTTHUMG00000130393	ENST00000317620.9:c.1022A>C	2.37:g.95943724A>C	ENSP00000318270:p.Glu341Ala	Somatic		Capture	Illumina HiSeq	Phase_I	95307451	NM_144707	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535756	0.45176	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.17	4.02	0.46733	.	0.195593	0.34959	N	0.003549	T	0.39733	0.1089	M	0.73962	2.25	0.32235	N	0.573458	B	0.28128	0.201	B	0.31442	0.13	T	0.44528	-0.9322	10	0.16896	T	0.51	-27.6497	7.3658	0.26772	0.9034:0.0:0.0966:0.0	.	341	Q8N271	PROM2_HUMAN	A	341	ENSP00000385716:E341A;ENSP00000318520:E341A;ENSP00000318270:E341A;ENSP00000442542:E341A	ENSP00000318270:E341A	E	+	2	0	PROM2	95307451	0.619000	0.27059	0.964000	0.40570	0.703000	0.40648	1.998000	0.40796	1.005000	0.39183	0.533000	0.62120	GAG		0.577	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707	
STARD7-AS1	285033	broad.mit.edu	37	2	96906137	96906137	+	RNA	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:96906137C>T	ENST00000446816.1	+	0	564																											TAATTTCTTCCGAATTCAAAA	0.408																																					p.R26X												.	.	0			c.C76T	2						.						72.0	72.0	72.0					2																	96906137		1872	4101	5973	96269864			285033	exon1																															2.37:g.96906137C>T		Somatic		Capture	Illumina HiSeq	Phase_I	96269864	NM_001037228		Nonsense_Mutation	SNP	ENST00000446816.1	37																																																																																					0.408	AC012307.3-001	KNOWN	basic|exp_conf	antisense	processed_transcript	OTTHUMT00000338796.1		
ANKRD39	51239	broad.mit.edu	37	2	97520143	97520143	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:97520143G>A	ENST00000393537.4	-	2	243	c.136C>T	c.(136-138)Cga>Tga	p.R46*		NM_016466.5	NP_057550.3	Q53RE8	ANR39_HUMAN	ankyrin repeat domain 39	46								p.R46*(1)		NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)	6						TGCTTCACTCGGCCCAGGTCT	0.572																																					p.R46X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C136T	2						.						93.0	92.0	93.0					2																	97520143		2203	4300	6503	96883870	SO:0001587	stop_gained	51239	exon2			BC031303	CCDS2028.1	2q11.2	2013-01-10			ENSG00000213337	ENSG00000213337		"""Ankyrin repeat domain containing"""	28640	protein-coding gene	gene with protein product						11042152	Standard	NM_016466		Approved	MGC41816	uc002sxd.4	Q53RE8	OTTHUMG00000130530	ENST00000393537.4:c.136C>T	2.37:g.97520143G>A	ENSP00000377170:p.Arg46*	Somatic		Capture	Illumina HiSeq	Phase_I	96883870	NM_016466	Q59FU2|Q8N5X5|Q9P0S5	Nonsense_Mutation	SNP	ENST00000393537.4	37	CCDS2028.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517869	0.85495	.	.	ENSG00000213337	ENST00000393537	.	.	.	4.95	4.03	0.46877	.	0.078383	0.48767	U	0.000164	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	-0.5856	11.3695	0.49692	0.0:0.0:0.6461:0.3539	.	.	.	.	X	46	.	ENSP00000377170:R46X	R	-	1	2	ANKRD39	96883870	0.997000	0.39634	1.000000	0.80357	0.876000	0.50452	2.070000	0.41491	2.574000	0.86865	0.591000	0.81541	CGA		0.572	ANKRD39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252951.2	NM_016466	
FAM178B	51252	broad.mit.edu	37	2	97559687	97559687	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:97559687C>A	ENST00000417561.3	-	18	2195	c.2196G>T	c.(2194-2196)aaG>aaT	p.K732N	FAM178B_ENST00000393526.2_Missense_Mutation_p.K24N|FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000490605.2_Missense_Mutation_p.K584N|FAM178B_ENST00000327896.3_Missense_Mutation_p.K552N			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	732								p.K732N(1)|p.K24N(1)		large_intestine(1)|ovary(1)	2						CGGCACTAGCCTTTGGCTGTT	0.632																																					p.K24N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G72T	2						.						106.0	90.0	96.0					2																	97559687		2203	4300	6503	96923414	SO:0001583	missense	51252	exon2			AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2196G>T	2.37:g.97559687C>A	ENSP00000413245:p.Lys732Asn	Somatic		Capture	Illumina HiSeq	Phase_I	96923414	NM_016490	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		.	.	.	.	.	.	.	.	.	.	C	10.88	1.476168	0.26511	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000393526;ENST00000490605	T;T;T;T	0.48836	0.8;0.83;0.86;0.82	4.73	1.4	0.22301	.	.	.	.	.	T	0.39835	0.1093	M	0.68317	2.08	0.25630	N	0.986311	P	0.45827	0.867	B	0.38616	0.277	T	0.26326	-1.0106	9	0.40728	T	0.16	-5.3251	5.2606	0.15571	0.0:0.5548:0.0:0.4452	.	732	Q8IXR5	F178B_HUMAN	N	732;552;24;584	ENSP00000413245:K732N;ENSP00000333553:K552N;ENSP00000377160:K24N;ENSP00000429896:K584N	ENSP00000333553:K552N	K	-	3	2	FAM178B	96923414	0.850000	0.29656	0.883000	0.34634	0.260000	0.26232	0.188000	0.17018	0.417000	0.25871	0.455000	0.32223	AAG		0.632	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
TMEM131	23505	broad.mit.edu	37	2	98373724	98373724	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:98373724G>A	ENST00000186436.5	-	41	5718	c.5490C>T	c.(5488-5490)ggC>ggT	p.G1830G		NM_015348.1	NP_056163.1	Q92545	TM131_HUMAN	transmembrane protein 131	1830						integral component of membrane (GO:0016021)		p.G1717G(1)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(4)|prostate(1)|skin(1)|stomach(1)	57						TGCCCATGAGGCCGATGCTTG	0.602																																					p.G1830G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C5490T	2						.						160.0	162.0	161.0					2																	98373724		2157	4251	6408	97740156	SO:0001819	synonymous_variant	23505	exon41			AK025852	CCDS46368.1	2q11.2	2006-04-12			ENSG00000075568	ENSG00000075568			30366	protein-coding gene	gene with protein product		615659				9039502, 10996388	Standard	NM_015348		Approved	CC28, YR-23, RW1, KIAA0257, PRO1048	uc002syh.4	Q92545	OTTHUMG00000153061	ENST00000186436.5:c.5490C>T	2.37:g.98373724G>A		Somatic		Capture	Illumina HiSeq	Phase_I	97740156	NM_015348		Silent	SNP	ENST00000186436.5	37	CCDS46368.1																																																																																				0.602	TMEM131-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329285.2	XM_371542	
CNGA3	1261	broad.mit.edu	37	2	99006148	99006148	+	Silent	SNP	C	C	T	rs150944260		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:99006148C>T	ENST00000272602.2	+	5	516	c.477C>T	c.(475-477)atC>atT	p.I159I	CNGA3_ENST00000436404.2_Silent_p.I141I|CNGA3_ENST00000409937.1_Silent_p.I163I|CNGA3_ENST00000393504.1_Silent_p.I159I			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	159					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)	p.I159I(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGGATGCGATCGTGGTGGACC	0.517																																					p.I159I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C477T	2						.	C	,	1,4405	2.1+/-5.4	0,1,2202	167.0	154.0	159.0		423,477	-9.4	0.0	2	dbSNP_134	159	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CNGA3	NM_001079878.1,NM_001298.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	141/677,159/695	99006148	1,13005	2203	4300	6503	98372580	SO:0001819	synonymous_variant	1261	exon6			S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.477C>T	2.37:g.99006148C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98372580	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Silent	SNP	ENST00000272602.2	37	CCDS2034.1																																																																																				0.517	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
MGAT4A	11320	broad.mit.edu	37	2	99294774	99294774	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:99294774C>T	ENST00000264968.3	-	2	618	c.255G>A	c.(253-255)aaG>aaA	p.K85K	MGAT4A_ENST00000409391.1_Silent_p.K85K|MGAT4A_ENST00000393487.1_Silent_p.K85K			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	85					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)	p.K85K(1)		NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						TACCTGAAAACTTATTCAACG	0.294																																					p.K85K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G255A	2						.						78.0	76.0	77.0					2																	99294774		2202	4300	6502	98661206	SO:0001819	synonymous_variant	11320	exon3			AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.255G>A	2.37:g.99294774C>T		Somatic		Capture	Illumina HiSeq	Phase_I	98661206	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Silent	SNP	ENST00000264968.3	37	CCDS2036.1																																																																																				0.294	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
TSGA10	80705	broad.mit.edu	37	2	99636944	99636944	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:99636944C>A	ENST00000393483.3	-	18	2460	c.1616G>T	c.(1615-1617)aGg>aTg	p.R539M	TSGA10_ENST00000539964.1_Splice_Site_p.R539M|TSGA10_ENST00000410001.1_Splice_Site_p.R539M|TSGA10_ENST00000355053.4_Splice_Site_p.R539M	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	539					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)		p.R539M(1)		NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CTCATTCTCCCTCTGTTCAAT	0.348																																					p.R539M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1616T	2						.						36.0	36.0	36.0					2																	99636944		2203	4300	6503	99003376	SO:0001630	splice_region_variant	80705	exon18			AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"""cancer/testis antigen 79"""	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.1615-1G>T	2.37:g.99636944C>A		Somatic		Capture	Illumina HiSeq	Phase_I	99003376	NM_025244	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	8.103	0.777111	0.16120	.	.	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482	T;T;T;T;T;T	0.77620	2.54;2.54;2.54;2.54;-1.11;2.54	5.39	4.24	0.50183	.	0.310429	0.32608	N	0.005866	T	0.56848	0.2013	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.48736	-0.9009	10	0.16420	T	0.52	-4.2019	12.1177	0.53873	0.8562:0.1438:0.0:0.0	.	539	Q9BZW7	TSG10_HUMAN	M	539;539;539;539;469;539	ENSP00000377123:R539M;ENSP00000386956:R539M;ENSP00000347161:R539M;ENSP00000444419:R539M;ENSP00000386508:R469M;ENSP00000377122:R539M	ENSP00000347161:R539M	R	-	2	0	TSGA10	99003376	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	2.656000	0.46716	1.065000	0.40693	-0.272000	0.10252	AGG		0.348	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	Missense_Mutation
SLC9A4	389015	broad.mit.edu	37	2	103125345	103125345	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:103125345delA	ENST00000295269.4	+	6	1898	c.1441delA	c.(1441-1443)aaafs	p.K482fs		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	482					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.T483fs*15(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCTGGATGTTAAAAAAACCAA	0.353																																					p.K481fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1441delA	2						.						123.0	128.0	127.0					2																	103125345		2203	4300	6503	102491777	SO:0001589	frameshift_variant	389015	exon6				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1441delA	2.37:g.103125345delA	ENSP00000295269:p.Lys482fs	Somatic		Capture	Illumina HiSeq	Phase_I	102491777	NM_001011552	Q69YK0	Frame_Shift_Del	DEL	ENST00000295269.4	37	CCDS33264.1																																																																																				0.353	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
CCDC148	130940	broad.mit.edu	37	2	159077217	159077217	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:159077217delT	ENST00000283233.5	-	11	1573	c.1260delA	c.(1258-1260)aaafs	p.K420fs	CCDC148-AS1_ENST00000412781.2_RNA|CCDC148_ENST00000409187.1_Frame_Shift_Del_p.K429fs	NM_138803.3	NP_620158.3	Q8NFR7	CC148_HUMAN	coiled-coil domain containing 148	420	Glu/Lys-rich.							p.K420fs*15(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23						TGGCCCAGTATTTTTTTATCT	0.318																																					p.K420fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1260delA	2						.						75.0	69.0	71.0					2																	159077217		2203	4300	6503	158785463	SO:0001589	frameshift_variant	130940	exon11				CCDS33304.1	2q24.1	2007-12-07			ENSG00000153237	ENSG00000153237			25191	protein-coding gene	gene with protein product							Standard	NM_138803		Approved	MGC125588	uc002tzq.3	Q8NFR7	OTTHUMG00000153973	ENST00000283233.5:c.1260delA	2.37:g.159077217delT	ENSP00000283233:p.Lys420fs	Somatic		Capture	Illumina HiSeq	Phase_I	158785463	NM_138803	F5H839|Q3B7I3|Q3B7I4|Q3KR41|Q4ZG12|Q4ZG23|Q53TM6|Q96BN5|Q96LM2	Frame_Shift_Del	DEL	ENST00000283233.5	37	CCDS33304.1																																																																																				0.318	CCDC148-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333270.1	NM_138803	
ASNSD1	54529	broad.mit.edu	37	2	190531834	190531834	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:190531834delT	ENST00000260952.4	+	4	1389	c.976delT	c.(976-978)tttfs	p.F326fs	ASNSD1_ENST00000607062.1_Intron	NM_019048.2	NP_061921	Q9NWL6	ASND1_HUMAN	asparagine synthetase domain containing 1	326	Asparagine synthetase.				asparagine biosynthetic process (GO:0006529)|glutamine metabolic process (GO:0006541)		asparagine synthase (glutamine-hydrolyzing) activity (GO:0004066)	p.S327fs*19(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(3)	25			OV - Ovarian serous cystadenocarcinoma(117;0.00318)|Epithelial(96;0.0449)|all cancers(119;0.118)			TGCAATCCTGTTTTCTGGGGG	0.398																																					p.F326fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.976delT	2						.						213.0	205.0	208.0					2																	190531834		2203	4300	6503	190240079	SO:0001589	frameshift_variant	54529	exon4			AY116969	CCDS2300.1	2q32.2	2012-09-20			ENSG00000138381	ENSG00000138381			24910	protein-coding gene	gene with protein product							Standard	NM_019048		Approved	NS3TP1, FLJ20752, NBLA00058	uc002uqt.3	Q9NWL6	OTTHUMG00000132665	ENST00000260952.4:c.976delT	2.37:g.190531834delT	ENSP00000260952:p.Phe326fs	Somatic		Capture	Illumina HiSeq	Phase_I	190240079	NM_019048	D3DPH6|Q3LIC3|Q4ZG45	Frame_Shift_Del	DEL	ENST00000260952.4	37	CCDS2300.1																																																																																				0.398	ASNSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255919.3	NM_019048	
MYO1B	4430	broad.mit.edu	37	2	192257904	192257904	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:192257904delA	ENST00000392318.3	+	20	2429	c.2182delA	c.(2182-2184)aaafs	p.K729fs	MYO1B_ENST00000304164.4_Frame_Shift_Del_p.K729fs|MYO1B_ENST00000339514.4_Frame_Shift_Del_p.K729fs|MYO1B_ENST00000439065.2_Frame_Shift_Del_p.K3fs|MYO1B_ENST00000392316.1_Frame_Shift_Del_p.K729fs	NM_001130158.1	NP_001123630.1	O43795	MYO1B_HUMAN	myosin IB	729	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.|IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.				actin filament bundle assembly (GO:0051017)|actin filament organization (GO:0007015)|actin filament-based movement (GO:0030048)|metabolic process (GO:0008152)|post-Golgi vesicle-mediated transport (GO:0006892)	actin filament (GO:0005884)|brush border (GO:0005903)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.S730fs*4(1)		NS(1)|central_nervous_system(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(19)|ovary(1)	55			OV - Ovarian serous cystadenocarcinoma(117;0.0112)|Epithelial(96;0.104)|all cancers(119;0.236)			CCTGCTAATGAAAAAAAGCCA	0.428																																					p.K728fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2182delA	2						.						97.0	94.0	95.0					2																	192257904		2203	4300	6503	191966149	SO:0001589	frameshift_variant	4430	exon20			L29138	CCDS2311.1, CCDS46477.1	2q12-q34	2011-09-27			ENSG00000128641	ENSG00000128641		"""Myosins / Myosin superfamily : Class I"""	7596	protein-coding gene	gene with protein product		606537				8022818, 8449985	Standard	NM_012223		Approved	myr1	uc010fsg.2	O43795	OTTHUMG00000132718	ENST00000392318.3:c.2182delA	2.37:g.192257904delA	ENSP00000376132:p.Lys729fs	Somatic		Capture	Illumina HiSeq	Phase_I	191966149	NM_012223	O43794|Q7Z6L5	Frame_Shift_Del	DEL	ENST00000392318.3	37	CCDS46477.1																																																																																				0.428	MYO1B-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334774.1	NM_012223	
INO80D	54891	broad.mit.edu	37	2	206921296	206921296	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:206921296delG	ENST00000403263.1	-	4	994	c.590delC	c.(589-591)cctfs	p.P198fs		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	198					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P92fs*23(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						AGGTGCAGGAGGGGGACTAAA	0.532																																					p.P197fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.590delC	2						.						45.0	49.0	48.0					2																	206921296		2077	4207	6284	206629541	SO:0001589	frameshift_variant	54891	exon4				CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.590delC	2.37:g.206921296delG	ENSP00000384198:p.Pro198fs	Somatic		Capture	Illumina HiSeq	Phase_I	206629541	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Frame_Shift_Del	DEL	ENST00000403263.1	37	CCDS46500.1																																																																																				0.532	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
ZDBF2	57683	broad.mit.edu	37	2	207176058	207176058	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:207176058delT	ENST00000374423.3	+	5	7192	c.6806delT	c.(6805-6807)cttfs	p.L2270fs		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	2270							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L2270fs*1(1)		endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						GCTAAAGTGCTTTTGAACTCT	0.488																																					p.L2269fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.6806delT	2						.						35.0	38.0	37.0					2																	207176058		1889	4118	6007	206884303	SO:0001589	frameshift_variant	57683	exon5			AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.6806delT	2.37:g.207176058delT	ENSP00000363545:p.Leu2270fs	Somatic		Capture	Illumina HiSeq	Phase_I	206884303	NM_020923	Q6ZNP7|Q6ZSN8	Frame_Shift_Del	DEL	ENST00000374423.3	37	CCDS46501.1																																																																																				0.488	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
HDLBP	3069	broad.mit.edu	37	2	242202314	242202314	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr2:242202314T>C	ENST00000391975.1	-	5	489	c.262A>G	c.(262-264)Aaa>Gaa	p.K88E	HDLBP_ENST00000427183.2_Missense_Mutation_p.K124E|HDLBP_ENST00000391976.2_Missense_Mutation_p.K88E|HDLBP_ENST00000310931.4_Missense_Mutation_p.K88E	NM_203346.3	NP_976221	Q00341	VIGLN_HUMAN	high density lipoprotein binding protein	88					cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)	cytoplasm (GO:0005737)|high-density lipoprotein particle (GO:0034364)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)|poly(A) RNA binding (GO:0044822)	p.K88E(1)		breast(7)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(11)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		all_cancers(19;7.77e-41)|all_epithelial(40;1.74e-18)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00338)|Ovarian(221;0.00556)|Lung NSC(271;0.0121)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;8.13e-34)|all cancers(36;4.71e-31)|OV - Ovarian serous cystadenocarcinoma(60;2.34e-15)|Kidney(56;3.72e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.76e-08)|BRCA - Breast invasive adenocarcinoma(100;3.38e-06)|Lung(119;0.000109)|LUSC - Lung squamous cell carcinoma(224;0.000964)|Colorectal(34;0.0132)|COAD - Colon adenocarcinoma(134;0.0928)		TCCTTGTATTTTCTCTCCTCC	0.418																																					p.K88E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A262G	2						.						156.0	129.0	138.0					2																	242202314		2203	4300	6503	241850987	SO:0001583	missense	3069	exon5				CCDS2547.1, CCDS58760.1	2q37.3	2008-07-18	2008-07-18		ENSG00000115677	ENSG00000115677			4857	protein-coding gene	gene with protein product		142695	"""vigilin"""	VGL		1318310, 8390966	Standard	NM_005336		Approved	HBP	uc002waz.3	Q00341	OTTHUMG00000133391	ENST00000391975.1:c.262A>G	2.37:g.242202314T>C	ENSP00000375836:p.Lys88Glu	Somatic		Capture	Illumina HiSeq	Phase_I	241850987	NM_005336	B4DTQ2|E7EM71|Q53QU2|Q9UCY3	Missense_Mutation	SNP	ENST00000391975.1	37	CCDS2547.1	.	.	.	.	.	.	.	.	.	.	T	16.93	3.258176	0.59321	.	.	ENSG00000115677	ENST00000391975;ENST00000391976;ENST00000310931;ENST00000427183;ENST00000422933;ENST00000428482;ENST00000442714;ENST00000452065;ENST00000444092;ENST00000430918;ENST00000441124;ENST00000426343	T;T;T;T;T;T;T;T;T;T;T;T	0.55760	2.18;2.18;2.18;2.18;1.43;0.84;0.5;0.75;0.61;0.61;0.53;0.64	6.17	2.44	0.29823	.	0.088371	0.85682	D	0.000000	T	0.44912	0.1316	M	0.79926	2.475	0.30427	N	0.777584	B;P	0.44627	0.059;0.839	B;B	0.30316	0.046;0.114	T	0.51593	-0.8686	10	0.44086	T	0.13	-10.4694	8.637	0.33955	0.0:0.0622:0.2443:0.6935	.	124;88	E7EM71;Q00341	.;VIGLN_HUMAN	E	88;88;88;124;88;88;88;88;88;88;88;88	ENSP00000375836:K88E;ENSP00000375837:K88E;ENSP00000312042:K88E;ENSP00000399139:K124E;ENSP00000403807:K88E;ENSP00000405109:K88E;ENSP00000413891:K88E;ENSP00000387782:K88E;ENSP00000416559:K88E;ENSP00000403913:K88E;ENSP00000396964:K88E;ENSP00000394205:K88E	ENSP00000312042:K88E	K	-	1	0	HDLBP	241850987	1.000000	0.71417	0.069000	0.20011	0.956000	0.61745	5.028000	0.64115	0.181000	0.19994	0.533000	0.62120	AAA		0.418	HDLBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257245.5	NM_203346	
SEC62	7095	broad.mit.edu	37	3	169700647	169700648	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:169700647_169700648insA	ENST00000337002.4	+	4	462_463	c.404_405insA	c.(403-408)acaaaafs	p.TK135fs	SEC62_ENST00000480708.1_Frame_Shift_Ins_p.TK135fs|SEC62-AS1_ENST00000479626.1_RNA	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	135					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.E138fs*9(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						gatgagaagacaaaaaaagaaa	0.252																																					p.T135fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.404_405insA	3						.																																			171183342	SO:0001589	frameshift_variant	7095	exon4			D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"""translocation protein 1"""	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.411dupA	3.37:g.169700654_169700654dupA	ENSP00000337688:p.Thr135fs	Somatic		Capture	Illumina HiSeq	Phase_I	171183341	NM_003262	D3DNQ0|O00682|O00729	Frame_Shift_Ins	INS	ENST00000337002.4	37	CCDS3210.1																																																																																				0.252	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1		
SYNPR	132204	broad.mit.edu	37	3	63466634	63466635	+	Splice_Site	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:63466634_63466635insA	ENST00000295894.5	+	2	518		c.e2+2		SYNPR-AS1_ENST00000488201.1_RNA|SYNPR_ENST00000479198.1_Splice_Site|SYNPR_ENST00000465156.1_Splice_Site|SYNPR_ENST00000478744.1_Splice_Site|SYNPR_ENST00000478300.1_Splice_Site|SYNPR_ENST00000460711.1_Splice_Site	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin							cell junction (GO:0030054)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)	transporter activity (GO:0005215)	p.?(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		CCCATTCAGGTAGGGAATGGTG	0.49																																					.	NSCLC(29;1052 1116 20025 32519)											.	.	1	Unknown(1)	large_intestine(1)	.	3						.																																			63441675	SO:0001630	splice_region_variant	132204	.			AF411860	CCDS46859.1, CCDS46860.1	3p14.3	2011-07-28			ENSG00000163630	ENSG00000163630			16507	protein-coding gene	gene with protein product						8034131, 12974474	Standard	NM_144642		Approved	MGC26651, SPO	uc003dlp.3	Q8TBG9	OTTHUMG00000158699	ENST00000295894.5:c.149+2->A	3.37:g.63466635_63466635dupA		Somatic		Capture	Illumina HiSeq	Phase_I	63441674	.	B2R675|G5E9W4	Splice_Site	INS	ENST00000295894.5	37	CCDS46860.1																																																																																				0.490	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1		Intron
FANCD2	2177	broad.mit.edu	37	3	10135979	10135979	+	Missense_Mutation	SNP	C	C	T	rs555348798		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:10135979C>T	ENST00000419585.1	+	40	4056	c.3895C>T	c.(3895-3897)Cgt>Tgt	p.R1299C	FANCD2_ENST00000383806.1_3'UTR|FANCD2OS_ENST00000436517.1_Intron|FANCD2OS_ENST00000524279.1_Intron|FANCD2_ENST00000287647.3_Missense_Mutation_p.R1299C|FANCD2_ENST00000383807.1_Missense_Mutation_p.R1299C			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	1299					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.R1299C(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TCAGTATGGGCGTCTCTTTGT	0.458			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.R1299C		yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3895T	3						.						270.0	282.0	278.0					3																	10135979		2203	4300	6503	10110979	SO:0001583	missense	2177	exon40	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.3895C>T	3.37:g.10135979C>T	ENSP00000398754:p.Arg1299Cys	Somatic		Capture	Illumina HiSeq	Phase_I	10110979	NM_033084	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	C	16.93	3.257572	0.59321	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000419585	T;T;T	0.61040	0.14;0.14;0.14	5.8	4.92	0.64577	.	0.101901	0.64402	D	0.000002	T	0.77123	0.4084	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.975;0.993	T	0.81129	-0.1073	10	0.87932	D	0	.	14.081	0.64922	0.1518:0.8482:0.0:0.0	.	1299;1299	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	C	1299	ENSP00000287647:R1299C;ENSP00000373318:R1299C;ENSP00000398754:R1299C	ENSP00000287647:R1299C	R	+	1	0	FANCD2	10110979	1.000000	0.71417	0.760000	0.31359	0.497000	0.33675	5.566000	0.67372	1.449000	0.47699	-0.195000	0.12781	CGT		0.458	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
FANCD2OS	115795	broad.mit.edu	37	3	10146398	10146398	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:10146398G>A	ENST00000450660.2	-	2	277	c.61C>T	c.(61-63)Cgg>Tgg	p.R21W	FANCD2OS_ENST00000524279.1_Missense_Mutation_p.R21W	NM_001164839.1	NP_001158311.1	Q96PS1	FACOS_HUMAN	FANCD2 opposite strand	21								p.R21W(1)									GTCGTGTGCCGCAGCCATTGG	0.547																																					p.R21W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C61T	3						.						166.0	169.0	168.0					3																	10146398		2203	4300	6503	10121398	SO:0001583	missense	115795	exon2			AF230334	CCDS2596.1	3p25.3	2012-11-12	2012-11-12	2012-11-12	ENSG00000163705	ENSG00000163705			28623	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 24"""	C3orf24		12477932	Standard	NM_001164839		Approved	MGC40179	uc003buz.3	Q96PS1	OTTHUMG00000128669	ENST00000450660.2:c.61C>T	3.37:g.10146398G>A	ENSP00000429608:p.Arg21Trp	Somatic		Capture	Illumina HiSeq	Phase_I	10121398	NM_001164839		Missense_Mutation	SNP	ENST00000450660.2	37	CCDS2596.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862661	0.71949	.	.	ENSG00000163705	ENST00000524279;ENST00000453223;ENST00000450660	.	.	.	5.62	3.79	0.43588	.	0.000000	0.64402	D	0.000015	T	0.32194	0.0821	L	0.29908	0.895	0.41884	D	0.99033	D	0.63046	0.992	B	0.37015	0.239	T	0.18840	-1.0324	9	0.87932	D	0	.	11.9843	0.53138	0.0:0.0:0.5449:0.4551	.	21	Q96PS1	CC024_HUMAN	W	21;19;21	.	ENSP00000429608:R21W	R	-	1	2	C3orf24	10121398	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.190000	0.42630	0.719000	0.32188	0.558000	0.71614	CGG		0.547	FANCD2OS-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339891.2	NM_173472	
SENP7	57337	broad.mit.edu	37	3	101060567	101060567	+	Silent	SNP	G	G	A	rs201255595		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:101060567G>A	ENST00000394095.2	-	15	2216	c.2163C>T	c.(2161-2163)agC>agT	p.S721S	SENP7_ENST00000358203.3_Silent_p.S557S|SENP7_ENST00000394094.2_Silent_p.S656S|SENP7_ENST00000314261.7_Silent_p.S655S|SENP7_ENST00000394091.1_Silent_p.S557S|SENP7_ENST00000348610.3_Silent_p.S688S	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	721						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)	p.S655S(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGTAGCAACCGCTACTTTGCT	0.443													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17523	0.0		0.0	False		,,,				2504	0.0				p.S721S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2163T	3						.						118.0	100.0	106.0					3																	101060567		2203	4300	6503	102543257	SO:0001819	synonymous_variant	57337	exon15				CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.2163C>T	3.37:g.101060567G>A		Somatic		Capture	Illumina HiSeq	Phase_I	102543257	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Silent	SNP	ENST00000394095.2	37	CCDS2941.2																																																																																				0.443	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
NFKBIZ	64332	broad.mit.edu	37	3	101572405	101572405	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:101572405T>C	ENST00000326172.5	+	5	1150	c.1035T>C	c.(1033-1035)ggT>ggC	p.G345G	NFKBIZ_ENST00000394054.2_Silent_p.G245G|NFKBIZ_ENST00000326151.5_Intron	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	345	Required for transcriptional activity. {ECO:0000250}.				inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.G345G(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						CCCTTCTTGGTGATCAAAGGG	0.468																																					p.G245G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T735C	3						.						123.0	126.0	125.0					3																	101572405		2203	4300	6503	103055095	SO:0001819	synonymous_variant	64332	exon6			AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"""Ankyrin repeat domain containing"""	29805	protein-coding gene	gene with protein product	"""IL-1 inducible nuclear ankyrin-repeat protein"""	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.1035T>C	3.37:g.101572405T>C		Somatic		Capture	Illumina HiSeq	Phase_I	103055095	NM_001005474	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Silent	SNP	ENST00000326172.5	37	CCDS2946.1																																																																																				0.468	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419	
CD47	961	broad.mit.edu	37	3	107789971	107789971	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:107789971T>C	ENST00000361309.5	-	3	564	c.459A>G	c.(457-459)atA>atG	p.I153M	CD47_ENST00000355354.7_Missense_Mutation_p.I153M	NM_001777.3	NP_001768.1	Q08722	CD47_HUMAN	CD47 molecule	153					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|opsonization (GO:0008228)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of inflammatory response (GO:0050729)|positive regulation of phagocytosis (GO:0050766)|positive regulation of T cell activation (GO:0050870)|response to bacterium (GO:0009617)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)	p.I153M(1)		endometrium(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(3;0.0191)|Epithelial(53;0.118)			AGAACAGGAGTATAGCAAAAA	0.289																																					p.I153M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A459G	3						.						34.0	32.0	32.0					3																	107789971		1785	4038	5823	109272661	SO:0001583	missense	961	exon3				CCDS43125.1, CCDS43126.1	3q13.1-q13.2	2013-01-11	2006-03-28		ENSG00000196776	ENSG00000196776		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1682	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibody 1D8"", ""antigenic surface determinant protein OA3"", ""integrin associated protein"", ""Rh-related antigen"", ""leukocyte surface antigen CD47"", ""CD47 glycoprotein"""	601028	"""CD47 antigen (Rh-related antigen, integrin-associated signal transducer)"""	MER6		8294396, 2277087	Standard	XM_005247908		Approved	IAP, OA3	uc003dwt.1	Q08722	OTTHUMG00000044216	ENST00000361309.5:c.459A>G	3.37:g.107789971T>C	ENSP00000355361:p.Ile153Met	Somatic		Capture	Illumina HiSeq	Phase_I	109272661	NM_198793	A8K198|D3DN59|Q53Y71|Q96A60	Missense_Mutation	SNP	ENST00000361309.5	37	CCDS43126.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.480970	0.63849	.	.	ENSG00000196776	ENST00000355354;ENST00000361309	.	.	.	5.79	0.0759	0.14401	CD47 transmembrane (1);	0.327507	0.30235	N	0.010087	T	0.52725	0.1752	M	0.65975	2.015	0.32517	N	0.536755	D;D;D;D	0.54397	0.958;0.958;0.966;0.966	P;P;P;P	0.55161	0.66;0.66;0.77;0.77	T	0.62091	-0.6927	9	0.72032	D	0.01	.	7.1429	0.25566	0.1365:0.0:0.3996:0.4639	.	153;153;153;153	Q08722-2;Q08722-3;E9PB22;Q08722	.;.;.;CD47_HUMAN	M	153	.	ENSP00000347512:I153M	I	-	3	3	CD47	109272661	0.996000	0.38824	0.999000	0.59377	0.911000	0.54048	0.035000	0.13797	0.420000	0.25954	-0.333000	0.08304	ATA		0.289	CD47-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000102793.1	NM_001777	
HHLA2	11148	broad.mit.edu	37	3	108072520	108072520	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:108072520C>T	ENST00000357759.5	+	4	725	c.311C>T	c.(310-312)gCg>gTg	p.A104V	HHLA2_ENST00000467761.1_Missense_Mutation_p.A104V|HHLA2_ENST00000467562.1_Intron|HHLA2_ENST00000491820.1_Missense_Mutation_p.A104V|HHLA2_ENST00000489514.2_Missense_Mutation_p.A104V	NM_007072.2	NP_009003.1	Q9UM44	HHLA2_HUMAN	HERV-H LTR-associating 2	104	Ig-like V-type 1.				positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytokine production (GO:0001819)|T cell costimulation (GO:0031295)	integral component of membrane (GO:0016021)		p.A104V(1)		endometrium(2)|large_intestine(1)|lung(14)|ovary(1)	18						AATGGGAATGCGTCGCTATTT	0.403																																					p.A104V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C311T	3						.						95.0	89.0	91.0					3																	108072520		1880	4113	5993	109555210	SO:0001583	missense	11148	exon4			AF126162	CCDS46883.1, CCDS63713.1, CCDS74975.1	3q13.13	2013-01-11			ENSG00000114455	ENSG00000114455		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	4905	protein-coding gene	gene with protein product		604371				10444326	Standard	NM_007072		Approved	B7H7	uc003dwz.3	Q9UM44	OTTHUMG00000159224	ENST00000357759.5:c.311C>T	3.37:g.108072520C>T	ENSP00000350402:p.Ala104Val	Somatic		Capture	Illumina HiSeq	Phase_I	109555210	NM_007072	B4DKN2|D3DN60|Q9NWQ6	Missense_Mutation	SNP	ENST00000357759.5	37	CCDS46883.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.272502	0.59649	.	.	ENSG00000114455	ENST00000467282;ENST00000463019;ENST00000491820;ENST00000482430;ENST00000357759;ENST00000467761;ENST00000489514	T;T;T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12;-0.12;-0.12	5.46	4.58	0.56647	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.000000	0.41294	D	0.000916	T	0.67335	0.2882	L	0.53617	1.68	0.34227	D	0.67604	D;D	0.71674	0.998;0.998	D;D	0.64237	0.923;0.923	T	0.69124	-0.5228	10	0.08381	T	0.77	-12.7028	10.6398	0.45586	0.0:0.9093:0.0:0.0907	.	104;104	C9J7D0;Q9UM44	.;HHLA2_HUMAN	V	71;104;104;104;104;104;104	ENSP00000420622:A71V;ENSP00000419940:A104V;ENSP00000418284:A104V;ENSP00000418174:A104V;ENSP00000350402:A104V;ENSP00000419207:A104V;ENSP00000417856:A104V	ENSP00000350402:A104V	A	+	2	0	HHLA2	109555210	0.999000	0.42202	0.986000	0.45419	0.141000	0.21300	2.347000	0.44036	1.265000	0.44215	0.655000	0.94253	GCG		0.403	HHLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353924.1	NM_007072	
CD200R1	131450	broad.mit.edu	37	3	112648345	112648345	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:112648345G>A	ENST00000471858.1	-	3	375	c.143C>T	c.(142-144)tCa>tTa	p.S48L	CD200R1_ENST00000440122.2_Missense_Mutation_p.S71L|CD200R1_ENST00000308611.3_Missense_Mutation_p.S71L|CD200R1_ENST00000295863.4_Missense_Mutation_p.S26L|CD200R1_ENST00000490004.1_Missense_Mutation_p.S48L	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	48					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TACAGGCCATGAAGTGTTAAC	0.358																																					p.S71L												.	.	0			c.C212T	3						.						66.0	64.0	65.0					3																	112648345		2202	4300	6502	114131035	SO:0001583	missense	131450	exon4			AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.143C>T	3.37:g.112648345G>A	ENSP00000418928:p.Ser48Leu	None		Capture	Illumina HiSeq	Phase_I	114131035	NM_138939	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	37	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	G	13.82	2.351315	0.41700	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.09911	2.93;2.93;2.93;2.93;2.93	5.5	0.0712	0.14381	Immunoglobulin subtype (1);	1.323710	0.05076	N	0.482632	T	0.20414	0.0491	L	0.54323	1.7	0.09310	N	1	D;B;B;B;B	0.65815	0.995;0.244;0.395;0.158;0.244	P;B;B;B;B	0.61477	0.889;0.082;0.143;0.038;0.082	T	0.15206	-1.0445	10	0.49607	T	0.09	.	1.4045	0.02278	0.1605:0.2769:0.3188:0.2438	.	26;48;71;48;71	B4E2U2;Q8TD46-3;Q8TD46-2;Q8TD46;Q8TD46-4	.;.;.;MO2R1_HUMAN;.	L	48;71;26;71;48	ENSP00000418928:S48L;ENSP00000311035:S71L;ENSP00000295863:S26L;ENSP00000405733:S71L;ENSP00000418801:S48L	ENSP00000295863:S26L	S	-	2	0	CD200R1	114131035	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.548000	0.06048	0.230000	0.21059	0.557000	0.71058	TCA		0.358	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
BOC	91653	broad.mit.edu	37	3	112969432	112969432	+	Missense_Mutation	SNP	C	C	T	rs34208374	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:112969432C>T	ENST00000495514.1	+	4	832	c.128C>T	c.(127-129)gCg>gTg	p.A43V	BOC_ENST00000355385.3_Missense_Mutation_p.A43V|BOC_ENST00000273395.4_Missense_Mutation_p.A43V|BOC_ENST00000484034.1_Missense_Mutation_p.A43V|BOC_ENST00000485230.1_Missense_Mutation_p.A43V			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	43	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.A43V(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GTCCAGCCTGCGTCCACCGTC	0.547													c|||	24	0.00479233	0.0182	0.0	5008	,	,		22089	0.0		0.0	False		,,,				2504	0.0				p.A43V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C128T	3						.		VAL/ALA	70,4336	63.5+/-100.7	0,70,2133	109.0	104.0	105.0		128	2.9	0.0	3	dbSNP_126	105	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BOC	NM_033254.2	64	0,71,6432	TT,TC,CC		0.0116,1.5887,0.5459	benign	43/1115	112969432	71,12935	2203	4300	6503	114452122	SO:0001583	missense	91653	exon4			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.128C>T	3.37:g.112969432C>T	ENSP00000418663:p.Ala43Val	Somatic		Capture	Illumina HiSeq	Phase_I	114452122	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	c	9.648	1.140699	0.21205	0.015887	1.16E-4	ENSG00000144857	ENST00000464546;ENST00000495514;ENST00000485230;ENST00000273395;ENST00000355385;ENST00000484034	T;T;T;T;T;T	0.76709	-1.04;0.96;0.96;0.96;0.96;0.96	5.68	2.91	0.33838	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.701300	0.13589	N	0.376727	T	0.44871	0.1314	N	0.17674	0.51	0.09310	N	1	B;B;B;P	0.41929	0.196;0.056;0.018;0.765	B;B;B;B	0.38106	0.019;0.017;0.029;0.265	T	0.32508	-0.9904	10	0.30078	T	0.28	.	8.5634	0.33525	0.0:0.7093:0.0:0.2907	rs34208374	43;43;43;43	C9J2L7;Q9BWV1-3;Q9BWV1;Q96DN7	.;.;BOC_HUMAN;.	V	43	ENSP00000417362:A43V;ENSP00000418663:A43V;ENSP00000420154:A43V;ENSP00000273395:A43V;ENSP00000347546:A43V;ENSP00000417337:A43V	ENSP00000273395:A43V	A	+	2	0	BOC	114452122	0.000000	0.05858	0.001000	0.08648	0.948000	0.59901	0.217000	0.17603	0.330000	0.23485	0.651000	0.88453	GCG		0.547	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
KIAA2018	205717	broad.mit.edu	37	3	113374121	113374121	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:113374121T>C	ENST00000478658.1	-	5	6425	c.6408A>G	c.(6406-6408)tcA>tcG	p.S2136S	KIAA2018_ENST00000316407.4_Silent_p.S2136S|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	2136						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)	p.S2136S(1)		NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TGCTAGGATTTGAGAACATCT	0.413																																					p.S2136S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A6408G	3						.						150.0	141.0	144.0					3																	113374121		1928	4121	6049	114856811	SO:0001819	synonymous_variant	205717	exon7			AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.6408A>G	3.37:g.113374121T>C		Somatic		Capture	Illumina HiSeq	Phase_I	114856811	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																				0.413	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
ZNF80	7634	broad.mit.edu	37	3	113955271	113955271	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:113955271G>A	ENST00000482457.2	-	1	1154	c.651C>T	c.(649-651)taC>taT	p.Y217Y	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Y217Y(1)		NS(1)|endometrium(1)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CTTTGCACTCGTAGGGCTTTC	0.488																																					p.Y217Y	GBM(23;986 1114 21716)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C651T	3						.						110.0	113.0	112.0					3																	113955271		2203	4300	6503	115437961	SO:0001819	synonymous_variant	7634	exon1			X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.651C>T	3.37:g.113955271G>A		Somatic		Capture	Illumina HiSeq	Phase_I	115437961	NM_007136	Q6NSW4|Q6NT14	Silent	SNP	ENST00000482457.2	37	CCDS2979.1																																																																																				0.488	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
ZBTB20	26137	broad.mit.edu	37	3	114070331	114070331	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:114070331G>A	ENST00000474710.1	-	4	772	c.594C>T	c.(592-594)ggC>ggT	p.G198G	ZBTB20_ENST00000471418.1_Silent_p.G125G|ZBTB20_ENST00000462705.1_Silent_p.G125G|ZBTB20_ENST00000464560.1_Silent_p.G125G|ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000481632.1_Silent_p.G125G|ZBTB20_ENST00000393785.2_Silent_p.G125G|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000357258.3_Silent_p.G125G|ZBTB20-AS1_ENST00000475939.1_RNA	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	198						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.G125G(1)		breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(8)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	48				LUSC - Lung squamous cell carcinoma(41;0.0581)|Lung(219;0.191)		GGAACACATCGCCCACGTTCT	0.647																																					p.G125G	NSCLC(69;748 1344 9802 11203 30933)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C375T	3						.						74.0	62.0	66.0					3																	114070331		2203	4300	6503	115553021	SO:0001819	synonymous_variant	26137	exon11			AF139460	CCDS2981.1, CCDS54626.1	3q13.2	2013-01-08	2004-07-16	2004-07-16	ENSG00000181722	ENSG00000181722		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	13503	protein-coding gene	gene with protein product		606025	"""zinc finger protein 288"""	ZNF288		10965110, 11352661	Standard	XM_005247339		Approved	ODA-8S, DKFZp566F123, DPZF	uc003ebi.3	Q9HC78	OTTHUMG00000159366	ENST00000474710.1:c.594C>T	3.37:g.114070331G>A		Somatic		Capture	Illumina HiSeq	Phase_I	115553021	NM_001164343	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	37	CCDS54626.1																																																																																				0.647	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642	
STXBP5L	9515	broad.mit.edu	37	3	120673816	120673816	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:120673816C>T	ENST00000273666.6	+	3	490	c.219C>T	c.(217-219)ccC>ccT	p.P73P	STXBP5L_ENST00000497029.1_Silent_p.P73P|STXBP5L_ENST00000492541.1_Silent_p.P73P|STXBP5L_ENST00000472879.1_Silent_p.P73P|STXBP5L_ENST00000471454.1_Silent_p.P73P	NM_014980.2	NP_055795.1	Q9Y2K9	STB5L_HUMAN	syntaxin binding protein 5-like	73					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|negative regulation of insulin secretion (GO:0046676)|positive regulation of protein secretion (GO:0050714)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P73P(2)		NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(12)|lung(28)|ovary(7)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				GBM - Glioblastoma multiforme(114;0.0694)		CTCATCAGCCCACAGCATTAG	0.378																																					p.P73P												.	.	2	Substitution - coding silent(2)	large_intestine(1)|lung(1)	c.C219T	3						.						121.0	114.0	116.0					3																	120673816		1894	4122	6016	122156506	SO:0001819	synonymous_variant	9515	exon3			AB023223	CCDS43137.1	3q13.33-q21.1	2013-01-10			ENSG00000145087	ENSG00000145087		"""WD repeat domain containing"""	30757	protein-coding gene	gene with protein product		609381				10231032, 14767561	Standard	NM_014980		Approved	KIAA1006, LLGL4	uc003eec.4	Q9Y2K9	OTTHUMG00000159426	ENST00000273666.6:c.219C>T	3.37:g.120673816C>T		Somatic		Capture	Illumina HiSeq	Phase_I	122156506	NM_014980	Q4G1B4|Q6PIC3	Silent	SNP	ENST00000273666.6	37	CCDS43137.1																																																																																				0.378	STXBP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355256.3		
POLQ	10721	broad.mit.edu	37	3	121258312	121258312	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:121258312C>T	ENST00000264233.5	-	4	727	c.599G>A	c.(598-600)cGc>cAc	p.R200H		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	200	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)	p.R333H(1)		NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTCTATGAGGCGATTGATCAG	0.383								DNA polymerases (catalytic subunits)																													p.R200H	Pancreas(152;907 1925 26081 31236 36904)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G599A	3						.						123.0	121.0	121.0					3																	121258312		2203	4300	6503	122741002	SO:0001583	missense	10721	exon4			AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.599G>A	3.37:g.121258312C>T	ENSP00000264233:p.Arg200His	Somatic		Capture	Illumina HiSeq	Phase_I	122741002	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	35	5.426896	0.96131	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.15603	2.41	5.97	5.97	0.96955	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.141423	0.64402	D	0.000008	T	0.41994	0.1183	M	0.67700	2.07	0.80722	D	1	D	0.62365	0.991	D	0.63381	0.914	T	0.08785	-1.0705	10	0.72032	D	0.01	.	20.4239	0.99064	0.0:1.0:0.0:0.0	.	200	O75417	DPOLQ_HUMAN	H	200;335	ENSP00000264233:R200H	ENSP00000264233:R200H	R	-	2	0	POLQ	122741002	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.738000	0.68613	2.828000	0.97474	0.655000	0.94253	CGC		0.383	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MYLK	4638	broad.mit.edu	37	3	123357034	123357034	+	Silent	SNP	C	C	T	rs370362666		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:123357034C>T	ENST00000475616.1	-	26	4844	c.4845G>A	c.(4843-4845)gcG>gcA	p.A1615A	MYLK_ENST00000346322.5_Silent_p.A1546A|MYLK_ENST00000354792.5_Silent_p.A415A|MYLK_ENST00000359169.1_Silent_p.A1615A|MYLK_ENST00000360772.3_Silent_p.A1615A|MYLK-AS1_ENST00000485162.1_RNA|MYLK_ENST00000360304.3_Silent_p.A1615A			Q15746	MYLK_HUMAN	myosin light chain kinase	1615	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.A1615A(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TCAGAGACCCCGCATTCTCTG	0.552																																					p.A1615A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G4845A	3						.	C	,,,	0,4406		0,0,2203	60.0	61.0	61.0		4845,4638,4845,4638	-10.3	0.0	3		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	1615/1915,1546/1846,1615/1864,1546/1795	123357034	1,13005	2203	4300	6503	124839724	SO:0001819	synonymous_variant	4638	exon29			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.4845G>A	3.37:g.123357034C>T		Somatic		Capture	Illumina HiSeq	Phase_I	124839724	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																				0.552	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CHCHD6	84303	broad.mit.edu	37	3	126423216	126423216	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:126423216C>T	ENST00000290913.3	+	1	154	c.61C>T	c.(61-63)Cgg>Tgg	p.R21W	CHCHD6_ENST00000508789.1_Missense_Mutation_p.R21W	NM_032343.2	NP_115719.1	Q9BRQ6	MIC25_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 6	21					cellular response to DNA damage stimulus (GO:0006974)|cristae formation (GO:0042407)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)		p.R21W(1)		endometrium(2)|large_intestine(3)|lung(3)	8						cgaggaggagcgggtccgggt	0.781																																					p.R21W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C61T	3						.						15.0	17.0	16.0					3																	126423216		2173	4265	6438	127905906	SO:0001583	missense	84303	exon1			BC006123	CCDS3041.1	3q21.3	2012-04-17			ENSG00000159685	ENSG00000159685		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28184	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 23"", ""coiled-coil-helix cristae morphology 1"""	615634				17624330, 22228767	Standard	NM_032343		Approved	MGC13016, PPP1R23, CHCM1	uc003ejf.2	Q9BRQ6	OTTHUMG00000159601	ENST00000290913.3:c.61C>T	3.37:g.126423216C>T	ENSP00000290913:p.Arg21Trp	Somatic		Capture	Illumina HiSeq	Phase_I	127905906	NM_032343	D6R9U0|D6RIB4|H8Y0Y7	Missense_Mutation	SNP	ENST00000290913.3	37	CCDS3041.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746134	0.89663	.	.	ENSG00000159685	ENST00000290913;ENST00000508789	T;T	0.53206	0.63;0.63	3.88	3.88	0.44766	.	0.198726	0.39759	N	0.001268	T	0.63236	0.2494	M	0.62723	1.935	0.58432	D	0.999991	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.66097	-0.6008	10	0.87932	D	0	-21.5255	11.63	0.51168	0.0:1.0:0.0:0.0	.	21;21	D6R9U0;Q9BRQ6	.;CHCH6_HUMAN	W	21	ENSP00000290913:R21W;ENSP00000422912:R21W	ENSP00000290913:R21W	R	+	1	2	CHCHD6	127905906	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.385000	0.34408	2.454000	0.82982	0.591000	0.81541	CGG		0.781	CHCHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356432.1	NM_032343	
SEC61A1	29927	broad.mit.edu	37	3	127774381	127774381	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:127774381T>C	ENST00000243253.3	+	3	282	c.98T>C	c.(97-99)cTg>cCg	p.L33P	SEC61A1_ENST00000464451.1_Missense_Mutation_p.L39P|SEC61A1_ENST00000424880.2_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	33					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell growth (GO:0016049)|endoplasmic reticulum organization (GO:0007029)|posttranslational protein targeting to membrane (GO:0006620)|protein targeting to ER (GO:0045047)|response to interferon-gamma (GO:0034341)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)	p.L33P(1)		central_nervous_system(1)|kidney(1)|large_intestine(5)|liver(1)|lung(8)|ovary(1)|prostate(4)	21						GAGAAAGTGCTGTGGACCGCT	0.438																																					p.L33P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T98C	3						.						166.0	159.0	162.0					3																	127774381		2203	4300	6503	129257071	SO:0001583	missense	29927	exon3			AF077032	CCDS3046.1	3q21.3	2008-02-05			ENSG00000058262	ENSG00000058262			18276	protein-coding gene	gene with protein product		609213					Standard	NM_013336		Approved		uc003ekb.3	P61619	OTTHUMG00000159624	ENST00000243253.3:c.98T>C	3.37:g.127774381T>C	ENSP00000243253:p.Leu33Pro	Somatic		Capture	Illumina HiSeq	Phase_I	129257071	NM_013336	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	37	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	T	24.1	4.499117	0.85069	.	.	ENSG00000058262	ENST00000464451;ENST00000243253	.	.	.	5.51	5.51	0.81932	SecY subunit domain (2);	0.000000	0.85682	D	0.000000	D	0.84051	0.5387	M	0.91038	3.17	0.80722	D	1	D	0.54207	0.965	P	0.61477	0.889	D	0.87787	0.2616	9	0.72032	D	0.01	.	15.6324	0.76920	0.0:0.0:0.0:1.0	.	33	P61619	S61A1_HUMAN	P	39;33	.	ENSP00000243253:L33P	L	+	2	0	SEC61A1	129257071	1.000000	0.71417	0.639000	0.29394	0.623000	0.37688	8.035000	0.88872	2.088000	0.63022	0.528000	0.53228	CTG		0.438	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336	
IFT122	55764	broad.mit.edu	37	3	129237951	129237951	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:129237951C>T	ENST00000348417.2	+	28	3470	c.3393C>T	c.(3391-3393)agC>agT	p.S1131S	IFT122_ENST00000504021.1_Splice_Site_p.S1008S|IFT122_ENST00000349441.2_Splice_Site_p.S1021S|IFT122_ENST00000347300.2_Splice_Site_p.S1072S|IFT122_ENST00000431818.2_Splice_Site_p.S981S|IFT122_ENST00000296266.3_Splice_Site_p.S1182S|IFT122_ENST00000507564.1_Splice_Site_p.S1124S|IFT122_ENST00000440957.2_Splice_Site_p.S922S	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1131					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)		p.S1182S(1)		breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						TCCCTCCAGGCTCCCAGATTC	0.572																																					p.S1021S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3063T	3						.						117.0	120.0	119.0					3																	129237951		2203	4300	6503	130720641	SO:0001630	splice_region_variant	55764	exon25			AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3392-1C>T	3.37:g.129237951C>T		Somatic		Capture	Illumina HiSeq	Phase_I	130720641	NM_052990	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																				0.572	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	Silent
PLXND1	23129	broad.mit.edu	37	3	129291743	129291743	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:129291743C>T	ENST00000324093.4	-	14	3057	c.2879G>A	c.(2878-2880)gGt>gAt	p.G960D	PLXND1_ENST00000393239.1_Missense_Mutation_p.G960D	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	960	IPT/TIG 1.				angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.G960D(1)	PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GGTCACCACACCTGAGAGTGG	0.682																																					p.G960D	Ovarian(97;366 1484 3738 22084 39045)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2879A	3						.						66.0	55.0	59.0					3																	129291743		2202	4300	6502	130774433	SO:0001583	missense	23129	exon14			AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.2879G>A	3.37:g.129291743C>T	ENSP00000317128:p.Gly960Asp	Somatic		Capture	Illumina HiSeq	Phase_I	130774433	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	C	0.272	-0.992435	0.02162	.	.	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.76186	-1.0;-1.0	5.1	2.63	0.31362	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.370048	0.28125	N	0.016505	T	0.52996	0.1769	N	0.21508	0.67	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.29640	-1.0005	10	0.10111	T	0.7	.	6.8329	0.23921	0.0:0.0778:0.1502:0.772	.	960	Q9Y4D7	PLXD1_HUMAN	D	960	ENSP00000317128:G960D;ENSP00000376931:G960D	ENSP00000317128:G960D	G	-	2	0	PLXND1	130774433	0.985000	0.35326	0.011000	0.14972	0.002000	0.02628	2.235000	0.43044	0.248000	0.21435	-0.294000	0.09567	GGT		0.682	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
COL6A6	131873	broad.mit.edu	37	3	130285811	130285811	+	Silent	SNP	C	C	T	rs368134547		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:130285811C>T	ENST00000358511.6	+	4	1579	c.1548C>T	c.(1546-1548)ggC>ggT	p.G516G	COL6A6_ENST00000453409.2_Silent_p.G516G	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	516	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.G516G(1)		NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CAAACACAGGCGCAGCACTGA	0.453																																					p.G516G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1548T	3						.	C		1,3857		0,1,1928	85.0	88.0	87.0		1548	-10.4	0.0	3		87	1,8293		0,1,4146	no	coding-synonymous	COL6A6	NM_001102608.1		0,2,6074	TT,TC,CC		0.0121,0.0259,0.0165		516/2264	130285811	2,12150	1929	4147	6076	131768501	SO:0001819	synonymous_variant	131873	exon4			AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.1548C>T	3.37:g.130285811C>T		Somatic		Capture	Illumina HiSeq	Phase_I	131768501	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																				0.453	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
CPNE4	131034	broad.mit.edu	37	3	131415449	131415449	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:131415449T>C	ENST00000512055.1	-	9	2570	c.444A>G	c.(442-444)gaA>gaG	p.E148E	CPNE4_ENST00000502818.1_Silent_p.E166E|CPNE4_ENST00000429747.1_Silent_p.E148E|CPNE4_ENST00000511604.1_Silent_p.E148E|CPNE4_ENST00000512332.1_Silent_p.E166E			Q96A23	CPNE4_HUMAN	copine IV	148	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CAGATAATTCTTCAGCAATCA	0.408																																					p.E148E												.	.	0			c.A444G	3						.						163.0	141.0	148.0					3																	131415449		2203	4300	6503	132898139	SO:0001819	synonymous_variant	131034	exon5			H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.444A>G	3.37:g.131415449T>C		None		Capture	Illumina HiSeq	Phase_I	132898139	NM_130808	D3DNC5|Q8TEX1	Silent	SNP	ENST00000512055.1	37	CCDS3072.1																																																																																				0.408	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
SRPRB	58477	broad.mit.edu	37	3	133538556	133538556	+	Silent	SNP	C	C	T	rs373850702		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:133538556C>T	ENST00000466490.2	+	8	1047	c.762C>T	c.(760-762)gaC>gaT	p.D254D		NM_021203.3	NP_067026.3	Q9Y5M8	SRPRB_HUMAN	signal recognition particle receptor, B subunit	254					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|small GTPase mediated signal transduction (GO:0007264)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)	p.D254D(1)		breast(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|urinary_tract(2)	12						GAAGAGGGGACGTGGGCTCTG	0.527																																					p.D254D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C762T	3						.	C		1,4405	2.1+/-5.4	0,1,2202	61.0	65.0	64.0		762	-2.3	0.0	3		64	0,8600		0,0,4300	no	coding-synonymous	SRPRB	NM_021203.3		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		254/272	133538556	1,13005	2203	4300	6503	135021246	SO:0001819	synonymous_variant	58477	exon8			AK075531	CCDS3081.1	3q22.1	2004-01-29			ENSG00000144867	ENSG00000144867			24085	protein-coding gene	gene with protein product						7844142, 10859309	Standard	NM_021203		Approved	APMCF1	uc003epx.2	Q9Y5M8	OTTHUMG00000159753	ENST00000466490.2:c.762C>T	3.37:g.133538556C>T		Somatic		Capture	Illumina HiSeq	Phase_I	135021246	NM_021203	Q6P595|Q8N2D8	Silent	SNP	ENST00000466490.2	37	CCDS3081.1																																																																																				0.527	SRPRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357170.2		
CEP63	80254	broad.mit.edu	37	3	134268999	134268999	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:134268999A>T	ENST00000337090.3	+	11	1450	c.1277A>T	c.(1276-1278)cAg>cTg	p.Q426L	CEP63_ENST00000332047.5_Missense_Mutation_p.Q380L|CEP63_ENST00000513612.2_Missense_Mutation_p.Q426L|CEP63_ENST00000606977.1_Missense_Mutation_p.Q426L|CEP63_ENST00000354446.3_Missense_Mutation_p.Q380L|CEP63_ENST00000383229.3_Missense_Mutation_p.Q426L			Q96MT8	CEP63_HUMAN	centrosomal protein 63kDa	426					centriole replication (GO:0007099)|DNA damage checkpoint (GO:0000077)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|signal transduction in response to DNA damage (GO:0042770)|spindle assembly (GO:0051225)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|spindle pole (GO:0000922)		p.Q426L(1)		kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						GAGTTACATCAGCGAGATATC	0.413																																					p.Q380L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1139T	3						.						107.0	103.0	104.0					3																	134268999		2203	4300	6503	135751689	SO:0001583	missense	80254	exon10			AK056465	CCDS3086.1, CCDS43152.1, CCDS43153.1, CCDS43154.1	3q22.1	2014-02-20			ENSG00000182923	ENSG00000182923			25815	protein-coding gene	gene with protein product		614724				14654843, 24240477	Standard	NM_001042383		Approved	FLJ13386	uc003eqo.1	Q96MT8	OTTHUMG00000159725	ENST00000337090.3:c.1277A>T	3.37:g.134268999A>T	ENSP00000336524:p.Gln426Leu	Somatic		Capture	Illumina HiSeq	Phase_I	135751689	NM_001042383	D3DND8|D3DND9|D3DNE0|Q96CR0|Q9H8F5|Q9H8N0	Missense_Mutation	SNP	ENST00000337090.3	37	CCDS3086.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.5|21.5	4.156912|4.156912	0.78114|0.78114	.|.	.|.	ENSG00000182923|ENSG00000182923	ENST00000332047;ENST00000354446;ENST00000337090;ENST00000383229;ENST00000513612;ENST00000514678|ENST00000504929	T;T;T;T;T;T|.	0.38560|.	1.18;1.55;1.76;1.13;1.76;1.14|.	5.67|5.67	5.67|5.67	0.87782|0.87782	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71099|0.71099	0.3300|0.3300	M|M	0.72894|0.72894	2.215|2.215	0.43489|0.43489	D|D	0.995727|0.995727	D;D;D;D|.	0.76494|.	0.997;0.996;0.999;0.996|.	D;D;D;P|.	0.79784|.	0.993;0.913;0.945;0.852|.	T|T	0.71774|0.71774	-0.4491|-0.4491	10|5	0.62326|.	D|.	0.03|.	-14.2423|-14.2423	11.1526|11.1526	0.48469|0.48469	0.846:0.154:0.0:0.0|0.846:0.154:0.0:0.0	.|.	426;426;380;380|.	Q96MT8;Q96MT8-2;Q96MT8-4;Q96MT8-3|.	CEP63_HUMAN;.;.;.|.	L|C	380;380;426;426;426;99|115	ENSP00000328382:Q380L;ENSP00000346432:Q380L;ENSP00000336524:Q426L;ENSP00000372716:Q426L;ENSP00000426129:Q426L;ENSP00000427526:Q99L|.	ENSP00000328382:Q380L|.	Q|S	+|+	2|1	0|0	CEP63|CEP63	135751689|135751689	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	5.044000|5.044000	0.64214|0.64214	2.157000|2.157000	0.67596|0.67596	0.528000|0.528000	0.53228|0.53228	CAG|AGC		0.413	CEP63-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000470139.1	NM_025180	
NCK1	4690	broad.mit.edu	37	3	136646930	136646930	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:136646930A>G	ENST00000481752.1	+	2	251	c.87A>G	c.(85-87)ttA>ttG	p.L29L	NCK1_ENST00000288986.2_Silent_p.L29L|NCK1_ENST00000469404.1_5'Flank			P16333	NCK1_HUMAN	NCK adaptor protein 1	29	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|axon guidance (GO:0007411)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of translation (GO:0006417)|response to other organism (GO:0051707)|signal complex assembly (GO:0007172)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	cytoskeletal adaptor activity (GO:0008093)|protein kinase inhibitor activity (GO:0004860)|receptor binding (GO:0005102)|receptor signaling complex scaffold activity (GO:0030159)|receptor tyrosine kinase binding (GO:0030971)	p.L29L(1)		cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	13						ATGAGAGATTATGGCTTCTGG	0.418																																					p.L29L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A87G	3						.						128.0	118.0	121.0					3																	136646930		2203	4300	6503	138129620	SO:0001819	synonymous_variant	4690	exon2			X17576	CCDS3092.1, CCDS54644.1	3q21	2013-02-14			ENSG00000158092	ENSG00000158092		"""SH2 domain containing"""	7664	protein-coding gene	gene with protein product		600508		NCK		7806213, 9737977	Standard	XM_005247498		Approved	NCKalpha	uc003erh.3	P16333	OTTHUMG00000159781	ENST00000481752.1:c.87A>G	3.37:g.136646930A>G		Somatic		Capture	Illumina HiSeq	Phase_I	138129620	NM_006153	B7Z751|D3DNE3	Silent	SNP	ENST00000481752.1	37	CCDS3092.1	.	.	.	.	.	.	.	.	.	.	A	10.05	1.244189	0.22796	.	.	ENSG00000158092	ENST00000496489	.	.	.	5.98	-1.93	0.07594	.	.	.	.	.	T	0.48169	0.1485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41342	-0.9514	4	.	.	.	-7.3615	4.7785	0.13190	0.4073:0.0:0.3859:0.2068	.	.	.	.	C	17	.	.	Y	+	2	0	NCK1	138129620	0.948000	0.32251	1.000000	0.80357	0.988000	0.76386	0.110000	0.15437	0.059000	0.16252	0.533000	0.62120	TAT		0.418	NCK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357307.1	NM_006153	
IL20RB	53833	broad.mit.edu	37	3	136708380	136708380	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:136708380C>A	ENST00000329582.4	+	4	753	c.504C>A	c.(502-504)gcC>gcA	p.A168A	IL20RB_ENST00000309741.5_Silent_p.A121A	NM_144717.3	NP_653318.2	Q6UXL0	I20RB_HUMAN	interleukin 20 receptor beta	168	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				homeostasis of number of cells within a tissue (GO:0048873)|immune response-inhibiting signal transduction (GO:0002765)|inflammatory response to antigenic stimulus (GO:0002437)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of type IV hypersensitivity (GO:0001808)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-4 production (GO:0032753)	integral component of membrane (GO:0016021)				kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14						TCCTTGTGGCCTACTGGAGGA	0.582																																					p.A168A												.	.	0			c.C504A	3						.						64.0	64.0	64.0					3																	136708380		2203	4300	6503	138191070	SO:0001819	synonymous_variant	53833	exon4			BC033292	CCDS3093.1	3q22.3	2013-02-11			ENSG00000174564	ENSG00000174564		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	6004	protein-coding gene	gene with protein product		605621	"""fibronectin type III domain containing 6"""	FNDC6		11163236, 16703417	Standard	NM_144717		Approved	DIRS1, IL-20R2, MGC34923	uc003eri.2	Q6UXL0	OTTHUMG00000159779	ENST00000329582.4:c.504C>A	3.37:g.136708380C>A		None		Capture	Illumina HiSeq	Phase_I	138191070	NM_144717	B4DL40|Q6P438|Q8IYY5|Q8TAJ7	Silent	SNP	ENST00000329582.4	37	CCDS3093.1																																																																																				0.582	IL20RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357277.2	NM_144717	
ARMC8	25852	broad.mit.edu	37	3	137942528	137942528	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:137942528C>T	ENST00000469044.1	+	5	659	c.388C>T	c.(388-390)Cgt>Tgt	p.R130C	ARMC8_ENST00000481646.1_Missense_Mutation_p.R116C|ARMC8_ENST00000358441.2_Missense_Mutation_p.R116C|ARMC8_ENST00000538260.1_Missense_Mutation_p.R130C|ARMC8_ENST00000470821.1_Missense_Mutation_p.R130C|ARMC8_ENST00000471453.1_Missense_Mutation_p.R116C|ARMC8_ENST00000489213.1_Missense_Mutation_p.R88C|ARMC8_ENST00000491704.1_Missense_Mutation_p.R88C|ARMC8_ENST00000461822.1_Missense_Mutation_p.R130C|ARMC8_ENST00000485396.1_Missense_Mutation_p.R88C|ARMC8_ENST00000393058.3_Missense_Mutation_p.R120C	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8	130								p.R116C(2)		endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						CCGATGCCTGCGTACCATCTT	0.413																																					p.R116C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C346T	3						.						105.0	99.0	101.0					3																	137942528		2203	4300	6503	139425218	SO:0001583	missense	25852	exon6				CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"""Armadillo repeat containing"""	24999	protein-coding gene	gene with protein product	"""GID complex subunit 5, VID28 homolog (S. cerevisiae)"""					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.388C>T	3.37:g.137942528C>T	ENSP00000419413:p.Arg130Cys	Somatic		Capture	Illumina HiSeq	Phase_I	139425218	NM_213654	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Missense_Mutation	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	C	22.7	4.321308	0.81580	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461600;ENST00000466749;ENST00000358441;ENST00000489213;ENST00000461822;ENST00000485396;ENST00000471453;ENST00000470821;ENST00000471709;ENST00000538260;ENST00000393058	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.9	5.9	0.94986	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.55768	0.1941	M	0.65498	2.005	0.80722	D	1	P;D;P;D;P;D;D	0.89917	0.854;1.0;0.92;1.0;0.953;1.0;1.0	B;D;B;D;B;D;D	0.83275	0.102;0.995;0.245;0.982;0.347;0.996;0.996	T	0.51725	-0.8669	10	0.51188	T	0.08	-15.4953	17.7564	0.88450	0.0:1.0:0.0:0.0	.	88;130;130;130;116;130;116	B7Z637;B7Z441;F5GWK4;Q8IUR7;Q8IUR7-2;G5E9V6;Q8IUR7-6	.;.;.;ARMC8_HUMAN;.;.;.	C	116;130;88;130;88;116;88;130;88;116;130;130;130;120	ENSP00000420333:R116C;ENSP00000419413:R130C;ENSP00000417304:R88C;ENSP00000418074:R130C;ENSP00000417699:R88C;ENSP00000351221:R116C;ENSP00000418412:R88C;ENSP00000420706:R130C;ENSP00000417049:R88C;ENSP00000420440:R116C;ENSP00000418405:R130C;ENSP00000420719:R130C;ENSP00000441592:R130C;ENSP00000376778:R120C	ENSP00000351221:R116C	R	+	1	0	ARMC8	139425218	1.000000	0.71417	0.949000	0.38748	0.963000	0.63663	6.219000	0.72231	2.802000	0.96397	0.650000	0.86243	CGT		0.413	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	
NME9	347736	broad.mit.edu	37	3	138025300	138025300	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:138025300G>T	ENST00000333911.3	-	7	510	c.483C>A	c.(481-483)acC>acA	p.T161T	NME9_ENST00000317876.4_Silent_p.T100T|NME9_ENST00000484930.1_Silent_p.T98T|NME9_ENST00000383180.2_Silent_p.T100T|NME9_ENST00000536478.1_Silent_p.T100T|NME9_ENST00000341790.5_Silent_p.T98T			Q86XW9	TXND6_HUMAN	NME/NM23 family member 9	161	NDK.				cell redox homeostasis (GO:0045454)|CTP biosynthetic process (GO:0006241)|GTP biosynthetic process (GO:0006183)|UTP biosynthetic process (GO:0006228)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)	p.T100T(1)									TGATGGCCAAGGTACAGGTCC	0.458																																					p.T100T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C300A	3						.						165.0	143.0	150.0					3																	138025300		2203	4300	6503	139507990	SO:0001819	synonymous_variant	347736	exon8			AF196568	CCDS3099.1	3q22.3	2012-05-18	2012-05-18	2011-08-24	ENSG00000181322	ENSG00000181322			21343	protein-coding gene	gene with protein product			"""thioredoxin domain containing 6"", ""NME gene family member 9"", ""NME family member 9"""	TXNDC6		12569107, 19852809	Standard	NM_178130		Approved	TXL-2, NM23-H9	uc003ese.1	Q86XW9	OTTHUMG00000159823	ENST00000333911.3:c.483C>A	3.37:g.138025300G>T		Somatic		Capture	Illumina HiSeq	Phase_I	139507990	NM_178130	Q7Z4A8|Q8N1V7	Silent	SNP	ENST00000333911.3	37		.	.	.	.	.	.	.	.	.	.	G	0.247	-1.009299	0.02112	.	.	ENSG00000181322	ENST00000474690	.	.	.	4.95	-1.81	0.07882	.	.	.	.	.	T	0.38931	0.1059	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31475	-0.9942	4	.	.	.	-23.5263	1.1664	0.01816	0.2482:0.1174:0.3838:0.2507	.	.	.	.	I	92	.	.	L	-	1	0	TXNDC6	139507990	0.004000	0.15560	0.543000	0.28128	0.129000	0.20672	-0.771000	0.04699	-0.037000	0.13646	-0.218000	0.12543	CTT		0.458	NME9-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357583.1	NM_178130	
CNTN6	27255	broad.mit.edu	37	3	1444145	1444145	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:1444145G>T	ENST00000446702.2	+	22	3588	c.2961G>T	c.(2959-2961)gaG>gaT	p.E987D	CNTN6_ENST00000350110.2_Missense_Mutation_p.E987D|CNTN6_ENST00000539053.1_Missense_Mutation_p.E915D			Q9UQ52	CNTN6_HUMAN	contactin 6	987	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|Notch signaling pathway (GO:0007219)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.E987D(1)		breast(6)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(34)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		all_cancers(2;0.000164)|all_epithelial(2;0.107)		Epithelial(13;0.000233)|all cancers(10;0.0013)|OV - Ovarian serous cystadenocarcinoma(96;0.0139)		GCAGCAGTGAGGAAATTAGGA	0.398																																					p.E987D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2961T	3						.						115.0	111.0	112.0					3																	1444145		2203	4299	6502	1419145	SO:0001583	missense	27255	exon22			AB003592	CCDS2557.1	3p26-p25	2013-02-11			ENSG00000134115	ENSG00000134115		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	2176	protein-coding gene	gene with protein product	"""neural adhesion molecule"""	607220				9486763	Standard	NM_014461		Approved	NB-3	uc003bpa.3	Q9UQ52	OTTHUMG00000119030	ENST00000446702.2:c.2961G>T	3.37:g.1444145G>T	ENSP00000407822:p.Glu987Asp	Somatic		Capture	Illumina HiSeq	Phase_I	1419145	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.447548	0.43429	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.48201	0.82;0.82;0.82	5.46	-0.0213	0.13952	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.209069	0.33161	N	0.005213	T	0.36826	0.0981	L	0.42245	1.32	0.29382	N	0.863218	B	0.20052	0.041	B	0.20577	0.03	T	0.35450	-0.9788	10	0.51188	T	0.08	.	10.8423	0.46722	0.4262:0.0:0.5738:0.0	.	987	Q9UQ52	CNTN6_HUMAN	D	987;915;987	ENSP00000407822:E987D;ENSP00000442791:E915D;ENSP00000341882:E987D	ENSP00000341882:E987D	E	+	3	2	CNTN6	1419145	0.971000	0.33674	0.998000	0.56505	0.999000	0.98932	0.075000	0.14686	0.037000	0.15575	0.655000	0.94253	GAG		0.398	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
PIK3CB	5291	broad.mit.edu	37	3	138478104	138478104	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:138478104C>T	ENST00000477593.1	-	2	155	c.82G>A	c.(82-84)Ggc>Agc	p.G28S	PIK3CB_ENST00000289153.2_Missense_Mutation_p.G28S			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	28	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)	p.G28S(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	GGTATGGAGCCATCAGATGCT	0.458																																					p.G28S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G82A	3						.						87.0	83.0	84.0					3																	138478104		2203	4300	6503	139960794	SO:0001583	missense	5291	exon1				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.82G>A	3.37:g.138478104C>T	ENSP00000418143:p.Gly28Ser	Somatic		Capture	Illumina HiSeq	Phase_I	139960794	NM_006219	D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	CCDS3104.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.494509	0.85069	.	.	ENSG00000051382	ENST00000477593;ENST00000289153;ENST00000483968;ENST00000461451;ENST00000465581	T;T;T;T	0.71461	-0.28;-0.28;-0.56;-0.57	5.84	5.84	0.93424	.	0.229455	0.45126	D	0.000383	T	0.49440	0.1557	N	0.03608	-0.345	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.46693	-0.9173	10	0.16896	T	0.51	-6.1226	18.3357	0.90287	0.0:1.0:0.0:0.0	.	28	P42338	PK3CB_HUMAN	S	28	ENSP00000418143:G28S;ENSP00000289153:G28S;ENSP00000419857:G28S;ENSP00000420399:G28S	ENSP00000289153:G28S	G	-	1	0	PIK3CB	139960794	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.752000	0.68728	2.760000	0.94817	0.655000	0.94253	GGC		0.458	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
PXYLP1	92370	broad.mit.edu	37	3	140998292	140998292	+	Missense_Mutation	SNP	A	A	G	rs200014913		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:140998292A>G	ENST00000286353.4	+	4	448	c.311A>G	c.(310-312)tAt>tGt	p.Y104C	ACPL2_ENST00000504264.1_Missense_Mutation_p.Y87C|ACPL2_ENST00000508812.1_Missense_Mutation_p.Y95C|ACPL2_ENST00000393010.2_Missense_Mutation_p.Y104C|ACPL2_ENST00000393007.1_Missense_Mutation_p.Y88C|ACPL2_ENST00000502783.1_Missense_Mutation_p.Y66C|RP11-438D8.2_ENST00000507698.1_RNA	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		104						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)	p.Y104C(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						TACCCACTGTATGTCATTCCC	0.448											OREG0015847	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y104C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A311G	3						.	A	CYS/TYR,CYS/TYR	0,4406		0,0,2203	159.0	139.0	146.0		311,311	5.8	1.0	3		146	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ACPL2	NM_001037172.1,NM_152282.3	194,194	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging,probably-damaging	104/481,104/481	140998292	1,13005	2203	4300	6503	142480982	SO:0001583	missense	92370	exon6																														ENST00000286353.4:c.311A>G	3.37:g.140998292A>G	ENSP00000286353:p.Tyr104Cys	Somatic	1660	Capture	Illumina HiSeq	Phase_I	142480982	NM_152282	D3DNF5|Q49AJ2|W0TR04	Missense_Mutation	SNP	ENST00000286353.4	37	CCDS3116.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.157946	0.78114	0.0	1.16E-4	ENSG00000155893	ENST00000505013;ENST00000286353;ENST00000502783;ENST00000393010;ENST00000512457;ENST00000504264;ENST00000508812;ENST00000393007	T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.55893	0.1949	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.58463	-0.7632	10	0.56958	D	0.05	.	14.1628	0.65457	1.0:0.0:0.0:0.0	.	87;104	B7Z3R9;Q8TE99	.;ACPL2_HUMAN	C	104;104;66;104;66;87;95;88	ENSP00000421271:Y104C;ENSP00000286353:Y104C;ENSP00000422558:Y66C;ENSP00000376733:Y104C;ENSP00000423702:Y66C;ENSP00000426877:Y87C;ENSP00000422901:Y95C;ENSP00000376731:Y88C	ENSP00000286353:Y104C	Y	+	2	0	ACPL2	142480982	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.628000	0.83189	2.232000	0.73038	0.533000	0.62120	TAT		0.448	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2		
ZBTB38	253461	broad.mit.edu	37	3	141161266	141161266	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:141161266C>T	ENST00000514251.1	+	4	315	c.36C>T	c.(34-36)gaC>gaT	p.D12D	ZBTB38_ENST00000441582.2_Silent_p.D12D|ZBTB38_ENST00000321464.5_Silent_p.D13D					zinc finger and BTB domain containing 38									p.D12D(1)		breast(3)|cervix(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|lung(14)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	41						ACCTCAAGGACGACTTTCACA	0.433																																					p.D12D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C36T	3						.						124.0	116.0	119.0					3																	141161266		1904	4127	6031	142643956	SO:0001819	synonymous_variant	253461	exon8			BC015444	CCDS43157.1	3q23	2014-06-13			ENSG00000177311	ENSG00000177311		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	26636	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 171"""	612218				12477932	Standard	NM_001080412		Approved	FLJ35036, CIBZ, ZNF921, PPP1R171	uc003etw.3	Q8NAP3	OTTHUMG00000160128	ENST00000514251.1:c.36C>T	3.37:g.141161266C>T		Somatic		Capture	Illumina HiSeq	Phase_I	142643956	NM_001080412		Silent	SNP	ENST00000514251.1	37	CCDS43157.1																																																																																				0.433	ZBTB38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359329.2		
PLOD2	5352	broad.mit.edu	37	3	145842007	145842007	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:145842007A>G	ENST00000360060.3	-	2	296	c.119T>C	c.(118-120)tTa>tCa	p.L40S	PLOD2_ENST00000282903.5_Missense_Mutation_p.L40S|PLOD2_ENST00000494950.1_5'UTR	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	40					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)	p.L40S(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	AGTTATGACTAATAATTTATC	0.318																																					p.L40S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T119C	3						.						96.0	97.0	97.0					3																	145842007		2203	4299	6502	147324697	SO:0001583	missense	5352	exon2			U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.119T>C	3.37:g.145842007A>G	ENSP00000353170:p.Leu40Ser	Somatic		Capture	Illumina HiSeq	Phase_I	147324697	NM_000935	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	18.06	3.540168	0.65085	.	.	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000469350	T;T;T	0.53423	0.62;0.62;0.62	4.71	3.53	0.40419	.	0.000000	0.64402	D	0.000001	T	0.71500	0.3347	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.988;0.995	T	0.75345	-0.3350	10	0.87932	D	0	-32.1881	11.1684	0.48556	0.8453:0.1547:0.0:0.0	.	40;40	O00469;O00469-2	PLOD2_HUMAN;.	S	40;40;12	ENSP00000282903:L40S;ENSP00000353170:L40S;ENSP00000419963:L12S	ENSP00000282903:L40S	L	-	2	0	PLOD2	147324697	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.964000	0.87933	0.637000	0.30526	0.386000	0.25728	TTA		0.318	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
TM4SF1	4071	broad.mit.edu	37	3	149095315	149095315	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:149095315G>A	ENST00000305366.3	-	1	337	c.20C>T	c.(19-21)gCa>gTa	p.A7V	TM4SF1_ENST00000472441.1_5'Flank|TM4SF1-AS1_ENST00000496491.1_RNA|TM4SF1-AS1_ENST00000484046.1_RNA	NM_014220.2	NP_055035.1	P30408	T4S1_HUMAN	transmembrane 4 L six family member 1	7						integral component of plasma membrane (GO:0005887)		p.A7V(1)		endometrium(3)|large_intestine(1)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			GATGCATCGTGCACACTTCCC	0.498																																					p.A7V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C20T	3						.						140.0	140.0	140.0					3																	149095315		2203	4300	6503	150578005	SO:0001583	missense	4071	exon1			M90657	CCDS3143.1	3q21-q25	2005-03-21	2005-03-21		ENSG00000169908	ENSG00000169908			11853	protein-coding gene	gene with protein product		191155	"""transmembrane 4 superfamily member 1"""	M3S1		1565644	Standard	NM_014220		Approved	L6	uc003exb.1	P30408	OTTHUMG00000159597	ENST00000305366.3:c.20C>T	3.37:g.149095315G>A	ENSP00000304277:p.Ala7Val	Somatic		Capture	Illumina HiSeq	Phase_I	150578005	NM_014220	Q6IB51	Missense_Mutation	SNP	ENST00000305366.3	37	CCDS3143.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.589015	0.66105	.	.	ENSG00000169908	ENST00000305366;ENST00000383054	T	0.35789	1.29	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.62660	0.2446	M	0.88450	2.955	0.80722	D	1	P	0.49090	0.919	P	0.54346	0.749	T	0.70132	-0.4956	10	0.72032	D	0.01	-20.367	19.4015	0.94632	0.0:0.0:1.0:0.0	.	7	P30408	T4S1_HUMAN	V	7	ENSP00000304277:A7V	ENSP00000304277:A7V	A	-	2	0	TM4SF1	150578005	0.812000	0.29077	0.143000	0.22291	0.004000	0.04260	4.226000	0.58606	2.585000	0.87301	0.655000	0.94253	GCA		0.498	TM4SF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356368.1		
ERICH6	131831	broad.mit.edu	37	3	150377751	150377751	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:150377751G>A	ENST00000295910.6	-	14	1972	c.1920C>T	c.(1918-1920)gcC>gcT	p.A640A	FAM194A_ENST00000491361.1_Silent_p.A494A	NM_152394.3	NP_689607.2												p.A640A(1)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TGTGACAAAGGGCAATTAGTT	0.313																																					p.A640A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1920T	3						.						95.0	101.0	99.0					3																	150377751		2203	4300	6503	151860441	SO:0001819	synonymous_variant	131831	exon14																														ENST00000295910.6:c.1920C>T	3.37:g.150377751G>A		Somatic		Capture	Illumina HiSeq	Phase_I	151860441	NM_152394		Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																				0.313	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
MED12L	116931	broad.mit.edu	37	3	151127075	151127075	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:151127075G>A	ENST00000474524.1	+	38	5798	c.5760G>A	c.(5758-5760)cgG>cgA	p.R1920R	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1920	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.R1920R(1)		NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CGCAAGCACGGCCCTCCCCTC	0.527																																					p.R1920R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G5760A	3						.						74.0	76.0	75.0					3																	151127075		2203	4300	6503	152609765	SO:0001819	synonymous_variant	116931	exon38			AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5760G>A	3.37:g.151127075G>A		Somatic		Capture	Illumina HiSeq	Phase_I	152609765	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																				0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
P2RY1	5028	broad.mit.edu	37	3	152553998	152553998	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:152553998A>G	ENST00000305097.3	+	1	1263	c.427A>G	c.(427-429)Aca>Gca	p.T143A		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	143					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|aging (GO:0007568)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cell surface receptor signaling pathway (GO:0007166)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of binding (GO:0051100)|negative regulation of norepinephrine secretion (GO:0010700)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of hormone secretion (GO:0046887)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of ion transport (GO:0043270)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to plasma membrane (GO:0072659)|regulation of receptor activity (GO:0010469)|regulation of vasodilation (GO:0042312)|relaxation of muscle (GO:0090075)|response to growth factor (GO:0070848)|response to mechanical stimulus (GO:0009612)|sensory perception of pain (GO:0019233)|signal transduction involved in regulation of gene expression (GO:0023019)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell body (GO:0044297)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ADP binding (GO:0043531)|ADP-activated nucleotide receptor activity (GO:0045032)|ATP binding (GO:0005524)|ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)	p.T143A(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)	23			LUSC - Lung squamous cell carcinoma(72;0.0628)|Lung(72;0.11)			CTTGTTTCTGACATGCATCAG	0.502																																					p.T143A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A427G	3						.						83.0	75.0	77.0					3																	152553998		2203	4300	6503	154036688	SO:0001583	missense	5028	exon1			U42029	CCDS3169.1	3q25.2	2012-08-08			ENSG00000169860	ENSG00000169860		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8539	protein-coding gene	gene with protein product		601167				8579591	Standard	NM_002563		Approved	P2Y1	uc003ezq.3	P47900	OTTHUMG00000159694	ENST00000305097.3:c.427A>G	3.37:g.152553998A>G	ENSP00000304767:p.Thr143Ala	Somatic		Capture	Illumina HiSeq	Phase_I	154036688	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	A	16.95	3.262344	0.59431	.	.	ENSG00000169860	ENST00000305097	T	0.72505	-0.66	5.76	4.6	0.57074	GPCR, rhodopsin-like superfamily (1);	0.054496	0.64402	D	0.000001	T	0.65544	0.2701	L	0.53249	1.67	0.80722	D	1	B	0.15930	0.015	B	0.20577	0.03	T	0.65874	-0.6062	10	0.62326	D	0.03	.	11.2454	0.48993	0.9276:0.0:0.0724:0.0	.	143	P47900	P2RY1_HUMAN	A	143	ENSP00000304767:T143A	ENSP00000304767:T143A	T	+	1	0	P2RY1	154036688	1.000000	0.71417	0.350000	0.25708	0.938000	0.57974	6.149000	0.71795	2.186000	0.69663	0.533000	0.62120	ACA		0.502	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563	
ANKRD28	23243	broad.mit.edu	37	3	15762452	15762452	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:15762452T>C	ENST00000399451.2	-	8	1243	c.876A>G	c.(874-876)ctA>ctG	p.L292L	ANKRD28_ENST00000497037.1_5'UTR|ANKRD28_ENST00000383777.1_Silent_p.L325L	NM_001195098.1|NM_001195099.1|NM_015199.3	NP_001182027.1|NP_001182028.1|NP_056014.2	O15084	ANR28_HUMAN	ankyrin repeat domain 28	292						nucleus (GO:0005634)		p.L325L(1)		breast(2)|endometrium(1)|large_intestine(2)|prostate(1)	6						CATTGCCAACTAGAAGCTCTA	0.373																																					p.L292L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A876G	3						.						111.0	105.0	107.0					3																	15762452		1890	4118	6008	15737456	SO:0001819	synonymous_variant	23243	exon8			AY367056	CCDS46769.1, CCDS74908.1	3p25.1	2013-01-10			ENSG00000206560	ENSG00000206560		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	29024	protein-coding gene	gene with protein product	"""phosphatase interactor targeting K protein"", ""protein phosphatase 6 ankyrin repeat subunit A"", ""protein phosphatase 1, regulatory subunit 65"""	611122				9205841	Standard	NM_015199		Approved	KIAA0379, PITK, PP6-ARS-A, PPP1R65	uc003caj.1	O15084	OTTHUMG00000155379	ENST00000399451.2:c.876A>G	3.37:g.15762452T>C		Somatic		Capture	Illumina HiSeq	Phase_I	15737456	NM_015199	B4DES5|Q1WWL4|Q29RW6|Q3B857|Q6ULS0|Q6ZT57	Silent	SNP	ENST00000399451.2	37	CCDS46769.1																																																																																				0.373	ANKRD28-003	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339758.1	NM_015199	
RFTN1	23180	broad.mit.edu	37	3	16535234	16535234	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:16535234G>A	ENST00000334133.4	-	2	415	c.143C>T	c.(142-144)gCt>gTt	p.A48V		NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	48					B cell receptor signaling pathway (GO:0050853)|dsRNA transport (GO:0033227)|growth (GO:0040007)|interleukin-17 production (GO:0032620)|membrane raft assembly (GO:0001765)|protein localization to membrane raft (GO:1903044)|protein transport into membrane raft (GO:0032596)|response to exogenous dsRNA (GO:0043330)|T cell antigen processing and presentation (GO:0002457)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 3 signaling pathway (GO:0034138)	cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	double-stranded RNA binding (GO:0003725)	p.A48V(1)		central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(8)|lung(8)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	38						GTACTCACCAGCACTCAGAGT	0.572																																					p.A48V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C143T	3						.						155.0	160.0	158.0					3																	16535234		2203	4300	6503	16510238	SO:0001583	missense	23180	exon2			D42043	CCDS33712.1	3p24.3	2010-04-09			ENSG00000131378	ENSG00000131378			30278	protein-coding gene	gene with protein product	"""raft-linking protein"""					7788527, 12805216	Standard	NM_015150		Approved	MIG2, KIAA0084, FLJ23866, Raftlin	uc003cay.3	Q14699	OTTHUMG00000156973	ENST00000334133.4:c.143C>T	3.37:g.16535234G>A	ENSP00000334153:p.Ala48Val	Somatic		Capture	Illumina HiSeq	Phase_I	16510238	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	G	16.33	3.093795	0.56075	.	.	ENSG00000131378	ENST00000334133;ENST00000451036;ENST00000449415;ENST00000441460;ENST00000431547	T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5	5.44	3.47	0.39725	.	0.462954	0.21337	N	0.076192	T	0.30823	0.0777	L	0.52573	1.65	0.09310	N	1	P	0.45827	0.867	P	0.47346	0.544	T	0.09143	-1.0688	10	0.42905	T	0.14	-17.2506	6.4882	0.22101	0.0958:0.0:0.5117:0.3926	.	48	Q14699	RFTN1_HUMAN	V	48	ENSP00000334153:A48V;ENSP00000403997:A48V;ENSP00000409427:A48V;ENSP00000388718:A48V;ENSP00000393216:A48V	ENSP00000334153:A48V	A	-	2	0	RFTN1	16510238	0.986000	0.35501	0.034000	0.17996	0.410000	0.31052	5.874000	0.69652	1.304000	0.44892	0.561000	0.74099	GCT		0.572	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150	
KCNAB1	7881	broad.mit.edu	37	3	155861197	155861197	+	Intron	SNP	G	G	A	rs183217804		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:155861197G>A	ENST00000490337.1	+	1	339				KCNAB1_ENST00000389636.5_Intron|KCNAB1_ENST00000471742.1_Missense_Mutation_p.G77D	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1						learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)	p.G77D(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GCAGAGACGGGCATGGCATAC	0.458																																					p.G77D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G230A	3						.						112.0	109.0	110.0					3																	155861197		2203	4300	6503	157343891	SO:0001627	intron_variant	7881	exon1			U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.275+22522G>A	3.37:g.155861197G>A		Somatic		Capture	Illumina HiSeq	Phase_I	157343891	NM_003471	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	37	CCDS3174.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219565	0.58560	.	.	ENSG00000169282	ENST00000471742	T	0.06768	3.26	5.29	5.29	0.74685	.	.	.	.	.	T	0.11324	0.0276	.	.	.	0.80722	D	1	B	0.26602	0.154	B	0.33254	0.16	T	0.09552	-1.0669	8	0.44086	T	0.13	.	16.7891	0.85583	0.0:0.0:1.0:0.0	.	77	Q14722-3	.	D	77	ENSP00000418956:G77D	ENSP00000418956:G77D	G	+	2	0	KCNAB1	157343891	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.688000	0.54699	2.622000	0.88805	0.561000	0.74099	GGC		0.458	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
MECOM	2122	broad.mit.edu	37	3	168833701	168833701	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:168833701C>A	ENST00000464456.1	-	7	2595	c.1395G>T	c.(1393-1395)gcG>gcT	p.A465A	MECOM_ENST00000472280.1_Silent_p.A466A|MECOM_ENST00000433243.2_Silent_p.A466A|MECOM_ENST00000264674.3_Silent_p.A530A|MECOM_ENST00000468789.1_Silent_p.A465A|MECOM_ENST00000460814.1_Silent_p.A465A|MECOM_ENST00000392736.3_Silent_p.A465A|MECOM_ENST00000494292.1_Silent_p.A653A	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A465A(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						CTCCTGACACCGCAGTCTGCT	0.393																																					p.A530A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1590T	3						.						289.0	261.0	270.0					3																	168833701		2203	4300	6503	170316395	SO:0001819	synonymous_variant	2122	exon8			S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.1395G>T	3.37:g.168833701C>A		Somatic		Capture	Illumina HiSeq	Phase_I	170316395	NM_001105077	Q13466|Q6FH90	Silent	SNP	ENST00000464456.1	37	CCDS54669.1																																																																																				0.393	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
CLDN11	5010	broad.mit.edu	37	3	170150441	170150441	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:170150441T>A	ENST00000064724.3	+	3	723	c.521T>A	c.(520-522)gTc>gAc	p.V174D	CLDN11_ENST00000489485.1_3'UTR|CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_005602.5	NP_005593.2	O75508	CLD11_HUMAN	claudin 11	174					axon ensheathment (GO:0008366)|calcium-independent cell-cell adhesion (GO:0016338)|spermatogenesis (GO:0007283)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)	p.V174D(1)		central_nervous_system(2)|endometrium(2)|large_intestine(1)|liver(2)|lung(3)|ovary(2)	12	all_cancers(22;5.62e-23)|all_epithelial(15;7.54e-28)|all_lung(20;2.51e-17)|Lung NSC(18;1.02e-16)|Ovarian(172;0.000567)|Breast(254;0.137)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.197)			GGTGGCTGTGTCATCCTCTGC	0.592																																					p.V174D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T521A	3						.						178.0	162.0	167.0					3																	170150441		2203	4300	6503	171633135	SO:0001583	missense	5010	exon3			AF068863	CCDS3213.1	3q26.2-q26.3	2008-08-01	2008-08-01		ENSG00000013297	ENSG00000013297		"""Claudins"""	8514	protein-coding gene	gene with protein product		601326	"""oligodendrocyte transmembrane protein"""	OTM		8661061, 8797478	Standard	NM_005602		Approved	OSP	uc003fgx.3	O75508	OTTHUMG00000158940	ENST00000064724.3:c.521T>A	3.37:g.170150441T>A	ENSP00000064724:p.Val174Asp	Somatic		Capture	Illumina HiSeq	Phase_I	171633135	NM_005602	B2R7C1|D3DNQ5|Q5U0P3	Missense_Mutation	SNP	ENST00000064724.3	37	CCDS3213.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.912436	0.92178	.	.	ENSG00000013297	ENST00000064724	D	0.87491	-2.26	5.83	5.83	0.93111	.	0.115109	0.64402	D	0.000020	D	0.87216	0.6122	L	0.55990	1.75	0.80722	D	1	P	0.51791	0.948	P	0.46026	0.501	D	0.88794	0.3280	10	0.87932	D	0	.	16.2127	0.82178	0.0:0.0:0.0:1.0	.	174	O75508	CLD11_HUMAN	D	174	ENSP00000064724:V174D	ENSP00000064724:V174D	V	+	2	0	CLDN11	171633135	1.000000	0.71417	0.995000	0.50966	0.967000	0.64934	5.733000	0.68571	2.236000	0.73375	0.533000	0.62120	GTC		0.592	CLDN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352403.1	NM_005602	
TBC1D5	9779	broad.mit.edu	37	3	17418097	17418097	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:17418097G>A	ENST00000253692.7	-	10	2285	c.621C>T	c.(619-621)caC>caT	p.H207H	TBC1D5_ENST00000446818.2_Silent_p.H207H|TBC1D5_ENST00000429924.2_Silent_p.H159H|TBC1D5_ENST00000414318.2_Intron|TBC1D5_ENST00000429383.4_Silent_p.H207H	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	207	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.					retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)	p.H207H(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						CTAACAGTTCGTGCATGCCCT	0.393																																					p.H207H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C621T	3						.						85.0	89.0	88.0					3																	17418097		2203	4300	6503	17393101	SO:0001819	synonymous_variant	9779	exon10			D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.621C>T	3.37:g.17418097G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17393101	NM_001134380	A6NP25|C9JP52	Silent	SNP	ENST00000253692.7	37	CCDS33714.1																																																																																				0.393	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
SLC7A14	57709	broad.mit.edu	37	3	170185083	170185083	+	Silent	SNP	C	C	T	rs200086652		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:170185083C>T	ENST00000231706.5	-	8	2391	c.2076G>A	c.(2074-2076)acG>acA	p.T692T	CLDN11_ENST00000451576.1_Intron|CLDN11_ENST00000486975.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	692					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)	amino acid transmembrane transporter activity (GO:0015171)	p.T692T(1)		central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(23)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(4)	53	all_cancers(22;2.41e-22)|all_epithelial(15;4.2e-27)|all_lung(20;1.17e-16)|Lung NSC(18;4.91e-16)|Ovarian(172;0.000902)|Breast(254;0.137)		Lung(28;6.23e-13)|LUSC - Lung squamous cell carcinoma(14;1.48e-12)			AGCGTTGGTACGTGCTTTGGT	0.587													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13566	0.0		0.0	False		,,,				2504	0.0				p.T692T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2076A	3						.						63.0	66.0	65.0					3																	170185083		2203	4300	6503	171667777	SO:0001819	synonymous_variant	57709	exon8			BC022968	CCDS33892.1	3q26.2	2014-06-13	2013-07-19		ENSG00000013293	ENSG00000013293		"""Solute carriers"""	29326	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 142"""	615720					Standard	NM_020949		Approved	KIAA1613, PPP1R142	uc003fgz.2	Q8TBB6	OTTHUMG00000158941	ENST00000231706.5:c.2076G>A	3.37:g.170185083C>T		Somatic		Capture	Illumina HiSeq	Phase_I	171667777	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																				0.587	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949	
PIK3CA	5290	broad.mit.edu	37	3	178952085	178952085	+	Missense_Mutation	SNP	A	A	G	rs121913279		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:178952085A>G	ENST00000263967.3	+	21	3297	c.3140A>G	c.(3139-3141)cAt>cGt	p.H1047R	RP11-245C23.3_ENST00000609807.1_RNA	NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	1047	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		H -> L (in BC; unknown pathological significance). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16353168}.|H -> R (in CLOVE, KERSEB, CRC, BC and OC; also found in an endometrial carcinoma sample; shows an increase in lipid kinase activity; oncogenic in vivo; requires binding to p85 regulatory subunit to induce cellular transformation but not interaction with RAS; may mimic the conformatitonal change triggered by the interaction with RAS; enhances invadopodia-mediated extracellular matrix degradation and invasion in breast cancer cells; increases lipid kinase activity; may alter the interaction of the PI3K/ PI4K kinase domain with the cell membrane). {ECO:0000269|PubMed:15016963, ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15520168, ECO:0000269|PubMed:15712344, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16114017, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|H -> Y (in MCAP; also found in an endometrial carcinoma sample). {ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H1047R(1387)|p.H1047L(194)|p.H1047P(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	AATGATGCACATCATGGTGGC	0.378	H1047L(EFM19_BREAST)|H1047R(BT20_BREAST)|H1047R(CAL29_URINARY_TRACT)|H1047R(CAL33_UPPER_AERODIGESTIVE_TRACT)|H1047R(DETROIT562_UPPER_AERODIGESTIVE_TRACT)|H1047R(HCC1954_BREAST)|H1047R(HCT116_LARGE_INTESTINE)|H1047R(HSC2_UPPER_AERODIGESTIVE_TRACT)|H1047R(LS180_LARGE_INTESTINE)|H1047R(MCAS_OVARY)|H1047R(MDAMB453_BREAST)|H1047R(NCIH1048_LUNG)|H1047R(RKO_LARGE_INTESTINE)|H1047R(SKOV3_OVARY)|H1047R(T47D_BREAST)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.H1047R	Colon(199;1504 1750 3362 26421 31210 32040)		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	PIK3CA,breast,NS,Substitution - Missense,0 	.	1582	Substitution - Missense(1582)	breast(961)|large_intestine(245)|endometrium(114)|ovary(77)|urinary_tract(36)|upper_aerodigestive_tract(26)|lung(19)|central_nervous_system(19)|stomach(19)|haematopoietic_and_lymphoid_tissue(11)|thyroid(10)|NS(9)|liver(7)|kidney(6)|soft_tissue(6)|skin(4)|prostate(4)|pituitary(3)|pancreas(3)|meninges(1)|cervix(1)|bone(1)	c.A3140G	3						.						99.0	89.0	92.0					3																	178952085		1912	4130	6042	180434779	SO:0001583	missense	5290	exon21				CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.3140A>G	3.37:g.178952085A>G	ENSP00000263967:p.His1047Arg	Somatic		Capture	Illumina HiSeq	Phase_I	180434779	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.506328	0.44558	.	.	ENSG00000121879	ENST00000263967	T	0.80214	-1.35	6.08	6.08	0.98989	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	T	0.62466	0.2430	N	0.08118	0	0.80722	D	1	P	0.38597	0.639	B	0.28011	0.085	T	0.67526	-0.5648	10	0.40728	T	0.16	-21.2893	16.6512	0.85203	1.0:0.0:0.0:0.0	.	1047	P42336	PK3CA_HUMAN	R	1047	ENSP00000263967:H1047R	ENSP00000263967:H1047R	H	+	2	0	PIK3CA	180434779	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.859000	0.92264	2.333000	0.79357	0.482000	0.46254	CAT		0.378	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
ACTL6A	86	broad.mit.edu	37	3	179292182	179292182	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:179292182A>C	ENST00000429709.2	+	5	616	c.403A>C	c.(403-405)Aaa>Caa	p.K135Q	ACTL6A_ENST00000450518.2_Missense_Mutation_p.K93Q|ACTL6A_ENST00000392662.1_Missense_Mutation_p.K93Q	NM_004301.3	NP_004292.1	O96019	ACL6A_HUMAN	actin-like 6A	135					ATP-dependent chromatin remodeling (GO:0043044)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|nervous system development (GO:0007399)|neural retina development (GO:0003407)|regulation of growth (GO:0040008)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|npBAF complex (GO:0071564)|NuA4 histone acetyltransferase complex (GO:0035267)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|transcription coactivator activity (GO:0003713)	p.K135Q(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|urinary_tract(1)	21	all_cancers(143;3.94e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)			AAAGAGAGAGAAACTGACAGA	0.363																																					p.K93Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A277C	3						.						174.0	174.0	174.0					3																	179292182		2203	4300	6503	180774876	SO:0001583	missense	86	exon5			AK098691	CCDS3231.1, CCDS43174.1	3q26.33	2011-07-06			ENSG00000136518	ENSG00000136518		"""INO80 complex subunits"""	24124	protein-coding gene	gene with protein product	"""BAF complex 53 kDa subunit"", ""BRG1-associated factor"", ""actin-related protein 4"", ""INO80 complex subunit K"""	604958				9845365, 10380635	Standard	NM_004301		Approved	Actl6, BAF53A, Arp4, Baf53a, INO80K	uc003fjw.3	O96019	OTTHUMG00000157782	ENST00000429709.2:c.403A>C	3.37:g.179292182A>C	ENSP00000397552:p.Lys135Gln	Somatic		Capture	Illumina HiSeq	Phase_I	180774876	NM_178042	B3KMN1|D3DNR9|Q8TAE5|Q9BVS8|Q9H0W6	Missense_Mutation	SNP	ENST00000429709.2	37	CCDS3231.1	.	.	.	.	.	.	.	.	.	.	A	31	5.079151	0.94050	.	.	ENSG00000136518	ENST00000429709;ENST00000450518;ENST00000392662	D;D;D	0.95588	-3.75;-3.75;-3.75	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.96131	0.8739	M	0.69523	2.12	0.80722	D	1	D	0.52996	0.957	P	0.50570	0.644	D	0.96226	0.9164	10	0.62326	D	0.03	.	16.5655	0.84588	1.0:0.0:0.0:0.0	.	135	O96019	ACL6A_HUMAN	Q	135;93;93	ENSP00000397552:K135Q;ENSP00000394014:K93Q;ENSP00000376430:K93Q	ENSP00000376430:K93Q	K	+	1	0	ACTL6A	180774876	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.316000	0.96319	2.302000	0.77476	0.533000	0.62120	AAA		0.363	ACTL6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349599.1	NM_004301	
CCDC39	339829	broad.mit.edu	37	3	180372696	180372696	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:180372696C>T	ENST00000442201.2	-	7	903	c.784G>A	c.(784-786)Gtt>Att	p.V262I	CCDC39_ENST00000273654.4_Missense_Mutation_p.V346I	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	262					axonemal dynein complex assembly (GO:0070286)|cilium-dependent cell motility (GO:0060285)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)		p.V346I(1)|p.V262I(1)		NS(1)|breast(1)|endometrium(4)|large_intestine(9)|lung(22)|ovary(6)|prostate(2)	45	all_cancers(143;9.31e-15)|Ovarian(172;0.0212)		OV - Ovarian serous cystadenocarcinoma(80;5.62e-23)|GBM - Glioblastoma multiforme(14;0.000558)			TTTTCTTTAACCAAATTTTCT	0.289																																					p.V262I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G784A	3						.						147.0	126.0	132.0					3																	180372696		1795	4071	5866	181855390	SO:0001583	missense	339829	exon7			BC047103	CCDS46964.1	3q26.33	2012-07-27			ENSG00000145075	ENSG00000145075			25244	protein-coding gene	gene with protein product		613798				21131972	Standard	NM_181426		Approved	DKFZp434A128, CILD14, FAP59	uc010hxe.3	Q9UFE4	OTTHUMG00000157857	ENST00000442201.2:c.784G>A	3.37:g.180372696C>T	ENSP00000405708:p.Val262Ile	Somatic		Capture	Illumina HiSeq	Phase_I	181855390	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	C	1.408	-0.576392	0.03882	.	.	ENSG00000145075	ENST00000273654;ENST00000442201	T;T	0.20332	2.08;2.08	5.5	2.26	0.28386	.	0.311787	0.31554	N	0.007453	T	0.06781	0.0173	N	0.04018	-0.295	0.24531	N	0.994117	B	0.29162	0.235	B	0.23419	0.046	T	0.31081	-0.9956	10	0.15952	T	0.53	-11.4302	4.4647	0.11684	0.0:0.3858:0.2246:0.3896	.	262	Q9UFE4	CCD39_HUMAN	I	346;262	ENSP00000273654:V346I;ENSP00000405708:V262I	ENSP00000273654:V346I	V	-	1	0	CCDC39	181855390	1.000000	0.71417	0.940000	0.37924	0.568000	0.35870	0.879000	0.28146	0.809000	0.34255	-0.253000	0.11424	GTT		0.289	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028	
EIF4G1	1981	broad.mit.edu	37	3	184037581	184037581	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:184037581C>T	ENST00000346169.2	+	7	800	c.529C>T	c.(529-531)Cgt>Tgt	p.R177C	EIF4G1_ENST00000441154.1_Missense_Mutation_p.R13C|EIF4G1_ENST00000319274.6_Missense_Mutation_p.R177C|EIF4G1_ENST00000392537.2_Missense_Mutation_p.R90C|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000435046.2_5'Flank|EIF4G1_ENST00000414031.1_Missense_Mutation_p.R137C|EIF4G1_ENST00000350481.5_Missense_Mutation_p.R13C|EIF4G1_ENST00000434061.2_5'Flank|EIF4G1_ENST00000382330.3_Missense_Mutation_p.R184C|EIF4G1_ENST00000427845.1_Missense_Mutation_p.R90C|EIF4G1_ENST00000342981.4_Missense_Mutation_p.R177C|EIF4G1_ENST00000424196.1_Missense_Mutation_p.R184C|EIF4G1_ENST00000411531.1_Missense_Mutation_p.R137C|EIF4G1_ENST00000352767.3_Missense_Mutation_p.R184C	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	177	PABPC1-binding.				cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)	p.R177C(1)		central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CAAGAGGGAGCGTAAGACGGT	0.597																																					p.R177C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C529T	3						.						23.0	19.0	21.0					3																	184037581		2202	4297	6499	185520275	SO:0001583	missense	1981	exon6			D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.529C>T	3.37:g.184037581C>T	ENSP00000316879:p.Arg177Cys	Somatic		Capture	Illumina HiSeq	Phase_I	185520275	NM_182917	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.968416	0.74131	.	.	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427141;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000456033;ENST00000411531;ENST00000444861;ENST00000441154	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.36340	2.0;2.0;2.0;2.0;2.0;2.0;2.0;3.26;2.0;1.26;2.0;2.0;2.0;2.0;2.0;2.0;1.82;3.23	4.68	4.68	0.58851	.	0.217827	0.40064	N	0.001187	T	0.53351	0.1791	L	0.55990	1.75	0.80722	D	1	D;D;D;B	0.89917	1.0;1.0;1.0;0.072	D;D;D;B	0.76575	0.982;0.988;0.988;0.012	T	0.53222	-0.8469	10	0.54805	T	0.06	-6.7788	13.1963	0.59740	0.0:0.9208:0.0:0.0792	.	184;177;177;184	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	C	177;137;90;177;184;184;118;13;184;144;90;177;177;184;127;137;13;13	ENSP00000316879:R177C;ENSP00000391935:R137C;ENSP00000376320:R90C;ENSP00000391412:R177C;ENSP00000413159:R184C;ENSP00000371767:R184C;ENSP00000403269:R118C;ENSP00000317600:R13C;ENSP00000338020:R184C;ENSP00000411214:R144C;ENSP00000407682:R90C;ENSP00000343450:R177C;ENSP00000323737:R177C;ENSP00000416255:R184C;ENSP00000415943:R127C;ENSP00000395974:R137C;ENSP00000398145:R13C;ENSP00000399858:R13C	ENSP00000323737:R177C	R	+	1	0	EIF4G1	185520275	1.000000	0.71417	0.942000	0.38095	0.773000	0.43773	5.190000	0.65104	2.414000	0.81942	0.462000	0.41574	CGT		0.597	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
CHRD	8646	broad.mit.edu	37	3	184102931	184102931	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:184102931G>T	ENST00000204604.1	+	14	1969	c.1723G>T	c.(1723-1725)Ggt>Tgt	p.G575C	CHRD_ENST00000545352.1_Missense_Mutation_p.G205C|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.G575C|CHRD_ENST00000348986.3_Missense_Mutation_p.G535C	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	575	CHRD 4. {ECO:0000255|PROSITE- ProRule:PRU00230}.				BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)	p.G575C(1)		NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGCTGGGCTTGGTGGCTCAGA	0.612																																					p.G575C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1723T	3						.						99.0	101.0	101.0					3																	184102931		2203	4300	6503	185585625	SO:0001583	missense	8646	exon14			AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.1723G>T	3.37:g.184102931G>T	ENSP00000204604:p.Gly575Cys	Somatic		Capture	Illumina HiSeq	Phase_I	185585625	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	.	.	.	.	.	.	.	.	.	.	G	18.01	3.527277	0.64860	.	.	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.46451	2.7;2.48;2.48;0.87	5.29	4.19	0.49359	CHRD (3);	0.150326	0.64402	D	0.000017	T	0.52008	0.1708	L	0.44542	1.39	0.39395	D	0.966494	D;D;D;D	0.89917	0.997;0.999;0.996;1.0	D;D;D;D	0.74348	0.954;0.957;0.95;0.983	T	0.54483	-0.8287	10	0.87932	D	0	-10.8141	9.3422	0.38087	0.1341:0.0:0.8659:0.0	.	205;535;575;575	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	C	575;575;535;205;288	ENSP00000204604:G575C;ENSP00000408972:G575C;ENSP00000334036:G535C;ENSP00000442948:G205C	ENSP00000204604:G575C	G	+	1	0	CHRD	185585625	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.461000	0.53035	2.662000	0.90505	0.655000	0.94253	GGT		0.612	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
MAP3K13	9175	broad.mit.edu	37	3	185169094	185169094	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:185169094C>T	ENST00000265026.3	+	7	1523	c.1189C>T	c.(1189-1191)Cga>Tga	p.R397*	MAP3K13_ENST00000424227.1_Nonsense_Mutation_p.R397*|MAP3K13_ENST00000535426.1_Nonsense_Mutation_p.R253*|MAP3K13_ENST00000446828.1_Nonsense_Mutation_p.R190*|MAP3K13_ENST00000443863.1_Nonsense_Mutation_p.R253*	NM_004721.4	NP_004712.1			mitogen-activated protein kinase kinase kinase 13									p.R397*(1)		NS(1)|biliary_tract(1)|breast(3)|endometrium(3)|kidney(1)|large_intestine(13)|lung(22)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54	all_cancers(143;7.21e-11)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.93e-20)			ACCTCGAAACCGACCTTCTTT	0.398																																					p.R397X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1189T	3						.						132.0	117.0	122.0					3																	185169094		2203	4300	6503	186651788	SO:0001587	stop_gained	9175	exon7			BC031677	CCDS3270.1, CCDS56298.1	3q27	2011-06-09			ENSG00000073803	ENSG00000073803		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6852	protein-coding gene	gene with protein product	"""leucine zipper-bearing kinase"""	604915				9353328	Standard	NM_004721		Approved	LZK, MEKK13	uc003fpi.3	O43283	OTTHUMG00000156673	ENST00000265026.3:c.1189C>T	3.37:g.185169094C>T	ENSP00000265026:p.Arg397*	Somatic		Capture	Illumina HiSeq	Phase_I	186651788	NM_004721		Nonsense_Mutation	SNP	ENST00000265026.3	37	CCDS3270.1	.	.	.	.	.	.	.	.	.	.	C	39	7.790644	0.98492	.	.	ENSG00000073803	ENST00000446828;ENST00000424227;ENST00000443863;ENST00000535426;ENST00000265026;ENST00000420577	.	.	.	5.76	3.9	0.45041	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.126	0.72483	0.2586:0.7413:0.0:0.0	.	.	.	.	X	190;397;253;253;397;142	.	ENSP00000265026:R397X	R	+	1	2	MAP3K13	186651788	0.976000	0.34144	0.991000	0.47740	0.993000	0.82548	1.472000	0.35376	0.826000	0.34661	0.655000	0.94253	CGA		0.398	MAP3K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345268.1	NM_004721	
ADIPOQ	9370	broad.mit.edu	37	3	186572481	186572481	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:186572481T>C	ENST00000412955.2	+	3	864	c.723T>C	c.(721-723)caT>caC	p.H241H	ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Silent_p.H241H|ADIPOQ_ENST00000320741.2_Silent_p.H241H			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	241	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		H -> P (in dbSNP:rs141205818). {ECO:0000269|PubMed:11812766, ECO:0000269|PubMed:12086969}.		adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)	p.H241H(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		TTCTCTACCATGACACCAACT	0.468																																					p.H241H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T723C	3						.						88.0	90.0	90.0					3																	186572481		2200	4298	6498	188055175	SO:0001819	synonymous_variant	9370	exon3			D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"""Endogenous ligands"""	13633	protein-coding gene	gene with protein product	"""adipose most abundant gene transcript 1"", ""adiponectin precursor"""	605441	"""adipocyte, C1Q and collagen domain containing"""	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.723T>C	3.37:g.186572481T>C		Somatic		Capture	Illumina HiSeq	Phase_I	188055175	NM_004797	Q58EX9	Silent	SNP	ENST00000412955.2	37	CCDS3284.1																																																																																				0.468	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797	
MASP1	5648	broad.mit.edu	37	3	186971086	186971086	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:186971086T>C	ENST00000337774.5	-	6	1151	c.762A>G	c.(760-762)aaA>aaG	p.K254K	MASP1_ENST00000392472.2_Silent_p.K141K|MASP1_ENST00000495249.1_Intron|MASP1_ENST00000296280.6_Silent_p.K254K|MASP1_ENST00000392470.2_Silent_p.K228K|MASP1_ENST00000169293.6_Silent_p.K254K	NM_001879.5	NP_001870.3	P48740	MASP1_HUMAN	mannan-binding lectin serine peptidase 1 (C4/C2 activating component of Ra-reactive factor)	254	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.|Interaction with FCN2.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|negative regulation of complement activation (GO:0045916)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|peptidase activity (GO:0008233)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase activity (GO:0004252)	p.K254N(2)|p.K254K(2)		NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(27)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	60	all_cancers(143;5.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.49e-18)	GBM - Glioblastoma multiforme(93;0.0366)		GCCCCAAAACTTTTGGACCAA	0.498																																					p.K254K												.	.	4	Substitution - Missense(2)|Substitution - coding silent(2)	large_intestine(2)|prostate(2)	c.A762G	3						.						139.0	156.0	150.0					3																	186971086		2203	4300	6503	188453780	SO:0001819	synonymous_variant	5648	exon6			D28593	CCDS33907.1, CCDS33908.1, CCDS33909.1	3q27-q28	2014-09-17	2005-08-17		ENSG00000127241	ENSG00000127241		"""Serine peptidases / Serine peptidases"""	6901	protein-coding gene	gene with protein product		600521	"""mannan-binding lectin serine protease 1 (C4/C2 activating component of Ra-reactive factor)"""	CRARF, PRSS5		8018603, 8240317	Standard	NR_033519		Approved	MASP	uc003fri.3	P48740	OTTHUMG00000156461	ENST00000337774.5:c.762A>G	3.37:g.186971086T>C		Somatic		Capture	Illumina HiSeq	Phase_I	188453780	NM_001031849	A8K542|A8K6M1|B4E2L7|O95570|Q68D21|Q8IUV8|Q96RS4|Q9UF09	Silent	SNP	ENST00000337774.5	37	CCDS33907.1																																																																																				0.498	MASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344262.1	NM_001879	
CPN2	1370	broad.mit.edu	37	3	194062734	194062734	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:194062734G>T	ENST00000323830.3	-	2	787	c.698C>A	c.(697-699)cCc>cAc	p.P233H	CPN2_ENST00000429275.1_Missense_Mutation_p.P233H	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	233					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)	p.P233H(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		CACCTGAGGGGGCAGCTCCGA	0.602																																					p.P233H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C698A	3						.						43.0	47.0	46.0					3																	194062734		2203	4300	6503	195544429	SO:0001583	missense	1370	exon2			J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.698C>A	3.37:g.194062734G>T	ENSP00000319464:p.Pro233His	Somatic		Capture	Illumina HiSeq	Phase_I	195544429	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	.	.	.	.	.	.	.	.	.	.	G	11.84	1.758272	0.31137	.	.	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.13420	2.59;2.59	5.05	4.16	0.48862	.	0.816163	0.10046	N	0.722833	T	0.21962	0.0529	M	0.73372	2.23	0.31077	N	0.712314	B	0.32717	0.381	B	0.32762	0.152	T	0.15838	-1.0423	10	0.72032	D	0.01	.	15.2257	0.73348	0.0:0.0:0.8584:0.1416	.	233	P22792	CPN2_HUMAN	H	233	ENSP00000319464:P233H;ENSP00000402232:P233H	ENSP00000319464:P233H	P	-	2	0	CPN2	195544429	0.998000	0.40836	0.422000	0.26621	0.374000	0.29953	6.313000	0.72844	1.233000	0.43693	0.561000	0.74099	CCC		0.602	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
GP5	2814	broad.mit.edu	37	3	194118665	194118665	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:194118665G>A	ENST00000401815.1	-	1	418	c.347C>T	c.(346-348)gCg>gTg	p.A116V	GP5_ENST00000323007.3_Missense_Mutation_p.A116V			P40197	GPV_HUMAN	glycoprotein V (platelet)	116					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|negative regulation of platelet activation (GO:0010544)|platelet activation (GO:0030168)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|central_nervous_system(2)|endometrium(2)|large_intestine(9)|lung(14)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	35	all_cancers(143;6.64e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;7.38e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.06e-05)		ATCCAGCAGCGCACCTGGAAG	0.517																																					p.A116V												.	.	0			c.C347T	3						.						83.0	85.0	84.0					3																	194118665		2203	4300	6503	195599954	SO:0001583	missense	2814	exon2			L11238	CCDS3307.1	3q29	2008-02-01			ENSG00000178732	ENSG00000178732		"""CD molecules"""	4443	protein-coding gene	gene with protein product		173511				7690959	Standard	NM_004488		Approved	CD42d	uc003ftv.1	P40197	OTTHUMG00000150345	ENST00000401815.1:c.347C>T	3.37:g.194118665G>A	ENSP00000383931:p.Ala116Val	None		Capture	Illumina HiSeq	Phase_I	195599954	NM_004488	D1MER9	Missense_Mutation	SNP	ENST00000401815.1	37	CCDS3307.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.775219	0.49786	.	.	ENSG00000178732	ENST00000401815;ENST00000323007	T;T	0.58210	0.35;0.35	4.49	3.53	0.40419	.	0.428415	0.17220	N	0.182361	T	0.51618	0.1685	L	0.35414	1.06	0.09310	N	1	D	0.67145	0.996	P	0.56216	0.794	T	0.35001	-0.9806	10	0.46703	T	0.11	.	9.1984	0.37242	0.0:0.2382:0.6136:0.1482	.	116	P40197	GPV_HUMAN	V	116	ENSP00000383931:A116V;ENSP00000319286:A116V	ENSP00000319286:A116V	A	-	2	0	GP5	195599954	0.000000	0.05858	0.061000	0.19648	0.635000	0.38103	0.032000	0.13732	2.418000	0.82041	0.555000	0.69702	GCG		0.517	GP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317710.1	NM_004488	
CNTN4	152330	broad.mit.edu	37	3	3085339	3085339	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:3085339G>T	ENST00000397461.1	+	22	3146	c.2762G>T	c.(2761-2763)tGg>tTg	p.W921L	CNTN4_ENST00000358480.3_Missense_Mutation_p.W702L|CNTN4_ENST00000427331.1_Missense_Mutation_p.W921L|CNTN4_ENST00000448906.2_Missense_Mutation_p.W593L|CNTN4_ENST00000397459.2_Missense_Mutation_p.W593L|CNTN4_ENST00000418658.1_Missense_Mutation_p.W921L|CNTN4-AS1_ENST00000442749.2_RNA	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	921	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)		p.W921L(1)|p.W593L(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		ATCCTGAATTGGGATCAAGTG	0.398																																					p.W593L												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1778T	3						.						70.0	71.0	70.0					3																	3085339		2203	4300	6503	3060339	SO:0001583	missense	152330	exon14			AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2762G>T	3.37:g.3085339G>T	ENSP00000380602:p.Trp921Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3060339	NM_175613	B2RAX3|Q8IX14|Q8TC35	Missense_Mutation	SNP	ENST00000397461.1	37	CCDS43041.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.796116	0.90453	.	.	ENSG00000144619	ENST00000418658;ENST00000397461;ENST00000427331;ENST00000358480;ENST00000397459;ENST00000448906	D;D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05;-2.05	5.61	5.61	0.85477	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.135440	0.53938	D	0.000048	D	0.94565	0.8249	M	0.92268	3.29	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95312	0.8413	10	0.87932	D	0	.	19.6476	0.95789	0.0:0.0:1.0:0.0	.	920;921	Q8IWV2-3;Q8IWV2	.;CNTN4_HUMAN	L	921;921;921;702;593;593	ENSP00000396010:W921L;ENSP00000380602:W921L;ENSP00000413642:W921L;ENSP00000351267:W702L;ENSP00000380600:W593L;ENSP00000392077:W593L	ENSP00000351267:W702L	W	+	2	0	CNTN4	3060339	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.640000	0.98453	2.653000	0.90120	0.655000	0.94253	TGG		0.398	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
IL5RA	3568	broad.mit.edu	37	3	3139615	3139615	+	Silent	SNP	G	G	A	rs185027967	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:3139615G>A	ENST00000446632.2	-	7	1222	c.648C>T	c.(646-648)aaC>aaT	p.N216N	IL5RA_ENST00000256452.3_Silent_p.N216N|IL5RA_ENST00000430514.2_Silent_p.N216N|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000418488.2_Silent_p.N216N|IL5RA_ENST00000311981.8_Silent_p.N216N|IL5RA_ENST00000438560.1_Silent_p.N216N|IL5RA_ENST00000456302.1_Silent_p.N216N|IL5RA_ENST00000383846.1_Silent_p.N216N	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	216					cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)	p.N216K(1)|p.N216N(1)		cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		TGCTGGAGCCGTTAACAAGCA	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		17303	0.002		0.0	False		,,,				2504	0.0				p.N216N	GBM(169;430 2801 24955 28528)											.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C648T	3						.						103.0	92.0	96.0					3																	3139615		2203	4300	6503	3114615	SO:0001819	synonymous_variant	3568	exon8			M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.648C>T	3.37:g.3139615G>A		Somatic		Capture	Illumina HiSeq	Phase_I	3114615	NM_000564	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Silent	SNP	ENST00000446632.2	37	CCDS2559.1																																																																																				0.488	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
GRM7	2917	broad.mit.edu	37	3	7721740	7721740	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:7721740A>G	ENST00000357716.4	+	9	2730	c.2456A>G	c.(2455-2457)tAc>tGc	p.Y819C	GRM7_ENST00000403881.1_Missense_Mutation_p.Y819C|GRM7_ENST00000402647.2_Missense_Mutation_p.Y819C|GRM7_ENST00000389336.4_Missense_Mutation_p.Y819C|GRM7_ENST00000486284.1_Missense_Mutation_p.Y819C	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	819					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)	p.Y819C(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TCCTAGCTCTACATACAAACT	0.443																																					p.Y819C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2456G	3						.						94.0	83.0	86.0					3																	7721740		2203	4300	6503	7696740	SO:0001583	missense	2917	exon9			U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2456A>G	3.37:g.7721740A>G	ENSP00000350348:p.Tyr819Cys	Somatic		Capture	Illumina HiSeq	Phase_I	7696740	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Missense_Mutation	SNP	ENST00000357716.4	37	CCDS43042.1	.	.	.	.	.	.	.	.	.	.	A	19.39	3.819068	0.71028	.	.	ENSG00000196277	ENST00000357716;ENST00000486284;ENST00000389336;ENST00000403881;ENST00000525747;ENST00000402647	D;D;D;D;D	0.90197	-2.59;-2.63;-2.63;-2.63;-2.63	4.97	4.97	0.65823	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93963	0.8067	M	0.62723	1.935	0.58432	D	0.999999	D;D;D;B	0.89917	1.0;0.999;1.0;0.021	D;P;D;B	0.87578	0.996;0.907;0.998;0.029	D	0.94089	0.7351	10	0.54805	T	0.06	.	13.7711	0.63026	1.0:0.0:0.0:0.0	.	819;574;819;819	Q14831-5;Q59G95;Q14831;Q14831-2	.;.;GRM7_HUMAN;.	C	819	ENSP00000350348:Y819C;ENSP00000417536:Y819C;ENSP00000373987:Y819C;ENSP00000385664:Y819C;ENSP00000384585:Y819C	ENSP00000350348:Y819C	Y	+	2	0	GRM7	7696740	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	1.988000	0.58038	0.477000	0.44152	TAC		0.443	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
BRPF1	7862	broad.mit.edu	37	3	9776020	9776020	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:9776020C>T	ENST00000457855.1	+	1	207	c.196C>T	c.(196-198)Cgc>Tgc	p.R66C	BRPF1_ENST00000302054.3_Missense_Mutation_p.R66C|BRPF1_ENST00000424362.1_Missense_Mutation_p.R66C|BRPF1_ENST00000383829.2_Missense_Mutation_p.R66C|BRPF1_ENST00000433861.2_Missense_Mutation_p.R66C			P55201	BRPF1_HUMAN	bromodomain and PHD finger containing, 1	66	Interaction with KAT6A and KAT6B.				chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R66C(2)		central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(15)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	49	Medulloblastoma(99;0.227)					GAAAAAGGGGCGCCAGTCACG	0.572																																					p.R66C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C196T	3						.						178.0	205.0	196.0					3																	9776020		2203	4300	6503	9751020	SO:0001583	missense	7862	exon2			M91585	CCDS2575.1, CCDS33692.1	3p26-p25	2008-07-18			ENSG00000156983	ENSG00000156983			14255	protein-coding gene	gene with protein product	"""peregrin"", ""bromodomain-containing protein, 140kD"""	602410				8946209, 7906940	Standard	NM_001003694		Approved	BR140	uc003bsf.3	P55201	OTTHUMG00000097033	ENST00000457855.1:c.196C>T	3.37:g.9776020C>T	ENSP00000410210:p.Arg66Cys	Somatic		Capture	Illumina HiSeq	Phase_I	9751020	NM_004634	B4DEZ6|Q7Z6E0|Q8TCM6|Q9UHI0	Missense_Mutation	SNP	ENST00000457855.1	37	CCDS2575.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.434743	0.83885	.	.	ENSG00000156983	ENST00000433861;ENST00000424362;ENST00000383829;ENST00000302054;ENST00000420291;ENST00000426583;ENST00000457855	T;T;T;T;T;T	0.52983	2.13;2.12;3.51;2.12;0.64;2.12	5.73	5.73	0.89815	.	0.051626	0.85682	D	0.000000	T	0.64735	0.2625	L	0.58101	1.795	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;P	0.76071	0.987;0.966;0.931;0.854	T	0.66172	-0.5990	10	0.87932	D	0	.	14.2034	0.65719	0.1502:0.8498:0.0:0.0	.	66;66;66;66	P55201-4;P55201-3;P55201-2;P55201	.;.;.;BRPF1_HUMAN	C	66	ENSP00000402485:R66C;ENSP00000398863:R66C;ENSP00000373340:R66C;ENSP00000306297:R66C;ENSP00000404235:R66C;ENSP00000410210:R66C	ENSP00000306297:R66C	R	+	1	0	BRPF1	9751020	0.996000	0.38824	1.000000	0.80357	0.980000	0.70556	3.602000	0.54066	2.709000	0.92574	0.563000	0.77884	CGC		0.572	BRPF1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338485.1	NM_001003694	
PRRT3	285368	broad.mit.edu	37	3	9991197	9991197	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:9991197G>A	ENST00000412055.1	-	2	732	c.603C>T	c.(601-603)ccC>ccT	p.P201P	PRRT3_ENST00000411976.2_Silent_p.P201P|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	201						integral component of membrane (GO:0016021)		p.P201P(1)		NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						GGTGGTCTGAGGGAGAAGTGG	0.587																																					p.P201P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C603T	3						.						69.0	79.0	75.0					3																	9991197		2077	4207	6284	9966197	SO:0001819	synonymous_variant	285368	exon2			AK090993	CCDS43049.1	3p25.3	2011-10-10			ENSG00000163704	ENSG00000163704		"""Proline-rich transmembrane proteins"""	26591	protein-coding gene	gene with protein product							Standard	NM_207351		Approved	FLJ33674	uc003bul.2	Q5FWE3	OTTHUMG00000155285	ENST00000412055.1:c.603C>T	3.37:g.9991197G>A		Somatic		Capture	Illumina HiSeq	Phase_I	9966197	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Silent	SNP	ENST00000412055.1	37	CCDS43049.1																																																																																				0.587	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351	
ZNF385D	79750	broad.mit.edu	37	3	21462861	21462861	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:21462861C>G	ENST00000281523.2	-	8	1551	c.1033G>C	c.(1033-1035)Gcc>Ccc	p.A345P		NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	345	Poly-Ala.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.A345P(1)		NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						gctgctgcggctgctgcagct	0.512																																					p.A345P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1033C	3						.						36.0	40.0	38.0					3																	21462861		2203	4300	6503	21437865	SO:0001583	missense	79750	exon8			BC007212	CCDS2636.1	3p24.3	2012-10-05	2007-12-06	2007-12-06	ENSG00000151789	ENSG00000151789			26191	protein-coding gene	gene with protein product			"""zinc finger protein 659"""	ZNF659		12477932	Standard	NM_024697		Approved	FLJ22419	uc003cce.3	Q9H6B1	OTTHUMG00000130484	ENST00000281523.2:c.1033G>C	3.37:g.21462861C>G	ENSP00000281523:p.Ala345Pro	Somatic		Capture	Illumina HiSeq	Phase_I	21437865	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025111	0.35701	.	.	ENSG00000151789	ENST00000281523	T	0.36157	1.27	6.08	5.21	0.72293	.	0.109105	0.64402	D	0.000010	T	0.44746	0.1308	L	0.38175	1.15	0.46167	D	0.998904	D	0.58268	0.982	P	0.55824	0.785	T	0.39099	-0.9630	10	0.52906	T	0.07	-44.8833	15.3853	0.74695	0.0:0.9334:0.0:0.0666	.	345	Q9H6B1	Z385D_HUMAN	P	345	ENSP00000281523:A345P	ENSP00000281523:A345P	A	-	1	0	ZNF385D	21437865	0.990000	0.36364	0.093000	0.20910	0.174000	0.22865	2.891000	0.48617	1.585000	0.49928	0.650000	0.86243	GCC		0.512	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697	
SCN5A	6331	broad.mit.edu	37	3	38596007	38596007	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:38596007T>C	ENST00000333535.4	-	27	4725	c.4576A>G	c.(4576-4578)Acc>Gcc	p.T1526A	SCN5A_ENST00000414099.2_Missense_Mutation_p.T1508A|SCN5A_ENST00000425664.1_Missense_Mutation_p.T1508A|SCN5A_ENST00000413689.1_Missense_Mutation_p.T1526A|SCN5A_ENST00000449557.2_Missense_Mutation_p.T1472A|SCN5A_ENST00000450102.2_Missense_Mutation_p.T1472A|SCN5A_ENST00000464652.1_5'UTR|SCN5A_ENST00000455624.2_Missense_Mutation_p.T1525A|SCN5A_ENST00000423572.2_Missense_Mutation_p.T1525A|SCN5A_ENST00000443581.1_Missense_Mutation_p.T1525A|SCN5A_ENST00000451551.2_Missense_Mutation_p.T1472A			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1526					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.T1526A(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GCCTGCTTGGTCACAATGTCG	0.483																																					p.T1508A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4522G	3						.						126.0	126.0	126.0					3																	38596007		2018	4190	6208	38571011	SO:0001583	missense	6331	exon26			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.4576A>G	3.37:g.38596007T>C	ENSP00000328968:p.Thr1526Ala	Somatic		Capture	Illumina HiSeq	Phase_I	38571011	NM_001099405	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.076900	0.55753	.	.	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96427	-3.96;-3.97;-3.97;-4.0;-3.97;-3.96;-3.98;-3.99;-4.0;-4.01	3.69	3.69	0.42338	.	0.385070	0.26923	N	0.021819	D	0.96787	0.8951	M	0.90759	3.145	0.31363	N	0.681181	B;B;B;B;B;B	0.31009	0.102;0.123;0.249;0.303;0.268;0.015	B;B;B;B;B;B	0.43225	0.024;0.075;0.103;0.078;0.412;0.016	D	0.97235	0.9887	10	0.87932	D	0	.	5.5962	0.17329	0.1773:0.0:0.1588:0.6639	.	1472;1525;1508;1526;1525;1526	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	A	1508;1525;1526;1472;1525;1508;1526;1525;1472;1472	ENSP00000398962:T1508A;ENSP00000398266:T1525A;ENSP00000410257:T1526A;ENSP00000388797:T1472A;ENSP00000397915:T1525A;ENSP00000416634:T1508A;ENSP00000328968:T1526A;ENSP00000399524:T1525A;ENSP00000403355:T1472A;ENSP00000413996:T1472A	ENSP00000328968:T1526A	T	-	1	0	SCN5A	38571011	0.995000	0.38212	1.000000	0.80357	0.960000	0.62799	0.292000	0.19011	1.552000	0.49463	0.379000	0.24179	ACC		0.483	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
SCN5A	6331	broad.mit.edu	37	3	38601827	38601827	+	Silent	SNP	G	G	A	rs587781165		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:38601827G>A	ENST00000333535.4	-	23	4205	c.4056C>T	c.(4054-4056)ggC>ggT	p.G1352G	SCN5A_ENST00000414099.2_Silent_p.G1352G|SCN5A_ENST00000425664.1_Silent_p.G1352G|SCN5A_ENST00000413689.1_Silent_p.G1352G|SCN5A_ENST00000449557.2_Silent_p.G1298G|SCN5A_ENST00000450102.2_Silent_p.G1298G|SCN5A_ENST00000455624.2_Silent_p.G1351G|SCN5A_ENST00000423572.2_Silent_p.G1351G|SCN5A_ENST00000443581.1_Silent_p.G1351G|SCN5A_ENST00000451551.2_Silent_p.G1298G			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1352					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)	p.G1352G(1)		NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	AGAGGTTCACGCCCATGATGC	0.547																																					p.G1352G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4056T	3						.						114.0	110.0	111.0					3																	38601827		2203	4300	6503	38576831	SO:0001819	synonymous_variant	6331	exon23			AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.4056C>T	3.37:g.38601827G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38576831	NM_001099405	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Silent	SNP	ENST00000333535.4	37	CCDS46796.1																																																																																				0.547	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
TTC21A	199223	broad.mit.edu	37	3	39159612	39159612	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:39159612C>T	ENST00000431162.2	+	7	903	c.769C>T	c.(769-771)Cat>Tat	p.H257Y	TTC21A_ENST00000301819.6_Missense_Mutation_p.H257Y|TTC21A_ENST00000440121.1_Missense_Mutation_p.H216Y			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	257								p.H257Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		TCTAACCGTGCATGAGCTTGC	0.418																																					p.H216Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C646T	3						.						164.0	164.0	164.0					3																	39159612		2041	4195	6236	39134616	SO:0001583	missense	199223	exon6			AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.769C>T	3.37:g.39159612C>T	ENSP00000398211:p.His257Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	39134616	NM_001105513	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	7.369	0.626362	0.14257	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.33865	1.39;1.39;1.39	5.43	2.7	0.31948	.	0.341006	0.28156	N	0.016389	T	0.37544	0.1007	L	0.38649	1.16	0.36968	D	0.893679	B;D;D;D;D	0.76494	0.314;0.999;0.999;0.998;0.999	B;D;D;P;D	0.64877	0.11;0.93;0.93;0.852;0.93	T	0.43556	-0.9384	10	0.02654	T	1	-3.2267	8.855	0.35223	0.0:0.7549:0.0:0.2451	.	216;257;257;257;257	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	Y	257;257;257;216	ENSP00000301819:H257Y;ENSP00000398211:H257Y;ENSP00000410882:H216Y	ENSP00000301819:H257Y	H	+	1	0	TTC21A	39134616	1.000000	0.71417	0.855000	0.33649	0.889000	0.51656	1.376000	0.34306	0.285000	0.22329	-0.251000	0.11542	CAT		0.418	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
ULK4	54986	broad.mit.edu	37	3	41746561	41746561	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:41746561G>A	ENST00000301831.4	-	27	3231	c.2769C>T	c.(2767-2769)gaC>gaT	p.D923D		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	923					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D75D(1)|p.D923D(1)		breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TGGAGCGATAGTCTTTCAATA	0.353																																					p.D923D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C2769T	3						.						84.0	79.0	80.0					3																	41746561		1826	4080	5906	41721565	SO:0001819	synonymous_variant	54986	exon27			AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2769C>T	3.37:g.41746561G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41721565	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Silent	SNP	ENST00000301831.4	37	CCDS43071.1																																																																																				0.353	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
TRAK1	22906	broad.mit.edu	37	3	42234687	42234687	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:42234687A>G	ENST00000327628.5	+	8	1290	c.890A>G	c.(889-891)aAg>aGg	p.K297R	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.K239R|TRAK1_ENST00000449246.1_Missense_Mutation_p.K223R|TRAK1_ENST00000341421.3_Missense_Mutation_p.K239R	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	297	HAP1 N-terminal.				endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						TTGCAGAAAAAGGCAAAAGCT	0.478																																					p.K297R	GBM(44;195 884 22595 31865 41850)											.	.	0			c.A890G	3						.						96.0	91.0	93.0					3																	42234687		2203	4300	6503	42209691	SO:0001583	missense	22906	exon8				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.890A>G	3.37:g.42234687A>G	ENSP00000328998:p.Lys297Arg	None		Capture	Illumina HiSeq	Phase_I	42209691	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.357523	0.61293	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000449246;ENST00000396175;ENST00000341421;ENST00000427771	T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.26810	0.0656	N	0.10645	0.015	0.58432	D	0.999996	D;D;D;D;P;D	0.89917	0.999;0.999;0.999;0.998;0.837;1.0	D;D;D;D;P;D	0.97110	0.996;0.996;0.998;0.994;0.583;1.0	T	0.27872	-1.0061	10	0.31617	T	0.26	.	15.4796	0.75514	1.0:0.0:0.0:0.0	.	223;239;297;239;223;297	B7Z218;C9JC32;B7Z347;Q9UPV9-2;E9PDS2;Q9UPV9	.;.;.;.;.;TRAK1_HUMAN	R	297;297;223;239;239;40	ENSP00000328998:K297R;ENSP00000410717:K223R;ENSP00000379478:K239R;ENSP00000340702:K239R;ENSP00000413729:K40R	ENSP00000328998:K297R	K	+	2	0	TRAK1	42209691	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	6.314000	0.72848	2.244000	0.73946	0.519000	0.50382	AAG		0.478	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
TRAK1	22906	broad.mit.edu	37	3	42264487	42264487	+	Missense_Mutation	SNP	C	C	T	rs367557305		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:42264487C>T	ENST00000327628.5	+	16	2520	c.2120C>T	c.(2119-2121)aCg>aTg	p.T707M	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.T649M|RNU4-78P_ENST00000410940.1_RNA	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	707					endosome to lysosome transport (GO:0008333)|protein O-linked glycosylation (GO:0006493)|protein targeting (GO:0006605)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.T649M(1)		central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(8)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	22						TTGAAATCCACGCCGGTGGCC	0.562																																					p.T707M	GBM(44;195 884 22595 31865 41850)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2120T	3						.	C	MET/THR	1,4115		0,1,2057	59.0	70.0	66.0		2120	5.2	1.0	3		66	0,8420		0,0,4210	no	missense	TRAK1	NM_001042646.1	81	0,1,6267	TT,TC,CC		0.0,0.0243,0.0080	probably-damaging	707/954	42264487	1,12535	2058	4210	6268	42239491	SO:0001583	missense	22906	exon16				CCDS2695.1, CCDS43072.1, CCDS58826.1, CCDS74922.1	3p22.1	2012-03-05			ENSG00000182606	ENSG00000182606			29947	protein-coding gene	gene with protein product	"""OGT(O Glc NAc transferase) interacting protein 106 KDa"", ""O-linked N-acetylglucosamine transferase interacting protein 106"", ""milton homolog 1 (Drosophila)"""	608112				10470851, 12435728, 16380713, 20230862	Standard	NM_014965		Approved	OIP106, KIAA1042, MILT1	uc003cky.4	Q9UPV9	OTTHUMG00000131795	ENST00000327628.5:c.2120C>T	3.37:g.42264487C>T	ENSP00000328998:p.Thr707Met	Somatic		Capture	Illumina HiSeq	Phase_I	42239491	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.855290	0.71719	2.43E-4	0.0	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175	T;T	0.10192	2.92;2.9	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.29524	0.0736	L	0.49126	1.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	T	0.00972	-1.1495	10	0.72032	D	0.01	.	17.7227	0.88356	0.0:1.0:0.0:0.0	.	649;707	C9JC32;Q9UPV9	.;TRAK1_HUMAN	M	707;686;649	ENSP00000328998:T707M;ENSP00000379478:T649M	ENSP00000328998:T707M	T	+	2	0	TRAK1	42239491	1.000000	0.71417	0.987000	0.45799	0.907000	0.53573	3.967000	0.56802	2.443000	0.82685	0.591000	0.81541	ACG		0.562	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965	
KIF15	56992	broad.mit.edu	37	3	44869760	44869760	+	Missense_Mutation	SNP	A	A	G	rs371462063		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:44869760A>G	ENST00000326047.4	+	24	3060	c.2911A>G	c.(2911-2913)Agt>Ggt	p.S971G	KIF15_ENST00000425755.1_Missense_Mutation_p.S606G	NM_020242.2	NP_064627.1	Q9NS87	KIF15_HUMAN	kinesin family member 15	971					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|plus-end kinesin complex (GO:0005873)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.S971G(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|liver(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(5)	36				BRCA - Breast invasive adenocarcinoma(193;0.0099)|KIRC - Kidney renal clear cell carcinoma(197;0.0564)|Kidney(197;0.0707)		AAAAGTGATCAGTTCCCTGGA	0.328																																					p.S971G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2911G	3						.	A	GLY/SER	0,4406		0,0,2203	80.0	80.0	80.0		2911	1.2	0.9	3		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIF15	NM_020242.2	56	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	971/1389	44869760	1,13005	2203	4300	6503	44844764	SO:0001583	missense	56992	exon24			AB035898	CCDS33744.1	3p21.31	2008-03-03	2005-03-15	2005-03-17	ENSG00000163808	ENSG00000163808		"""Kinesins"""	17273	protein-coding gene	gene with protein product			"""kinesin-like 7"""	KNSL7		10878014	Standard	NM_020242		Approved	HKLP2, NY-BR-62	uc003cnx.4	Q9NS87	OTTHUMG00000156307	ENST00000326047.4:c.2911A>G	3.37:g.44869760A>G	ENSP00000324020:p.Ser971Gly	Somatic		Capture	Illumina HiSeq	Phase_I	44844764	NM_020242	Q17RV9|Q69YL6|Q96JX7|Q9H280	Missense_Mutation	SNP	ENST00000326047.4	37	CCDS33744.1	.	.	.	.	.	.	.	.	.	.	A	14.02	2.410625	0.42715	0.0	1.16E-4	ENSG00000163808	ENST00000326047;ENST00000396031;ENST00000425755	T;T	0.42513	0.97;0.97	6.01	1.2	0.21068	.	0.636054	0.14606	N	0.309340	T	0.27349	0.0671	L	0.36672	1.1	0.09310	N	1	B	0.21309	0.054	B	0.21360	0.034	T	0.15093	-1.0449	10	0.33141	T	0.24	.	4.1603	0.10280	0.5188:0.19:0.2912:0.0	.	971	Q9NS87	KIF15_HUMAN	G	971;970;606	ENSP00000324020:S971G;ENSP00000389982:S606G	ENSP00000324020:S971G	S	+	1	0	KIF15	44844764	0.954000	0.32549	0.875000	0.34327	0.951000	0.60555	1.217000	0.32455	0.528000	0.28580	0.528000	0.53228	AGT		0.328	KIF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343831.2		
NBEAL2	23218	broad.mit.edu	37	3	47043264	47043264	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:47043264C>T	ENST00000450053.3	+	30	4909	c.4730C>T	c.(4729-4731)gCg>gTg	p.A1577V	NBEAL2_ENST00000383740.2_5'UTR|NBEAL2_ENST00000292309.5_Missense_Mutation_p.A1393V	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	1577					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.A954V(1)|p.A1577V(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CGTGAGATGGCGCAGATTGGC	0.597																																					p.A1577V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C4730T	3						.						92.0	96.0	95.0					3																	47043264		2125	4258	6383	47018268	SO:0001583	missense	23218	exon30			AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.4730C>T	3.37:g.47043264C>T	ENSP00000415034:p.Ala1577Val	Somatic		Capture	Illumina HiSeq	Phase_I	47018268	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Missense_Mutation	SNP	ENST00000450053.3	37	CCDS46817.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.378736|5.378736	0.95945|0.95945	.|.	.|.	ENSG00000160796|ENSG00000160796	ENST00000292309;ENST00000450053|ENST00000416683	T;T|.	0.59638|.	0.3;0.25|.	5.2|5.2	5.2|5.2	0.72013|0.72013	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69024|0.69024	0.3065|0.3065	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	P|.	0.47962|.	0.903|.	B|.	0.38296|.	0.27|.	T|T	0.66396|0.66396	-0.5934|-0.5934	10|5	0.59425|.	D|.	0.04|.	.|.	17.308|17.308	0.87200|0.87200	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1577|.	Q6ZNJ1|.	NBEL2_HUMAN|.	V|C	1393;1577|865	ENSP00000292309:A1393V;ENSP00000415034:A1577V|.	ENSP00000292309:A1393V|.	A|R	+|+	2|1	0|0	NBEAL2|NBEAL2	47018268|47018268	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.983000|0.983000	0.72400|0.72400	7.743000|7.743000	0.85020|0.85020	2.433000|2.433000	0.82419|0.82419	0.563000|0.563000	0.77884|0.77884	GCG|CGC		0.597	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
SETD2	29072	broad.mit.edu	37	3	47162622	47162622	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:47162622A>G	ENST00000409792.3	-	3	3546	c.3504T>C	c.(3502-3504)gtT>gtC	p.V1168V		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2	1168					angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)	p.V1168V(1)|p.V665V(1)		breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		TTGTACTATCAACCCCATCAC	0.428			"""N, F, S, Mis"""		clear cell renal carcinoma																																p.V1168V			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T3504C	3						.						133.0	140.0	137.0					3																	47162622		2203	4300	6503	47137626	SO:0001819	synonymous_variant	29072	exon3			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.3504T>C	3.37:g.47162622A>G		Somatic		Capture	Illumina HiSeq	Phase_I	47137626	NM_014159	O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Silent	SNP	ENST00000409792.3	37	CCDS2749.2																																																																																				0.428	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	NM_014159	
CELSR3	1951	broad.mit.edu	37	3	48699661	48699661	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:48699661C>T	ENST00000164024.4	-	1	687	c.407G>A	c.(406-408)cGc>cAc	p.R136H	CELSR3_ENST00000544264.1_Missense_Mutation_p.R136H|RP11-148G20.1_ENST00000421275.1_RNA	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	136					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.R136H(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		GACCTCTGGGCGCCAGTATAA	0.632																																					p.R136H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G407A	3						.						75.0	85.0	81.0					3																	48699661		2195	4290	6485	48674665	SO:0001583	missense	1951	exon1			AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.407G>A	3.37:g.48699661C>T	ENSP00000164024:p.Arg136His	Somatic		Capture	Illumina HiSeq	Phase_I	48674665	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	C	6.397	0.441371	0.12164	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.70869	-0.52;-0.51	4.83	2.55	0.30701	.	.	.	.	.	T	0.44664	0.1304	N	0.08118	0	0.24727	N	0.993117	B;B	0.11235	0.001;0.004	B;B	0.04013	0.0;0.001	T	0.26326	-1.0106	9	0.12103	T	0.63	.	6.9775	0.24683	0.0:0.6051:0.2552:0.1397	.	136;206	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	H	136	ENSP00000164024:R136H;ENSP00000445694:R136H	ENSP00000164024:R136H	R	-	2	0	CELSR3	48674665	0.979000	0.34478	0.987000	0.45799	0.490000	0.33462	1.414000	0.34736	0.995000	0.38917	0.655000	0.94253	CGC		0.632	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
ARIH2	10425	broad.mit.edu	37	3	48965066	48965066	+	Silent	SNP	A	A	G	rs367899872		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:48965066A>G	ENST00000356401.4	+	3	414	c.75A>G	c.(73-75)gaA>gaG	p.E25E	ARIH2_ENST00000490095.1_Intron|ARIH2_ENST00000449376.1_Silent_p.E25E	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	25	Asp/Glu-rich (acidic).|Poly-Glu.				developmental cell growth (GO:0048588)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organismal development (GO:0007275)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.E25E(1)		cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13				BRCA - Breast invasive adenocarcinoma(193;9.42e-05)|Kidney(197;0.00258)|KIRC - Kidney renal clear cell carcinoma(197;0.00269)		aggaagaggaagaagaagaag	0.517																																					p.E25E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A75G	3						.						49.0	52.0	51.0					3																	48965066		2203	4300	6503	48940070	SO:0001819	synonymous_variant	10425	exon3			AF099149	CCDS2780.1	3p21	2013-10-03	2013-10-03		ENSG00000177479	ENSG00000177479			690	protein-coding gene	gene with protein product	"""all-trans retinoic acid inducible RING finger"""	605615	"""ariadne (Drosophila) homolog 2"", ""ariadne homolog 2 (Drosophila)"""			10422847, 24058416	Standard	XM_005264798		Approved	TRIAD1	uc003cvb.3	O95376	OTTHUMG00000133547	ENST00000356401.4:c.75A>G	3.37:g.48965066A>G		Somatic		Capture	Illumina HiSeq	Phase_I	48940070	NM_006321	Q9HBZ6|Q9UEM9	Silent	SNP	ENST00000356401.4	37	CCDS2780.1																																																																																				0.517	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321	
USP19	10869	broad.mit.edu	37	3	49152539	49152539	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:49152539C>T	ENST00000398888.2	-	13	2043	c.1725G>A	c.(1723-1725)gcG>gcA	p.A575A	USP19_ENST00000434032.2_Silent_p.A676A|USP19_ENST00000398898.2_Silent_p.A615A|USP19_ENST00000398896.1_Silent_p.A383A|USP19_ENST00000453664.1_Silent_p.A666A|USP19_ENST00000417901.1_Silent_p.A678A|USP19_ENST00000398892.3_Silent_p.A615A|USP19_ENST00000488993.1_5'Flank	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	575	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)	p.A663A(1)		NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGCCTTACTCGCCACAATGG	0.602																																					p.A666A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1998A	3						.						61.0	65.0	64.0					3																	49152539		2133	4232	6365	49127543	SO:0001819	synonymous_variant	10869	exon14			AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.1725G>A	3.37:g.49152539C>T		Somatic		Capture	Illumina HiSeq	Phase_I	49127543	NM_001199162	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Silent	SNP	ENST00000398888.2	37	CCDS43090.1																																																																																				0.602	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
CCDC71	64925	broad.mit.edu	37	3	49200644	49200644	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:49200644G>A	ENST00000321895.6	-	2	1104	c.998C>T	c.(997-999)gCc>gTc	p.A333V		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	333								p.A333V(1)		endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		catgactttggccttggcctt	0.637																																					p.A333V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C998T	3						.						79.0	62.0	68.0					3																	49200644		2203	4300	6503	49175648	SO:0001583	missense	64925	exon2			AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.998C>T	3.37:g.49200644G>A	ENSP00000319006:p.Ala333Val	Somatic		Capture	Illumina HiSeq	Phase_I	49175648	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	g	7.933	0.741106	0.15642	.	.	ENSG00000177352	ENST00000321895	T	0.38240	1.15	4.91	3.1	0.35709	.	0.869953	0.09613	N	0.778606	T	0.32436	0.0829	L	0.51422	1.61	0.20489	N	0.999895	P	0.36909	0.573	B	0.36666	0.23	T	0.16129	-1.0413	10	0.36615	T	0.2	-19.0649	7.8812	0.29623	0.0872:0.1625:0.7503:0.0	.	333	Q8IV32	CCD71_HUMAN	V	333	ENSP00000319006:A333V	ENSP00000319006:A333V	A	-	2	0	CCDC71	49175648	0.996000	0.38824	0.312000	0.25196	0.016000	0.09150	2.452000	0.44961	0.783000	0.33636	0.556000	0.70494	GCC		0.637	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
CCDC36	339834	broad.mit.edu	37	3	49294518	49294518	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:49294518C>T	ENST00000438782.1	+	8	1824	c.1588C>T	c.(1588-1590)Cag>Tag	p.Q530*	CCDC36_ENST00000296449.5_Nonsense_Mutation_p.Q530*|CCDC36_ENST00000452691.2_Nonsense_Mutation_p.Q530*|RP11-3B7.1_ENST00000440528.3_5'Flank			Q8IYA8	CCD36_HUMAN	coiled-coil domain containing 36	530								p.Q520*(1)		endometrium(1)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|ovary(1)|urinary_tract(3)	14				BRCA - Breast invasive adenocarcinoma(193;9.11e-05)|Kidney(197;0.00248)|KIRC - Kidney renal clear cell carcinoma(197;0.00262)		AAGGGCAGTGCAGGGAAGACT	0.557																																					p.Q530X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1588T	3						.						75.0	78.0	77.0					3																	49294518		2203	4300	6503	49269522	SO:0001587	stop_gained	339834	exon10			AK058049	CCDS33755.2	3p21.31	2009-08-06			ENSG00000173421	ENSG00000173421			27945	protein-coding gene	gene with protein product	"""cancer/testis antigen 74"""						Standard	NM_178173		Approved	FLJ25320, CT74	uc011bck.1	Q8IYA8	OTTHUMG00000155920	ENST00000438782.1:c.1588C>T	3.37:g.49294518C>T	ENSP00000391788:p.Gln530*	Somatic		Capture	Illumina HiSeq	Phase_I	49269522	NM_178173	C9JJL0|Q05DG9|Q96LP7	Nonsense_Mutation	SNP	ENST00000438782.1	37	CCDS33755.2	.	.	.	.	.	.	.	.	.	.	C	18.34	3.601938	0.66445	.	.	ENSG00000173421	ENST00000296449;ENST00000438782;ENST00000452691;ENST00000309062	.	.	.	4.66	2.74	0.32292	.	1.140060	0.06618	N	0.756874	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	1.8788	7.1818	0.25776	0.1797:0.57:0.2504:0.0	.	.	.	.	X	530;530;530;510	.	ENSP00000296449:Q530X	Q	+	1	0	CCDC36	49269522	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.640000	0.24705	0.571000	0.29365	0.561000	0.74099	CAG		0.557	CCDC36-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342332.1	NM_178173	
BSN	8927	broad.mit.edu	37	3	49688334	49688334	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:49688334G>A	ENST00000296452.4	+	4	1922	c.1808G>A	c.(1807-1809)aGc>aAc	p.S603N		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	603					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)	p.S603N(1)		breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AAGACCCCAAGCAGTGTCCAG	0.617																																					p.S603N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1808A	3						.						95.0	113.0	107.0					3																	49688334		2203	4300	6503	49663338	SO:0001583	missense	8927	exon4			AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.1808G>A	3.37:g.49688334G>A	ENSP00000296452:p.Ser603Asn	Somatic		Capture	Illumina HiSeq	Phase_I	49663338	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	G	12.12	1.842730	0.32606	.	.	ENSG00000164061	ENST00000296452	T	0.18338	2.22	5.34	3.39	0.38822	.	0.384615	0.30781	N	0.008884	T	0.13243	0.0321	L	0.47716	1.5	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.15896	-1.0421	10	0.39692	T	0.17	.	4.6249	0.12474	0.0829:0.1538:0.6043:0.1591	.	603	Q9UPA5	BSN_HUMAN	N	603	ENSP00000296452:S603N	ENSP00000296452:S603N	S	+	2	0	BSN	49663338	0.078000	0.21339	0.962000	0.40283	0.734000	0.41952	2.320000	0.43797	1.227000	0.43598	0.655000	0.94253	AGC		0.617	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
IFRD2	7866	broad.mit.edu	37	3	50325659	50325659	+	Missense_Mutation	SNP	C	C	T	rs369995042		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:50325659C>T	ENST00000429673.2	-	12	1483	c.1484G>A	c.(1483-1485)cGa>cAa	p.R495Q	IFRD2_ENST00000484043.1_5'Flank|IFRD2_ENST00000336089.4_Missense_Mutation_p.R597Q|IFRD2_ENST00000417626.2_Missense_Mutation_p.R431Q|IFRD2_ENST00000436390.1_Missense_Mutation_p.R431Q			Q12894	IFRD2_HUMAN	interferon-related developmental regulator 2	495						nucleus (GO:0005634)		p.R597Q(1)		breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)	14				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CACACGGCTTCGAGCCTTGGT	0.572																																					p.R495Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1484A	3						.	C	GLN/ARG	0,3952		0,0,1976	39.0	41.0	40.0		1484	5.9	0.8	3		40	1,8329		0,1,4164	no	missense	IFRD2	NM_006764.4	43	0,1,6140	TT,TC,CC		0.012,0.0,0.0081	probably-damaging	495/507	50325659	1,12281	1976	4165	6141	50300663	SO:0001583	missense	7866	exon12			U09585		3p21.3	2008-07-18			ENSG00000214706	ENSG00000214706			5457	protein-coding gene	gene with protein product	"""interferon-related protein"""	602725				9050919	Standard	NM_006764		Approved	SKMc15, SM15, IFNRP	uc011bdp.2	Q12894	OTTHUMG00000156935	ENST00000429673.2:c.1484G>A	3.37:g.50325659C>T	ENSP00000398971:p.Arg495Gln	Somatic		Capture	Illumina HiSeq	Phase_I	50300663	NM_006764	Q9BVB4|Q9UJ88	Missense_Mutation	SNP	ENST00000429673.2	37	CCDS46831.1	.	.	.	.	.	.	.	.	.	.	C	36	5.761389	0.96906	0.0	1.2E-4	ENSG00000214706	ENST00000417626;ENST00000426499;ENST00000436390;ENST00000336089;ENST00000429673	T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13	5.93	5.93	0.95920	Interferon-related developmental regulator, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.83514	0.5271	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.86068	0.1536	10	0.87932	D	0	-17.4696	17.8477	0.88736	0.0:1.0:0.0:0.0	.	495;597	Q12894;Q9UJ88	IFRD2_HUMAN;.	Q	431;60;431;597;495	ENSP00000402849:R431Q;ENSP00000408549:R60Q;ENSP00000392316:R431Q;ENSP00000336936:R597Q;ENSP00000398971:R495Q	ENSP00000336936:R597Q	R	-	2	0	IFRD2	50300663	1.000000	0.71417	0.785000	0.31869	0.989000	0.77384	7.302000	0.78861	2.826000	0.97356	0.655000	0.94253	CGA		0.572	IFRD2-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_006764	
CACNA2D2	9254	broad.mit.edu	37	3	50513589	50513589	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:50513589C>T	ENST00000479441.1	-	2	247	c.248G>A	c.(247-249)gGc>gAc	p.G83D	CACNA2D2_ENST00000423994.2_Missense_Mutation_p.G83D|CACNA2D2_ENST00000487413.1_5'UTR|CACNA2D2_ENST00000424201.2_Missense_Mutation_p.G83D|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.G83D|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.G83D|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.G83D|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.G83D|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.G14D			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	83					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G83D(1)		breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CCGCATCACGCCGTCGACCTC	0.632																																					p.G83D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G248A	3						.						56.0	52.0	54.0					3																	50513589		2201	4300	6501	50488593	SO:0001583	missense	9254	exon2			AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.248G>A	3.37:g.50513589C>T	ENSP00000418081:p.Gly83Asp	Somatic		Capture	Illumina HiSeq	Phase_I	50488593	NM_006030	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	37	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	14.02	2.411005	0.42817	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.05139	3.49;3.5;3.5;3.49;3.49;3.5;3.5;3.49	5.01	5.01	0.66863	.	0.076344	0.52532	D	0.000067	T	0.07098	0.0180	L	0.29908	0.895	0.37643	D	0.922123	P;P	0.38863	0.65;0.632	B;B	0.43728	0.247;0.429	T	0.44205	-0.9343	10	0.11485	T	0.65	-12.2834	13.6709	0.62424	0.0:1.0:0.0:0.0	.	83;83	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	D	83;83;83;14;83;83;83;83	ENSP00000407393:G83D;ENSP00000404631:G83D;ENSP00000266039:G83D;ENSP00000354228:G14D;ENSP00000390526:G83D;ENSP00000378519:G83D;ENSP00000390329:G83D;ENSP00000418081:G83D	ENSP00000266039:G83D	G	-	2	0	CACNA2D2	50488593	0.866000	0.29940	0.881000	0.34555	0.972000	0.66771	3.985000	0.56930	2.591000	0.87537	0.561000	0.74099	GGC		0.632	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	
DNAH1	25981	broad.mit.edu	37	3	52383372	52383372	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:52383372G>A	ENST00000420323.2	+	14	2723	c.2462G>A	c.(2461-2463)cGc>cAc	p.R821H		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	821	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R821H(1)		cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCCAAGAAACGCAAGGCCCTG	0.577																																					p.R821H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2462A	3						.						81.0	89.0	87.0					3																	52383372		2157	4248	6405	52358412	SO:0001583	missense	25981	exon14			U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.2462G>A	3.37:g.52383372G>A	ENSP00000401514:p.Arg821His	Somatic		Capture	Illumina HiSeq	Phase_I	52358412	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	11.66	1.706353	0.30232	.	.	ENSG00000114841	ENST00000420323	T	0.23348	1.91	5.45	3.6	0.41247	.	0.706661	0.12878	N	0.431661	T	0.24812	0.0602	M	0.73319	2.225	0.30868	N	0.7328	B;B	0.20261	0.001;0.043	B;B	0.13407	0.001;0.009	T	0.32322	-0.9911	10	0.13470	T	0.59	.	7.0945	0.25301	0.1577:0.0:0.6927:0.1496	.	821;821	C9JXH6;Q9P2D7-3	.;.	H	821	ENSP00000401514:R821H	ENSP00000401514:R821H	R	+	2	0	DNAH1	52358412	0.966000	0.33281	0.998000	0.56505	0.987000	0.75469	3.311000	0.51919	0.624000	0.30286	0.655000	0.94253	CGC		0.577	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
ITIH1	3697	broad.mit.edu	37	3	52820380	52820380	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:52820380G>T	ENST00000273283.2	+	13	1687	c.1663G>T	c.(1663-1665)Ggc>Tgc	p.G555C	ITIH1_ENST00000405128.3_5'Flank|ITIH1_ENST00000542827.1_Missense_Mutation_p.G555C|ITIH1_ENST00000540715.1_Missense_Mutation_p.G413C|ITIH1_ENST00000537050.1_Missense_Mutation_p.G267C	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	555	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.G555C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		CCGAGAGCGTGGCCACATGCT	0.602																																					p.G413C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1237T	3						.						58.0	44.0	49.0					3																	52820380		2201	4297	6498	52795420	SO:0001583	missense	3697	exon11				CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.1663G>T	3.37:g.52820380G>T	ENSP00000273283:p.Gly555Cys	Somatic		Capture	Illumina HiSeq	Phase_I	52795420	NM_001166434	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.951639	0.73787	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133	T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76	5.49	5.49	0.81192	.	0.302386	0.36893	N	0.002343	T	0.32224	0.0822	M	0.83012	2.62	0.41216	D	0.986471	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.76071	0.987;0.98;0.981	T	0.07849	-1.0751	10	0.72032	D	0.01	-31.1309	8.0558	0.30604	0.0843:0.1612:0.7544:0.0	.	413;156;555	F5H165;Q9P1C5;P19827	.;.;ITIH1_HUMAN	C	555;555;413;267;108	ENSP00000442584:G555C;ENSP00000273283:G555C;ENSP00000443973:G413C;ENSP00000443847:G267C;ENSP00000395836:G108C	ENSP00000273283:G555C	G	+	1	0	ITIH1	52795420	0.589000	0.26807	1.000000	0.80357	0.967000	0.64934	1.500000	0.35682	2.582000	0.87167	0.462000	0.41574	GGC		0.602	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
ATXN7	6314	broad.mit.edu	37	3	63976433	63976433	+	Missense_Mutation	SNP	G	G	A	rs201198489		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:63976433G>A	ENST00000295900.6	+	11	2130	c.1580G>A	c.(1579-1581)cGg>cAg	p.R527Q	ATXN7_ENST00000398590.3_Missense_Mutation_p.R527Q|ATXN7_ENST00000484332.1_Missense_Mutation_p.R382Q|ATXN7_ENST00000487717.1_Missense_Mutation_p.R527Q|ATXN7_ENST00000538065.1_Missense_Mutation_p.R527Q	NM_000333.3	NP_000324.1	O15265	ATX7_HUMAN	ataxin 7	527					cell death (GO:0008219)|chromatin organization (GO:0006325)|histone deubiquitination (GO:0016578)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|nucleus organization (GO:0006997)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	chromatin binding (GO:0003682)	p.R527Q(1)		NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(12)|prostate(2)|stomach(1)|urinary_tract(3)	35		Prostate(884;0.0181)		BRCA - Breast invasive adenocarcinoma(55;0.000614)|KIRC - Kidney renal clear cell carcinoma(15;0.00294)|Kidney(15;0.00305)		TTTGGGAGCCGGCAGATAGGA	0.527																																					p.R527Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1580A	3						.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4086		0,0,2043	135.0	132.0	133.0		1580,1145,1580	4.6	1.0	3		133	2,8408		0,2,4203	no	missense,missense,missense	ATXN7	NM_000333.3,NM_001128149.2,NM_001177387.1	43,43,43	0,2,6246	AA,AG,GG		0.0238,0.0,0.016	possibly-damaging,possibly-damaging,possibly-damaging	527/893,382/748,527/946	63976433	2,12494	2043	4205	6248	63951473	SO:0001583	missense	6314	exon10			AJ000517	CCDS43102.1, CCDS46861.1, CCDS46861.2, CCDS54603.1	3p21.1-p12	2014-09-17	2004-08-12	2004-08-12	ENSG00000163635	ENSG00000163635		"""Ataxins"""	10560	protein-coding gene	gene with protein product		607640	"""spinocerebellar ataxia 7 (olivopontocerebellar atrophy with retinal degeneration)"""	SCA7		7647798, 10598805	Standard	NM_000333		Approved	OPCA3, ADCAII	uc021wzy.1	O15265	OTTHUMG00000158763	ENST00000295900.6:c.1580G>A	3.37:g.63976433G>A	ENSP00000295900:p.Arg527Gln	Somatic		Capture	Illumina HiSeq	Phase_I	63951473	NM_001177387	B4E207|E9PHP9|O75328|O75329|Q9Y6P8	Missense_Mutation	SNP	ENST00000295900.6	37	CCDS43102.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.498316	0.85069	0.0	2.38E-4	ENSG00000163635	ENST00000398590;ENST00000295900;ENST00000487717;ENST00000538065;ENST00000484332	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	5.47	4.58	0.56647	.	0.061202	0.64402	D	0.000003	T	0.45558	0.1348	L	0.55990	1.75	0.80722	D	1	P;P;B	0.45283	0.553;0.855;0.204	B;B;B	0.37508	0.032;0.252;0.052	T	0.52313	-0.8592	10	0.56958	D	0.05	-10.871	12.3502	0.55144	0.1338:0.0:0.8662:0.0	.	382;527;527	E9PHP9;O15265-2;O15265	.;.;ATX7_HUMAN	Q	527;527;527;527;382	ENSP00000381590:R527Q;ENSP00000295900:R527Q;ENSP00000420234:R527Q;ENSP00000439585:R527Q;ENSP00000428277:R382Q	ENSP00000295900:R527Q	R	+	2	0	ATXN7	63951473	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.501000	0.66950	2.728000	0.93425	0.655000	0.94253	CGG		0.527	ATXN7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352070.1	NM_000333	
LRIG1	26018	broad.mit.edu	37	3	66434674	66434674	+	Silent	SNP	C	C	T	rs140903952	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:66434674C>T	ENST00000273261.3	-	14	2336	c.1812G>A	c.(1810-1812)acG>acA	p.T604T	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Silent_p.T628T|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	604	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.T604T(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TGTCGTGGGGCGTTTTGGTGA	0.547													c|||	7	0.00139776	0.0	0.0029	5008	,	,		18000	0.0		0.001	False		,,,				2504	0.0041				p.T604T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1812A	3						.	T		2,4404	4.2+/-10.8	0,2,2201	233.0	225.0	228.0		1812	-1.0	0.8	3	dbSNP_134	228	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRIG1	NM_015541.2		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		604/1094	66434674	24,12982	2203	4300	6503	66517364	SO:0001819	synonymous_variant	26018	exon14			AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1812G>A	3.37:g.66434674C>T		Somatic		Capture	Illumina HiSeq	Phase_I	66517364	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																				0.547	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
PDZRN3	23024	broad.mit.edu	37	3	73433004	73433004	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:73433004T>A	ENST00000263666.4	-	10	2827	c.2713A>T	c.(2713-2715)Atg>Ttg	p.M905L	PDZRN3_ENST00000466780.1_Missense_Mutation_p.M562L|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000462146.2_Missense_Mutation_p.M562L|PDZRN3_ENST00000535920.1_Missense_Mutation_p.M627L|PDZRN3_ENST00000479530.1_Missense_Mutation_p.M622L	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	905					neuromuscular junction development (GO:0007528)|protein ubiquitination (GO:0016567)	neuromuscular junction (GO:0031594)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.M905L(1)		breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(31)|ovary(4)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69		Prostate(10;0.114)|Lung NSC(201;0.187)|Lung SC(41;0.236)		BRCA - Breast invasive adenocarcinoma(55;0.00041)|Epithelial(33;0.0023)|LUSC - Lung squamous cell carcinoma(21;0.0048)|Lung(16;0.0105)|KIRC - Kidney renal clear cell carcinoma(39;0.111)|Kidney(39;0.134)		TCCTTGCACATGCTCACCAGG	0.637																																					p.M905L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2713T	3						.						67.0	58.0	61.0					3																	73433004		2203	4300	6503	73515694	SO:0001583	missense	23024	exon10			AB029018	CCDS33789.1	3p14.1	2013-01-09	2008-08-14		ENSG00000121440	ENSG00000121440		"""RING-type (C3HC4) zinc fingers"""	17704	protein-coding gene	gene with protein product	"""likely ortholog of mouse semaF cytoplasmic domain associated protein 3"""	609729				10470851	Standard	XM_005264718		Approved	KIAA1095, SEMACAP3, LNX3	uc003dpl.1	Q9UPQ7	OTTHUMG00000158865	ENST00000263666.4:c.2713A>T	3.37:g.73433004T>A	ENSP00000263666:p.Met905Leu	Somatic		Capture	Illumina HiSeq	Phase_I	73515694	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Missense_Mutation	SNP	ENST00000263666.4	37	CCDS33789.1	.	.	.	.	.	.	.	.	.	.	T	1.217	-0.628113	0.03610	.	.	ENSG00000121440	ENST00000263666;ENST00000535920;ENST00000462146;ENST00000466780;ENST00000479530	T;T;T;T;T	0.40756	1.02;1.02;1.02;1.02;1.02	5.4	0.296	0.15757	.	0.912470	0.09465	N	0.798421	T	0.21387	0.0515	N	0.20401	0.57	0.49299	D	0.99977	B;B;B;B	0.32350	0.003;0.098;0.017;0.366	B;B;B;B	0.24269	0.004;0.012;0.009;0.052	T	0.15809	-1.0424	10	0.08381	T	0.77	.	8.9394	0.35720	0.0:0.3072:0.0:0.6928	.	627;622;622;905	F5H8I9;B7ZAG0;B7Z5X9;Q9UPQ7	.;.;.;PZRN3_HUMAN	L	905;627;562;562;622	ENSP00000263666:M905L;ENSP00000442026:M627L;ENSP00000418168:M562L;ENSP00000418484:M562L;ENSP00000418624:M622L	ENSP00000263666:M905L	M	-	1	0	PDZRN3	73515694	1.000000	0.71417	0.996000	0.52242	0.431000	0.31685	2.087000	0.41653	-0.175000	0.10725	-0.912000	0.02778	ATG		0.637	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363	
CNTN3	5067	broad.mit.edu	37	3	74347112	74347112	+	Missense_Mutation	SNP	T	T	G	rs202118462		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:74347112T>G	ENST00000263665.6	-	17	2424	c.2397A>C	c.(2395-2397)gaA>gaC	p.E799D		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	799	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.E799D(1)		NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		CCATACCTTCTTCTGCAGAGA	0.358																																					p.E799D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2397C	3						.						118.0	116.0	117.0					3																	74347112		2203	4300	6503	74429802	SO:0001583	missense	5067	exon17			AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2397A>C	3.37:g.74347112T>G	ENSP00000263665:p.Glu799Asp	Somatic		Capture	Illumina HiSeq	Phase_I	74429802	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	.	.	.	.	.	.	.	.	.	.	T	15.08	2.728644	0.48833	.	.	ENSG00000113805	ENST00000263665	T	0.56103	0.48	5.82	-0.829	0.10796	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.56587	0.1995	M	0.86805	2.84	0.47374	D	0.999404	B	0.25521	0.128	B	0.29524	0.103	T	0.61422	-0.7066	10	0.66056	D	0.02	.	12.8491	0.57848	0.0:0.509:0.0:0.491	.	799	Q9P232	CNTN3_HUMAN	D	799	ENSP00000263665:E799D	ENSP00000263665:E799D	E	-	3	2	CNTN3	74429802	0.997000	0.39634	0.998000	0.56505	0.998000	0.95712	0.305000	0.19254	-0.093000	0.12396	0.533000	0.62120	GAA		0.358	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
ROBO1	6091	broad.mit.edu	37	3	78795908	78795908	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:78795908T>C	ENST00000464233.1	-	5	755	c.642A>G	c.(640-642)aaA>aaG	p.K214K	ROBO1_ENST00000436010.2_Silent_p.K175K|ROBO1_ENST00000467549.1_Silent_p.K175K|ROBO1_ENST00000495273.1_Silent_p.K175K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	214	Ig-like C2-type 2.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.K191K(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTCTTTCATCTTTATCATCCA	0.413																																					p.K214K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A642G	3						.						113.0	112.0	113.0					3																	78795908		1870	4100	5970	78878598	SO:0001819	synonymous_variant	6091	exon5			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.642A>G	3.37:g.78795908T>C		Somatic		Capture	Illumina HiSeq	Phase_I	78878598	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																				0.413	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
ROBO1	6091	broad.mit.edu	37	3	78987879	78987879	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:78987879C>A	ENST00000464233.1	-	4	484	c.371G>T	c.(370-372)aGt>aTt	p.S124I	RN7SL751P_ENST00000473281.2_RNA|ROBO1_ENST00000436010.2_Missense_Mutation_p.S85I|ROBO1_ENST00000467549.1_Missense_Mutation_p.S85I|ROBO1_ENST00000495273.1_Missense_Mutation_p.S85I	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	124	Ig-like C2-type 1.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)	p.S101I(1)		breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TAAAGATCCACTCGGCAGCAA	0.488																																					p.S124I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G371T	3						.						120.0	114.0	116.0					3																	78987879		1948	4144	6092	79070569	SO:0001583	missense	6091	exon4			AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.371G>T	3.37:g.78987879C>A	ENSP00000420321:p.Ser124Ile	Somatic		Capture	Illumina HiSeq	Phase_I	79070569	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.426914	0.83667	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.53	5.53	0.82687	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.044040	0.85682	D	0.000000	T	0.57403	0.2051	L	0.39566	1.225	0.53005	D	0.999963	D;D;D;D	0.89917	1.0;0.996;0.999;0.994	D;P;D;D	0.81914	0.995;0.9;0.987;0.977	T	0.51036	-0.8756	9	.	.	.	.	19.4697	0.94958	0.0:1.0:0.0:0.0	.	124;85;85;85	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	I	85;85;124;85;85;124	ENSP00000406043:S85I;ENSP00000420321:S124I;ENSP00000420637:S85I;ENSP00000417992:S85I	.	S	-	2	0	ROBO1	79070569	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.562000	0.36353	2.611000	0.88343	0.462000	0.41574	AGT		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
CRYBG3	131544	broad.mit.edu	37	3	97596644	97596644	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:97596644A>T	ENST00000182096.4	+	1	826	c.762A>T	c.(760-762)gaA>gaT	p.E254D		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2202							carbohydrate binding (GO:0030246)	p.E254D(1)		breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TGCCAAATGAACCTACTACCT	0.423																																					.												.	.	1	Substitution - Missense(1)	large_intestine(1)	.	3						.						84.0	83.0	83.0					3																	97596644		1931	4138	6069	99079334	SO:0001583	missense	131544	.					3q11.2	2008-09-30			ENSG00000080200	ENSG00000080200			34427	protein-coding gene	gene with protein product							Standard	NM_153605		Approved	DKFZp667G2110	uc021xbn.2	Q68DQ2	OTTHUMG00000159187	ENST00000182096.4:c.762A>T	3.37:g.97596644A>T	ENSP00000182096:p.Glu254Asp	Somatic		Capture	Illumina HiSeq	Phase_I	99079334	.	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	A	10.58	1.389640	0.25118	.	.	ENSG00000080200	ENST00000182096	T	0.77620	-1.11	5.66	0.427	0.16489	.	0.760458	0.12015	N	0.507517	T	0.76688	0.4022	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.63793	0.918	T	0.70475	-0.4861	10	0.52906	T	0.07	.	5.3147	0.15849	0.5307:0.255:0.2143:0.0	.	254	Q68DQ2	CRBG3_HUMAN	D	254	ENSP00000182096:E254D	ENSP00000182096:E254D	E	+	3	2	CRYBG3	99079334	0.859000	0.29813	0.909000	0.35828	0.313000	0.28021	0.335000	0.19806	-0.140000	0.11394	-0.440000	0.05779	GAA		0.423	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605	
ST3GAL6	10402	broad.mit.edu	37	3	98503842	98503842	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:98503842A>G	ENST00000483910.1	+	6	678	c.389A>G	c.(388-390)aAg>aGg	p.K130R	ST3GAL6_ENST00000265261.6_Intron|ST3GAL6_ENST00000394162.1_Missense_Mutation_p.K130R|ST3GAL6_ENST00000462152.1_3'UTR	NM_001271146.1	NP_001258075.1	Q9Y274	SIA10_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 6	130					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|cellular response to interleukin-6 (GO:0071354)|glycolipid metabolic process (GO:0006664)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|oligosaccharide metabolic process (GO:0009311)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	beta-galactoside alpha-2,3-sialyltransferase activity (GO:0052798)	p.K130R(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(1)	19						TTGAAGAATAAGACATTAGGA	0.343																																					p.K130R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A389G	3						.						101.0	108.0	106.0					3																	98503842		2203	4300	6503	99986532	SO:0001583	missense	10402	exon7			AF119391	CCDS2933.1, CCDS59452.1, CCDS74968.1	3q12.2	2013-03-01	2005-02-07	2005-02-07	ENSG00000064225	ENSG00000064225		"""Sialyltransferases"""	18080	protein-coding gene	gene with protein product		607156	"""sialyltransferase 10 (alpha-2,3-sialyltransferase VI)"""	SIAT10		10206952	Standard	NM_006100		Approved	ST3GALVI	uc010hpd.4	Q9Y274	OTTHUMG00000159047	ENST00000483910.1:c.389A>G	3.37:g.98503842A>G	ENSP00000417376:p.Lys130Arg	Somatic		Capture	Illumina HiSeq	Phase_I	99986532	NM_006100	B2RCH2|B3KMI1|D3DN39|F8W6U0	Missense_Mutation	SNP	ENST00000483910.1	37	CCDS2933.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.386515	0.61956	.	.	ENSG00000064225	ENST00000483910;ENST00000486334;ENST00000394162;ENST00000492254;ENST00000477574;ENST00000485145	T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5	5.1	3.91	0.45181	.	0.220226	0.40302	N	0.001132	T	0.38054	0.1026	L	0.46741	1.465	0.80722	D	1	D;D	0.61080	0.989;0.98	P;P	0.60117	0.869;0.714	T	0.16247	-1.0409	10	0.46703	T	0.11	-20.8911	5.1876	0.15193	0.7258:0.1837:0.0905:0.0	.	153;130	C9J480;Q9Y274	.;SIA10_HUMAN	R	130;130;130;153;95;44	ENSP00000417376:K130R;ENSP00000418896:K130R;ENSP00000377717:K130R;ENSP00000417201:K153R;ENSP00000419987:K95R;ENSP00000419202:K44R	ENSP00000377717:K130R	K	+	2	0	ST3GAL6	99986532	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.504000	0.53347	1.024000	0.39682	0.533000	0.62120	AAG		0.343	ST3GAL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353013.2	NM_006100	
MYLK	4638	broad.mit.edu	37	3	123457860	123457860	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:123457860delC	ENST00000475616.1	-	4	471	c.472delG	c.(472-474)gagfs	p.E158fs	MYLK_ENST00000346322.5_Frame_Shift_Del_p.E158fs|MYLK_ENST00000359169.1_Frame_Shift_Del_p.E158fs|MYLK_ENST00000360772.3_Frame_Shift_Del_p.E158fs|MYLK_ENST00000360304.3_Frame_Shift_Del_p.E158fs			Q15746	MYLK_HUMAN	myosin light chain kinase	158					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)	p.E158fs*79(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		GGTGGGCACTCCCCCCAGATG	0.547																																					p.E158fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.472delG	3						.						71.0	61.0	64.0					3																	123457860		2203	4300	6503	124940550	SO:0001589	frameshift_variant	4638	exon7			X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.472delG	3.37:g.123457860delC	ENSP00000418335:p.Glu158fs	Somatic		Capture	Illumina HiSeq	Phase_I	124940550	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Frame_Shift_Del	DEL	ENST00000475616.1	37	CCDS46896.1																																																																																				0.547	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
CCDC37	348807	broad.mit.edu	37	3	126142183	126142183	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:126142183delC	ENST00000352312.1	+	12	1197	c.1098delC	c.(1096-1098)atcfs	p.I366fs	CCDC37_ENST00000393425.1_Frame_Shift_Del_p.I367fs|CCDC37_ENST00000505024.1_Frame_Shift_Del_p.I367fs	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	366								p.T369fs*36(1)		NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		ACTCTCCCATCCCCCCCACGC	0.657																																					p.I366fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1098delC	3						.			1,4265		0,1,2132	42.0	37.0	39.0			0.5	0.0	3		39	1,8253		0,1,4126	no	frameshift	CCDC37	NM_182628.2		0,2,6258	A1A1,A1R,RR		0.0121,0.0234,0.016			126142183	2,12518	2203	4300	6503	127624873	SO:0001589	frameshift_variant	348807	exon12			AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1098delC	3.37:g.126142183delC	ENSP00000344749:p.Ile366fs	Somatic		Capture	Illumina HiSeq	Phase_I	127624873	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Frame_Shift_Del	DEL	ENST00000352312.1	37	CCDS3037.1																																																																																				0.657	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
SLCO2A1	6578	broad.mit.edu	37	3	133664061	133664061	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:133664061delC	ENST00000310926.4	-	10	1612	c.1339delG	c.(1339-1341)gacfs	p.D447fs	SLCO2A1_ENST00000493729.1_Frame_Shift_Del_p.D371fs	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	447	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				lipid transport (GO:0006869)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lipid transporter activity (GO:0005319)|prostaglandin transmembrane transporter activity (GO:0015132)	p.D447fs*33(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)|skin(2)|stomach(2)	30					Alprostadil(DB00770)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Furosemide(DB00695)|Iloprost(DB01088)|Phenobarbital(DB01174)|Pyruvic acid(DB00119)	CACGAGCAGTCCCTGCGGCAG	0.522																																					p.D447fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1339delG	3						.						146.0	157.0	154.0					3																	133664061		2203	4300	6503	135146751	SO:0001589	frameshift_variant	6578	exon10				CCDS3084.1	3q21	2013-05-22	2003-11-25	2003-11-26	ENSG00000174640	ENSG00000174640		"""Solute carriers"""	10955	protein-coding gene	gene with protein product		601460	"""solute carrier family 21 (prostaglandin transporter), member 2"", ""matrin F/G 1"""	SLC21A2, MATR1		8787677, 9618293	Standard	NM_005630		Approved	PGT, OATP2A1	uc003eqa.4	Q92959	OTTHUMG00000159745	ENST00000310926.4:c.1339delG	3.37:g.133664061delC	ENSP00000311291:p.Asp447fs	Somatic		Capture	Illumina HiSeq	Phase_I	135146751	NM_005630	Q86V98|Q8IUN2	Frame_Shift_Del	DEL	ENST00000310926.4	37	CCDS3084.1																																																																																				0.522	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
ABCC5	10057	broad.mit.edu	37	3	183667851	183667853	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	AGA	AGA	AGA	-	AGA	AGA	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:183667851_183667853delAGA	ENST00000334444.6	-	21	3245_3247	c.3005_3007delTCT	c.(3004-3009)ttctgt>tgt	p.F1002del	ABCC5_ENST00000265586.6_In_Frame_Del_p.F1002del	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	1002	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)	p.F1002delF(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(32)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	62	all_cancers(143;1.85e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cisplatin(DB00515)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Glutathione(DB00143)|Mercaptopurine(DB01033)|Probenecid(DB01032)|Rifampicin(DB01045)|Sildenafil(DB00203)|Sulfinpyrazone(DB01138)|Zidovudine(DB00495)	ATTCCCACACAGAAGAACACCAG	0.517																																					p.1002_1003del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.3005_3007del	3						.																																			185150547	SO:0001651	inframe_deletion	10057	exon21			AF104942	CCDS33898.1, CCDS43176.1	3q27	2012-03-14			ENSG00000114770	ENSG00000114770		"""ATP binding cassette transporters / subfamily C"""	56	protein-coding gene	gene with protein product		605251				8894702, 9827529	Standard	XM_005247058		Approved	MRP5, SMRP, EST277145, MOAT-C	uc003fmg.3	O15440	OTTHUMG00000156871	ENST00000334444.6:c.3005_3007delTCT	3.37:g.183667854_183667856delAGA	ENSP00000333926:p.Phe1002del	Somatic		Capture	Illumina HiSeq	Phase_I	185150545	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	In_Frame_Del	DEL	ENST00000334444.6	37	CCDS43176.1																																																																																				0.517	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
LIPH	200879	broad.mit.edu	37	3	185236947	185236947	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:185236947delT	ENST00000296252.4	-	6	1010	c.869delA	c.(868-870)gagfs	p.E290fs	LIPH_ENST00000424591.2_Frame_Shift_Del_p.E256fs	NM_139248.2	NP_640341.1	Q8WWY8	LIPH_HUMAN	lipase, member H	290					lipid catabolic process (GO:0016042)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|phospholipase activity (GO:0004620)	p.E290fs*17(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(2)	20	all_cancers(143;8.87e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			GGGACAGGACTCTTTTTGTGA	0.458																																					p.E290fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.869delA	3						.						132.0	132.0	132.0					3																	185236947		2203	4300	6503	186719641	SO:0001589	frameshift_variant	200879	exon6			AY093498	CCDS3272.1	3q27	2012-07-31			ENSG00000163898	ENSG00000163898			18483	protein-coding gene	gene with protein product		607365				12213196, 12063250	Standard	XM_006713529		Approved	mPA-PLA1, PLA1B, mPA-PLA1alpha, LPDLR	uc003fpm.3	Q8WWY8	OTTHUMG00000156657	ENST00000296252.4:c.869delA	3.37:g.185236947delT	ENSP00000296252:p.Glu290fs	Somatic		Capture	Illumina HiSeq	Phase_I	186719641	NM_139248	A2IBA7|Q8TEC7	Frame_Shift_Del	DEL	ENST00000296252.4	37	CCDS3272.1																																																																																				0.458	LIPH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345153.1		
TMEM44	93109	broad.mit.edu	37	3	194337941	194337941	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr3:194337941C>T	ENST00000392432.2	-	7	1016	c.811G>A	c.(811-813)Gct>Act	p.A271T	TMEM44_ENST00000347147.4_Missense_Mutation_p.A224T|TMEM44_ENST00000473092.1_Missense_Mutation_p.A224T|TMEM44_ENST00000273580.7_Missense_Mutation_p.A224T|TMEM44_ENST00000381975.3_Missense_Mutation_p.A224T	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	271						integral component of membrane (GO:0016021)		p.A224T(1)		breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		AGGAGGCCAGCCAGGGCCGAC	0.682																																					p.A224T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G670A	3						.						17.0	16.0	17.0					3																	194337941		2121	4158	6279	195819230	SO:0001583	missense	93109	exon6			AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.811G>A	3.37:g.194337941C>T	ENSP00000376227:p.Ala271Thr	Somatic		Capture	Illumina HiSeq	Phase_I	195819230	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518895	0.85495	.	.	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000013	T	0.63200	0.2491	M	0.66939	2.045	0.50813	D	0.999895	D;D;D;D;D	0.89917	0.987;1.0;1.0;1.0;0.987	P;D;D;D;P	0.87578	0.889;0.998;0.998;0.998;0.889	T	0.65043	-0.6264	10	0.72032	D	0.01	-11.8494	15.1688	0.72854	0.0:1.0:0.0:0.0	.	224;271;224;224;224	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	T	271;224;224;224;224	ENSP00000376227:A271T;ENSP00000273580:A224T;ENSP00000333355:A224T;ENSP00000371402:A224T;ENSP00000418674:A224T	ENSP00000273580:A224T	A	-	1	0	TMEM44	195819230	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	4.166000	0.58203	2.632000	0.89209	0.655000	0.94253	GCT		0.682	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
SNX25	83891	broad.mit.edu	37	4	186267704	186267705	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:186267704_186267705insA	ENST00000504273.1	+	13	2003_2004	c.1709_1710insA	c.(1708-1713)ttaaaafs	p.LK570fs	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Frame_Shift_Ins_p.LK570fs			Q9H3E2	SNX25_HUMAN	sorting nexin 25	570	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.V573fs*7(1)		NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		GTCCCTTCTTTAAAAAAAGTCC	0.292																																					p.L570fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1709_1710insA	4						.																																			186504699	SO:0001589	frameshift_variant	83891	exon13			AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"""Sorting nexins"""	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1716dupA	4.37:g.186267711_186267711dupA	ENSP00000426255:p.Leu570fs	Somatic		Capture	Illumina HiSeq	Phase_I	186504698	NM_031953	Q3ZT30|Q8N6K3	Frame_Shift_Ins	INS	ENST00000504273.1	37	CCDS34116.1																																																																																				0.292	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953	
NKX6-1	4825	broad.mit.edu	37	4	85419365	85419366	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:85419365_85419366insC	ENST00000295886.4	-	1	237_238	c.16_17insG	c.(16-18)gcafs	p.A6fs	NKX6-1_ENST00000515820.2_5'Flank	NM_006168.2	NP_006159.2	P78426	NKX61_HUMAN	NK6 homeobox 1	6					cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|cellular response to peptide hormone stimulus (GO:0071375)|detection of glucose (GO:0051594)|endocrine pancreas development (GO:0031018)|negative regulation of glial cell differentiation (GO:0045686)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|oligodendrocyte differentiation (GO:0048709)|organ morphogenesis (GO:0009887)|pancreas development (GO:0031016)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of insulin secretion (GO:0032024)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of axon extension (GO:0030516)|regulation of neuron migration (GO:2001222)|regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification (GO:0021912)|regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification (GO:0021913)|response to drug (GO:0042493)|response to nicotine (GO:0035094)|smoothened signaling pathway (GO:0007224)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A6fs*159(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	15		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.0013)		GCCCTCCATTGCCCCCACCGCT	0.723																																					p.A6fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.17_18insG	4						.																																			85638390	SO:0001589	frameshift_variant	4825	exon1			AH007313	CCDS3607.1	4q21.33	2012-03-09	2007-07-09	2002-10-04	ENSG00000163623	ENSG00000163623		"""Homeoboxes / ANTP class : NKL subclass"""	7839	protein-coding gene	gene with protein product		602563	"""NK homeobox (Drosophila), family 6, A"", ""NK6 transcription factor related, locus 1 (Drosophila)"""	NKX6A		9119408	Standard	NM_006168		Approved	Nkx6.1	uc003hpa.1	P78426	OTTHUMG00000130426	ENST00000295886.4:c.17dupG	4.37:g.85419370_85419370dupC	ENSP00000295886:p.Ala6fs	Somatic		Capture	Illumina HiSeq	Phase_I	85638389	NM_006168		Frame_Shift_Ins	INS	ENST00000295886.4	37	CCDS3607.1																																																																																				0.723	NKX6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252814.2	NM_006168	
DKK2	27123	broad.mit.edu	37	4	107847035	107847035	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:107847035C>A	ENST00000285311.3	-	2	999	c.294G>T	c.(292-294)tcG>tcT	p.S98S	DKK2_ENST00000513208.1_5'UTR|DKK2_ENST00000510463.1_Silent_p.S52S	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	98	DKK-type Cys-1.				multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)		p.S98S(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(7)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	32		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.34e-06)		CCATGCAGGCCGATGATCCTT	0.512																																					p.S98S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G294T	4						.						180.0	156.0	164.0					4																	107847035		2203	4300	6503	108066484	SO:0001819	synonymous_variant	27123	exon2			AB033208	CCDS3675.1	4q25	2013-05-15	2013-05-15		ENSG00000155011	ENSG00000155011			2892	protein-coding gene	gene with protein product		605415	"""dickkopf (Xenopus laevis) homolog 2"", ""dickkopf 2 homolog (Xenopus laevis)"""			10570958	Standard	NM_014421		Approved		uc003hyi.3	Q9UBU2	OTTHUMG00000131216	ENST00000285311.3:c.294G>T	4.37:g.107847035C>A		Somatic		Capture	Illumina HiSeq	Phase_I	108066484	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Silent	SNP	ENST00000285311.3	37	CCDS3675.1																																																																																				0.512	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4		
CCDC109B	55013	broad.mit.edu	37	4	110581505	110581505	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:110581505A>G	ENST00000394650.4	+	3	463	c.330A>G	c.(328-330)gcA>gcG	p.A110A		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	110					mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)	calcium channel complex (GO:0034704)|integral component of mitochondrial inner membrane (GO:0031305)|intrinsic component of membrane (GO:0031224)|mitochondrion (GO:0005739)|uniplex complex (GO:1990246)	calcium channel inhibitor activity (GO:0019855)	p.A22A(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(1)	9				OV - Ovarian serous cystadenocarcinoma(123;6.65e-06)		TCAAAACTGCAGCCATCTTCA	0.368																																					p.A110A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A330G	4						.						81.0	70.0	74.0					4																	110581505		2203	4300	6503	110800954	SO:0001819	synonymous_variant	55013	exon3			BC002633	CCDS3683.2	4q25	2011-05-24			ENSG00000005059	ENSG00000005059			26076	protein-coding gene	gene with protein product						12477932	Standard	NM_017918		Approved	FLJ20647	uc011cfs.2	Q9NWR8	OTTHUMG00000161103	ENST00000394650.4:c.330A>G	4.37:g.110581505A>G		Somatic		Capture	Illumina HiSeq	Phase_I	110800954	NM_017918	A8K4Y3|Q6IAC1	Silent	SNP	ENST00000394650.4	37	CCDS3683.2																																																																																				0.368	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918	
PITX2	5308	broad.mit.edu	37	4	111539551	111539551	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:111539551G>T	ENST00000354925.2	-	7	2389	c.684C>A	c.(682-684)ccC>ccA	p.P228P	RP11-380D23.2_ENST00000503456.1_lincRNA|PITX2_ENST00000355080.5_Silent_p.P182P|PITX2_ENST00000306732.3_Silent_p.P235P|PITX2_ENST00000394595.3_Missense_Mutation_p.L160I|PITX2_ENST00000556049.1_5'Flank|PITX2_ENST00000394598.2_Silent_p.P228P	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	228					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		TCACTGCTGAGGGCACCATGC	0.562																																					p.P228P												.	.	0			c.C684A	4						.						72.0	71.0	71.0					4																	111539551		2203	4300	6503	111759000	SO:0001819	synonymous_variant	5308	exon5			U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.684C>A	4.37:g.111539551G>T		None		Capture	Illumina HiSeq	Phase_I	111759000	NM_153426	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Silent	SNP	ENST00000354925.2	37	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	G	7.500	0.652436	0.14580	.	.	ENSG00000164093	ENST00000394595	.	.	.	5.25	4.4	0.53042	.	.	.	.	.	T	0.48519	0.1504	.	.	.	0.23107	N	0.998283	.	.	.	.	.	.	T	0.43702	-0.9375	5	0.87932	D	0	.	11.3839	0.49773	0.0702:0.127:0.8028:0.0	.	.	.	.	I	160	.	ENSP00000378095:L160I	L	-	1	0	PITX2	111759000	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.054000	0.30455	1.427000	0.47276	0.563000	0.77884	CTC		0.562	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2		
PITX2	5308	broad.mit.edu	37	4	111553635	111553635	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:111553635G>A	ENST00000354925.2	-	5	1753	c.48C>T	c.(46-48)ggC>ggT	p.G16G	PITX2_ENST00000355080.5_Intron|PITX2_ENST00000394595.3_Splice_Site_p.G16G|PITX2_ENST00000394598.2_Splice_Site_p.G16G	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	16					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.G16G(1)		breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		CCGGCTGCACGCCTGGGCCAC	0.682																																					p.G16G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C48T	4						.						38.0	50.0	46.0					4																	111553635		2201	4300	6501	111773084	SO:0001630	splice_region_variant	5308	exon3			U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.47-1C>T	4.37:g.111553635G>A		Somatic		Capture	Illumina HiSeq	Phase_I	111773084	NM_153426	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Silent	SNP	ENST00000354925.2	37	CCDS3692.1																																																																																				0.682	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2		Silent
ALPK1	80216	broad.mit.edu	37	4	113353404	113353404	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:113353404C>A	ENST00000458497.1	+	11	2980	c.2701C>A	c.(2701-2703)Ctc>Atc	p.L901I	ALPK1_ENST00000177648.9_Missense_Mutation_p.L901I|ALPK1_ENST00000504176.2_Missense_Mutation_p.L823I	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	901							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.L901I(1)		NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		CTTCCCTGTCCTCAGCGAGGA	0.552																																					p.L901I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2701A	4						.						116.0	114.0	115.0					4																	113353404		2203	4300	6503	113572853	SO:0001583	missense	80216	exon11			AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2701C>A	4.37:g.113353404C>A	ENSP00000398048:p.Leu901Ile	Somatic		Capture	Illumina HiSeq	Phase_I	113572853	NM_025144	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	37	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465016	0.43839	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02812	4.23;4.23;4.15	5.33	1.44	0.22558	.	1.405740	0.04250	N	0.338455	T	0.03564	0.0102	M	0.67953	2.075	0.09310	N	1	B;P;B	0.38922	0.041;0.651;0.003	B;B;B	0.27887	0.018;0.084;0.003	T	0.43766	-0.9371	10	0.36615	T	0.2	0.0715	2.652	0.05002	0.2583:0.4726:0.1254:0.1437	.	823;823;901	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	I	901;901;823	ENSP00000398048:L901I;ENSP00000177648:L901I;ENSP00000426044:L823I	ENSP00000177648:L901I	L	+	1	0	ALPK1	113572853	0.000000	0.05858	0.000000	0.03702	0.246000	0.25737	-0.518000	0.06267	-0.056000	0.13221	0.655000	0.94253	CTC		0.552	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
NEUROG2	63973	broad.mit.edu	37	4	113436339	113436339	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:113436339C>T	ENST00000313341.3	-	2	619	c.293G>A	c.(292-294)cGa>cAa	p.R98Q	RP11-402J6.1_ENST00000506057.1_RNA|RP11-402J6.1_ENST00000504009.1_RNA	NM_024019.3	NP_076924.1	Q9H2A3	NGN2_HUMAN	neurogenin 2	98					axon guidance (GO:0007411)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|central nervous system neuron development (GO:0021954)|forebrain development (GO:0030900)|neuron migration (GO:0001764)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	E-box binding (GO:0070888)|sequence-specific DNA binding (GO:0043565)	p.R98Q(1)		central_nervous_system(1)|large_intestine(3)|lung(6)|skin(2)	12		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.00168)		CTTGGCGCCTCGGGAGACGGC	0.697																																					p.R98Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G293A	4						.						20.0	21.0	21.0					4																	113436339		2197	4289	6486	113655788	SO:0001583	missense	63973	exon2			AF303002	CCDS3698.1	4q25	2013-05-21			ENSG00000178403	ENSG00000178403		"""Basic helix-loop-helix proteins"""	13805	protein-coding gene	gene with protein product		606624					Standard	NM_024019		Approved	Atoh4, Math4A, ngn-2, bHLHa8, NGN2	uc003ias.3	Q9H2A3	OTTHUMG00000132907	ENST00000313341.3:c.293G>A	4.37:g.113436339C>T	ENSP00000317333:p.Arg98Gln	Somatic		Capture	Illumina HiSeq	Phase_I	113655788	NM_024019	Q8N416	Missense_Mutation	SNP	ENST00000313341.3	37	CCDS3698.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.347613	0.24426	.	.	ENSG00000178403	ENST00000313341	D	0.91945	-2.94	3.64	3.64	0.41730	.	0.180896	0.25872	U	0.027748	D	0.85401	0.5688	N	0.24115	0.695	0.18873	N	0.999982	D	0.64830	0.994	P	0.47645	0.553	T	0.76105	-0.3081	10	0.12766	T	0.61	-7.0247	9.0215	0.36202	0.0:0.7733:0.2267:0.0	.	98	Q9H2A3	NGN2_HUMAN	Q	98	ENSP00000317333:R98Q	ENSP00000317333:R98Q	R	-	2	0	NEUROG2	113655788	0.957000	0.32711	0.487000	0.27428	0.014000	0.08584	5.678000	0.68153	1.865000	0.54081	0.467000	0.42956	CGA		0.697	NEUROG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256414.1	NM_024019	
SPON2	10417	broad.mit.edu	37	4	1165696	1165696	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:1165696G>A	ENST00000290902.5	-	2	496	c.164C>T	c.(163-165)gCc>gTc	p.A55V	SPON2_ENST00000431380.1_Missense_Mutation_p.A55V	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	55	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)	p.A55V(1)		central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CTTGGGGAAGGCCGTCTGGCT	0.667																																					p.A55V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C164T	4						.						56.0	76.0	70.0					4																	1165696		2190	4290	6480	1155696	SO:0001583	missense	10417	exon4			AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.164C>T	4.37:g.1165696G>A	ENSP00000290902:p.Ala55Val	Somatic		Capture	Illumina HiSeq	Phase_I	1155696	NM_001199021	D3DVN9|Q4W5N4|Q9ULW1	Missense_Mutation	SNP	ENST00000290902.5	37	CCDS3347.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.619911	0.87460	.	.	ENSG00000159674	ENST00000290902;ENST00000431380;ENST00000503765;ENST00000515004;ENST00000502483	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.74	4.74	0.60224	Spondin, N-terminal (2);	0.107611	0.64402	D	0.000006	T	0.52964	0.1767	M	0.65975	2.015	0.80722	D	1	P;D;D	0.54601	0.9;0.967;0.967	P;P;B	0.51615	0.675;0.478;0.344	T	0.51537	-0.8693	10	0.25106	T	0.35	.	17.7011	0.88295	0.0:0.0:1.0:0.0	.	55;55;55	D6RB12;D3DVN9;Q9BUD6	.;.;SPON2_HUMAN	V	55	ENSP00000290902:A55V;ENSP00000394832:A55V;ENSP00000424542:A55V;ENSP00000425871:A55V;ENSP00000422516:A55V	ENSP00000290902:A55V	A	-	2	0	SPON2	1155696	1.000000	0.71417	0.998000	0.56505	0.981000	0.71138	9.062000	0.93920	2.174000	0.68829	0.407000	0.27541	GCC		0.667	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
ZGRF1	55345	broad.mit.edu	37	4	113539102	113539102	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:113539102G>A	ENST00000505019.1	-	6	2221	c.2096C>T	c.(2095-2097)gCt>gTt	p.A699V	C4orf21_ENST00000309071.5_Missense_Mutation_p.A699V|C4orf21_ENST00000445203.2_Missense_Mutation_p.A668V	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		699						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.A699V(2)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ACTGTTTTCAGCAATCTGGTT	0.318																																					p.A699V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2096T	4						.						44.0	47.0	46.0					4																	113539102		2203	4298	6501	113758551	SO:0001583	missense	55345	exon6																														ENST00000505019.1:c.2096C>T	4.37:g.113539102G>A	ENSP00000424737:p.Ala699Val	Somatic		Capture	Illumina HiSeq	Phase_I	113758551	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Missense_Mutation	SNP	ENST00000505019.1	37		.	.	.	.	.	.	.	.	.	.	G	13.92	2.382033	0.42207	.	.	ENSG00000138658	ENST00000505019;ENST00000309071;ENST00000445203	D;T;T	0.82433	-1.61;1.88;1.47	5.37	4.29	0.51040	.	0.458425	0.18864	N	0.129027	T	0.71517	0.3349	N	0.22421	0.69	0.09310	N	1	B;B	0.25105	0.118;0.103	B;B	0.22601	0.037;0.04	T	0.63954	-0.6520	10	0.54805	T	0.06	-6.8029	10.6802	0.45811	0.1276:0.0:0.8724:0.0	.	699;699	Q86YA3;G5EA02	CD021_HUMAN;.	V	699;699;668	ENSP00000424737:A699V;ENSP00000309095:A699V;ENSP00000390505:A668V	ENSP00000309095:A699V	A	-	2	0	C4orf21	113758551	0.011000	0.17503	0.046000	0.18839	0.302000	0.27658	1.486000	0.35530	2.683000	0.91414	0.557000	0.71058	GCT		0.318	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
PRSS12	8492	broad.mit.edu	37	4	119203216	119203216	+	Missense_Mutation	SNP	C	C	T	rs139833696		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:119203216C>T	ENST00000296498.3	-	13	2785	c.2503G>A	c.(2503-2505)Gga>Aga	p.G835R	SNHG8_ENST00000384096.1_lincRNA|PRSS12_ENST00000510903.1_5'Flank	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	835	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G835R(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						CAGCTCTCTCCGGGCCGTTCA	0.547																																					p.G835R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2503A	4						.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	80.0	82.0	81.0		2503	6.2	0.0	4	dbSNP_134	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRSS12	NM_003619.3	125	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	835/876	119203216	2,13004	2203	4300	6503	119422664	SO:0001583	missense	8492	exon13			AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2503G>A	4.37:g.119203216C>T	ENSP00000296498:p.Gly835Arg	Somatic		Capture	Illumina HiSeq	Phase_I	119422664	NM_003619	Q9UP16	Missense_Mutation	SNP	ENST00000296498.3	37	CCDS3709.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.594280	0.66219	2.27E-4	1.16E-4	ENSG00000164099	ENST00000296498	D	0.93366	-3.21	6.17	6.17	0.99709	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.394294	0.30338	N	0.009857	D	0.93943	0.8061	L	0.28556	0.865	0.37830	D	0.92869	D	0.89917	1.0	D	0.71656	0.974	D	0.94576	0.7775	10	0.62326	D	0.03	.	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	835	P56730	NETR_HUMAN	R	835	ENSP00000296498:G835R	ENSP00000296498:G835R	G	-	1	0	PRSS12	119422664	0.997000	0.39634	0.034000	0.17996	0.379000	0.30106	4.465000	0.60141	2.941000	0.99782	0.655000	0.94253	GGA		0.547	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
KIAA1109	84162	broad.mit.edu	37	4	123257358	123257358	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:123257358G>T	ENST00000264501.4	+	70	12233	c.11860G>T	c.(11860-11862)Gga>Tga	p.G3954*	KIAA1109_ENST00000388738.3_Nonsense_Mutation_p.G3954*			Q2LD37	K1109_HUMAN	KIAA1109	3954					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)		p.G3954*(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CAAAGGAAAAGGAAGTGGAGG	0.323																																					p.G3954X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G11860T	4						.						74.0	69.0	70.0					4																	123257358		1814	4069	5883	123476808	SO:0001587	stop_gained	84162	exon68			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.11860G>T	4.37:g.123257358G>T	ENSP00000264501:p.Gly3954*	Somatic		Capture	Illumina HiSeq	Phase_I	123476808	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Nonsense_Mutation	SNP	ENST00000264501.4	37	CCDS43267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	37|37	6.178700|6.178700	0.97352|0.97352	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707|ENST00000306802	.|T	.|0.33865	.|1.39	5.54|5.54	5.54|5.54	0.83059|0.83059	.|.	0.065870|.	0.64402|.	D|.	0.000012|.	.|T	.|0.59569	.|0.2203	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.60520	.|-0.7247	.|6	0.40728|0.54805	T|T	0.16|0.06	.|.	19.4796|19.4796	0.95003|0.95003	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|N	3954;3954;623|329	.|ENSP00000304374:K329N	ENSP00000264501:G3954X|ENSP00000304374:K329N	G|K	+|+	1|3	0|2	KIAA1109|KIAA1109	123476808|123476808	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	5.750000|5.750000	0.68712|0.68712	2.595000|2.595000	0.87683|0.87683	0.650000|0.650000	0.86243|0.86243	GGA|AAG		0.323	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
NUDT6	11162	broad.mit.edu	37	4	123838805	123838805	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:123838805G>T	ENST00000304430.5	-	2	326	c.293C>A	c.(292-294)cCc>cAc	p.P98H	NUDT6_ENST00000339154.2_5'UTR	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	98						mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)	p.P98H(1)		endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TTGGAGGATGGGAATGTGCAG	0.468																																					p.P98H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C293A	4						.						116.0	117.0	117.0					4																	123838805		2000	4180	6180	124058255	SO:0001583	missense	11162	exon2			AF019632	CCDS3729.1, CCDS43268.1	4q26	2011-02-21			ENSG00000170917	ENSG00000170917		"""Nudix motif containing"""	8053	protein-coding gene	gene with protein product		606261				7984147, 10022609	Standard	NM_198041		Approved	gfg-1, gfg, FGF2AS, FGF-AS	uc003iew.3	P53370	OTTHUMG00000039507	ENST00000304430.5:c.293C>A	4.37:g.123838805G>T	ENSP00000306070:p.Pro98His	Somatic		Capture	Illumina HiSeq	Phase_I	124058255	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.188896	0.78789	.	.	ENSG00000170917	ENST00000304430	T	0.26518	1.73	4.63	4.63	0.57726	.	0.000000	0.85682	D	0.000000	T	0.56202	0.1969	M	0.84773	2.715	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62374	-0.6868	10	0.51188	T	0.08	-17.3204	17.3065	0.87196	0.0:0.0:1.0:0.0	.	98	P53370	NUDT6_HUMAN	H	98	ENSP00000306070:P98H	ENSP00000306070:P98H	P	-	2	0	NUDT6	124058255	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.268000	0.89876	2.410000	0.81850	0.561000	0.74099	CCC		0.468	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
SPATA5	166378	broad.mit.edu	37	4	123850276	123850276	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:123850276A>C	ENST00000274008.4	+	3	439	c.370A>C	c.(370-372)Agg>Cgg	p.R124R	SPATA5_ENST00000422835.2_3'UTR	NM_145207.2	NP_660208.2	Q8NB90	SPAT5_HUMAN	spermatogenesis associated 5	124					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.R124R(1)		endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24						TGTGGGTGTGAGGCCTGGTGA	0.532																																					p.R124R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A370C	4						.						133.0	119.0	123.0					4																	123850276		2203	4300	6503	124069726	SO:0001819	synonymous_variant	166378	exon3			AF361489	CCDS3730.1	4q28.1	2010-04-21			ENSG00000145375	ENSG00000145375		"""ATPases / AAA-type"""	18119	protein-coding gene	gene with protein product	"""ATPase family gene 2 homolog (S. cerevisiae)"""	613940				16465403	Standard	NM_145207		Approved	SPAF, AFG2	uc003iez.4	Q8NB90	OTTHUMG00000133074	ENST00000274008.4:c.370A>C	4.37:g.123850276A>C		Somatic		Capture	Illumina HiSeq	Phase_I	124069726	NM_145207	C9JT97|Q86XW1|Q8NI20|Q8TDL7	Silent	SNP	ENST00000274008.4	37	CCDS3730.1																																																																																				0.532	SPATA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256714.2	NM_145207	
FAT4	79633	broad.mit.edu	37	4	126238394	126238394	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:126238394C>T	ENST00000394329.3	+	1	841	c.828C>T	c.(826-828)gaC>gaT	p.D276D		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	276	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.D276D(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						CGGCGGCGGACGCGGACGAGG	0.652											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D276D												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C828T	4						.						18.0	23.0	22.0					4																	126238394		1963	4119	6082	126457844	SO:0001819	synonymous_variant	79633	exon1			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.828C>T	4.37:g.126238394C>T		Somatic	1548	Capture	Illumina HiSeq	Phase_I	126457844	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																				0.652	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126240183	126240183	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:126240183G>A	ENST00000394329.3	+	1	2630	c.2617G>A	c.(2617-2619)Gtg>Atg	p.V873M		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	873	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.V873M(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGGGGGCACAGTGACTGGAGA	0.448																																					p.V873M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2617A	4						.						61.0	60.0	60.0					4																	126240183		1969	4152	6121	126459633	SO:0001583	missense	79633	exon1			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.2617G>A	4.37:g.126240183G>A	ENSP00000377862:p.Val873Met	Somatic		Capture	Illumina HiSeq	Phase_I	126459633	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204195	0.38905	.	.	ENSG00000196159	ENST00000394329	T	0.01787	4.64	5.13	4.29	0.51040	Cadherin (4);Cadherin-like (1);	0.000000	0.31233	U	0.008019	T	0.05273	0.0140	L	0.43701	1.375	0.80722	D	1	D	0.53151	0.958	D	0.65573	0.936	T	0.53443	-0.8438	10	0.33141	T	0.24	.	10.3117	0.43712	0.2082:0.0:0.7918:0.0	.	873	Q6V0I7	FAT4_HUMAN	M	873	ENSP00000377862:V873M	ENSP00000377862:V873M	V	+	1	0	FAT4	126459633	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	4.308000	0.59129	1.175000	0.42826	0.655000	0.94253	GTG		0.448	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
FAT4	79633	broad.mit.edu	37	4	126372024	126372024	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:126372024A>G	ENST00000394329.3	+	9	9866	c.9853A>G	c.(9853-9855)Aat>Gat	p.N3285D	FAT4_ENST00000335110.5_Missense_Mutation_p.N1583D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3285	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.N3285D(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TGCCACTGTTAATATACAATT	0.398																																					p.N3285D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A9853G	4						.						53.0	54.0	54.0					4																	126372024		2203	4300	6503	126591474	SO:0001583	missense	79633	exon9			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.9853A>G	4.37:g.126372024A>G	ENSP00000377862:p.Asn3285Asp	Somatic		Capture	Illumina HiSeq	Phase_I	126591474	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	1.190	-0.635532	0.03584	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01725	4.67;4.67	5.48	2.91	0.33838	Cadherin (4);Cadherin-like (1);	0.211150	0.21834	N	0.068422	T	0.02156	0.0067	L	0.48218	1.51	0.09310	N	0.999999	B;B;B	0.15473	0.001;0.001;0.013	B;B;B	0.15484	0.003;0.006;0.013	T	0.42599	-0.9442	10	0.36615	T	0.2	.	8.555	0.33476	0.8013:0.1305:0.0682:0.0	.	1583;3285;3285	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	3285;1583	ENSP00000377862:N3285D;ENSP00000335169:N1583D	ENSP00000335169:N1583D	N	+	1	0	FAT4	126591474	0.992000	0.36948	0.002000	0.10522	0.022000	0.10575	3.439000	0.52878	0.336000	0.23639	-0.313000	0.08912	AAT		0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
JADE1	79960	broad.mit.edu	37	4	129773353	129773353	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:129773353G>A	ENST00000226319.6	+	6	906	c.626G>A	c.(625-627)tGc>tAc	p.C209Y	PHF17_ENST00000512960.1_Missense_Mutation_p.C209Y|PHF17_ENST00000511647.1_Missense_Mutation_p.C209Y|PHF17_ENST00000452328.2_Missense_Mutation_p.C197Y|PHF17_ENST00000413543.2_Missense_Mutation_p.C209Y	NM_199320.2	NP_955352.1												p.C209Y(1)		NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TGTGATGTCTGCCAGTCTCCT	0.493																																					p.C209Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G626A	4						.						196.0	162.0	174.0					4																	129773353		2203	4300	6503	129992803	SO:0001583	missense	79960	exon6																														ENST00000226319.6:c.626G>A	4.37:g.129773353G>A	ENSP00000226319:p.Cys209Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	129992803	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	G	18.69	3.677551	0.68042	.	.	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000512960;ENST00000535321;ENST00000413543	D;D;D;D;D	0.99954	-8.82;-8.82;-8.82;-8.82;-8.82	5.38	5.38	0.77491	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.99947	0.9977	M	0.77313	2.365	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.95592	0.8655	9	.	.	.	.	19.3333	0.94303	0.0:0.0:1.0:0.0	.	197;209;209	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	Y	209;209;197;209;209;209	ENSP00000226319:C209Y;ENSP00000423737:C209Y;ENSP00000388015:C197Y;ENSP00000425730:C209Y;ENSP00000404211:C209Y	.	C	+	2	0	PHF17	129992803	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	9.294000	0.96088	2.793000	0.96121	0.655000	0.94253	TGC		0.493	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
JADE1	79960	broad.mit.edu	37	4	129782863	129782863	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:129782863C>T	ENST00000226319.6	+	9	1266	c.986C>T	c.(985-987)tCt>tTt	p.S329F	PHF17_ENST00000512960.1_Missense_Mutation_p.S329F|PHF17_ENST00000511647.1_Missense_Mutation_p.S329F|PHF17_ENST00000452328.2_Missense_Mutation_p.S317F|PHF17_ENST00000413543.2_Missense_Mutation_p.S329F	NM_199320.2	NP_955352.1														NS(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TGACAGTGCTCTGTGAAGAAC	0.488																																					p.S329F												.	.	0			c.C986T	4						.						78.0	81.0	80.0					4																	129782863		2203	4300	6503	130002313	SO:0001583	missense	79960	exon9																														ENST00000226319.6:c.986C>T	4.37:g.129782863C>T	ENSP00000226319:p.Ser329Phe	None		Capture	Illumina HiSeq	Phase_I	130002313	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.557301	0.86231	.	.	ENSG00000077684	ENST00000226319;ENST00000511647;ENST00000452328;ENST00000512960;ENST00000535321;ENST00000413543	T;T;T;T;T	0.64085	-0.08;-0.08;-0.08;-0.08;-0.08	5.08	5.08	0.68730	Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.83385	0.5243	M	0.90369	3.11	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.996;1.0;0.99	D	0.86356	0.1714	9	.	.	.	.	18.654	0.91441	0.0:1.0:0.0:0.0	.	317;329;329	Q6IE81-2;Q6IE81;Q6IE81-3	.;JADE1_HUMAN;.	F	329;329;317;329;329;329	ENSP00000226319:S329F;ENSP00000423737:S329F;ENSP00000388015:S317F;ENSP00000425730:S329F;ENSP00000404211:S329F	.	S	+	2	0	PHF17	130002313	1.000000	0.71417	0.988000	0.46212	0.963000	0.63663	7.039000	0.76544	2.640000	0.89533	0.655000	0.94253	TCT		0.488	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1		
PCDH18	54510	broad.mit.edu	37	4	138452072	138452072	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:138452072G>A	ENST00000344876.4	-	1	1557	c.1171C>T	c.(1171-1173)Ctg>Ttg	p.L391L	PCDH18_ENST00000507846.1_Silent_p.L171L|PCDH18_ENST00000412923.2_Silent_p.L391L|PCDH18_ENST00000510305.1_Intron|PCDH18_ENST00000511115.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	391	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				brain development (GO:0007420)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L391L(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(27)|lung(21)|ovary(2)|pancreas(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	86	all_hematologic(180;0.24)					TCTCCATTCAGCCCAGAATCC	0.363																																					p.L391L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1171T	4						.						81.0	87.0	85.0					4																	138452072		2203	4300	6503	138671522	SO:0001819	synonymous_variant	54510	exon1			AL137471	CCDS34064.1, CCDS75193.1	4q28.3	2010-01-26			ENSG00000189184	ENSG00000189184		"""Cadherins / Protocadherins : Non-clustered"""	14268	protein-coding gene	gene with protein product		608287				10835267, 11549318	Standard	XM_005263070		Approved	KIAA1562, PCDH68L	uc003ihe.4	Q9HCL0	OTTHUMG00000161348	ENST00000344876.4:c.1171C>T	4.37:g.138452072G>A		Somatic		Capture	Illumina HiSeq	Phase_I	138671522	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Silent	SNP	ENST00000344876.4	37	CCDS34064.1																																																																																				0.363	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035	
NAA15	80155	broad.mit.edu	37	4	140283014	140283014	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:140283014G>A	ENST00000296543.5	+	14	1999	c.1676G>A	c.(1675-1677)aGa>aAa	p.R559K	NAA15_ENST00000398947.1_Missense_Mutation_p.R559K	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	559	Interaction with HYPK.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.R559K(1)		NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						AAGGCAGCAAGAATTGCTATA	0.358																																					p.R559K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1676A	4						.						119.0	111.0	114.0					4																	140283014		1849	4084	5933	140502464	SO:0001583	missense	80155	exon14			AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.1676G>A	4.37:g.140283014G>A	ENSP00000296543:p.Arg559Lys	Somatic		Capture	Illumina HiSeq	Phase_I	140502464	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	G	8.285	0.816478	0.16607	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.39592	1.07;1.07	5.73	5.73	0.89815	.	0.063232	0.64402	D	0.000004	T	0.23649	0.0572	N	0.05230	-0.09	0.80722	D	1	B	0.06786	0.001	B	0.14023	0.01	T	0.18587	-1.0332	10	0.02654	T	1	-16.1983	20.2699	0.98469	0.0:0.0:1.0:0.0	.	559	Q9BXJ9	NAA15_HUMAN	K	559;433;559	ENSP00000296543:R559K;ENSP00000381920:R559K	ENSP00000296543:R559K	R	+	2	0	NAA15	140502464	0.665000	0.27466	1.000000	0.80357	0.999000	0.98932	2.166000	0.42406	2.854000	0.98071	0.655000	0.94253	AGA		0.358	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
TBC1D9	23158	broad.mit.edu	37	4	141560521	141560522	+	Missense_Mutation	DNP	AC	AC	CA			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	AC	AC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:141560521_141560522AC>CA	ENST00000442267.2	-	14	2472_2473	c.2398_2399GT>TG	c.(2398-2400)GTg>TGg	p.V800W		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	800							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.V800>?(2)		endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	31	all_hematologic(180;0.162)	Medulloblastoma(177;0.00498)				CGTCTGGATCACTTTCAGTCTC	0.436																																					.												.	.	2	Complex(2)	large_intestine(2)	c.2398_2399TG	4						.																																			141779972	SO:0001583	missense	23158	exon14			AB020689	CCDS47136.1	4q31.1	2013-01-10	2006-07-12		ENSG00000109436	ENSG00000109436		"""EF-hand domain containing"""	21710	protein-coding gene	gene with protein product			"""TBC1 domain family, member 9"""			12970790	Standard	NM_015130		Approved	KIAA0882, MDR1	uc010ioj.3	Q6ZT07	OTTHUMG00000161405	ENST00000442267.2:c.2398_2399delinsCA	4.37:g.141560521_141560522delinsCA	ENSP00000411197:p.Val800Trp	Somatic		Capture	Illumina HiSeq	Phase_I	141779971	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	DNP	ENST00000442267.2	37	CCDS47136.1																																																																																				0.436	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130	
RNF150	57484	broad.mit.edu	37	4	142053482	142053482	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:142053482C>T	ENST00000515673.2	-	1	514	c.481G>A	c.(481-483)Gcg>Acg	p.A161T	RNF150_ENST00000420921.2_Intron|RNF150_ENST00000507500.1_Missense_Mutation_p.A161T|RNF150_ENST00000306799.3_Missense_Mutation_p.A161T			Q9ULK6	RN150_HUMAN	ring finger protein 150	161	PA.					integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.A161T(1)|p.A70T(1)		breast(1)|large_intestine(10)|lung(7)|ovary(1)	19	all_hematologic(180;0.162)					CACTCACCCGCGTGGGGCATG	0.667																																					p.A161T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G481A	4						.						19.0	17.0	18.0					4																	142053482		2197	4297	6494	142272932	SO:0001583	missense	57484	exon1			AB033040	CCDS34065.1	4q31.1	2013-01-09			ENSG00000170153	ENSG00000170153		"""RING-type (C3HC4) zinc fingers"""	23138	protein-coding gene	gene with protein product						10574462	Standard	XM_005263150		Approved	KIAA1214	uc003iio.1	Q9ULK6	OTTHUMG00000161380	ENST00000515673.2:c.481G>A	4.37:g.142053482C>T	ENSP00000425840:p.Ala161Thr	Somatic		Capture	Illumina HiSeq	Phase_I	142272932	NM_020724	Q3T1D0|Q6ZNW6	Missense_Mutation	SNP	ENST00000515673.2	37	CCDS34065.1	.	.	.	.	.	.	.	.	.	.	C	16.29	3.081966	0.55861	.	.	ENSG00000170153	ENST00000306799;ENST00000515673;ENST00000507500	T;T;T	0.06768	3.26;3.26;3.26	4.81	3.92	0.45320	Protease-associated domain, PA (1);	0.272984	0.37012	N	0.002287	T	0.07548	0.0190	L	0.38175	1.15	0.80722	D	1	B;B;B	0.26975	0.137;0.003;0.165	B;B;B	0.23419	0.045;0.005;0.046	T	0.31558	-0.9939	10	0.19147	T	0.46	.	14.3742	0.66862	0.0:0.7354:0.2646:0.0	.	161;161;161	Q9ULK6-2;Q9ULK6-3;Q9ULK6	.;.;RN150_HUMAN	T	161	ENSP00000304321:A161T;ENSP00000425840:A161T;ENSP00000425568:A161T	ENSP00000304321:A161T	A	-	1	0	RNF150	142272932	0.927000	0.31430	1.000000	0.80357	0.977000	0.68977	0.966000	0.29331	2.400000	0.81607	0.455000	0.32223	GCG		0.667	RNF150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364739.2	XM_291090	
IL15	3600	broad.mit.edu	37	4	142653933	142653933	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:142653933G>A	ENST00000296545.7	+	8	1265	c.421G>A	c.(421-423)Gaa>Aaa	p.E141K	IL15_ENST00000477265.1_Missense_Mutation_p.E114K|IL15_ENST00000514653.1_Missense_Mutation_p.E114K|IL15_ENST00000320650.4_Missense_Mutation_p.E141K|IL15_ENST00000529613.1_Missense_Mutation_p.E141K|IL15_ENST00000394159.1_Missense_Mutation_p.E114K			P40933	IL15_HUMAN	interleukin 15	141				E -> K (in Ref. 4; AAB97518). {ECO:0000305}.	aging (GO:0007568)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|cellular response to vitamin D (GO:0071305)|extrathymic T cell selection (GO:0045062)|hyaluronan metabolic process (GO:0030212)|immune response (GO:0006955)|inflammatory response (GO:0006954)|lymph node development (GO:0048535)|natural killer cell differentiation (GO:0001779)|negative regulation of smooth muscle cell proliferation (GO:0048662)|NK T cell proliferation (GO:0001866)|positive regulation of cell proliferation (GO:0008284)|positive regulation of immune response (GO:0050778)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of natural killer cell proliferation (GO:0032819)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of defense response to virus by host (GO:0050691)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|lung(2)|stomach(1)	5	all_hematologic(180;0.158)					GGAACTGGAGGAAAAAAATAT	0.274																																					p.E141K	Pancreas(10;184 986 25902)											.	.	0			c.G421A	4						.						80.0	92.0	88.0					4																	142653933		2203	4298	6501	142873383	SO:0001583	missense	3600	exon8			U14407	CCDS3755.1, CCDS3756.1	4q31	2011-07-14			ENSG00000164136	ENSG00000164136		"""Interleukins and interleukin receptors"""	5977	protein-coding gene	gene with protein product		600554				8178155	Standard	NM_000585		Approved	IL-15, MGC9721	uc003iis.3	P40933	OTTHUMG00000133418	ENST00000296545.7:c.421G>A	4.37:g.142653933G>A	ENSP00000296545:p.Glu141Lys	None		Capture	Illumina HiSeq	Phase_I	142873383	NM_172174	D3DNZ2|O00440|O43512|Q495Z8|Q6FGX7|Q93058|Q9UBA3	Missense_Mutation	SNP	ENST00000296545.7	37	CCDS3755.1	.	.	.	.	.	.	.	.	.	.	G	19.17	3.774974	0.70107	.	.	ENSG00000164136	ENST00000320650;ENST00000296545;ENST00000514653;ENST00000529613;ENST00000477265;ENST00000394159	.	.	.	5.77	5.77	0.91146	.	0.000000	0.64402	D	0.000001	T	0.76026	0.3930	L	0.58428	1.81	0.46028	D	0.998825	D	0.76494	0.999	D	0.80764	0.994	T	0.76149	-0.3065	9	0.62326	D	0.03	-11.1264	15.8376	0.78811	0.0:0.0:1.0:0.0	.	141	P40933	IL15_HUMAN	K	141;141;114;141;114;114	.	ENSP00000296545:E141K	E	+	1	0	IL15	142873383	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	4.742000	0.62103	2.890000	0.99128	0.650000	0.86243	GAA		0.274	IL15-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257278.2	NM_172175	
ANAPC10	10393	broad.mit.edu	37	4	146017246	146017246	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:146017246A>C	ENST00000507656.1	-	2	99	c.6T>G	c.(4-6)acT>acG	p.T2T	ANAPC10_ENST00000512680.1_Silent_p.T2T|ANAPC10_ENST00000510270.1_5'UTR|ABCE1_ENST00000296577.4_5'Flank|ANAPC10_ENST00000309439.5_Silent_p.T2T|ANAPC10_ENST00000451299.2_Silent_p.T2T	NM_001256706.1	NP_001243635.1	Q9UM13	APC10_HUMAN	anaphase promoting complex subunit 10	2	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|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 ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.T2T(1)		endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	all_hematologic(180;0.151)					TGTTTGGTGTAGTCATTTTTA	0.388																																					p.T2T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T6G	4						.						165.0	165.0	165.0					4																	146017246		1843	4091	5934	146236696	SO:0001819	synonymous_variant	10393	exon2			AF132794	CCDS43273.1	4q31	2011-06-15			ENSG00000164162	ENSG00000164162		"""Anaphase promoting complex subunits"""	24077	protein-coding gene	gene with protein product		613745				10318877, 11230166	Standard	NM_001256706		Approved	APC10, DOC1, DKFZP564L0562	uc031shk.1	Q9UM13	OTTHUMG00000161477	ENST00000507656.1:c.6T>G	4.37:g.146017246A>C		Somatic		Capture	Illumina HiSeq	Phase_I	146236696	NM_014885	D3DNZ7|Q2V500|Q9UG51|Q9Y5R0	Silent	SNP	ENST00000507656.1	37	CCDS43273.1																																																																																				0.388	ANAPC10-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365090.1	NM_014885	
ZNF827	152485	broad.mit.edu	37	4	146696959	146696959	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:146696959T>G	ENST00000508784.1	-	10	2902	c.2675A>C	c.(2674-2676)aAa>aCa	p.K892T	ZNF827_ENST00000379448.4_Missense_Mutation_p.K892T|ZNF827_ENST00000513320.1_Missense_Mutation_p.K542T			Q17R98	ZN827_HUMAN	zinc finger protein 827	892					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K892T(2)		NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48	all_hematologic(180;0.151)					ATAAGGATGTTTCTTCCCATC	0.498																																					p.K892T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A2675C	4						.						146.0	131.0	136.0					4																	146696959		2203	4300	6503	146916409	SO:0001583	missense	152485	exon10			AK091130	CCDS34072.1	4q31.22	2013-01-08			ENSG00000151612	ENSG00000151612		"""Zinc fingers, C2H2-type"""	27193	protein-coding gene	gene with protein product						12477932	Standard	NM_178835		Approved		uc003ikm.3	Q17R98	OTTHUMG00000161362	ENST00000508784.1:c.2675A>C	4.37:g.146696959T>G	ENSP00000421863:p.Lys892Thr	Somatic		Capture	Illumina HiSeq	Phase_I	146916409	NM_178835	B7ZL52|Q7Z4S7|Q8N279	Missense_Mutation	SNP	ENST00000508784.1	37		.	.	.	.	.	.	.	.	.	.	T	21.5	4.153334	0.78114	.	.	ENSG00000151612	ENST00000508784;ENST00000513320;ENST00000379448;ENST00000281318;ENST00000440280	T;T;T	0.08282	3.19;3.11;3.23	5.82	5.82	0.92795	.	0.041552	0.85682	D	0.000000	T	0.12050	0.0293	N	0.14661	0.345	0.49798	D	0.999824	D;D;D	0.56287	0.965;0.958;0.975	P;P;P	0.58077	0.832;0.549;0.736	T	0.40905	-0.9538	10	0.22706	T	0.39	-22.4056	16.1839	0.81934	0.0:0.0:0.0:1.0	.	542;892;892	G5E9Z1;Q17R98;Q17R98-2	.;ZN827_HUMAN;.	T	892;542;892;891;542	ENSP00000421863:K892T;ENSP00000423130:K542T;ENSP00000368761:K892T	ENSP00000281318:K891T	K	-	2	0	ZNF827	146916409	1.000000	0.71417	0.997000	0.53966	0.910000	0.53928	7.596000	0.82721	2.222000	0.72286	0.533000	0.62120	AAA		0.498	ZNF827-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000364654.2	NM_178835	
DCLK2	166614	broad.mit.edu	37	4	151000255	151000255	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:151000255G>T	ENST00000296550.7	+	1	830	c.76G>T	c.(76-78)Ggg>Tgg	p.G26W	DCLK2_ENST00000506325.1_Missense_Mutation_p.G26W|DCLK2_ENST00000302176.8_Missense_Mutation_p.G26W	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	26					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.G26W(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GTCGCGGAGAGGGGCCCCCAG	0.706																																					p.G26W	GBM(195;186 2215 13375 16801 37459)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G76T	4						.						11.0	16.0	14.0					4																	151000255		2173	4277	6450	151219705	SO:0001583	missense	166614	exon1			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.76G>T	4.37:g.151000255G>T	ENSP00000296550:p.Gly26Trp	Somatic		Capture	Illumina HiSeq	Phase_I	151219705	NM_001040260	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.086434	0.76642	.	.	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.69435	-0.39;-0.4;-0.37	4.51	4.51	0.55191	.	0.184593	0.47093	D	0.000254	T	0.60919	0.2306	N	0.08118	0	0.40104	D	0.976402	D;D;D	0.71674	0.998;0.998;0.973	D;D;P	0.66351	0.943;0.943;0.624	T	0.66791	-0.5834	10	0.87932	D	0	.	8.4797	0.33034	0.1749:0.0:0.8251:0.0	.	26;26;26	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	W	26	ENSP00000296550:G26W;ENSP00000427235:G26W;ENSP00000303887:G26W	ENSP00000296550:G26W	G	+	1	0	DCLK2	151219705	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.370000	0.34238	2.483000	0.83821	0.557000	0.71058	GGG		0.706	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	
KIAA0922	23240	broad.mit.edu	37	4	154523386	154523386	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:154523386G>A	ENST00000409663.3	+	22	2398	c.2346G>A	c.(2344-2346)tcG>tcA	p.S782S	KIAA0922_ENST00000440693.1_Silent_p.S699S|KIAA0922_ENST00000409959.3_Silent_p.S783S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	782						integral component of membrane (GO:0016021)		p.S635S(1)		breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TAACTGTTTCGTCTCTGAAAA	0.378																																					p.S782S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2346A	4						.						119.0	119.0	119.0					4																	154523386		2203	4300	6503	154742836	SO:0001819	synonymous_variant	23240	exon22			AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.2346G>A	4.37:g.154523386G>A		Somatic		Capture	Illumina HiSeq	Phase_I	154742836	NM_015196	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																				0.378	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
PLRG1	5356	broad.mit.edu	37	4	155465613	155465613	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:155465613G>A	ENST00000499023.2	-	7	704	c.578C>T	c.(577-579)cCg>cTg	p.P193L	RNU6-1285P_ENST00000363480.1_RNA|PLRG1_ENST00000393905.2_Missense_Mutation_p.P193L|PLRG1_ENST00000302078.5_Missense_Mutation_p.P184L	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	193					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.P193L(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				GAGTTTCCACGGTGGGTGCCA	0.428																																					p.P193L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C578T	4						.						122.0	123.0	123.0					4																	155465613		2203	4300	6503	155685063	SO:0001583	missense	5356	exon7			AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.578C>T	4.37:g.155465613G>A	ENSP00000424417:p.Pro193Leu	Somatic		Capture	Illumina HiSeq	Phase_I	155685063	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	37	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	G	31	5.090370	0.94149	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078;ENST00000504341	D;D;D	0.82526	-1.62;-1.62;-1.62	6.16	6.16	0.99307	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.91851	0.7421	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.76575	0.988;0.982	D	0.91447	0.5178	10	0.87932	D	0	-14.6024	20.8598	0.99761	0.0:0.0:1.0:0.0	.	184;193	O43660-2;O43660	.;PLRG1_HUMAN	L	193;193;184;191	ENSP00000424417:P193L;ENSP00000377483:P193L;ENSP00000303191:P184L	ENSP00000303191:P184L	P	-	2	0	PLRG1	155685063	1.000000	0.71417	0.996000	0.52242	0.793000	0.44817	9.869000	0.99810	2.937000	0.99478	0.650000	0.86243	CCG		0.428	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
TAPT1	202018	broad.mit.edu	37	4	16189885	16189885	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:16189885T>G	ENST00000405303.2	-	5	789	c.706A>C	c.(706-708)Att>Ctt	p.I236L	TAPT1_ENST00000304584.8_Missense_Mutation_p.I62L|TAPT1_ENST00000399920.3_Missense_Mutation_p.I125L|TAPT1_ENST00000508888.1_5'UTR	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	236					embryonic skeletal system development (GO:0048706)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|post-embryonic development (GO:0009791)	integral component of membrane (GO:0016021)	growth hormone-releasing hormone receptor activity (GO:0016520)	p.I236L(1)		NS(1)|breast(2)|cervix(1)|kidney(2)|large_intestine(2)|lung(1)|prostate(1)	10						ATCACCCCAATGTGGGCTCTT	0.383																																					p.I236L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A706C	4						.						78.0	78.0	78.0					4																	16189885		1800	4065	5865	15798983	SO:0001583	missense	202018	exon5			AK074494	CCDS47030.1	4p15.32	2014-01-28			ENSG00000169762	ENSG00000169762			26887	protein-coding gene	gene with protein product		612758				12477932	Standard	NM_153365		Approved	FLJ90013	uc010ied.1	Q6NXT6	OTTHUMG00000160177	ENST00000405303.2:c.706A>C	4.37:g.16189885T>G	ENSP00000385347:p.Ile236Leu	Somatic		Capture	Illumina HiSeq	Phase_I	15798983	NM_153365	Q8N2S3|Q9NZK9	Missense_Mutation	SNP	ENST00000405303.2	37	CCDS47030.1	.	.	.	.	.	.	.	.	.	.	T	14.19	2.460166	0.43736	.	.	ENSG00000169762	ENST00000405303;ENST00000542770;ENST00000399920;ENST00000304584	T;T	0.29397	1.57;1.59	6.17	6.17	0.99709	.	0.042126	0.85682	D	0.000000	T	0.16557	0.0398	N	0.11023	0.085	0.54753	D	0.999981	B	0.14805	0.011	B	0.18561	0.022	T	0.15607	-1.0431	10	0.10636	T	0.68	-4.415	12.6398	0.56702	0.0:0.0:0.1377:0.8623	.	236	Q6NXT6	TAPT1_HUMAN	L	236;236;125;62	ENSP00000385347:I236L;ENSP00000382803:I125L	ENSP00000305198:I62L	I	-	1	0	TAPT1	15798983	1.000000	0.71417	0.887000	0.34795	0.974000	0.67602	5.873000	0.69644	2.371000	0.80710	0.533000	0.62120	ATT		0.383	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365	
GUCY1A3	2982	broad.mit.edu	37	4	156632102	156632102	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:156632102C>T	ENST00000296518.7	+	6	994	c.785C>T	c.(784-786)aCc>aTc	p.T262I	GUCY1A3_ENST00000513574.1_Missense_Mutation_p.T262I|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.T262I|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.T4I|GUCY1A3_ENST00000506455.1_Missense_Mutation_p.T262I|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.T262I|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.T262I			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	262					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of blood pressure (GO:0008217)|relaxation of vascular smooth muscle (GO:0060087)|response to defense-related host nitric oxide production (GO:0052565)	guanylate cyclase complex, soluble (GO:0008074)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)|receptor activity (GO:0004872)	p.T262I(1)		central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|liver(2)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.17)		ATGAAAAGCACCAAGCCATCC	0.478																																					p.T262I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C785T	4						.						124.0	117.0	119.0					4																	156632102		2203	4300	6503	156851552	SO:0001583	missense	2982	exon6				CCDS34085.1, CCDS54812.1	4q31.3-q33	2008-03-18				ENSG00000164116	4.6.1.2		4685	protein-coding gene	gene with protein product		139396		GUC1A3		1352257	Standard	NM_001130687		Approved	GC-SA3	uc003iow.3	Q02108		ENST00000296518.7:c.785C>T	4.37:g.156632102C>T	ENSP00000296518:p.Thr262Ile	Somatic		Capture	Illumina HiSeq	Phase_I	156851552	NM_001130682	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	C	9.118	1.008232	0.19199	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.86164	-1.95;-1.95;-1.8;-1.95;-2.08;-1.95;-1.95	5.76	2.99	0.34606	.	0.578033	0.17504	N	0.171867	D	0.82360	0.5020	L	0.54323	1.7	0.29932	N	0.821808	B;B;B	0.19935	0.008;0.008;0.04	B;B;B	0.24155	0.008;0.008;0.051	T	0.73401	-0.3994	10	0.35671	T	0.21	.	7.6118	0.28135	0.1264:0.6864:0.1216:0.0656	.	262;262;262	B3KU69;Q02108;D6RDW3	.;GCYA3_HUMAN;.	I	262;262;262;262;4;262;262	ENSP00000424361:T262I;ENSP00000421493:T262I;ENSP00000426968:T262I;ENSP00000412201:T262I;ENSP00000377418:T4I;ENSP00000296518:T262I;ENSP00000426040:T262I	ENSP00000296518:T262I	T	+	2	0	GUCY1A3	156851552	0.826000	0.29277	0.008000	0.14137	0.399000	0.30720	3.527000	0.53517	0.394000	0.25230	0.643000	0.83706	ACC		0.478	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2		
LAP3	51056	broad.mit.edu	37	4	17590506	17590506	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:17590506G>A	ENST00000226299.4	+	7	1043	c.769G>A	c.(769-771)Gag>Aag	p.E257K	AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000503467.1_3'UTR|LAP3_ENST00000606142.1_Missense_Mutation_p.E226K	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	257					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)	p.E257K(1)		endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|urinary_tract(1)	20						AGGATCTGACGAGCCCCCAGT	0.458																																					p.E257K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G769A	4						.						108.0	106.0	107.0					4																	17590506		2203	4300	6503	17199604	SO:0001583	missense	51056	exon7			AF061738	CCDS3422.1	4p15.33	2012-07-25	2003-09-12		ENSG00000002549	ENSG00000002549	3.4.11.1		18449	protein-coding gene	gene with protein product		170250	"""peptidase S"""	PEPS		6350155, 689684	Standard	NM_015907		Approved	LAPEP, LAP	uc003gph.1	P28838	OTTHUMG00000048214	ENST00000226299.4:c.769G>A	4.37:g.17590506G>A	ENSP00000226299:p.Glu257Lys	Somatic		Capture	Illumina HiSeq	Phase_I	17199604	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352769	0.95830	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.42513	0.97;0.97	5.12	5.12	0.69794	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65616	0.2708	M	0.70787	2.145	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.68861	-0.5297	10	0.72032	D	0.01	-35.76	18.9237	0.92536	0.0:0.0:1.0:0.0	.	257	P28838	AMPL_HUMAN	K	257;91	ENSP00000226299:E257K;ENSP00000424724:E91K	ENSP00000226299:E257K	E	+	1	0	LAP3	17199604	1.000000	0.71417	0.951000	0.38953	0.799000	0.45148	7.846000	0.86887	2.534000	0.85438	0.557000	0.71058	GAG		0.458	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1		
NCAPG	64151	broad.mit.edu	37	4	17826620	17826620	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:17826620G>A	ENST00000251496.2	+	10	1589	c.1413G>A	c.(1411-1413)gcG>gcA	p.A471A		NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	471					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)		p.A471A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	27				STAD - Stomach adenocarcinoma(129;0.18)		AGATTCGGGCGCCCATTGTTA	0.328																																					p.A471A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1413A	4						.						76.0	76.0	76.0					4																	17826620		2203	4300	6503	17435718	SO:0001819	synonymous_variant	64151	exon10			AF331796	CCDS3424.1	4p15.32	2014-01-15			ENSG00000109805	ENSG00000109805			24304	protein-coding gene	gene with protein product	"""chromosome condensation protein G"""	606280				10910072, 11136719	Standard	NM_022346		Approved	FLJ12450, hCAP-G, CAP-G, YCG1	uc003gpp.4	Q9BPX3	OTTHUMG00000128539	ENST00000251496.2:c.1413G>A	4.37:g.17826620G>A		Somatic		Capture	Illumina HiSeq	Phase_I	17435718	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Silent	SNP	ENST00000251496.2	37	CCDS3424.1																																																																																				0.328	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346	
FSTL5	56884	broad.mit.edu	37	4	162697122	162697122	+	Missense_Mutation	SNP	C	C	T	rs199735797		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:162697122C>T	ENST00000306100.5	-	5	950	c.514G>A	c.(514-516)Gac>Aac	p.D172N	FSTL5_ENST00000427802.2_Missense_Mutation_p.D171N|FSTL5_ENST00000379164.4_Missense_Mutation_p.D171N|FSTL5_ENST00000536695.1_Missense_Mutation_p.D171N	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	172						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D172N(2)		central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		CGAGATATGTCGTCGCCATTA	0.303													C|||	1	0.000199681	0.0	0.0	5008	,	,		15201	0.0		0.001	False		,,,				2504	0.0				p.D172N												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G514A	4						.						101.0	101.0	101.0					4																	162697122		2203	4294	6497	162916572	SO:0001583	missense	56884	exon5			BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.514G>A	4.37:g.162697122C>T	ENSP00000305334:p.Asp172Asn	Somatic		Capture	Illumina HiSeq	Phase_I	162916572	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	4.894	0.166215	0.09339	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	5.3	4.4	0.53042	.	0.443811	0.27362	N	0.019710	T	0.14917	0.0360	L	0.47716	1.5	0.34415	D	0.696831	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.04013	0.0;0.001;0.0	T	0.14531	-1.0469	10	0.18276	T	0.48	.	4.8665	0.13611	0.0:0.6349:0.1962:0.1689	.	171;171;172	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	N	172;171;171;171	ENSP00000305334:D172N;ENSP00000368462:D171N;ENSP00000389270:D171N;ENSP00000440409:D171N	ENSP00000305334:D172N	D	-	1	0	FSTL5	162916572	1.000000	0.71417	0.908000	0.35775	0.044000	0.14063	3.321000	0.51999	2.625000	0.88918	0.650000	0.86243	GAC		0.303	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
ADAM29	11086	broad.mit.edu	37	4	175898338	175898338	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:175898338T>G	ENST00000359240.3	+	5	2332	c.1662T>G	c.(1660-1662)atT>atG	p.I554M	ADAM29_ENST00000404450.4_Missense_Mutation_p.I554M|ADAM29_ENST00000514159.1_Missense_Mutation_p.I554M|ADAM29_ENST00000445694.1_Missense_Mutation_p.I554M|RP13-577H12.2_ENST00000507525.1_RNA	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	554	Cys-rich.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		GTGGAAGAATTCAGTGTGAGA	0.388																																					p.I554M	Ovarian(140;1727 1835 21805 25838 41440)											.	.	0			c.T1662G	4						.						133.0	132.0	132.0					4																	175898338		2203	4300	6503	176134913	SO:0001583	missense	11086	exon3			AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.1662T>G	4.37:g.175898338T>G	ENSP00000352177:p.Ile554Met	None		Capture	Illumina HiSeq	Phase_I	176134913	NM_001130705	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.421637	0.43020	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.26067	1.76;1.76;1.76;1.76	3.69	3.69	0.42338	ADAM, cysteine-rich (2);	0.986860	0.08200	U	0.982503	T	0.50837	0.1639	M	0.80028	2.48	0.23834	N	0.996712	D	0.67145	0.996	D	0.72625	0.978	T	0.27088	-1.0084	9	.	.	.	.	7.2863	0.26342	0.0:0.0:0.2257:0.7743	.	554	Q9UKF5	ADA29_HUMAN	M	554	ENSP00000352177:I554M;ENSP00000414544:I554M;ENSP00000384229:I554M;ENSP00000423517:I554M	.	I	+	3	3	ADAM29	176134913	0.923000	0.31300	0.977000	0.42913	0.554000	0.35429	-0.129000	0.10515	1.904000	0.55121	0.523000	0.50628	ATT		0.388	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
TENM3	55714	broad.mit.edu	37	4	183675700	183675700	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:183675700G>A	ENST00000511685.1	+	22	4303	c.4180G>A	c.(4180-4182)Ggg>Agg	p.G1394R	TENM3_ENST00000406950.2_Missense_Mutation_p.G1394R|TENM3_ENST00000502950.1_3'UTR			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	1394					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1394R(1)									ATATCCTGTGGGGAAGCACGC	0.478																																					p.G1394R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4180A	4						.						56.0	56.0	56.0					4																	183675700		2020	4178	6198	183912694	SO:0001583	missense	55714	exon21			AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.4180G>A	4.37:g.183675700G>A	ENSP00000424226:p.Gly1394Arg	Somatic		Capture	Illumina HiSeq	Phase_I	183912694	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	16.58	3.163907	0.57476	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.87571	-2.27;-2.27	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	.	.	.	.	D	0.92270	0.7548	L	0.60957	1.885	0.58432	D	0.999997	D	0.76494	0.999	D	0.66716	0.946	D	0.91989	0.5601	9	0.66056	D	0.02	.	19.9142	0.97043	0.0:0.0:1.0:0.0	.	1394	Q9P273	TEN3_HUMAN	R	1394	ENSP00000424226:G1394R;ENSP00000385276:G1394R	ENSP00000385276:G1394R	G	+	1	0	ODZ3	183912694	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	9.290000	0.96065	2.941000	0.99782	0.655000	0.94253	GGG		0.478	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
WWC2	80014	broad.mit.edu	37	4	184129264	184129264	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:184129264C>T	ENST00000403733.3	+	3	599	c.400C>T	c.(400-402)Cga>Tga	p.R134*	WWC2_ENST00000504005.1_5'Flank|WWC2_ENST00000448232.2_Nonsense_Mutation_p.R134*|WWC2_ENST00000378925.3_Nonsense_Mutation_p.R36*|WWC2_ENST00000513834.1_Nonsense_Mutation_p.R134*	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	134					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		TGAATACGTGCGATTAAATGA	0.483																																					p.R134X												.	.	0			c.C400T	4						.						66.0	71.0	69.0					4																	184129264		2107	4218	6325	184366258	SO:0001587	stop_gained	80014	exon3			BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.400C>T	4.37:g.184129264C>T	ENSP00000384222:p.Arg134*	None		Capture	Illumina HiSeq	Phase_I	184366258	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Nonsense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	38	6.899491	0.97920	.	.	ENSG00000151718	ENST00000403733;ENST00000378925;ENST00000513834;ENST00000448232	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	-11.2498	18.8047	0.92032	0.0:1.0:0.0:0.0	.	.	.	.	X	134;36;134;134	.	ENSP00000368205:R36X	R	+	1	2	WWC2	184366258	1.000000	0.71417	0.386000	0.26170	0.810000	0.45777	5.893000	0.69798	2.680000	0.91292	0.563000	0.77884	CGA		0.483	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
TRAPPC11	60684	broad.mit.edu	37	4	184618882	184618882	+	Silent	SNP	G	G	A	rs200191432		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:184618882G>A	ENST00000334690.6	+	25	2947	c.2745G>A	c.(2743-2745)acG>acA	p.T915T	TRAPPC11_ENST00000512476.1_Silent_p.T521T|TRAPPC11_ENST00000357207.4_Silent_p.T915T	NM_021942.5	NP_068761.4	Q7Z392	TPC11_HUMAN	trafficking protein particle complex 11	915					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)		p.T915T(1)									TGTTGATGACGGACCTCTTAA	0.483																																					p.T915T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2745A	4						.						134.0	126.0	129.0					4																	184618882		2203	4300	6503	184855876	SO:0001819	synonymous_variant	60684	exon25				CCDS34112.1, CCDS47166.1	4q35.1	2011-12-12	2011-12-12	2011-12-12	ENSG00000168538	ENSG00000168538		"""Trafficking protein particle complex"""	25751	protein-coding gene	gene with protein product	"""gryzun homolog (Drosophila)"", ""foie gras homolog (zebrafish)"""	614138	"""chromosome 4 open reading frame 41"""	C4orf41		19942856, 21525244	Standard	NM_021942		Approved	FLJ12716, gry, foigr	uc003ivx.3	Q7Z392	OTTHUMG00000160673	ENST00000334690.6:c.2745G>A	4.37:g.184618882G>A		Somatic		Capture	Illumina HiSeq	Phase_I	184855876	NM_199053	A4QPB8|B2RCD6|Q5U5I7|Q6FI73|Q86T25|Q9H0L1|Q9H5K9|Q9H8Q1|Q9H9I7	Silent	SNP	ENST00000334690.6	37	CCDS34112.1																																																																																				0.483	TRAPPC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361654.2	NM_021942	
ENPP6	133121	broad.mit.edu	37	4	185074884	185074884	+	Missense_Mutation	SNP	G	G	A	rs147410353		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:185074884G>A	ENST00000296741.2	-	2	385	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C		NM_153343.3	NP_699174.1	Q6UWR7	ENPP6_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 6	82					choline metabolic process (GO:0019695)|lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glycerophosphocholine cholinephosphodiesterase activity (GO:0047390)|glycerophosphodiester phosphodiesterase activity (GO:0008889)|phosphoric diester hydrolase activity (GO:0008081)	p.R82C(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|skin(2)	15		all_lung(41;7.99e-12)|Lung NSC(41;1.46e-11)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;4.98e-27)|Epithelial(43;3.15e-24)|OV - Ovarian serous cystadenocarcinoma(60;4.09e-12)|Colorectal(24;3.78e-05)|STAD - Stomach adenocarcinoma(60;4.5e-05)|COAD - Colon adenocarcinoma(29;0.000154)|GBM - Glioblastoma multiforme(59;0.000167)|BRCA - Breast invasive adenocarcinoma(30;0.000378)|LUSC - Lung squamous cell carcinoma(40;0.0151)		TCACAATGGCGGCCTATGTCA	0.448																																					p.R82C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C244T	4						.	G	CYS/ARG	0,4406		0,0,2203	107.0	99.0	102.0		244	4.6	1.0	4	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	no	missense	ENPP6	NM_153343.3	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	82/441	185074884	1,13005	2203	4300	6503	185311878	SO:0001583	missense	133121	exon2			AK057370	CCDS3834.1	4q35.1	2008-02-05			ENSG00000164303	ENSG00000164303			23409	protein-coding gene	gene with protein product							Standard	NM_153343		Approved	MGC33971	uc003iwc.3	Q6UWR7	OTTHUMG00000160617	ENST00000296741.2:c.244C>T	4.37:g.185074884G>A	ENSP00000296741:p.Arg82Cys	Somatic		Capture	Illumina HiSeq	Phase_I	185311878	NM_153343	Q4W5Q1|Q96M57	Missense_Mutation	SNP	ENST00000296741.2	37	CCDS3834.1	.	.	.	.	.	.	.	.	.	.	G	16.22	3.060268	0.55432	0.0	1.16E-4	ENSG00000164303	ENST00000296741	T	0.73469	-0.75	5.44	4.58	0.56647	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.84115	0.5401	L	0.61387	1.9	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.85723	0.1326	10	0.72032	D	0.01	-18.2652	15.171	0.72872	0.0:0.0:0.8448:0.1552	.	82	Q6UWR7	ENPP6_HUMAN	C	82	ENSP00000296741:R82C	ENSP00000296741:R82C	R	-	1	0	ENPP6	185311878	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	7.585000	0.82584	1.229000	0.43630	0.655000	0.94253	CGC		0.448	ENPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361428.1	NM_153343	
SNX25	83891	broad.mit.edu	37	4	186253779	186253779	+	Missense_Mutation	SNP	G	G	A	rs199546139		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:186253779G>A	ENST00000504273.1	+	10	1582	c.1288G>A	c.(1288-1290)Gtg>Atg	p.V430M	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Missense_Mutation_p.V430M			Q9H3E2	SNX25_HUMAN	sorting nexin 25	430					negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)	p.V430M(1)		NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		TGAGGAAGCCGTGGATGATGG	0.403																																					p.V430M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1288A	4						.	G	MET/VAL	0,4406		0,0,2203	68.0	64.0	65.0		1288	0.2	0.0	4		65	2,8598		0,2,4298	yes	missense	SNX25	NM_031953.2	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	430/841	186253779	2,13004	2203	4300	6503	186490773	SO:0001583	missense	83891	exon10			AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"""Sorting nexins"""	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.1288G>A	4.37:g.186253779G>A	ENSP00000426255:p.Val430Met	Somatic		Capture	Illumina HiSeq	Phase_I	186490773	NM_031953	Q3ZT30|Q8N6K3	De_novo_Start_OutOfFrame	SNP	ENST00000504273.1	37	CCDS34116.1	.	.	.	.	.	.	.	.	.	.	.	11.25	1.582766	0.28268	0.0	2.33E-4	ENSG00000109762	ENST00000504273;ENST00000264694	T;T	0.10573	2.86;2.86	5.82	0.218	0.15270	.	2.105100	0.01592	N	0.021616	T	0.07098	0.0180	N	0.16478	0.41	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.30031	-0.9992	10	0.30854	T	0.27	-2.7954	3.3937	0.07298	0.0827:0.213:0.2722:0.432	.	201;430	Q8N6K3;Q9H3E2	.;SNX25_HUMAN	M	430	ENSP00000426255:V430M;ENSP00000264694:V430M	ENSP00000264694:V430M	V	+	1	0	SNX25	186490773	0.017000	0.18338	0.000000	0.03702	0.037000	0.13140	0.313000	0.19415	0.060000	0.16281	0.579000	0.79373	GTG		0.403	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953	
UFSP2	55325	broad.mit.edu	37	4	186336962	186336962	+	Silent	SNP	C	C	T	rs138402181		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:186336962C>T	ENST00000264689.6	-	5	509	c.393G>A	c.(391-393)acG>acA	p.T131T	UFSP2_ENST00000502282.1_5'UTR|Y_RNA_ENST00000384502.1_RNA	NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	131						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	small conjugating protein-specific protease activity (GO:0019783)|thiolester hydrolase activity (GO:0016790)	p.T131T(1)		endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		CAATGATGGGCGTTACAGCTG	0.383																																					p.T131T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G393A	4						.	C		0,4406		0,0,2203	107.0	95.0	99.0		393	-3.7	0.7	4	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	UFSP2	NM_018359.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		131/470	186336962	2,13004	2203	4300	6503	186573956	SO:0001819	synonymous_variant	55325	exon5			AK002062	CCDS3842.1	4q35.1	2008-03-25	2008-03-25	2008-03-25	ENSG00000109775	ENSG00000109775			25640	protein-coding gene	gene with protein product		611482	"""chromosome 4 open reading frame 20"""	C4orf20		17182609	Standard	NM_018359		Approved	FLJ11200	uc003ixo.2	Q9NUQ7	OTTHUMG00000160441	ENST00000264689.6:c.393G>A	4.37:g.186336962C>T		Somatic		Capture	Illumina HiSeq	Phase_I	186573956	NM_018359	Q6IA77|Q96FS3	Silent	SNP	ENST00000264689.6	37	CCDS3842.1	.	.	.	.	.	.	.	.	.	.	C	3.061	-0.193155	0.06259	0.0	2.33E-4	ENSG00000109775	ENST00000511485	.	.	.	5.22	-3.74	0.04385	.	.	.	.	.	T	0.37348	0.1000	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32375	-0.9909	4	.	.	.	-18.7127	1.0407	0.01558	0.2804:0.2078:0.3254:0.1864	.	.	.	.	T	45	.	.	A	-	1	0	UFSP2	186573956	0.836000	0.29430	0.715000	0.30552	0.451000	0.32288	-0.178000	0.09782	-0.870000	0.04047	-3.309000	0.00045	GCC		0.383	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359	
SORBS2	8470	broad.mit.edu	37	4	186544619	186544619	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:186544619C>T	ENST00000284776.7	-	13	2461	c.1952G>A	c.(1951-1953)cGc>cAc	p.R651H	SORBS2_ENST00000431808.1_Missense_Mutation_p.R651H|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.R555H|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000355634.5_Missense_Mutation_p.R751H|SORBS2_ENST00000449407.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	651	His-rich.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.R651H(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GATGAggtggcggtggtggtg	0.522																																					p.R651H	Esophageal Squamous(153;41 2433 9491 36028)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1952A	4						.						59.0	61.0	60.0					4																	186544619		2203	4299	6502	186781613	SO:0001583	missense	8470	exon13				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1952G>A	4.37:g.186544619C>T	ENSP00000284776:p.Arg651His	Somatic		Capture	Illumina HiSeq	Phase_I	186781613	NM_021069	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	C	16.88	3.245583	0.59103	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.45276	0.94;0.94;0.9;0.96	5.88	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.53249	1.67	0.51482	D	0.999927	D;D;D	0.61080	0.989;0.964;0.989	P;B;P	0.49421	0.61;0.432;0.514	T	0.47045	-0.9147	10	0.87932	D	0	-20.4882	11.7113	0.51626	0.0:0.866:0.0:0.134	.	555;751;651	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	H	651;651;555;751	ENSP00000284776:R651H;ENSP00000411764:R651H;ENSP00000397482:R555H;ENSP00000347852:R751H	ENSP00000284776:R651H	R	-	2	0	SORBS2	186781613	0.989000	0.36119	1.000000	0.80357	0.558000	0.35554	3.724000	0.54962	2.797000	0.96272	0.561000	0.74099	CGC		0.522	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
ZNF141	7700	broad.mit.edu	37	4	366976	366976	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:366976T>A	ENST00000240499.7	+	4	899	c.750T>A	c.(748-750)acT>acA	p.T250T	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	250					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T250T(1)		breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						TAATTCATACTGGAGAAAAAC	0.363																																					p.T250T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T750A	4						.						71.0	80.0	77.0					4																	366976		2200	4298	6498	356976	SO:0001819	synonymous_variant	7700	exon4			L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.750T>A	4.37:g.366976T>A		Somatic		Capture	Illumina HiSeq	Phase_I	356976	NM_003441	Q6DK07	Silent	SNP	ENST00000240499.7	37	CCDS33931.1																																																																																				0.363	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441	
ZNF721	170960	broad.mit.edu	37	4	435607	435607	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:435607A>G	ENST00000338977.5	-	2	2661	c.2613T>C	c.(2611-2613)caT>caC	p.H871H	ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Silent_p.H883H|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000506646.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	871					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H883H(1)|p.H653H(1)		endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						GAATTTTCTTATGCGCATAAA	0.388																																					p.H883H												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T2649C	4						.						65.0	67.0	67.0					4																	435607		2021	4217	6238	425607	SO:0001819	synonymous_variant	170960	exon3			AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.2613T>C	4.37:g.435607A>G		Somatic		Capture	Illumina HiSeq	Phase_I	425607	NM_133474	Q69YG7	Silent	SNP	ENST00000338977.5	37																																																																																					0.388	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
GAK	2580	broad.mit.edu	37	4	853435	853435	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:853435T>C	ENST00000314167.4	-	24	3352	c.3242A>G	c.(3241-3243)gAc>gGc	p.D1081G	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Missense_Mutation_p.D1002G	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1081					cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D1081G(1)		autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		AGCAAATGGGTCCGGGTTCTG	0.602																																					p.D1081G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A3242G	4						.						69.0	72.0	71.0					4																	853435		2203	4300	6503	843435	SO:0001583	missense	2580	exon24			D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3242A>G	4.37:g.853435T>C	ENSP00000314499:p.Asp1081Gly	Somatic		Capture	Illumina HiSeq	Phase_I	843435	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.8|22.8	4.335089|4.335089	0.81801|0.81801	.|.	.|.	ENSG00000178950|ENSG00000178950	ENST00000398567;ENST00000314167;ENST00000511163|ENST00000511980	T;D|.	0.84800|.	-1.29;-1.9|.	4.68|4.68	4.68|4.68	0.58851|0.58851	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71160|0.71160	0.3307|0.3307	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.999;0.997;0.999;0.997|.	D;P;D;D|.	0.66602|.	0.945;0.884;0.945;0.921|.	T|T	0.71909|0.71909	-0.4450|-0.4450	10|5	0.72032|.	D|.	0.01|.	-37.4464|-37.4464	12.0536|12.0536	0.53522|0.53522	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	983;1002;1081;966|.	B4DS37;E9PGR2;O14976;Q59HA5|.	.;.;GAK_HUMAN;.|.	G|A	357;1081;1002|193	ENSP00000314499:D1081G;ENSP00000421361:D1002G|.	ENSP00000314499:D1081G|.	D|T	-|-	2|1	0|0	GAK|GAK	843435|843435	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.974000|0.974000	0.67602|0.67602	7.782000|7.782000	0.85680|0.85680	1.730000|1.730000	0.51580|0.51580	0.418000|0.418000	0.28097|0.28097	GAC|ACC		0.602	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
ZFYVE28	57732	broad.mit.edu	37	4	2343241	2343241	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:2343241G>A	ENST00000290974.2	-	3	621	c.282C>T	c.(280-282)caC>caT	p.H94H	ZFYVE28_ENST00000503000.1_Silent_p.H94H|ZFYVE28_ENST00000511071.1_Silent_p.H94H|ZFYVE28_ENST00000515312.1_Silent_p.H24H|ZFYVE28_ENST00000505421.1_5'Flank|ZFYVE28_ENST00000515169.1_Silent_p.H24H|ZFYVE28_ENST00000509171.1_Silent_p.H47H	NM_020972.2	NP_066023.2	Q9HCC9	LST2_HUMAN	zinc finger, FYVE domain containing 28	94					negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)	p.H94H(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	31						CCAGGTTGTCGTGCCGGATCT	0.612																																					p.H94H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C282T	4						.						42.0	43.0	43.0					4																	2343241		2203	4300	6503	2313039	SO:0001819	synonymous_variant	57732	exon3			AK126692	CCDS33942.1, CCDS54708.1, CCDS54709.1, CCDS54710.1, CCDS54711.1, CCDS54712.1	4p16.3	2008-05-02			ENSG00000159733	ENSG00000159733		"""Zinc fingers, FYVE domain containing"""	29334	protein-coding gene	gene with protein product		614176				10997877	Standard	NM_020972		Approved	KIAA1643	uc003gex.2	Q9HCC9	OTTHUMG00000160292	ENST00000290974.2:c.282C>T	4.37:g.2343241G>A		Somatic		Capture	Illumina HiSeq	Phase_I	2313039	NM_001172656	B2RP83|B3KX50|B7Z1Q7|B7Z2G9|B7Z2M2|B7ZB19|E9PB54|E9PB64|E9PG77|Q7Z6J3	Silent	SNP	ENST00000290974.2	37	CCDS33942.1																																																																																				0.612	ZFYVE28-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360078.1	XM_035371	
FAM193A	8603	broad.mit.edu	37	4	2695373	2695373	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:2695373G>T	ENST00000324666.5	+	14	2342	c.1991G>T	c.(1990-1992)aGg>aTg	p.R664M	FAM193A_ENST00000545951.1_Missense_Mutation_p.R664M|FAM193A_ENST00000505311.1_Missense_Mutation_p.R664M|FAM193A_ENST00000382839.3_Missense_Mutation_p.R664M|FAM193A_ENST00000502458.1_Missense_Mutation_p.R686M	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	664								p.R664M(1)		NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GCCGCCCCGAGGAATAGCCCC	0.612																																					p.R664M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1991T	4						.						78.0	91.0	87.0					4																	2695373		2203	4300	6503	2665171	SO:0001583	missense	8603	exon14			AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.1991G>T	4.37:g.2695373G>T	ENSP00000324587:p.Arg664Met	Somatic		Capture	Illumina HiSeq	Phase_I	2665171	NM_003704	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.363833	0.82353	.	.	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	5.85	5.85	0.93711	.	0.093720	0.64402	D	0.000001	T	0.74665	0.3746	L	0.47716	1.5	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.998;0.998;0.998	T	0.74234	-0.3731	10	0.54805	T	0.06	-32.0499	17.3213	0.87236	0.0:0.0:1.0:0.0	.	664;686;664;686;664	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	M	664;664;664;686;518	ENSP00000372290:R664M;ENSP00000324587:R664M;ENSP00000443617:R664M;ENSP00000427505:R686M;ENSP00000427260:R518M	ENSP00000324587:R664M	R	+	2	0	FAM193A	2665171	1.000000	0.71417	0.928000	0.36995	0.513000	0.34164	7.423000	0.80229	2.768000	0.95171	0.655000	0.94253	AGG		0.612	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
HTT	3064	broad.mit.edu	37	4	3133020	3133020	+	Missense_Mutation	SNP	G	G	A	rs556061424		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:3133020G>A	ENST00000355072.5	+	15	2139	c.1994G>A	c.(1993-1995)cGc>cAc	p.R665H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	665					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.R665H(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TAGCCTTGCCGCATCAAAGGT	0.428													G|||	1	0.000199681	0.0	0.0	5008	,	,		23847	0.0		0.0	False		,,,				2504	0.001				p.R665H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1994A	4						.						112.0	109.0	110.0					4																	3133020		2029	4188	6217	3102818	SO:0001583	missense	3064	exon15			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1994G>A	4.37:g.3133020G>A	ENSP00000347184:p.Arg665His	Somatic		Capture	Illumina HiSeq	Phase_I	3102818	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	33	5.251512	0.95305	.	.	ENSG00000197386	ENST00000355072	T	0.05996	3.36	5.07	5.07	0.68467	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.19046	0.0457	M	0.72118	2.19	0.58432	D	0.999999	D	0.71674	0.998	P	0.55161	0.77	T	0.00138	-1.2003	10	0.66056	D	0.02	.	16.3972	0.83613	0.0:0.0:1.0:0.0	.	665	P42858	HD_HUMAN	H	665	ENSP00000347184:R665H	ENSP00000347184:R665H	R	+	2	0	HTT	3102818	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	6.590000	0.74085	2.643000	0.89663	0.655000	0.94253	CGC		0.428	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HTT	3064	broad.mit.edu	37	4	3176516	3176516	+	Missense_Mutation	SNP	G	G	A	rs201053245		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:3176516G>A	ENST00000355072.5	+	32	4380	c.4235G>A	c.(4234-4236)cGt>cAt	p.R1412H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1412					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.R1412H(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		ACAAAGAACCGTGCAGATAAG	0.463													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19573	0.0		0.0	False		,,,				2504	0.0				p.R1412H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4235A	4						.						122.0	113.0	116.0					4																	3176516		1967	4151	6118	3146314	SO:0001583	missense	3064	exon32			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.4235G>A	4.37:g.3176516G>A	ENSP00000347184:p.Arg1412His	Somatic		Capture	Illumina HiSeq	Phase_I	3146314	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	33	5.288424	0.95517	.	.	ENSG00000197386	ENST00000355072	T	0.05649	3.41	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.23926	0.0579	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00137	-1.2004	10	0.72032	D	0.01	.	19.2953	0.94119	0.0:0.0:1.0:0.0	.	1412	P42858	HD_HUMAN	H	1412	ENSP00000347184:R1412H	ENSP00000347184:R1412H	R	+	2	0	HTT	3146314	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	9.434000	0.97515	2.557000	0.86248	0.555000	0.69702	CGT		0.463	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
HTT	3064	broad.mit.edu	37	4	3230642	3230642	+	Missense_Mutation	SNP	C	C	T	rs202216456		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:3230642C>T	ENST00000355072.5	+	59	8160	c.8015C>T	c.(8014-8016)tCg>tTg	p.S2672L	HTT_ENST00000513806.1_3'UTR	NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	2672					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)	p.S2672L(1)		breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		CACTCCTGTTCGCAGTTTTTG	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		19704	0.0		0.001	False		,,,				2504	0.0				p.S2672L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8015T	4						.						86.0	89.0	88.0					4																	3230642		2026	4188	6214	3200440	SO:0001583	missense	3064	exon59			L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.8015C>T	4.37:g.3230642C>T	ENSP00000347184:p.Ser2672Leu	Somatic		Capture	Illumina HiSeq	Phase_I	3200440	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.712	0.695388	0.15106	.	.	ENSG00000197386	ENST00000355072	T	0.03772	3.81	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.03477	0.0100	L	0.29908	0.895	0.80722	D	1	P	0.46859	0.885	B	0.34093	0.175	T	0.41520	-0.9504	10	0.02654	T	1	.	18.3626	0.90380	0.0:1.0:0.0:0.0	.	2672	P42858	HD_HUMAN	L	2672	ENSP00000347184:S2672L	ENSP00000347184:S2672L	S	+	2	0	HTT	3200440	1.000000	0.71417	0.910000	0.35882	0.164000	0.22412	7.469000	0.80959	2.350000	0.79820	0.563000	0.77884	TCG		0.527	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
ZBTB49	166793	broad.mit.edu	37	4	4322569	4322569	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:4322569C>T	ENST00000337872.4	+	8	1945	c.1824C>T	c.(1822-1824)ctC>ctT	p.L608L	ZBTB49_ENST00000355834.3_Silent_p.L486L|ZBTB49_ENST00000538529.1_Silent_p.L91L|RP11-265O12.1_ENST00000509015.1_lincRNA	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	608					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.L608L(1)		breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	28						CCTCCGACCTCGAGAAATCTC	0.567																																					p.L608L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1824T	4						.						56.0	52.0	54.0					4																	4322569		2203	4300	6503	4373470	SO:0001819	synonymous_variant	166793	exon8			AK095878	CCDS3375.1	4p16.2	2013-01-08	2010-01-26	2010-01-26	ENSG00000168826	ENSG00000168826		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	19883	protein-coding gene	gene with protein product			"""zinc finger protein 509"""	ZNF509		12477932	Standard	NM_145291		Approved	FLJ38559	uc003ghu.3	Q6ZSB9	OTTHUMG00000090325	ENST00000337872.4:c.1824C>T	4.37:g.4322569C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4373470	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Silent	SNP	ENST00000337872.4	37	CCDS3375.1																																																																																				0.567	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291	
EVC	2121	broad.mit.edu	37	4	5795383	5795383	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:5795383C>T	ENST00000264956.6	+	13	2009	c.1825C>T	c.(1825-1827)Cgg>Tgg	p.R609W	EVC_ENST00000382674.2_Missense_Mutation_p.R609W|EVC_ENST00000515113.1_3'UTR	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	609					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.R609W(1)		NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GACACACCTGCGGGAGGACCA	0.617																																					p.R609W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1825T	4						.						30.0	26.0	27.0					4																	5795383		2163	4214	6377	5846284	SO:0001583	missense	2121	exon13			AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1825C>T	4.37:g.5795383C>T	ENSP00000264956:p.Arg609Trp	Somatic		Capture	Illumina HiSeq	Phase_I	5846284	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199340	0.58126	.	.	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.54866	0.55;0.55	5.21	0.0981	0.14496	.	0.974268	0.08453	N	0.943635	T	0.42268	0.1195	L	0.51422	1.61	0.09310	N	0.999999	B	0.15141	0.012	B	0.12837	0.008	T	0.43426	-0.9392	10	0.72032	D	0.01	.	2.6771	0.05084	0.3445:0.3042:0.0:0.3512	.	609	P57679	EVC_HUMAN	W	609	ENSP00000264956:R609W;ENSP00000372120:R609W	ENSP00000264956:R609W	R	+	1	2	EVC	5846284	0.213000	0.23551	0.232000	0.24009	0.726000	0.41606	0.282000	0.18829	0.073000	0.16731	0.655000	0.94253	CGG		0.617	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
KIAA0232	9778	broad.mit.edu	37	4	6860228	6860228	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:6860228G>A	ENST00000307659.5	+	6	968	c.513G>A	c.(511-513)gtG>gtA	p.V171V	KIAA0232_ENST00000425103.1_Silent_p.V171V	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	171							ATP binding (GO:0005524)	p.V171V(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(12)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	41						AGGATCAAGTGGAAATGTATG	0.358																																					p.V171V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G513A	4						.						42.0	40.0	41.0					4																	6860228		1837	4081	5918	6911129	SO:0001819	synonymous_variant	9778	exon6			D86985	CCDS43209.1	4p16.1	2012-11-29			ENSG00000170871	ENSG00000170871			28992	protein-coding gene	gene with protein product						9039502	Standard	NM_014743		Approved		uc003gjq.4	Q92628	OTTHUMG00000160072	ENST00000307659.5:c.513G>A	4.37:g.6860228G>A		Somatic		Capture	Illumina HiSeq	Phase_I	6911129	NM_014743	A7E2D2	Silent	SNP	ENST00000307659.5	37	CCDS43209.1																																																																																				0.358	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743	
SLC2A9	56606	broad.mit.edu	37	4	10022953	10022953	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:10022953A>C	ENST00000264784.3	-	1	154	c.101T>G	c.(100-102)cTg>cGg	p.L34R	SLC2A9_ENST00000506583.1_Intron|SLC2A9_ENST00000309065.3_Intron	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	34					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)	p.L34R(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	GTCACACTCCAGCAGTGCCCT	0.592																																					p.L34R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T101G	4						.						141.0	144.0	143.0					4																	10022953		2203	4300	6503	9632051	SO:0001583	missense	56606	exon1			AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.101T>G	4.37:g.10022953A>C	ENSP00000264784:p.Leu34Arg	Somatic		Capture	Illumina HiSeq	Phase_I	9632051	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	37	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	A	8.272	0.813622	0.16537	.	.	ENSG00000109667	ENST00000264784	D	0.81579	-1.51	2.71	0.73	0.18271	Major facilitator superfamily domain, general substrate transporter (1);	90.666600	0.00166	N	0.000000	T	0.62913	0.2467	N	0.08118	0	0.09310	N	0.999996	B	0.15141	0.012	B	0.20955	0.032	T	0.52586	-0.8556	9	.	.	.	.	4.3813	0.11295	0.3522:0.0:0.6478:0.0	.	34	Q9NRM0	GTR9_HUMAN	R	34	ENSP00000264784:L34R	.	L	-	2	0	SLC2A9	9632051	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.701000	0.25616	0.426000	0.26116	-0.177000	0.13119	CTG		0.592	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
WDR1	9948	broad.mit.edu	37	4	10084670	10084670	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:10084670G>A	ENST00000499869.2	-	10	1365	c.1172C>T	c.(1171-1173)aCc>aTc	p.T391I	WDR1_ENST00000515743.1_5'UTR|WDR1_ENST00000382452.2_Missense_Mutation_p.T391I|WDR1_ENST00000502702.1_Missense_Mutation_p.T251I|WDR1_ENST00000382451.2_Missense_Mutation_p.T251I			O75083	WDR1_HUMAN	WD repeat domain 1	391					blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)		p.T391I(1)		endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CATGAGGCTGGTGTACCGCAC	0.632																																					p.T391I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1172T	4						.						52.0	60.0	57.0					4																	10084670		2131	4231	6362	9693768	SO:0001583	missense	9948	exon10			AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.1172C>T	4.37:g.10084670G>A	ENSP00000427687:p.Thr391Ile	Somatic		Capture	Illumina HiSeq	Phase_I	9693768	NM_017491	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	37	CCDS54740.1	.	.	.	.	.	.	.	.	.	.	G	17.14	3.314080	0.60414	.	.	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000382451;ENST00000502702;ENST00000439733	T;T;T;T	0.48836	0.8;0.8;1.18;1.18	5.42	5.42	0.78866	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.49287	0.1548	N	0.11427	0.14	0.80722	D	1	D;P	0.69078	0.997;0.647	D;B	0.63033	0.91;0.091	T	0.56171	-0.8023	10	0.46703	T	0.11	-44.1168	18.2079	0.89860	0.0:0.0:1.0:0.0	.	251;391	O75083-3;O75083	.;WDR1_HUMAN	I	391;391;251;251;226	ENSP00000427687:T391I;ENSP00000371890:T391I;ENSP00000371889:T251I;ENSP00000426725:T251I	ENSP00000371889:T251I	T	-	2	0	WDR1	9693768	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	9.117000	0.94347	2.538000	0.85594	0.462000	0.41574	ACC		0.632	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
PPARGC1A	10891	broad.mit.edu	37	4	23815656	23815656	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:23815656G>C	ENST00000264867.2	-	8	1569	c.1450C>G	c.(1450-1452)Ctg>Gtg	p.L484V	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	484	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.L484V(1)		central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				CTGTCCCTCAGTTCACCGGTC	0.458																																					p.L484V	Esophageal Squamous(29;694 744 13796 34866 44181)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1450G	4						.						132.0	122.0	125.0					4																	23815656		2203	4300	6503	23424754	SO:0001583	missense	10891	exon8			AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.1450C>G	4.37:g.23815656G>C	ENSP00000264867:p.Leu484Val	Somatic		Capture	Illumina HiSeq	Phase_I	23424754	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	37	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.140106	0.37728	.	.	ENSG00000109819	ENST00000264867	T	0.22945	1.93	6.16	5.32	0.75619	.	0.316177	0.30410	N	0.009695	T	0.33614	0.0869	M	0.61703	1.905	0.80722	D	1	P	0.51351	0.944	P	0.46659	0.523	T	0.07195	-1.0785	10	0.30078	T	0.28	-3.7647	15.3585	0.74448	0.0661:0.0:0.9339:0.0	.	484	Q9UBK2	PRGC1_HUMAN	V	484	ENSP00000264867:L484V	ENSP00000264867:L484V	L	-	1	2	PPARGC1A	23424754	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.608000	0.46308	1.627000	0.50400	0.650000	0.86243	CTG		0.458	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
SEL1L3	23231	broad.mit.edu	37	4	25760567	25760567	+	Missense_Mutation	SNP	C	C	T	rs200213966		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:25760567C>T	ENST00000399878.3	-	21	3201	c.3079G>A	c.(3079-3081)Gaa>Aaa	p.E1027K	SEL1L3_ENST00000502949.1_Missense_Mutation_p.E874K|SEL1L3_ENST00000264868.5_Missense_Mutation_p.E992K	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	1027						integral component of membrane (GO:0016021)		p.E874K(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						GCTCACCTTTCGTACAGTTCC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		17540	0.001		0.0	False		,,,				2504	0.0				p.E1027K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3079A	4						.						108.0	104.0	105.0					4																	25760567		1868	4104	5972	25369665	SO:0001583	missense	23231	exon21			BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.3079G>A	4.37:g.25760567C>T	ENSP00000382767:p.Glu1027Lys	Somatic		Capture	Illumina HiSeq	Phase_I	25369665	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	19.89	3.911325	0.72983	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949;ENST00000507618	T;T;T	0.13196	2.82;2.83;2.61	5.67	5.67	0.87782	.	0.306550	0.36200	N	0.002732	T	0.15869	0.0382	L	0.56769	1.78	0.40337	D	0.978995	B;B	0.32620	0.254;0.378	B;B	0.24701	0.013;0.055	T	0.01643	-1.1305	10	0.51188	T	0.08	.	15.4663	0.75403	0.147:0.853:0.0:0.0	.	434;1027	B4DTH5;Q68CR1	.;SE1L3_HUMAN	K	1027;992;874;118	ENSP00000382767:E1027K;ENSP00000264868:E992K;ENSP00000425438:E874K	ENSP00000264868:E992K	E	-	1	0	SEL1L3	25369665	0.990000	0.36364	0.965000	0.40720	0.786000	0.44442	2.912000	0.48782	2.665000	0.90641	0.591000	0.81541	GAA		0.408	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
WDR19	57728	broad.mit.edu	37	4	39276477	39276477	+	Silent	SNP	C	C	T	rs202102903		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:39276477C>T	ENST00000399820.3	+	33	3769	c.3615C>T	c.(3613-3615)ggC>ggT	p.G1205G	WDR19_ENST00000288634.7_Silent_p.G1045G	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1205					ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)		p.G1205G(1)		large_intestine(1)	1						ACAGGGCAGGCCTGAAGAACT	0.488													C|||	1	0.000199681	0.0	0.0	5008	,	,		21678	0.0		0.001	False		,,,				2504	0.0				p.G1205G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3615T	4						.	C		0,3988		0,0,1994	153.0	142.0	146.0		3615	3.7	1.0	4		146	1,8355		0,1,4177	no	coding-synonymous	WDR19	NM_025132.3		0,1,6171	TT,TC,CC		0.012,0.0,0.0081		1205/1343	39276477	1,12343	1994	4178	6172	38952872	SO:0001819	synonymous_variant	57728	exon33			AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3615C>T	4.37:g.39276477C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38952872	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Silent	SNP	ENST00000399820.3	37	CCDS47042.1																																																																																				0.488	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
GABRG1	2565	broad.mit.edu	37	4	46060335	46060335	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:46060335T>A	ENST00000295452.4	-	7	982	c.815A>T	c.(814-816)tAt>tTt	p.Y272F		NM_173536.3	NP_775807.2	Q8N1C3	GBRG1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 1	272					gamma-aminobutyric acid signaling pathway (GO:0007214)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.Y272F(1)		breast(2)|central_nervous_system(5)|endometrium(3)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(2)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	76				Lung(65;0.106)|LUSC - Lung squamous cell carcinoma(721;0.23)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATAGTGAAATATCCCATTCT	0.338																																					p.Y272F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A815T	4						.						103.0	105.0	104.0					4																	46060335		2203	4300	6503	45755092	SO:0001583	missense	2565	exon7			BC031087	CCDS3470.1	4p12	2012-06-22			ENSG00000163285	ENSG00000163285		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4086	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma"""	137166				1321425	Standard	NM_173536		Approved		uc003gxb.3	Q8N1C3	OTTHUMG00000128609	ENST00000295452.4:c.815A>T	4.37:g.46060335T>A	ENSP00000295452:p.Tyr272Phe	Somatic		Capture	Illumina HiSeq	Phase_I	45755092	NM_173536	Q5H9T8	Missense_Mutation	SNP	ENST00000295452.4	37	CCDS3470.1	.	.	.	.	.	.	.	.	.	.	T	16.24	3.067176	0.55539	.	.	ENSG00000163285	ENST00000295452;ENST00000540030	D	0.84070	-1.8	5.82	4.57	0.56435	Neurotransmitter-gated ion-channel transmembrane domain (1);	0.062065	0.64402	D	0.000002	T	0.78162	0.4240	L	0.49778	1.585	0.51482	D	0.999923	B	0.23735	0.09	B	0.23852	0.049	T	0.76669	-0.2874	10	0.54805	T	0.06	.	11.2436	0.48982	0.1368:0.0:0.0:0.8632	.	272	Q8N1C3	GBRG1_HUMAN	F	272	ENSP00000295452:Y272F	ENSP00000295452:Y272F	Y	-	2	0	GABRG1	45755092	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.104000	0.71498	2.236000	0.73375	0.524000	0.50904	TAT		0.338	GABRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250470.1	NM_173536	
CORIN	10699	broad.mit.edu	37	4	47765575	47765575	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:47765575C>G	ENST00000273857.4	-	4	437	c.438G>C	c.(436-438)caG>caC	p.Q146H	CORIN_ENST00000502252.1_Missense_Mutation_p.Q79H|CORIN_ENST00000505909.1_Missense_Mutation_p.Q146H|CORIN_ENST00000508498.1_Missense_Mutation_p.Q7H|CORIN_ENST00000504584.1_Missense_Mutation_p.Q146H	NM_006587.2	NP_006578.2	Q9Y5Q5	CORIN_HUMAN	corin, serine peptidase	146	FZ 1. {ECO:0000255|PROSITE- ProRule:PRU00090}.				female pregnancy (GO:0007565)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)|regulation of blood pressure (GO:0008217)|regulation of renal sodium excretion (GO:0035813)|regulation of systemic arterial blood pressure by atrial natriuretic peptide (GO:0003050)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)	p.Q146H(1)		NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(18)|lung(39)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	79						GCATCTGACACTGGCTGTGGG	0.433																																					p.Q146H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G438C	4						.						127.0	122.0	124.0					4																	47765575		2203	4300	6503	47460332	SO:0001583	missense	10699	exon4			AF133845	CCDS3477.1, CCDS63958.1, CCDS75122.1	4p13-p12	2011-08-31	2005-08-17		ENSG00000145244	ENSG00000145244		"""Serine peptidases / Transmembrane"""	19012	protein-coding gene	gene with protein product		605236	"""corin, serine protease"""			10329693	Standard	NM_006587		Approved	PRSC, CRN, ATC2, Lrp4, TMPRSS10	uc003gxm.3	Q9Y5Q5	OTTHUMG00000099441	ENST00000273857.4:c.438G>C	4.37:g.47765575C>G	ENSP00000273857:p.Gln146His	Somatic		Capture	Illumina HiSeq	Phase_I	47460332	NM_006587	B0ZBE3|Q2TBD2|Q4W5E5|Q4W5G6|Q9UHY2	Missense_Mutation	SNP	ENST00000273857.4	37	CCDS3477.1	.	.	.	.	.	.	.	.	.	.	C	14.46	2.540558	0.45176	.	.	ENSG00000145244	ENST00000273857;ENST00000508498;ENST00000502252;ENST00000505909;ENST00000504584	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	4.99	1.06	0.20224	Frizzled domain (5);	0.000000	0.85682	D	0.000000	T	0.82181	0.4981	M	0.72894	2.215	0.35897	D	0.830133	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;0.999;1.0;0.999	T	0.83023	-0.0166	10	0.66056	D	0.02	.	9.2402	0.37491	0.0:0.5297:0.0:0.4703	.	146;146;79;7;146	B7Z4R1;B4E2W9;B4E1Y7;B4DZA3;Q9Y5Q5	.;.;.;.;CORIN_HUMAN	H	146;7;79;146;146	ENSP00000273857:Q146H;ENSP00000425597:Q7H;ENSP00000424212:Q79H;ENSP00000425401:Q146H;ENSP00000423216:Q146H	ENSP00000273857:Q146H	Q	-	3	2	CORIN	47460332	0.871000	0.30034	0.998000	0.56505	0.556000	0.35491	-0.096000	0.11059	-0.057000	0.13199	-0.216000	0.12614	CAG		0.433	CORIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216906.2		
PDGFRA	5156	broad.mit.edu	37	4	55156543	55156543	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:55156543G>A	ENST00000257290.5	+	22	3275	c.2944G>A	c.(2944-2946)Gtg>Atg	p.V982M	FIP1L1_ENST00000507166.1_Missense_Mutation_p.V742M	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	982					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.V982L(1)|p.V982M(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)	ACGCATGCGTGTGGACTCAGA	0.448			"""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.V982M	Pancreas(151;208 1913 7310 23853 37092)		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G2944A	4						.						156.0	135.0	142.0					4																	55156543		2203	4300	6503	54851300	SO:0001583	missense	5156	exon22	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.2944G>A	4.37:g.55156543G>A	ENSP00000257290:p.Val982Met	Somatic		Capture	Illumina HiSeq	Phase_I	54851300	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.236703	0.22711	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	T;T	0.77489	-1.1;-0.9	5.77	5.77	0.91146	.	0.000000	0.29522	U	0.011903	T	0.68100	0.2964	L	0.34521	1.04	0.80722	D	1	B	0.18863	0.031	B	0.09377	0.004	T	0.63070	-0.6719	10	0.41790	T	0.15	.	13.2254	0.59912	0.0725:0.0:0.9275:0.0	.	982	P16234	PGFRA_HUMAN	M	742;982	ENSP00000423325:V742M;ENSP00000257290:V982M	ENSP00000423325:V742M	V	+	1	0	FIP1L1;PDGFRA	54851300	0.999000	0.42202	0.962000	0.40283	0.226000	0.24999	2.695000	0.47043	2.740000	0.93945	0.557000	0.71058	GTG		0.448	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
LPHN3	23284	broad.mit.edu	37	4	62599071	62599071	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:62599071A>G	ENST00000514591.1	+	7	1323	c.994A>G	c.(994-996)Aat>Gat	p.N332D	LPHN3_ENST00000512091.2_Missense_Mutation_p.N332D|LPHN3_ENST00000506700.1_Missense_Mutation_p.N332D|LPHN3_ENST00000508693.1_Missense_Mutation_p.N400D|LPHN3_ENST00000506720.1_Missense_Mutation_p.N400D|LPHN3_ENST00000511324.1_Missense_Mutation_p.N400D|LPHN3_ENST00000545650.1_Missense_Mutation_p.N332D|LPHN3_ENST00000507164.1_Missense_Mutation_p.N400D|LPHN3_ENST00000506746.1_Missense_Mutation_p.N400D|LPHN3_ENST00000514157.1_Missense_Mutation_p.N332D|LPHN3_ENST00000507625.1_Missense_Mutation_p.N400D|LPHN3_ENST00000514996.1_Missense_Mutation_p.N332D|LPHN3_ENST00000508946.1_Missense_Mutation_p.N332D|LPHN3_ENST00000509896.1_Missense_Mutation_p.N400D|LPHN3_ENST00000504896.1_Missense_Mutation_p.N332D			Q9HAR2	LPHN3_HUMAN	latrophilin 3	332	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)	p.N332D(2)		breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GGATGATGACAATGAGGCTAC	0.383																																					p.N332D												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A994G	4						.						122.0	108.0	113.0					4																	62599071		1942	4146	6088	62281666	SO:0001583	missense	23284	exon5			AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.994A>G	4.37:g.62599071A>G	ENSP00000422533:p.Asn332Asp	Somatic		Capture	Illumina HiSeq	Phase_I	62281666	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.223483	0.58668	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78;-2.78	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.89361	0.6693	N	0.08118	0	0.45946	D	0.998773	D;D;D	0.76494	0.999;0.999;0.974	D;D;D	0.81914	0.995;0.995;0.969	D	0.90510	0.4480	10	0.41790	T	0.15	.	14.4261	0.67218	1.0:0.0:0.0:0.0	.	332;400;332	E9PE04;E7EN28;Q9HAR2-2	.;.;.	D	332;332;400;400;332;332;332;332;332;400;400;400;332;332;332;400;400;332	ENSP00000423388:N332D;ENSP00000422533:N332D;ENSP00000423787:N400D;ENSP00000425033:N400D;ENSP00000424120:N332D;ENSP00000439831:N332D;ENSP00000421476:N400D;ENSP00000424030:N400D;ENSP00000421372:N400D;ENSP00000425201:N332D;ENSP00000423434:N332D;ENSP00000421627:N332D;ENSP00000420931:N400D;ENSP00000425884:N400D;ENSP00000424258:N332D	ENSP00000280009:N332D	N	+	1	0	LPHN3	62281666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	1.999000	0.58509	0.455000	0.32223	AAT		0.383	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
CSN2	1447	broad.mit.edu	37	4	70823400	70823400	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:70823400C>A	ENST00000353151.3	-	5	278	c.267G>T	c.(265-267)gtG>gtT	p.V89V		NM_001891.2	NP_001882.1	P61201	CSN2_HUMAN	casein beta	0					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)	p.V89V(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|skin(2)	12						CAGGCAGCACCACAGCAGGCT	0.488																																					p.V89V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G267T	4						.						123.0	116.0	118.0					4																	70823400		2203	4300	6503	70857989	SO:0001819	synonymous_variant	1447	exon5			X17070	CCDS3532.1	4q21.1	2008-02-05			ENSG00000135222	ENSG00000135222			2447	protein-coding gene	gene with protein product		115460		CASB		1577486	Standard	NM_001891		Approved		uc003hes.4	P05814	OTTHUMG00000129409	ENST00000353151.3:c.267G>T	4.37:g.70823400C>A		Somatic		Capture	Illumina HiSeq	Phase_I	70857989	NM_001891	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Silent	SNP	ENST00000353151.3	37	CCDS3532.1																																																																																				0.488	CSN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251565.1		
HTN1	3346	broad.mit.edu	37	4	70921264	70921264	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:70921264C>A	ENST00000511674.1	+	5	223	c.152C>A	c.(151-153)tCa>tAa	p.S51*	HTN1_ENST00000246896.3_Nonsense_Mutation_p.S51*			P15515	HIS1_HUMAN	histatin 1	51					biomineral tissue development (GO:0031214)|defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)		p.S51*(1)		endometrium(1)|large_intestine(1)|lung(2)|skin(2)	6						GACTATGGATCAAATTATCTA	0.368																																					p.S51X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C152A	4						.						110.0	100.0	104.0					4																	70921264		2202	4298	6500	70955853	SO:0001587	stop_gained	3346	exon5				CCDS3534.1	4q13	2008-02-05			ENSG00000126550	ENSG00000126550			5283	protein-coding gene	gene with protein product		142701					Standard	NM_002159		Approved	HIS1	uc003hex.3	P15515	OTTHUMG00000129397	ENST00000511674.1:c.152C>A	4.37:g.70921264C>A	ENSP00000424501:p.Ser51*	Somatic		Capture	Illumina HiSeq	Phase_I	70955853	NM_002159		Nonsense_Mutation	SNP	ENST00000511674.1	37	CCDS3534.1	.	.	.	.	.	.	.	.	.	.	C	3.276	-0.147995	0.06627	.	.	ENSG00000126550	ENST00000246896;ENST00000511674	.	.	.	0.781	-1.56	0.08532	.	.	.	.	.	.	.	.	.	.	.	0.20703	N	0.999866	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	2.8127	0.05446	0.3049:0.3917:0.3034:0.0	.	.	.	.	X	51	.	ENSP00000246896:S51X	S	+	2	0	HTN1	70955853	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-6.634000	0.00059	-1.527000	0.01758	-1.918000	0.00516	TCA		0.368	HTN1-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362220.2		
RUFY3	22902	broad.mit.edu	37	4	71654558	71654558	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:71654558G>T	ENST00000226328.4	+	11	1670	c.1107G>T	c.(1105-1107)atG>atT	p.M369I	RUFY3_ENST00000381006.3_Missense_Mutation_p.M369I|RUFY3_ENST00000536664.1_Missense_Mutation_p.M353I|RUFY3_ENST00000417478.2_Missense_Mutation_p.M429I|RUFY3_ENST00000502653.1_Missense_Mutation_p.M316I	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	369					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)		p.M369I(1)		endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			AGATCAGCATGAGGCAGGAGA	0.463																																					p.M369I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1107T	4						.						132.0	111.0	118.0					4																	71654558		2203	4300	6503	71873422	SO:0001583	missense	22902	exon11			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.1107G>T	4.37:g.71654558G>T	ENSP00000226328:p.Met369Ile	Somatic		Capture	Illumina HiSeq	Phase_I	71873422	NM_014961	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	37	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.832998	0.91036	.	.	ENSG00000018189	ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000502653	T;T;T;T;T	0.13538	2.58;2.58;2.58;2.58;2.58	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.37100	0.0991	L	0.58810	1.83	0.80722	D	1	D;D;P;P	0.65815	0.995;0.981;0.851;0.869	D;P;P;P	0.77004	0.989;0.692;0.838;0.66	T	0.03773	-1.1005	10	0.87932	D	0	-25.9442	19.6014	0.95563	0.0:0.0:1.0:0.0	.	353;369;369;429	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	I	429;369;369;353;316	ENSP00000399771:M429I;ENSP00000370394:M369I;ENSP00000226328:M369I;ENSP00000443652:M353I;ENSP00000425400:M316I	ENSP00000226328:M369I	M	+	3	0	RUFY3	71873422	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	9.476000	0.97823	2.622000	0.88805	0.650000	0.86243	ATG		0.463	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961	
RUFY3	22902	broad.mit.edu	37	4	71665904	71665904	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:71665904C>A	ENST00000381006.3	+	15	2183	c.1604C>A	c.(1603-1605)cCc>cAc	p.P535H	RUFY3_ENST00000512331.1_3'UTR|RUFY3_ENST00000502653.1_Missense_Mutation_p.P482H	NM_001037442.2	NP_001032519.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	0					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			CTAAAAAAGCCCCTGGAAGAA	0.358																																					p.P535H												.	.	0			c.C1604A	4						.						51.0	52.0	51.0					4																	71665904		2203	4300	6503	71884768	SO:0001583	missense	22902	exon15			AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000381006.3:c.1604C>A	4.37:g.71665904C>A	ENSP00000370394:p.Pro535His	None		Capture	Illumina HiSeq	Phase_I	71884768	NM_001037442	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000381006.3	37	CCDS34001.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.591893	0.66219	.	.	ENSG00000018189	ENST00000381006;ENST00000502653	T;T	0.76709	-1.04;-1.04	5.59	5.59	0.84812	.	0.765590	0.12022	N	0.506853	T	0.79857	0.4518	.	.	.	0.80722	D	1	P	0.41569	0.755	P	0.44946	0.465	T	0.77335	-0.2626	9	0.44086	T	0.13	-0.0054	16.7679	0.85528	0.0:1.0:0.0:0.0	.	535	Q7L099-3	.	H	535;482	ENSP00000370394:P535H;ENSP00000425400:P482H	ENSP00000370394:P535H	P	+	2	0	RUFY3	71884768	0.018000	0.18449	0.963000	0.40424	0.981000	0.71138	2.991000	0.49409	2.648000	0.89879	0.563000	0.77884	CCC		0.358	RUFY3-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252162.1	NM_014961	
ADAMTS3	9508	broad.mit.edu	37	4	73161388	73161388	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:73161388T>G	ENST00000286657.4	-	19	2742	c.2706A>C	c.(2704-2706)caA>caC	p.Q902H		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	902	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.Q902H(1)		NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTGTACACTCTTGAATATTGC	0.368																																					p.Q902H	NSCLC(168;1941 2048 2918 13048 43078)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2706C	4						.						235.0	197.0	210.0					4																	73161388		2203	4300	6503	73380252	SO:0001583	missense	9508	exon19			AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.2706A>C	4.37:g.73161388T>G	ENSP00000286657:p.Gln902His	Somatic		Capture	Illumina HiSeq	Phase_I	73380252	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	37	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	T	9.892	1.204376	0.22205	.	.	ENSG00000156140	ENST00000286657	T	0.55052	0.54	5.28	-6.15	0.02105	.	0.000000	0.64402	D	0.000001	T	0.41351	0.1155	L	0.31845	0.965	0.46774	D	0.999199	B	0.27594	0.182	B	0.36464	0.225	T	0.13335	-1.0513	10	0.19590	T	0.45	.	18.6469	0.91413	0.0:0.775:0.0:0.225	.	902	O15072	ATS3_HUMAN	H	902	ENSP00000286657:Q902H	ENSP00000286657:Q902H	Q	-	3	2	ADAMTS3	73380252	0.983000	0.35010	0.948000	0.38648	0.603000	0.37013	0.246000	0.18160	-1.133000	0.02903	-1.069000	0.02264	CAA		0.368	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
NAAA	27163	broad.mit.edu	37	4	76861241	76861241	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:76861241A>G	ENST00000286733.4	-	2	385	c.284T>C	c.(283-285)tTc>tCc	p.F95S	NAAA_ENST00000505594.1_5'UTR|NAAA_ENST00000399497.3_Missense_Mutation_p.F95S|NAAA_ENST00000507187.2_Missense_Mutation_p.F95S|NAAA_ENST00000507956.1_Missense_Mutation_p.F95S	NM_014435.3	NP_055250.2	Q02083	NAAA_HUMAN	N-acylethanolamine acid amidase	95					lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds (GO:0016810)|transcription factor binding (GO:0008134)	p.F95S(1)		endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	11						CTCGCCGGTGAAGGGCTGGGG	0.592																																					p.F95S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T284C	4						.						52.0	60.0	57.0					4																	76861241		2034	4185	6219	77080265	SO:0001583	missense	27163	exon2			M92449	CCDS43239.1	4q21.1	2011-09-23	2008-04-24	2008-04-24	ENSG00000138744	ENSG00000138744	3.5.1.-		736	protein-coding gene	gene with protein product		607469	"""N-acylsphingosine amidohydrolase (acid ceramidase)-like"""	ASAHL		10610717, 1446826	Standard	NM_001042402		Approved		uc003hjb.3	Q02083	OTTHUMG00000160855	ENST00000286733.4:c.284T>C	4.37:g.76861241A>G	ENSP00000286733:p.Phe95Ser	Somatic		Capture	Illumina HiSeq	Phase_I	77080265	NM_001042402	Q5KTF2|Q96EY2|Q9BRA8	Missense_Mutation	SNP	ENST00000286733.4	37	CCDS43239.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405654	0.62288	.	.	ENSG00000138744	ENST00000399497;ENST00000286733;ENST00000507956;ENST00000399490;ENST00000507187	T;T;T;T	0.53640	0.61;0.61;0.61;0.61	5.1	-2.81	0.05805	.	0.131674	0.53938	D	0.000047	T	0.53932	0.1827	M	0.70275	2.135	0.19300	N	0.999972	D;P	0.58268	0.982;0.911	P;P	0.55577	0.779;0.467	T	0.55256	-0.8169	10	0.62326	D	0.03	-6.1781	10.5379	0.45016	0.3168:0.0:0.0:0.6832	.	95;95	D6R9S9;Q02083	.;NAAA_HUMAN	S	95	ENSP00000382420:F95S;ENSP00000286733:F95S;ENSP00000427641:F95S;ENSP00000423142:F95S	ENSP00000286733:F95S	F	-	2	0	NAAA	77080265	0.997000	0.39634	0.074000	0.20217	0.992000	0.81027	1.403000	0.34612	-0.584000	0.05913	0.477000	0.44152	TTC		0.592	NAAA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362843.4		
CNOT6L	246175	broad.mit.edu	37	4	78652580	78652580	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:78652580C>T	ENST00000504123.1	-	9	1115	c.985G>A	c.(985-987)Gct>Act	p.A329T	CNOT6L_ENST00000264903.4_Missense_Mutation_p.A329T			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	329	Nuclease domain.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)	p.A329T(1)		kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						AATACCACAGCGACACCAATG	0.398																																					p.A329T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G985A	4						.						108.0	105.0	106.0					4																	78652580		2166	4294	6460	78871604	SO:0001583	missense	246175	exon9			AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.985G>A	4.37:g.78652580C>T	ENSP00000424896:p.Ala329Thr	Somatic		Capture	Illumina HiSeq	Phase_I	78871604	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.11|17.11	3.306617|3.306617	0.60305|0.60305	.|.	.|.	ENSG00000138767|ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000505983|ENST00000515506	T;T;T;T|.	0.80824|.	-1.42;-1.42;-1.42;-1.42|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Endonuclease/exonuclease/phosphatase (2);|.	0.096228|.	0.64402|.	N|.	0.000001|.	T|T	0.79015|0.79015	0.4375|0.4375	M|M	0.87827|0.87827	2.91|2.91	0.80722|0.80722	D|D	1|1	B;B|.	0.32101|.	0.356;0.067|.	B;B|.	0.30105|.	0.111;0.052|.	T|T	0.81398|0.81398	-0.0951|-0.0951	10|5	0.45353|.	T|.	0.12|.	-3.5178|-3.5178	13.1205|13.1205	0.59323|0.59323	0.0:0.9269:0.0:0.073|0.0:0.9269:0.0:0.073	.|.	302;329|.	Q96LI5-2;Q96LI5|.	.;CNO6L_HUMAN|.	T|H	329;329;336;104|357	ENSP00000424896:A329T;ENSP00000264903:A329T;ENSP00000425571:A336T;ENSP00000426320:A104T|.	ENSP00000264903:A329T|.	A|R	-|-	1|2	0|0	CNOT6L|CNOT6L	78871604|78871604	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.855000|0.855000	0.48748|0.48748	6.091000|6.091000	0.71406|0.71406	2.690000|2.690000	0.91761|0.91761	0.591000|0.591000	0.81541|0.81541	GCT|CGC		0.398	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
BMP3	651	broad.mit.edu	37	4	81967426	81967426	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:81967426A>T	ENST00000282701.2	+	2	1171	c.851A>T	c.(850-852)gAg>gTg	p.E284V		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	284					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)	p.E284V(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						CTTTCCATTGAGCGGAGGAAG	0.522																																					p.E284V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A851T	4						.						70.0	76.0	74.0					4																	81967426		2203	4299	6502	82186450	SO:0001583	missense	651	exon2			M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.851A>T	4.37:g.81967426A>T	ENSP00000282701:p.Glu284Val	Somatic		Capture	Illumina HiSeq	Phase_I	82186450	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	A	5.563	0.288783	0.10513	.	.	ENSG00000152785	ENST00000282701	T	0.74421	-0.84	5.27	4.01	0.46588	.	0.371038	0.30809	N	0.008821	T	0.69006	0.3063	L	0.50333	1.59	0.09310	N	0.999998	B	0.27380	0.177	B	0.31547	0.132	T	0.64824	-0.6316	10	0.54805	T	0.06	.	11.8258	0.52267	0.8537:0.1463:0.0:0.0	.	284	P12645	BMP3_HUMAN	V	284	ENSP00000282701:E284V	ENSP00000282701:E284V	E	+	2	0	BMP3	82186450	0.231000	0.23751	0.513000	0.27749	0.049000	0.14656	3.428000	0.52792	2.129000	0.65627	0.533000	0.62120	GAG		0.522	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
THAP9	79725	broad.mit.edu	37	4	83838382	83838382	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:83838382delT	ENST00000302236.5	+	5	1068	c.1017delT	c.(1015-1017)tatfs	p.Y339fs	LIN54_ENST00000505905.1_Intron	NM_024672.4	NP_078948.3	Q9H5L6	THAP9_HUMAN	THAP domain containing 9	339					DNA integration (GO:0015074)|DNA recombination (GO:0006310)|transposition, DNA-mediated (GO:0006313)		metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transferase activity (GO:0016740)|transposase activity (GO:0004803)	p.F341fs*2(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(13)|lung(5)|ovary(2)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(3)	33		Hepatocellular(203;0.114)				CTCTTGGTTATTTTTTTGTAA	0.413																																					p.Y339fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1017delT	4						.						104.0	105.0	105.0					4																	83838382		2203	4300	6503	84057406	SO:0001589	frameshift_variant	79725	exon5			AK091412	CCDS3598.1	4q21.3	2013-01-25			ENSG00000168152	ENSG00000168152		"""THAP (C2CH-type zinc finger) domain containing"""	23192	protein-coding gene	gene with protein product		612537				12575992	Standard	NM_024672		Approved	FLJ34093	uc003hnt.2	Q9H5L6	OTTHUMG00000130291	ENST00000302236.5:c.1017delT	4.37:g.83838382delT	ENSP00000305533:p.Tyr339fs	Somatic		Capture	Illumina HiSeq	Phase_I	84057406	NM_024672	B3KRE2|Q59AC9	Frame_Shift_Del	DEL	ENST00000302236.5	37	CCDS3598.1																																																																																				0.413	THAP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252633.1	NM_024672	
COPS4	51138	broad.mit.edu	37	4	83956441	83956441	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:83956441C>A	ENST00000264389.2	+	1	199	c.64C>A	c.(64-66)Ctg>Atg	p.L22M	COPS4_ENST00000503682.1_Missense_Mutation_p.L22M|COPS4_ENST00000509093.1_Missense_Mutation_p.L22M|COPS4_ENST00000511653.1_Missense_Mutation_p.L22M	NM_016129.2	NP_057213.2	Q9BT78	CSN4_HUMAN	COP9 signalosome subunit 4	22					cullin deneddylation (GO:0010388)|protein deneddylation (GO:0000338)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)		p.L22M(1)		endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|urinary_tract(2)	13		Hepatocellular(203;0.114)				TCATAAAGATCTGGCTGGCAA	0.582																																					p.L22M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C64A	4						.						39.0	39.0	39.0					4																	83956441		2203	4300	6503	84175465	SO:0001583	missense	51138	exon1			AF100757	CCDS3600.1, CCDS58909.1	4q21.22	2013-03-14	2013-03-14		ENSG00000138663	ENSG00000138663			16702	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 4"", ""COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)"""			9707402	Standard	NM_016129		Approved	CSN4	uc003hoa.3	Q9BT78	OTTHUMG00000130298	ENST00000264389.2:c.64C>A	4.37:g.83956441C>A	ENSP00000264389:p.Leu22Met	Somatic		Capture	Illumina HiSeq	Phase_I	84175465	NM_016129	B3KN88|B3KST5|Q561W7|Q9NW31|Q9Y677	Missense_Mutation	SNP	ENST00000264389.2	37	CCDS3600.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.828985	0.50845	.	.	ENSG00000138663	ENST00000509093;ENST00000264389;ENST00000509317;ENST00000503682;ENST00000511653	T;T;T;T;T	0.51071	0.93;0.93;0.72;0.93;0.91	6.02	4.3	0.51218	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000001	T	0.46776	0.1410	L	0.54323	1.7	0.49687	D	0.999817	P;P;P;P	0.49961	0.498;0.71;0.93;0.883	B;B;P;P	0.48030	0.22;0.284;0.564;0.564	T	0.36939	-0.9727	10	0.39692	T	0.17	-8.0421	8.2431	0.31671	0.0:0.7582:0.0:0.2418	.	22;22;22;22	B3KST5;D6RFN0;D6RAX7;Q9BT78	.;.;.;CSN4_HUMAN	M	22	ENSP00000425976:L22M;ENSP00000264389:L22M;ENSP00000425486:L22M;ENSP00000424791:L22M;ENSP00000424655:L22M	ENSP00000264389:L22M	L	+	1	2	COPS4	84175465	1.000000	0.71417	0.999000	0.59377	0.948000	0.59901	1.511000	0.35801	0.875000	0.35847	0.655000	0.94253	CTG		0.582	COPS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252643.1		
WDFY3	23001	broad.mit.edu	37	4	85710928	85710928	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:85710928delT	ENST00000295888.4	-	22	4027	c.3620delA	c.(3619-3621)aacfs	p.N1207fs	WDFY3_ENST00000322366.6_Frame_Shift_Del_p.N1207fs	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	1207					aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)	p.N1207fs*16(1)		breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		TGCAGTACTGTTTTTCAACAT	0.413																																					p.N1207fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3620delA	4						.						125.0	120.0	122.0					4																	85710928		2203	4300	6503	85929952	SO:0001589	frameshift_variant	23001	exon22			AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.3620delA	4.37:g.85710928delT	ENSP00000295888:p.Asn1207fs	Somatic		Capture	Illumina HiSeq	Phase_I	85929952	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Frame_Shift_Del	DEL	ENST00000295888.4	37	CCDS3609.1																																																																																				0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
PTPN13	5783	broad.mit.edu	37	4	87705637	87705637	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:87705637A>G	ENST00000411767.2	+	38	6107	c.6044A>G	c.(6043-6045)aAt>aGt	p.N2015S	PTPN13_ENST00000436978.1_Missense_Mutation_p.N2020S|PTPN13_ENST00000427191.2_Missense_Mutation_p.N1996S|PTPN13_ENST00000511467.1_Missense_Mutation_p.N2020S|PTPN13_ENST00000316707.6_Missense_Mutation_p.N1824S			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	2015					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)	p.N2020S(1)		NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GAAGAAATAAATGAAATATCG	0.388																																					p.N1824S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A5471G	4						.						128.0	123.0	124.0					4																	87705637		1855	4087	5942	87924661	SO:0001583	missense	5783	exon35				CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.6044A>G	4.37:g.87705637A>G	ENSP00000407249:p.Asn2015Ser	Somatic		Capture	Illumina HiSeq	Phase_I	87924661	NM_080684	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.864491	0.00547	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.50001	0.76;0.79;0.86;0.76;0.79	5.12	-9.69	0.00524	.	1.501820	0.04144	N	0.320098	T	0.12732	0.0309	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.0;0.001	T	0.12837	-1.0532	10	0.07482	T	0.82	.	1.3165	0.02108	0.2008:0.2876:0.2983:0.2134	.	1824;1996;2015;2020	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	S	1996;2020;1824;2015;2020;1964	ENSP00000408368:N1996S;ENSP00000394794:N2020S;ENSP00000322675:N1824S;ENSP00000407249:N2015S;ENSP00000426626:N2020S	ENSP00000322675:N1824S	N	+	2	0	PTPN13	87924661	0.001000	0.12720	0.000000	0.03702	0.015000	0.08874	-0.951000	0.03885	-1.862000	0.01151	-1.607000	0.00807	AAT		0.388	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
HSD17B13	345275	broad.mit.edu	37	4	88238298	88238298	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:88238298G>T	ENST00000328546.4	-	3	460	c.396C>A	c.(394-396)acC>acA	p.T132T	RP11-529H2.2_ENST00000508163.1_RNA|HSD17B13_ENST00000302219.6_Silent_p.T96T	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	132						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)	p.T132T(1)		endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		CTTCATCCTTGGTGCTGAGAA	0.403																																					p.T96T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C288A	4						.						152.0	140.0	144.0					4																	88238298		2203	4300	6503	88457322	SO:0001819	synonymous_variant	345275	exon2				CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18685	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 3"""	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.396C>A	4.37:g.88238298G>T		Somatic		Capture	Illumina HiSeq	Phase_I	88457322	NM_001136230	A8K9R9|Q2M1L5|Q86W22|Q86W23	Silent	SNP	ENST00000328546.4	37	CCDS3618.1																																																																																				0.403	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135	
HERC3	8916	broad.mit.edu	37	4	89591061	89591061	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:89591061C>A	ENST00000402738.1	+	15	1923	c.1684C>A	c.(1684-1686)Ctc>Atc	p.L562I	HERC3_ENST00000543130.1_Missense_Mutation_p.L6I|HERC3_ENST00000264345.3_Missense_Mutation_p.L562I	NM_001271602.1|NM_014606.1	NP_001258531.1|NP_055421.1	Q15034	HERC3_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 3	562					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.L562I(1)		NS(1)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|prostate(2)|skin(2)	45				OV - Ovarian serous cystadenocarcinoma(123;0.000319)		GCTGGTAAACCTCTATAAAGG	0.373																																					p.L562I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1684A	4						.						104.0	107.0	106.0					4																	89591061		2203	4300	6503	89810084	SO:0001583	missense	8916	exon15			D25215	CCDS34028.1	4q21	2012-02-23	2012-02-23		ENSG00000138641	ENSG00000138641			4876	protein-coding gene	gene with protein product		605200	"""hect domain and RLD 3"""			10702688	Standard	NM_014606		Approved	KIAA0032	uc003hrw.2	Q15034	OTTHUMG00000150436	ENST00000402738.1:c.1684C>A	4.37:g.89591061C>A	ENSP00000385684:p.Leu562Ile	Somatic		Capture	Illumina HiSeq	Phase_I	89810084	NM_014606	A8K1S5|Q8IXX3	Missense_Mutation	SNP	ENST00000402738.1	37	CCDS34028.1	.	.	.	.	.	.	.	.	.	.	C	12.50	1.956643	0.34565	.	.	ENSG00000138641	ENST00000402738;ENST00000264345;ENST00000543130	T;T;T	0.39787	1.06;1.06;1.21	5.08	5.08	0.68730	.	0.124528	0.56097	D	0.000025	T	0.26085	0.0636	N	0.11313	0.125	0.47949	D	0.999556	P	0.35456	0.502	B	0.30572	0.117	T	0.07271	-1.0781	10	0.30078	T	0.28	.	19.0331	0.92965	0.0:1.0:0.0:0.0	.	562	Q15034	HERC3_HUMAN	I	562;562;6	ENSP00000385684:L562I;ENSP00000264345:L562I;ENSP00000441703:L6I	ENSP00000264345:L562I	L	+	1	0	HERC3	89810084	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.643000	0.61390	2.802000	0.96397	0.655000	0.94253	CTC		0.373	HERC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318081.2	NM_014606	
CCSER1	401145	broad.mit.edu	37	4	91229441	91229441	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:91229441G>A	ENST00000509176.1	+	2	294	c.6G>A	c.(4-6)ggG>ggA	p.G2G	CCSER1_ENST00000432775.2_Silent_p.G2G|CCSER1_ENST00000333691.8_Silent_p.G2G	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	2								p.G2G(1)									TCCCAATGGGGGACTCAGGAT	0.408																																					p.G2G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6A	4						.						32.0	29.0	30.0					4																	91229441		1842	4089	5931	91448464	SO:0001819	synonymous_variant	401145	exon2				CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.6G>A	4.37:g.91229441G>A		Somatic		Capture	Illumina HiSeq	Phase_I	91448464	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																				0.408	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
TSPAN5	10098	broad.mit.edu	37	4	99399877	99399877	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:99399877G>A	ENST00000305798.3	-	5	937	c.535C>T	c.(535-537)Cga>Tga	p.R179*	TSPAN5_ENST00000505184.1_Nonsense_Mutation_p.R108*|TSPAN5_ENST00000509168.1_5'UTR	NM_005723.3	NP_005714.2	P62079	TSN5_HUMAN	tetraspanin 5	179					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)	p.R179*(1)		kidney(2)|large_intestine(6)|lung(5)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(123;1.89e-07)		ACGCCACATCGCTCTCGACTT	0.478																																					p.R179X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C535T	4						.						126.0	112.0	117.0					4																	99399877		2203	4300	6503	99618900	SO:0001587	stop_gained	10098	exon5				CCDS3646.1	4q22.3	2013-02-14	2005-03-21	2005-03-21	ENSG00000168785	ENSG00000168785		"""Tetraspanins"""	17753	protein-coding gene	gene with protein product		613136	"""transmembrane 4 superfamily member 9"""	TM4SF9			Standard	NM_005723		Approved	Tspan-5, NET-4	uc003hub.3	P62079	OTTHUMG00000131008	ENST00000305798.3:c.535C>T	4.37:g.99399877G>A	ENSP00000307701:p.Arg179*	Somatic		Capture	Illumina HiSeq	Phase_I	99618900	NM_005723	B2RDY2|O60628|O60746|Q6FHE5|Q9JLY1	Nonsense_Mutation	SNP	ENST00000305798.3	37	CCDS3646.1	.	.	.	.	.	.	.	.	.	.	G	36	5.749871	0.96890	.	.	ENSG00000168785	ENST00000305798;ENST00000505184;ENST00000515287	.	.	.	5.13	4.28	0.50868	.	0.056384	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	12.7732	0.57434	0.0:0.0:0.7018:0.2982	.	.	.	.	X	179;108;108	.	ENSP00000307701:R179X	R	-	1	2	TSPAN5	99618900	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.884000	0.63135	1.127000	0.42034	0.555000	0.69702	CGA		0.478	TSPAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253641.2	NM_005723	
ARSJ	79642	broad.mit.edu	37	4	114823494	114823494	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:114823494delT	ENST00000315366.7	-	2	2602	c.1736delA	c.(1735-1737)aagfs	p.K582fs	ARSJ_ENST00000541197.1_Frame_Shift_Del_p.K582fs	NM_024590.3	NP_078866.3	Q5FYB0	ARSJ_HUMAN	arylsulfatase family, member J	582					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.K579fs*>21(1)		endometrium(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	21		Ovarian(17;0.0035)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00194)		tttcttcttcttttttttgct	0.388																																					p.K579fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1736delA	4						.						66.0	60.0	61.0					4																	114823494		1854	4092	5946	115042943	SO:0001589	frameshift_variant	79642	exon2				CCDS43264.1	4q26	2013-02-14	2006-03-07		ENSG00000180801	ENSG00000180801		"""Arylsulfatase family"""	26286	protein-coding gene	gene with protein product		610010	"""arylsulfatase J"""			12975309, 16174644	Standard	NM_024590		Approved	FLJ23548	uc003ibq.1	Q5FYB0	OTTHUMG00000161067	ENST00000315366.7:c.1736delA	4.37:g.114823494delT	ENSP00000320219:p.Lys582fs	Somatic		Capture	Illumina HiSeq	Phase_I	115042943	NM_024590	A2RUG0|B7ZM45|Q1HA39|Q5FWE4|Q6UWT9	Frame_Shift_Del	DEL	ENST00000315366.7	37	CCDS43264.1																																																																																				0.388	ARSJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363650.1	NM_024590	
FAT4	79633	broad.mit.edu	37	4	126238447	126238447	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	-	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:126238447delC	ENST00000394329.3	+	1	894	c.881delC	c.(880-882)accfs	p.T294fs		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	294	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F296fs*45(2)		NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						GACGAGGGGACCCCCTTCCAA	0.667											OREG0016317	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T294fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.881delC	4						.						20.0	26.0	24.0					4																	126238447		1995	4148	6143	126457897	SO:0001589	frameshift_variant	79633	exon1			AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.881delC	4.37:g.126238447delC	ENSP00000377862:p.Thr294fs	Somatic	1548	Capture	Illumina HiSeq	Phase_I	126457897	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Frame_Shift_Del	DEL	ENST00000394329.3	37	CCDS3732.3																																																																																				0.667	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
DCLK2	166614	broad.mit.edu	37	4	151177332	151177332	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:151177332delC	ENST00000296550.7	+	16	2988	c.2234delC	c.(2233-2235)accfs	p.T745fs	DCLK2_ENST00000506325.1_Frame_Shift_Del_p.T744fs|DCLK2_ENST00000302176.8_Frame_Shift_Del_p.T762fs	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	745	Pro-rich.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.H747fs*>20(1)|p.H764fs*>20(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					GAATCTCCCACCCCCCACCCT	0.706																																					p.T745fs	GBM(195;186 2215 13375 16801 37459)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2234delC	4						.						4.0	5.0	5.0					4																	151177332		2077	4122	6199	151396782	SO:0001589	frameshift_variant	166614	exon16			BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"""doublecortin and CaM kinase-like 2"""	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.2234delC	4.37:g.151177332delC	ENSP00000296550:p.Thr745fs	Somatic		Capture	Illumina HiSeq	Phase_I	151396782	NM_001040260	C9J5Q9|Q59GC8|Q8N399	Frame_Shift_Del	DEL	ENST00000296550.7	37	CCDS34076.1																																																																																				0.706	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260	
DCHS2	54798	broad.mit.edu	37	4	155219319	155219319	+	Frame_Shift_Del	DEL	G	G	-	rs140771226		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:155219319delG	ENST00000357232.4	-	18	4781	c.4782delC	c.(4780-4782)cccfs	p.P1594fs		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1594	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.E1595fs*11(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TAGGCGACTCGGGGGAAAGAA	0.433																																					p.P1594fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4782delC	4						.						90.0	91.0	91.0					4																	155219319		2203	4300	6503	155438769	SO:0001589	frameshift_variant	54798	exon18			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4782delC	4.37:g.155219319delG	ENSP00000349768:p.Pro1594fs	Somatic		Capture	Illumina HiSeq	Phase_I	155438769	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Frame_Shift_Del	DEL	ENST00000357232.4	37	CCDS3785.1																																																																																				0.433	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
FAT1	2195	broad.mit.edu	37	4	187538941	187538941	+	Frame_Shift_Del	DEL	T	T	-	rs113224498		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:187538941delT	ENST00000441802.2	-	10	9008	c.8799delA	c.(8797-8799)caafs	p.Q2933fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2933	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G2934fs*3(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TCACCCCACCTTGGGGGTCAT	0.448										HNSCC(5;0.00058)																											p.Q2933fs	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.8799delA	4						.			2047,1659		852,343,658	114.0	112.0	113.0			4.0	0.0	4	dbSNP_132	115	3089,4803		1093,903,1950	no	frameshift	FAT1	NM_005245.3		1945,1246,2608	A1A1,A1R,RR		39.1409,44.7652,44.2835			187538941	5136,6462	1924	4121	6045	187775935	SO:0001589	frameshift_variant	2195	exon10			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8799delA	4.37:g.187538941delT	ENSP00000406229:p.Gln2933fs	Somatic		Capture	Illumina HiSeq	Phase_I	187775935	NM_005245		Frame_Shift_Del	DEL	ENST00000441802.2	37	CCDS47177.1																																																																																				0.448	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
FAT1	2195	broad.mit.edu	37	4	187630712	187630712	+	Silent	SNP	G	G	A	rs373265178		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr4:187630712G>A	ENST00000441802.2	-	2	479	c.270C>T	c.(268-270)ctC>ctT	p.L90L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	90	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L90L(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AAAAGTCTCCGAGAATGTACT	0.393										HNSCC(5;0.00058)																											p.L90L	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C270T	4						.	G		1,3767		0,1,1883	90.0	83.0	85.0		270	-4.1	0.7	4		85	0,8226		0,0,4113	no	coding-synonymous	FAT1	NM_005245.3		0,1,5996	AA,AG,GG		0.0,0.0265,0.0083		90/4589	187630712	1,11993	1884	4113	5997	187867706	SO:0001819	synonymous_variant	2195	exon2			X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.270C>T	4.37:g.187630712G>A		Somatic		Capture	Illumina HiSeq	Phase_I	187867706	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																				0.393	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ITK	3702	broad.mit.edu	37	5	156671433	156671434	+	Frame_Shift_Ins	INS	-	-	TG			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	TG	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:156671433_156671434insTG	ENST00000422843.3	+	13	1546_1547	c.1394_1395insTG	c.(1393-1398)gatgtgfs	p.DV465fs	ITK_ENST00000519749.1_3'UTR	NM_005546.3	NP_005537.3	Q08881	ITK_HUMAN	IL2-inducible T-cell kinase	465	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cellular defense response (GO:0006968)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|intracellular signal transduction (GO:0035556)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|signal transduction (GO:0007165)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.E468fs*37(1)		breast(4)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(25)|ovary(8)|prostate(2)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	70	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.1)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)		Pazopanib(DB06589)	ATGTGTCTGGATGTGTGTGAGG	0.559			T	SYK	peripheral T-cell lymphoma																																p.D465fs	Esophageal Squamous(70;1378 1469 8785 19883)		Dom	yes		5	5q31-q32	3702	IL2-inducible T-cell kinase		L	.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1394_1395insTG	5						.																																			156604012	SO:0001589	frameshift_variant	3702	exon13			D13720	CCDS4336.1	5q31-q32	2014-09-17			ENSG00000113263	ENSG00000113263		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	6171	protein-coding gene	gene with protein product		186973				8364206	Standard	NM_005546		Approved	EMT, PSCTK2, LYK	uc003lwo.1	Q08881	OTTHUMG00000130245	ENST00000422843.3:c.1401_1402dupTG	5.37:g.156671440_156671441dupTG	ENSP00000398655:p.Asp465fs	Somatic		Capture	Illumina HiSeq	Phase_I	156604011	NM_005546	B2R752|Q32ML7	Frame_Shift_Ins	INS	ENST00000422843.3	37	CCDS4336.1																																																																																				0.559	ITK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252569.2		
DROSHA	29102	broad.mit.edu	37	5	31493321	31493322	+	Frame_Shift_Ins	INS	-	-	G	rs61354118	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:31493321_31493322insG	ENST00000511367.2	-	12	2078_2079	c.1834_1835insC	c.(1834-1836)ctgfs	p.L612fs	DROSHA_ENST00000344624.3_Frame_Shift_Ins_p.L612fs|DROSHA_ENST00000513349.1_Frame_Shift_Ins_p.L575fs|DROSHA_ENST00000442743.1_Frame_Shift_Ins_p.L575fs	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	612	Necessary for interaction with DGCR8 and pri-miRNA processing activity.			L -> P (in Ref. 4; CAB45133). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.L612fs*8(1)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						TACATTGGTCAGGGGGGCATGT	0.421																																					p.L612fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1835_1836insC	5						.																																			31529079	SO:0001589	frameshift_variant	29102	exon12			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.1835dupC	5.37:g.31493327_31493327dupG	ENSP00000425979:p.Leu612fs	Somatic		Capture	Illumina HiSeq	Phase_I	31529078	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Frame_Shift_Ins	INS	ENST00000511367.2	37	CCDS47195.1																																																																																				0.421	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
RAD1	5810	broad.mit.edu	37	5	34913593	34913594	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:34913593_34913594insA	ENST00000382038.2	-	3	1707_1708	c.288_289insT	c.(286-291)tttggafs	p.G97fs	RAD1_ENST00000341754.4_Frame_Shift_Ins_p.G97fs|BRIX1_ENST00000336767.5_5'Flank	NM_002853.3	NP_002844.1	O60671	RAD1_HUMAN	RAD1 checkpoint DNA exonuclease	97					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|meiotic recombination checkpoint (GO:0051598)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|substantia nigra development (GO:0021762)	chromosome (GO:0005694)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|damaged DNA binding (GO:0003684)|exodeoxyribonuclease III activity (GO:0008853)	p.G97fs*44(1)		endometrium(3)|large_intestine(1)|lung(5)|urinary_tract(1)	10	all_lung(31;0.000107)	Lung NSC(810;5.19e-05)|Ovarian(839;0.0448)|Breast(839;0.198)	COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			GGACTTGATCCAAAAATAGATA	0.312								Other conserved DNA damage response genes																													p.G97fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.289_290insT	5						.																																			34949351	SO:0001589	frameshift_variant	5810	exon3			AF074717	CCDS3905.1	5p13	2014-08-08	2014-08-08		ENSG00000113456	ENSG00000113456	3.1.11.2		9806	protein-coding gene	gene with protein product	"""exonuclease homolog RAD1"", ""checkpoint control protein HRAD1"", ""cell cycle checkpoint protein Hrad1"", ""Rad1-like DNA damage checkpoint"", ""DNA repair exonuclease REC1"""	603153	"""RAD1 (S. pombe) homolog"", ""RAD1 homolog (S. pombe)"""			9716408, 9828137	Standard	NR_026591		Approved	HRAD1, REC1	uc003jix.3	O60671	OTTHUMG00000090783	ENST00000382038.2:c.289dupT	5.37:g.34913598_34913598dupA	ENSP00000371469:p.Gly97fs	Somatic		Capture	Illumina HiSeq	Phase_I	34949350	NM_002853	O75572|O95304|Q1W161|Q5KSM0|Q5KSM1|Q9UEP1	Frame_Shift_Ins	INS	ENST00000382038.2	37	CCDS3905.1																																																																																				0.312	RAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207567.1	NM_002853	
SLCO4C1	353189	broad.mit.edu	37	5	101631703	101631703	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:101631703G>A	ENST00000310954.6	-	1	550	c.264C>T	c.(262-264)taC>taT	p.Y88Y		NM_180991.4	NP_851322.3			solute carrier organic anion transporter family, member 4C1											breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	50		all_cancers(142;1.86e-08)|all_epithelial(76;5.24e-12)|Prostate(80;0.00124)|Colorectal(57;0.00332)|Ovarian(225;0.024)|Lung NSC(167;0.0402)|all_lung(232;0.0486)		Epithelial(69;4.07e-14)|COAD - Colon adenocarcinoma(37;0.00986)		TCCTCCAGCCGTAAGACCCCT	0.572																																					p.Y88Y												.	.	0			c.C264T	5						.						82.0	83.0	83.0					5																	101631703		2203	4300	6503	101659602	SO:0001819	synonymous_variant	353189	exon1			AY273896	CCDS34205.1	5q21	2013-05-22	2003-11-25		ENSG00000173930	ENSG00000173930		"""Solute carriers"""	23612	protein-coding gene	gene with protein product		609013					Standard	NM_180991		Approved	SLC21A20, OATP4C1, OATPX, OATP-H	uc003knm.3	Q6ZQN7	OTTHUMG00000162757	ENST00000310954.6:c.264C>T	5.37:g.101631703G>A		None		Capture	Illumina HiSeq	Phase_I	101659602	NM_180991		Silent	SNP	ENST00000310954.6	37	CCDS34205.1																																																																																				0.572	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991	
CTNND2	1501	broad.mit.edu	37	5	11022928	11022928	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:11022928G>A	ENST00000304623.8	-	17	3141	c.2952C>T	c.(2950-2952)gcC>gcT	p.A984A	CTNND2_ENST00000503622.1_Silent_p.A647A|CTNND2_ENST00000511377.1_Silent_p.A893A|CTNND2_ENST00000458100.2_Silent_p.A551A|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000359640.2_Silent_p.A926A	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	984					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.A984A(2)		NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						CGATGCCACCGGCATCCCGTA	0.502																																					p.A984A												.	.	2	Substitution - coding silent(2)	upper_aerodigestive_tract(1)|large_intestine(1)	c.C2952T	5						.						188.0	148.0	162.0					5																	11022928		2203	4300	6503	11075928	SO:0001819	synonymous_variant	1501	exon17			U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.2952C>T	5.37:g.11022928G>A		Somatic		Capture	Illumina HiSeq	Phase_I	11075928	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Silent	SNP	ENST00000304623.8	37	CCDS3881.1																																																																																				0.502	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
FER	2241	broad.mit.edu	37	5	108207188	108207188	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:108207188T>C	ENST00000281092.4	+	7	1172	c.788T>C	c.(787-789)tTc>tCc	p.F263S	FER_ENST00000438717.2_Missense_Mutation_p.F88S|FER_ENST00000536402.1_Missense_Mutation_p.F263S	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	263	Important for interaction with membranes containing phosphoinositides.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.F263S(1)		NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		TACAATAATTTCATAGATGTT	0.313																																					p.F263S	Colon(146;1051 1799 9836 27344 47401)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T788C	5						.						99.0	104.0	102.0					5																	108207188		2201	4298	6499	108235087	SO:0001583	missense	2241	exon7			J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.788T>C	5.37:g.108207188T>C	ENSP00000281092:p.Phe263Ser	Somatic		Capture	Illumina HiSeq	Phase_I	108235087	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	T	19.78	3.891492	0.72524	.	.	ENSG00000151422	ENST00000281092;ENST00000536402;ENST00000438717	T;T;T	0.66460	-0.21;-0.21;-0.21	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	T	0.70369	0.3216	M	0.78637	2.42	0.80722	D	1	P	0.48764	0.915	B	0.41764	0.366	T	0.76721	-0.2855	10	0.87932	D	0	-13.6229	16.5285	0.84344	0.0:0.0:0.0:1.0	.	263	P16591	FER_HUMAN	S	263;263;88	ENSP00000281092:F263S;ENSP00000442627:F263S;ENSP00000394297:F88S	ENSP00000281092:F263S	F	+	2	0	FER	108235087	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.601000	0.67606	2.307000	0.77673	0.528000	0.53228	TTC		0.313	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
CAMK4	814	broad.mit.edu	37	5	110784900	110784900	+	Splice_Site	SNP	C	C	T	rs199946284		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:110784900C>T	ENST00000282356.4	+	7	1022	c.624C>T	c.(622-624)tgC>tgT	p.C208C	CAMK4_ENST00000512453.1_Splice_Site_p.C208C	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)	p.C208C(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		CAGGGTACTGCGGTATGCTCT	0.274																																					p.C208C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C624T	5						.	C		0,4404		0,0,2202	59.0	61.0	61.0		624	1.0	1.0	5		61	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	CAMK4	NM_001744.4		0,3,6499	TT,TC,CC		0.0349,0.0,0.0231		208/474	110784900	3,13001	2202	4300	6502	110812799	SO:0001630	splice_region_variant	814	exon7			D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.625+1C>T	5.37:g.110784900C>T		Somatic		Capture	Illumina HiSeq	Phase_I	110812799	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	37	CCDS4103.1																																																																																				0.274	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744	Silent
TSSK1B	83942	broad.mit.edu	37	5	112770140	112770140	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:112770140C>T	ENST00000390666.3	-	1	588	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	CTD-2201G3.1_ENST00000510381.2_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000383058.4_RNA|CTD-2201G3.1_ENST00000416046.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	133	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.V133I(2)		large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		TCCCGGTGGACGACGTCCAGG	0.557																																					p.V133I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G397A	5						.						86.0	82.0	84.0					5																	112770140		2202	4300	6502	112798039	SO:0001583	missense	83942	exon1			AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.397G>A	5.37:g.112770140C>T	ENSP00000375081:p.Val133Ile	Somatic		Capture	Illumina HiSeq	Phase_I	112798039	NM_032028	B2R8D9	Missense_Mutation	SNP	ENST00000390666.3	37	CCDS4112.1	.	.	.	.	.	.	.	.	.	.	C	8.919	0.960571	0.18583	.	.	ENSG00000212122	ENST00000390666	T	0.22336	1.96	1.24	0.218	0.15270	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	0.31301	U	0.007881	T	0.18635	0.0447	N	0.16743	0.435	0.21325	N	0.999729	D	0.60160	0.987	P	0.58820	0.846	T	0.10941	-1.0608	10	0.54805	T	0.06	.	4.3273	0.11046	0.0:0.5479:0.0:0.4521	.	133	Q9BXA7	TSSK1_HUMAN	I	133	ENSP00000375081:V133I	ENSP00000375081:V133I	V	-	1	0	TSSK1B	112798039	0.555000	0.26530	0.902000	0.35471	0.143000	0.21401	0.822000	0.27352	-0.335000	0.08451	-0.657000	0.03884	GTC		0.557	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
YTHDC2	64848	broad.mit.edu	37	5	112901648	112901648	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:112901648T>G	ENST00000161863.4	+	21	2987	c.2774T>G	c.(2773-2775)cTt>cGt	p.L925R		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	925					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.L925R(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AAGAATTTTCTTTCACAGGCT	0.383																																					p.L925R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T2774G	5						.						90.0	93.0	92.0					5																	112901648		2202	4300	6502	112929547	SO:0001583	missense	64848	exon21			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2774T>G	5.37:g.112901648T>G	ENSP00000161863:p.Leu925Arg	Somatic		Capture	Illumina HiSeq	Phase_I	112929547	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	37	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.427303	0.83667	.	.	ENSG00000047188	ENST00000161863;ENST00000511372	T	0.07800	3.16	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.32615	0.0835	M	0.86178	2.8	0.80722	D	1	D	0.69078	0.997	D	0.70935	0.971	T	0.19679	-1.0298	10	0.87932	D	0	.	15.0991	0.72258	0.0:0.0:0.0:1.0	.	925	Q9H6S0	YTDC2_HUMAN	R	925;835	ENSP00000161863:L925R	ENSP00000161863:L925R	L	+	2	0	YTHDC2	112929547	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.819000	0.86621	1.968000	0.57251	0.460000	0.39030	CTT		0.383	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
SEMA6A	57556	broad.mit.edu	37	5	115782397	115782397	+	Missense_Mutation	SNP	C	C	T	rs200942463	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:115782397C>T	ENST00000343348.6	-	19	3792	c.3005G>A	c.(3004-3006)cGt>cAt	p.R1002H	SEMA6A_ENST00000257414.8_Missense_Mutation_p.R1019H|CTB-118N6.3_ENST00000512128.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.R1002H|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000503865.1_Missense_Mutation_p.R381H|CTB-118N6.3_ENST00000510682.1_RNA|SEMA6A_ENST00000282394.6_Missense_Mutation_p.R479H|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000513137.1_Missense_Mutation_p.R429H	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	1002					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.R1002H(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		CGAGGGCGTACGCTTCAGCCC	0.597																																					p.R1002H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3005A	5						.						29.0	32.0	31.0					5																	115782397		2109	4232	6341	115810296	SO:0001583	missense	57556	exon19			AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.3005G>A	5.37:g.115782397C>T	ENSP00000345512:p.Arg1002His	Somatic		Capture	Illumina HiSeq	Phase_I	115810296	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	37	CCDS47256.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.29|18.29	3.590547|3.590547	0.66219|0.66219	.|.	.|.	ENSG00000092421|ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263|ENST00000515129	T;T;T;T;T;T|.	0.60040|.	1.71;1.71;0.22;2.14;0.27;1.71|.	4.36|4.36	4.36|4.36	0.52297|0.52297	.|.	1.000120|.	0.08080|.	N|.	1.000000|.	T|T	0.66925|0.66925	0.2839|0.2839	L|L	0.47190|0.47190	1.495|1.495	0.51482|0.51482	D|D	0.999923|0.999923	D;D;D;D;D;D|.	0.89917|.	0.998;0.994;0.999;0.991;1.0;0.998|.	D;P;P;P;D;D|.	0.78314|.	0.991;0.656;0.862;0.747;0.991;0.991|.	T|T	0.65142|0.65142	-0.6240|-0.6240	10|5	0.87932|.	D|.	0|.	.|.	16.6789|16.6789	0.85286|0.85286	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	381;1002;546;1019;479;429|.	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01|.	.;SEM6A_HUMAN;.;.;.;.|.	H|I	1002;1019;429;479;381;1002|517	ENSP00000345512:R1002H;ENSP00000257414:R1019H;ENSP00000422997:R429H;ENSP00000282394:R479H;ENSP00000425364:R381H;ENSP00000424388:R1002H|.	ENSP00000257414:R1019H|.	R|V	-|-	2|1	0|0	SEMA6A|SEMA6A	115810296|115810296	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.915000|0.915000	0.54546|0.54546	5.494000|5.494000	0.66905|0.66905	2.254000|2.254000	0.74563|0.74563	0.462000|0.462000	0.41574|0.41574	CGT|GTA		0.597	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
MEGF10	84466	broad.mit.edu	37	5	126776451	126776451	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:126776451G>T	ENST00000274473.6	+	19	2521	c.2254G>T	c.(2254-2256)Gga>Tga	p.G752*	MEGF10_ENST00000503335.2_Nonsense_Mutation_p.G752*	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	752	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)		p.G752*(1)		breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGGGTTTTATGGAAAAGATTG	0.512																																					p.G752X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G2254T	5						.						143.0	134.0	137.0					5																	126776451		2203	4300	6503	126804350	SO:0001587	stop_gained	84466	exon19			AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.2254G>T	5.37:g.126776451G>T	ENSP00000274473:p.Gly752*	Somatic		Capture	Illumina HiSeq	Phase_I	126804350	NM_032446	Q68DE5|Q8WUL3	Nonsense_Mutation	SNP	ENST00000274473.6	37	CCDS4142.1	.	.	.	.	.	.	.	.	.	.	G	41	8.615588	0.98886	.	.	ENSG00000145794	ENST00000503335;ENST00000274473	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-17.3397	20.5948	0.99439	0.0:0.0:1.0:0.0	.	.	.	.	X	752	.	ENSP00000274473:G752X	G	+	1	0	MEGF10	126804350	1.000000	0.71417	1.000000	0.80357	0.761000	0.43186	9.869000	0.99810	2.873000	0.98535	0.563000	0.77884	GGA		0.512	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
FBN2	2201	broad.mit.edu	37	5	127873218	127873218	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:127873218C>T	ENST00000508053.1	-	7	1053	c.79G>A	c.(79-81)Gcc>Acc	p.A27T	FBN2_ENST00000262464.4_Missense_Mutation_p.A27T|FBN2_ENST00000508989.1_Missense_Mutation_p.A27T			P35556	FBN2_HUMAN	fibrillin 2	27					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.A27T(1)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGCTGGCCGGCCGTGCCCTGC	0.711																																					p.A27T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G79A	5						.						13.0	14.0	14.0					5																	127873218		2149	4230	6379	127901117	SO:0001583	missense	2201	exon1			U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.79G>A	5.37:g.127873218C>T	ENSP00000424571:p.Ala27Thr	Somatic		Capture	Illumina HiSeq	Phase_I	127901117	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086654	0.55861	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989;ENST00000502468	D;D;D;T	0.87334	-1.9;-1.9;-2.24;-0.74	4.77	2.94	0.34122	.	0.387849	0.21368	N	0.075694	T	0.70325	0.3211	N	0.08118	0	0.09310	N	1	B;B;B;B	0.19583	0.001;0.001;0.008;0.037	B;B;B;B	0.16289	0.002;0.002;0.009;0.015	T	0.56805	-0.7918	10	0.23891	T	0.37	.	7.5229	0.27639	0.1656:0.7479:0.0:0.0865	.	27;27;27;27	P35556-2;E9PHW4;D6RJI3;P35556	.;.;.;FBN2_HUMAN	T	27	ENSP00000262464:A27T;ENSP00000424571:A27T;ENSP00000425596:A27T;ENSP00000424753:A27T	ENSP00000262464:A27T	A	-	1	0	FBN2	127901117	0.398000	0.25279	0.017000	0.16124	0.997000	0.91878	2.160000	0.42348	1.114000	0.41781	0.591000	0.81541	GCC		0.711	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
SLC6A18	348932	broad.mit.edu	37	5	1240677	1240677	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:1240677G>A	ENST00000324642.3	+	7	1000	c.877G>A	c.(877-879)Gcc>Acc	p.A293T	SLC6A18_ENST00000296821.4_Missense_Mutation_p.A288T	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	293					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)			endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			GGTGGTCATCGCCCTGGTCAA	0.572																																					p.A293T												.	.	0			c.G877A	5						.						212.0	153.0	173.0					5																	1240677		2203	4300	6503	1293677	SO:0001583	missense	348932	exon7			AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.877G>A	5.37:g.1240677G>A	ENSP00000323549:p.Ala293Thr	None		Capture	Illumina HiSeq	Phase_I	1293677	NM_182632		Missense_Mutation	SNP	ENST00000324642.3	37	CCDS3860.1	.	.	.	.	.	.	.	.	.	.	G	16.44	3.123985	0.56613	.	.	ENSG00000164363	ENST00000324642;ENST00000296821	T;T	0.74421	-0.84;-0.84	4.51	1.59	0.23543	.	0.327125	0.28515	N	0.015080	T	0.62514	0.2434	L	0.42245	1.32	0.21290	N	0.999735	P	0.49358	0.923	B	0.43658	0.426	T	0.55573	-0.8120	10	0.46703	T	0.11	.	4.2915	0.10881	0.1741:0.0:0.5098:0.3162	.	293	Q96N87	S6A18_HUMAN	T	293;288	ENSP00000323549:A293T;ENSP00000296821:A288T	ENSP00000296821:A288T	A	+	1	0	SLC6A18	1293677	1.000000	0.71417	0.946000	0.38457	0.897000	0.52465	3.818000	0.55678	0.310000	0.22990	0.655000	0.94253	GCC		0.572	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
SLC27A6	28965	broad.mit.edu	37	5	128320999	128320999	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:128320999T>C	ENST00000262462.4	+	2	1665	c.655T>C	c.(655-657)Tgt>Cgt	p.C219R	SLC27A6_ENST00000506176.1_Missense_Mutation_p.C219R|SLC27A6_ENST00000395266.1_Missense_Mutation_p.C219R			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	219					long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty acid transport (GO:0015909)|transmembrane transport (GO:0055085)|very long-chain fatty acid metabolic process (GO:0000038)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	long-chain fatty acid-CoA ligase activity (GO:0004467)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)	p.C219R(1)		NS(2)|endometrium(1)|kidney(3)|large_intestine(11)|liver(1)|lung(20)|prostate(1)|skin(4)|stomach(1)	44		all_cancers(142;0.0483)|Prostate(80;0.055)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Epithelial(69;0.171)|OV - Ovarian serous cystadenocarcinoma(64;0.186)		CAAGTCTACTTGTCTTTACAT	0.423																																					p.C219R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T655C	5						.						115.0	96.0	103.0					5																	128320999		2203	4300	6503	128348898	SO:0001583	missense	28965	exon2			AF064254	CCDS4145.1	5q23.3	2013-05-22			ENSG00000113396	ENSG00000113396		"""Acyl-CoA synthetase family"", ""Solute carriers"""	11000	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 2"""	604196				12556534, 10479480	Standard	XM_005271967		Approved	FATP6, VLCS-H1, FACVL2, ACSVL2	uc003kuy.3	Q9Y2P4	OTTHUMG00000128991	ENST00000262462.4:c.655T>C	5.37:g.128320999T>C	ENSP00000262462:p.Cys219Arg	Somatic		Capture	Illumina HiSeq	Phase_I	128348898	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	T	4.297	0.054285	0.08291	.	.	ENSG00000113396	ENST00000508645;ENST00000262462;ENST00000395266;ENST00000506176	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.47	0.43	0.16515	AMP-dependent synthetase/ligase (1);	0.793468	0.12382	N	0.473797	T	0.29783	0.0744	L	0.38733	1.17	0.09310	N	0.999999	B	0.27951	0.195	B	0.36335	0.222	T	0.31052	-0.9957	9	.	.	.	-8.7702	2.0268	0.03520	0.1281:0.3544:0.1479:0.3696	.	219	Q9Y2P4	S27A6_HUMAN	R	38;219;219;219	ENSP00000421759:C38R;ENSP00000262462:C219R;ENSP00000378684:C219R;ENSP00000421024:C219R	.	C	+	1	0	SLC27A6	128348898	0.000000	0.05858	0.000000	0.03702	0.403000	0.30841	-0.174000	0.09839	0.076000	0.16826	0.533000	0.62120	TGT		0.423	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031	
ACSL6	23305	broad.mit.edu	37	5	131326645	131326645	+	Missense_Mutation	SNP	G	G	A	rs151127186	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:131326645G>A	ENST00000379240.1	-	3	364	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	ACSL6_ENST00000431707.1_Missense_Mutation_p.R36W|ACSL6_ENST00000379246.1_Missense_Mutation_p.R82W|ACSL6_ENST00000379272.2_Missense_Mutation_p.R71W|ACSL6_ENST00000477640.1_5'Flank|ACSL6_ENST00000379255.1_Missense_Mutation_p.R36W|ACSL6_ENST00000357096.1_Missense_Mutation_p.R36W|ACSL6_ENST00000543479.1_Missense_Mutation_p.R71W|ACSL6_ENST00000296869.4_Missense_Mutation_p.R96W|ACSL6_ENST00000379249.3_Missense_Mutation_p.R71W|ACSL6_ENST00000544770.1_De_novo_Start_OutOfFrame|ACSL6_ENST00000379264.2_Missense_Mutation_p.R96W|ACSL6_ENST00000379244.1_Missense_Mutation_p.R71W			Q9UKU0	ACSL6_HUMAN	acyl-CoA synthetase long-chain family member 6	71					acyl-CoA metabolic process (GO:0006637)|cellular lipid metabolic process (GO:0044255)|cellular response to insulin stimulus (GO:0032869)|fatty acid transport (GO:0015908)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|phospholipid biosynthetic process (GO:0008654)|positive regulation of neuron projection development (GO:0010976)|positive regulation of plasma membrane long-chain fatty acid transport (GO:0010747)|positive regulation of triglyceride biosynthetic process (GO:0010867)|response to gravity (GO:0009629)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein homodimerization activity (GO:0042803)	p.R96W(2)		NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	35		all_cancers(142;0.107)|Breast(839;0.198)|Lung NSC(810;0.216)|all_lung(232;0.248)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			ACAGATCGCCGTGCCCCGCCA	0.612													g|||	4	0.000798722	0.0023	0.0014	5008	,	,		15329	0.0		0.0	False		,,,				2504	0.0				p.R96W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C286T	5						.		TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	70.0	57.0	62.0		286,181,211,244,106,286	2.8	1.0	5	dbSNP_134	62	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	ACSL6	NM_001009185.2,NM_001205247.1,NM_001205248.1,NM_001205250.1,NM_001205251.1,NM_015256.3	101,101,101,101,101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	96/723,61/688,71/698,82/709,36/623,96/723	131326645	1,13005	2203	4300	6503	131354544	SO:0001583	missense	23305	exon3			AB020644	CCDS34228.1, CCDS34229.1, CCDS56381.1, CCDS56382.1, CCDS56383.1	5q31	2008-02-05	2004-02-19	2004-02-20	ENSG00000164398	ENSG00000164398		"""Acyl-CoA synthetase family"""	16496	protein-coding gene	gene with protein product		604443	"""fatty-acid-Coenzyme A ligase, long-chain 6"""	FACL6		10502316, 10548543	Standard	NM_015256		Approved	KIAA0837, ACS2, LACS5, LACS2	uc003kvy.2	Q9UKU0	OTTHUMG00000150692	ENST00000379240.1:c.211C>T	5.37:g.131326645G>A	ENSP00000368542:p.Arg71Trp	Somatic		Capture	Illumina HiSeq	Phase_I	131354544	NM_001009185	J3KPG3|O94924|O95829|Q108M9|Q108N0|Q4G191|Q86TN7	Missense_Mutation	SNP	ENST00000379240.1	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	g	16.95	3.263690	0.59431	2.27E-4	0.0	ENSG00000164398	ENST00000379249;ENST00000379264;ENST00000379272;ENST00000357096;ENST00000379255;ENST00000296869;ENST00000379246;ENST00000379244;ENST00000379240;ENST00000431707;ENST00000543479;ENST00000434099;ENST00000430403;ENST00000419502;ENST00000416557;ENST00000414078;ENST00000441995	T;T;T;T;T;T;T;T;T;T;T;T;T	0.54071	1.74;2.48;2.35;3.27;3.27;2.49;2.49;2.5;2.5;2.5;2.5;0.61;0.59	5.7	2.78	0.32641	.	0.000000	0.85682	D	0.000000	T	0.71400	0.3335	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.996;1.0;1.0;1.0;0.996;0.996	D;P;D;D;D;P;P	0.97110	1.0;0.885;0.998;1.0;1.0;0.849;0.885	T	0.74671	-0.3587	10	0.52906	T	0.07	.	14.6264	0.68624	0.0:0.0:0.6202:0.3798	.	71;71;61;71;36;96;96	Q9UKU0-3;Q9UKU0-6;B4DFW3;Q9UKU0;Q9UKU0-7;Q9UKU0-1;Q9UKU0-8	.;.;.;ACSL6_HUMAN;.;.;.	W	71;96;71;36;36;96;82;71;71;36;71;36;71;71;71;71;36	ENSP00000368551:R71W;ENSP00000368566:R96W;ENSP00000368574:R71W;ENSP00000349608:R36W;ENSP00000368557:R36W;ENSP00000296869:R96W;ENSP00000368548:R82W;ENSP00000368546:R71W;ENSP00000368542:R71W;ENSP00000413329:R36W;ENSP00000442124:R71W;ENSP00000397507:R36W;ENSP00000398423:R71W	ENSP00000296869:R96W	R	-	1	2	ACSL6	131354544	1.000000	0.71417	0.999000	0.59377	0.418000	0.31294	4.316000	0.59178	0.760000	0.33108	-0.463000	0.05309	CGG		0.612	ACSL6-004	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000132622.1	NM_015256	
JADE2	23338	broad.mit.edu	37	5	133895621	133895621	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:133895621A>G	ENST00000402835.1	+	5	668	c.413A>G	c.(412-414)gAc>gGc	p.D138G	PHF15_ENST00000361895.2_Missense_Mutation_p.D138G|PHF15_ENST00000395003.1_Missense_Mutation_p.D138G|PHF15_ENST00000282605.4_Missense_Mutation_p.D138G														p.D138G(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCCGCTATGACTTGGACGAG	0.602																																					p.D138G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A413G	5						.						67.0	59.0	62.0					5																	133895621		2203	4300	6503	133923520	SO:0001583	missense	23338	exon5																														ENST00000402835.1:c.413A>G	5.37:g.133895621A>G	ENSP00000384671:p.Asp138Gly	Somatic		Capture	Illumina HiSeq	Phase_I	133923520	NM_015288		Missense_Mutation	SNP	ENST00000402835.1	37		.	.	.	.	.	.	.	.	.	.	A	32	5.119083	0.94385	.	.	ENSG00000043143	ENST00000512386;ENST00000413974;ENST00000448712;ENST00000282605;ENST00000361895;ENST00000432594;ENST00000402835;ENST00000395003;ENST00000431355	T;T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0;0.0	5.67	5.67	0.87782	Enhancer of polycomb-like, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.82222	0.4990	M	0.88775	2.98	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.999;0.996;0.999	D	0.85850	0.1403	10	0.87932	D	0	.	15.0855	0.72148	1.0:0.0:0.0:0.0	.	138;138;138;138;154	Q9NQC1;B5MBX1;D3DQA3;Q9NQC1-3;B3KPL2	JADE2_HUMAN;.;.;.;.	G	138;138;154;138;138;138;138;138;138	ENSP00000422991:D138G;ENSP00000282605:D138G;ENSP00000354425:D138G;ENSP00000384671:D138G;ENSP00000378451:D138G;ENSP00000406189:D138G	ENSP00000282605:D138G	D	+	2	0	PHF15	133923520	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.962000	0.93254	2.169000	0.68431	0.459000	0.35465	GAC		0.602	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1		
LECT2	3950	broad.mit.edu	37	5	135276335	135276335	+	5'UTR	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:135276335A>G	ENST00000471827.1	-	0	426				LECT2_ENST00000522943.1_Intron|FBXL21_ENST00000297158.9_RNA|FBXL21_ENST00000467490.1_RNA			O14960	LECT2_HUMAN	leukocyte cell-derived chemotaxin 2						chemotaxis (GO:0006935)|negative regulation of Wnt signaling pathway (GO:0030178)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	identical protein binding (GO:0042802)	p.H216R(1)|p.H58R(1)		large_intestine(1)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGCTGTCCTCATGTTTCATCT	0.308																																					p.H216R												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A647G	5						.						106.0	101.0	103.0					5																	135276335		1850	4097	5947	135304234	SO:0001623	5_prime_UTR_variant	26223	exon7			AB007546	CCDS4190.1	5q31.1	2008-05-15			ENSG00000145826	ENSG00000145826			6550	protein-coding gene	gene with protein product		602882				9545637	Standard	NM_002302		Approved	chm-II, chm2	uc003lbe.1	O14960	OTTHUMG00000129146	ENST00000471827.1:c.-386T>C	5.37:g.135276335A>G		Somatic		Capture	Illumina HiSeq	Phase_I	135304234	NM_012159	B2RA90|O14565|Q52M49	Missense_Mutation	SNP	ENST00000471827.1	37																																																																																					0.308	LECT2-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000342497.1	NM_002302	
FAM13B	51306	broad.mit.edu	37	5	137346786	137346786	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:137346786T>G	ENST00000033079.3	-	6	1052	c.601A>C	c.(601-603)Atg>Ctg	p.M201L	FAM13B_ENST00000420893.2_Missense_Mutation_p.M201L|FAM13B_ENST00000425075.2_Missense_Mutation_p.M83L	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	201	Glu-rich.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.M201L(1)		endometrium(4)|kidney(2)|lung(5)	11						AGTCCAGCCATTATCCTGCTC	0.333																																					p.M201L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A601C	5						.						147.0	141.0	143.0					5																	137346786		2203	4300	6503	137374685	SO:0001583	missense	51306	exon6			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.601A>C	5.37:g.137346786T>G	ENSP00000033079:p.Met201Leu	Somatic		Capture	Illumina HiSeq	Phase_I	137374685	NM_016603	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	T	18.47	3.631023	0.67015	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.38240	1.15;2.17;1.15	5.59	5.59	0.84812	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.153392	0.64402	D	0.000019	T	0.47507	0.1449	L	0.41573	1.285	0.41127	D	0.985859	P;B;B	0.44090	0.826;0.034;0.07	P;B;B	0.57009	0.811;0.015;0.087	T	0.33727	-0.9857	10	0.35671	T	0.21	-10.0756	15.7689	0.78149	0.0:0.0:0.0:1.0	.	83;201;201	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	L	201;83;201	ENSP00000033079:M201L;ENSP00000394669:M83L;ENSP00000388521:M201L	ENSP00000033079:M201L	M	-	1	0	FAM13B	137374685	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.248000	0.65421	2.134000	0.65973	0.533000	0.62120	ATG		0.333	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1		
DNAH5	1767	broad.mit.edu	37	5	13719090	13719090	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:13719090C>A	ENST00000265104.4	-	72	12504	c.12400G>T	c.(12400-12402)Gct>Tct	p.A4134S		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4134	AAA 6. {ECO:0000250}.		A -> V (in dbSNP:rs30168). {ECO:0000269|PubMed:10997877}.		cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A4134S(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGCTTATGAGCCTCGGTGGTC	0.468									Kartagener syndrome																												p.A4134S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G12400T	5						.						147.0	144.0	145.0					5																	13719090		2203	4300	6503	13772090	SO:0001583	missense	1767	exon72	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.12400G>T	5.37:g.13719090C>A	ENSP00000265104:p.Ala4134Ser	Somatic		Capture	Illumina HiSeq	Phase_I	13772090	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	12.96	2.094177	0.36952	.	.	ENSG00000039139	ENST00000265104	T	0.08458	3.09	5.59	5.59	0.84812	Dynein heavy chain (1);	0.198108	0.41823	D	0.000814	T	0.06280	0.0162	N	0.11698	0.16	0.22796	N	0.998725	B	0.15930	0.015	B	0.24155	0.051	T	0.33266	-0.9875	10	0.42905	T	0.14	.	13.3078	0.60363	0.0:0.9185:0.0:0.0815	.	4134	Q8TE73	DYH5_HUMAN	S	4134	ENSP00000265104:A4134S	ENSP00000265104:A4134S	A	-	1	0	DNAH5	13772090	0.998000	0.40836	0.960000	0.40013	0.024000	0.10985	3.242000	0.51384	2.625000	0.88918	0.650000	0.86243	GCT		0.468	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
WNT8A	7478	broad.mit.edu	37	5	137424707	137424707	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:137424707G>A	ENST00000398754.1	+	5	464	c.459G>A	c.(457-459)ggG>ggA	p.G153G	WNT8A_ENST00000506684.1_Silent_p.G171G	NM_058244.2	NP_490645.1	Q9H1J5	WNT8A_HUMAN	wingless-type MMTV integration site family, member 8A	153					canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|canonical Wnt signaling pathway involved in neural crest cell differentiation (GO:0044335)|endoderm development (GO:0007492)|establishment of organ orientation (GO:0048561)|neural crest cell fate commitment (GO:0014034)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|polarity specification of anterior/posterior axis (GO:0009949)|polarity specification of proximal/distal axis (GO:0010085)|regulation of protein localization (GO:0032880)|regulation of transcription involved in anterior/posterior axis specification (GO:0044324)|response to retinoic acid (GO:0032526)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)	p.G153G(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			TGGAGAAGGGGAAGGATGCCA	0.522																																					p.G153G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G459A	5						.						125.0	140.0	135.0					5																	137424707		2203	4300	6503	137452606	SO:0001819	synonymous_variant	7478	exon5			AB057725	CCDS43368.1, CCDS75311.1	5q31	2008-07-18			ENSG00000061492	ENSG00000061492		"""Wingless-type MMTV integration sites"""	12788	protein-coding gene	gene with protein product		606360				11408932	Standard	XM_005272076		Approved	WNT8D	uc003lcd.1	Q9H1J5	OTTHUMG00000129196	ENST00000398754.1:c.459G>A	5.37:g.137424707G>A		Somatic		Capture	Illumina HiSeq	Phase_I	137452606	NM_058244	Q96S51	Silent	SNP	ENST00000398754.1	37	CCDS43368.1																																																																																				0.522	WNT8A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280395.1	NM_058244	
HSPA9	3313	broad.mit.edu	37	5	137891797	137891797	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:137891797A>G	ENST00000297185.3	-	17	2094	c.1969T>C	c.(1969-1971)Tct>Cct	p.S657P	SNORD63_ENST00000411005.1_RNA|HSPA9_ENST00000501917.2_Intron	NM_004134.6	NP_004125.3	P38646	GRP75_HUMAN	heat shock 70kDa protein 9 (mortalin)	657					cellular protein metabolic process (GO:0044267)|negative regulation of apoptotic process (GO:0043066)|protein export from nucleus (GO:0006611)|protein folding (GO:0006457)|protein targeting to mitochondrion (GO:0006626)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)	p.S657P(1)		breast(2)|endometrium(1)|kidney(4)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			TCTCGCTCAGATGCCATCTGT	0.423																																					p.S657P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1969C	5						.						109.0	101.0	104.0					5																	137891797		2203	4300	6503	137919696	SO:0001583	missense	3313	exon17			L11066	CCDS4208.1	5q31.1	2011-09-02	2006-10-31	2006-10-31	ENSG00000113013	ENSG00000113013		"""Heat shock proteins / HSP70"""	5244	protein-coding gene	gene with protein product		600548	"""heat shock 70kDa protein 9B (mortalin-2)"""	HSPA9B		7684501	Standard	NM_004134		Approved	GRP75, PBP74, mot-2, mthsp75	uc003ldf.3	P38646	OTTHUMG00000129206	ENST00000297185.3:c.1969T>C	5.37:g.137891797A>G	ENSP00000297185:p.Ser657Pro	Somatic		Capture	Illumina HiSeq	Phase_I	137919696	NM_004134	B2RCM1|P30036|P31932|Q1HB43|Q53H23|Q6GU03|Q9BWB7|Q9UC56	Missense_Mutation	SNP	ENST00000297185.3	37	CCDS4208.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.355040	0.61293	.	.	ENSG00000113013	ENST00000297185;ENST00000541333;ENST00000540484	T	0.01092	5.35	5.45	4.25	0.50352	.	0.107611	0.64402	D	0.000004	T	0.02533	0.0077	N	0.19112	0.55	0.58432	D	0.99999	P	0.48350	0.909	D	0.63033	0.91	T	0.68432	-0.5410	10	0.52906	T	0.07	-12.7632	12.3434	0.55107	0.8593:0.1407:0.0:0.0	.	657	P38646	GRP75_HUMAN	P	657;610;643	ENSP00000297185:S657P	ENSP00000297185:S657P	S	-	1	0	HSPA9	137919696	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.453000	0.66645	2.086000	0.62901	0.533000	0.62120	TCT		0.423	HSPA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251285.1	NM_004134	
DNAH5	1767	broad.mit.edu	37	5	13919407	13919407	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:13919407C>T	ENST00000265104.4	-	7	957	c.853G>A	c.(853-855)Gcg>Acg	p.A285T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	285	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.A285T(1)		NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCCAGCTCCGCTCGTGGCCCA	0.532									Kartagener syndrome																												p.A285T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G853A	5						.						139.0	151.0	147.0					5																	13919407		2203	4300	6503	13972407	SO:0001583	missense	1767	exon7	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.853G>A	5.37:g.13919407C>T	ENSP00000265104:p.Ala285Thr	Somatic		Capture	Illumina HiSeq	Phase_I	13972407	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	.	15.37	2.812471	0.50527	.	.	ENSG00000039139	ENST00000265104	T	0.55588	0.51	5.5	5.5	0.81552	Dynein heavy chain, domain-1 (1);	0.000000	0.85682	D	0.000000	T	0.47192	0.1432	L	0.47716	1.5	0.80722	D	1	B	0.24576	0.106	B	0.24006	0.05	T	0.39251	-0.9623	10	0.13108	T	0.6	.	18.3809	0.90451	0.0:1.0:0.0:0.0	.	285	Q8TE73	DYH5_HUMAN	T	285	ENSP00000265104:A285T	ENSP00000265104:A285T	A	-	1	0	DNAH5	13972407	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.729000	0.84864	2.593000	0.87608	0.491000	0.48974	GCG		0.532	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
NRG2	9542	broad.mit.edu	37	5	139422207	139422207	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:139422207G>A	ENST00000361474.1	-	1	672	c.448C>T	c.(448-450)Cga>Tga	p.R150*	NRG2_ENST00000394770.1_Nonsense_Mutation_p.R150*|NRG2_ENST00000289422.7_Nonsense_Mutation_p.R150*|NRG2_ENST00000545385.1_Nonsense_Mutation_p.R150*|NRG2_ENST00000358522.3_Nonsense_Mutation_p.R150*|NRG2_ENST00000289409.4_Nonsense_Mutation_p.R150*|NRG2_ENST00000541337.1_Nonsense_Mutation_p.R150*	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	150					embryo development (GO:0009790)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)	p.R58*(1)|p.R150*(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	25			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCGGCTCTCGGGTGCTGTTG	0.697																																					p.R150X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C448T	5						.						6.0	9.0	8.0					5																	139422207		2106	4185	6291	139402391	SO:0001587	stop_gained	9542	exon1				CCDS4217.1, CCDS54910.1	5q23-q33	2013-01-11			ENSG00000158458	ENSG00000158458		"""Immunoglobulin superfamily / I-set domain containing"""	7998	protein-coding gene	gene with protein product	"""neural- and thymus-derived activator for ErbB kinases"", ""divergent of neuregulin-1"""	603818				9168114, 9168115	Standard	NM_004883		Approved	Don-1, NTAK, HRG2	uc003lev.2	O14511	OTTHUMG00000129241	ENST00000361474.1:c.448C>T	5.37:g.139422207G>A	ENSP00000354910:p.Arg150*	Somatic		Capture	Illumina HiSeq	Phase_I	139402391	NM_013981		Nonsense_Mutation	SNP	ENST00000361474.1	37	CCDS4217.1	.	.	.	.	.	.	.	.	.	.	G	39	7.340378	0.98221	.	.	ENSG00000158458	ENST00000541337;ENST00000289422;ENST00000361474;ENST00000446269;ENST00000545385;ENST00000394770;ENST00000289409;ENST00000358522;ENST00000544729;ENST00000378238	.	.	.	4.14	4.14	0.48551	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.8102	14.2064	0.65737	0.0:0.0:1.0:0.0	.	.	.	.	X	150;150;150;150;150;150;150;150;58;150	.	ENSP00000289409:R150X	R	-	1	2	NRG2	139402391	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	2.896000	0.48656	1.867000	0.54127	0.305000	0.20034	CGA		0.697	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	
TMCO6	55374	broad.mit.edu	37	5	140021323	140021323	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140021323G>A	ENST00000394671.3	+	3	373	c.272G>A	c.(271-273)cGt>cAt	p.R91H	TMCO6_ENST00000252100.6_Missense_Mutation_p.R91H|TMCO6_ENST00000511410.1_Missense_Mutation_p.R91H|TMCO6_ENST00000537378.1_5'UTR|NDUFA2_ENST00000510680.1_Intron	NM_018502.3	NP_060972.3	Q96DC7	TMCO6_HUMAN	transmembrane and coiled-coil domains 6	91					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein transporter activity (GO:0008565)	p.R91H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(1)|urinary_tract(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCAGCCTTCGTCGAGGCTTG	0.602																																					p.R91H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G272A	5						.						47.0	50.0	49.0					5																	140021323		2033	4195	6228	140001507	SO:0001583	missense	55374	exon3			BC001910	CCDS4233.2, CCDS75320.1	5q31.3	2008-11-06			ENSG00000113119	ENSG00000113119			28814	protein-coding gene	gene with protein product						12477932	Standard	XM_005268476		Approved	FLJ39769, PRO1580	uc003lgl.3	Q96DC7	OTTHUMG00000129497	ENST00000394671.3:c.272G>A	5.37:g.140021323G>A	ENSP00000378166:p.Arg91His	Somatic		Capture	Illumina HiSeq	Phase_I	140001507	NM_018502	Q9BUU0|Q9P198	Missense_Mutation	SNP	ENST00000394671.3	37	CCDS4233.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.239201	0.79800	.	.	ENSG00000113119	ENST00000394671;ENST00000511410;ENST00000252100	T;T;T	0.32753	1.44;1.44;1.44	5.29	5.29	0.74685	Armadillo-like helical (1);Armadillo-type fold (1);	0.879866	0.09168	U	0.839302	T	0.60818	0.2298	M	0.77486	2.375	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.997;0.997	T	0.55483	-0.8134	10	0.87932	D	0	-1.536	15.6551	0.77126	0.0:0.0:1.0:0.0	.	91;91;91	E7ESN7;Q96DC7-2;Q96DC7	.;.;TMCO6_HUMAN	H	91	ENSP00000378166:R91H;ENSP00000422154:R91H;ENSP00000252100:R91H	ENSP00000252100:R91H	R	+	2	0	TMCO6	140001507	1.000000	0.71417	0.998000	0.56505	0.771000	0.43674	4.000000	0.57039	2.484000	0.83849	0.563000	0.77884	CGT		0.602	TMCO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251666.2	NM_018502	
NDUFA2	4695	broad.mit.edu	37	5	140026866	140026866	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140026866C>T	ENST00000252102.4	-	2	384	c.183G>A	c.(181-183)gtG>gtA	p.V61V	NDUFA2_ENST00000512088.1_Silent_p.V61V|IK_ENST00000417647.2_5'Flank|NDUFA2_ENST00000510680.1_5'UTR|MIR3655_ENST00000581765.1_RNA	NM_001185012.1|NM_002488.4	NP_001171941.1|NP_002479.1	O43678	NDUA2_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa	61					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.V61V(1)		breast(1)|endometrium(3)|large_intestine(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCTTGGGCTGCACATCGGAGC	0.627																																					p.V61V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G183A	5						.						81.0	72.0	75.0					5																	140026866		2203	4300	6503	140007050	SO:0001819	synonymous_variant	4695	exon2			AF047185	CCDS4234.1, CCDS54911.1	5q31.2	2011-07-04	2002-08-29		ENSG00000131495	ENSG00000131495		"""Mitochondrial respiratory chain complex / Complex I"""	7685	protein-coding gene	gene with protein product	"""complex I B8 subunit"""	602137	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 (8kD, B8)"""			9425316, 9763676	Standard	NM_002488		Approved	B8	uc003lgp.3	O43678	OTTHUMG00000129505	ENST00000252102.4:c.183G>A	5.37:g.140026866C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140007050	NM_001185012	D6RJD6|Q6IAY8	Silent	SNP	ENST00000252102.4	37	CCDS4234.1																																																																																				0.627	NDUFA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251679.2	NM_002488	
PCDHA3	56145	broad.mit.edu	37	5	140181188	140181188	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140181188G>A	ENST00000522353.2	+	1	406	c.406G>A	c.(406-408)Gct>Act	p.A136T	PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.A136T|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	136	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A136T(2)		NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTCCAATGGCTGTAAAGAA	0.502																																					p.A136T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G406A	5						.						113.0	123.0	120.0					5																	140181188		2203	4300	6503	140161372	SO:0001583	missense	56145	exon1			AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.406G>A	5.37:g.140181188G>A	ENSP00000429808:p.Ala136Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140161372	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	.	.	.	.	.	.	.	.	.	.	g	5.730	0.319234	0.10845	.	.	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.19938	2.11;2.11	4.51	-1.43	0.08884	Cadherin (2);Cadherin-like (1);	0.860042	0.09613	U	0.778660	T	0.06142	0.0159	N	0.04994	-0.135	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.12156	0.007;0.001	T	0.37430	-0.9706	10	0.02654	T	1	.	0.8006	0.01074	0.3123:0.1191:0.3269:0.2418	.	136;136	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	T	136	ENSP00000429808:A136T;ENSP00000434086:A136T	ENSP00000429808:A136T	A	+	1	0	PCDHA3	140161372	0.000000	0.05858	0.001000	0.08648	0.783000	0.44284	-1.501000	0.02281	-0.122000	0.11766	-0.353000	0.07706	GCT		0.502	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
PCDHA5	56143	broad.mit.edu	37	5	140203213	140203213	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140203213G>A	ENST00000529859.1	+	1	1853	c.1853G>A	c.(1852-1854)cGc>cAc	p.R618H	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.R618H|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.R618H|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	618	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R618H(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCAGTGCGCGCATCCCGTTC	0.652																																					p.R618H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1853A	5						.						74.0	77.0	76.0					5																	140203213		2203	4300	6503	140183397	SO:0001583	missense	56143	exon1			AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1853G>A	5.37:g.140203213G>A	ENSP00000436557:p.Arg618His	Somatic		Capture	Illumina HiSeq	Phase_I	140183397	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	g	0.473	-0.883725	0.02530	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.52526	0.66;0.66;0.66	3.87	2.06	0.26882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.35508	0.0934	L	0.44542	1.39	0.23421	N	0.997713	B;B;B	0.29301	0.241;0.171;0.171	B;B;B	0.27715	0.082;0.03;0.046	T	0.22941	-1.0202	9	0.41790	T	0.15	.	5.4247	0.16419	0.1933:0.1635:0.6433:0.0	.	618;618;618	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	H	618	ENSP00000433416:R618H;ENSP00000436557:R618H;ENSP00000367366:R618H	ENSP00000367366:R618H	R	+	2	0	PCDHA5	140183397	0.000000	0.05858	0.173000	0.22940	0.289000	0.27227	-0.561000	0.05957	0.264000	0.21851	-0.699000	0.03677	CGC		0.652	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
PCDHA6	56142	broad.mit.edu	37	5	140207831	140207831	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140207831T>C	ENST00000529310.1	+	1	269	c.155T>C	c.(154-156)cTg>cCg	p.L52P	PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Missense_Mutation_p.L52P|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	52	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.L52P(2)		NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCAGGACCTGGGGCTGGAG	0.637																																					p.L52P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T155C	5						.						55.0	66.0	62.0					5																	140207831		2203	4298	6501	140188015	SO:0001583	missense	56142	exon1			AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.155T>C	5.37:g.140207831T>C	ENSP00000433378:p.Leu52Pro	Somatic		Capture	Illumina HiSeq	Phase_I	140188015	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.345440	0.41498	.	.	ENSG00000081842	ENST00000529310;ENST00000527624	T;T	0.60299	0.2;0.2	3.87	3.87	0.44632	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.000000	0.29609	U	0.011672	D	0.85168	0.5635	H	0.99347	4.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;0.999	D	0.90670	0.4597	10	0.87932	D	0	.	13.1114	0.59275	0.0:0.0:0.0:1.0	.	52;52;52	Q9UN73-3;Q9UN73;Q9UN73-2	.;PCDA6_HUMAN;.	P	52	ENSP00000433378:L52P;ENSP00000434113:L52P	ENSP00000434113:L52P	L	+	2	0	PCDHA6	140188015	1.000000	0.71417	1.000000	0.80357	0.131000	0.20780	6.052000	0.71080	1.736000	0.51660	0.260000	0.18958	CTG		0.637	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
PCDHA7	56141	broad.mit.edu	37	5	140214108	140214108	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140214108G>A	ENST00000525929.1	+	1	140	c.140G>A	c.(139-141)cGc>cAc	p.R47H	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000378125.3_Missense_Mutation_p.R47H|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	47	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R47H(2)		NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCGTGGGCCGCATCGCGCAG	0.602																																					p.R47H	NSCLC(160;258 2013 5070 22440 28951)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G140A	5						.						58.0	72.0	68.0					5																	140214108		2203	4299	6502	140194292	SO:0001583	missense	56141	exon1			AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.140G>A	5.37:g.140214108G>A	ENSP00000436426:p.Arg47His	Somatic		Capture	Illumina HiSeq	Phase_I	140194292	NM_018910	O75282	Missense_Mutation	SNP	ENST00000525929.1	37	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.288036	0.59976	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.27256	1.68;1.68	4.17	4.17	0.49024	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.34890	0.0913	M	0.64630	1.985	0.31293	N	0.689194	P;D	0.54047	0.806;0.964	B;P	0.45577	0.133;0.486	T	0.49457	-0.8938	9	0.72032	D	0.01	.	16.9132	0.86145	0.0:0.0:1.0:0.0	.	47;47	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	H	47	ENSP00000436426:R47H;ENSP00000367365:R47H	ENSP00000367365:R47H	R	+	2	0	PCDHA7	140194292	0.014000	0.17966	1.000000	0.80357	0.982000	0.71751	2.165000	0.42396	2.028000	0.59812	0.449000	0.29647	CGC		0.602	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
PCDHAC2	56134	broad.mit.edu	37	5	140348558	140348558	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140348558C>T	ENST00000289269.5	+	1	2739	c.2207C>T	c.(2206-2208)gCg>gTg	p.A736V	PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	736					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A736V(2)		NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCTACACTGCGTATGGCACT	0.418																																					p.A736V	Melanoma(190;638 2083 3390 11909 52360)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2207T	5						.						86.0	83.0	84.0					5																	140348558		2203	4300	6503	140328742	SO:0001583	missense	56134	exon1			AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.2207C>T	5.37:g.140348558C>T	ENSP00000289269:p.Ala736Val	Somatic		Capture	Illumina HiSeq	Phase_I	140328742	NM_018899	Q2M3V1|Q9Y5F4	Missense_Mutation	SNP	ENST00000289269.5	37	CCDS4242.1	.	.	.	.	.	.	.	.	.	.	C	8.295	0.818566	0.16607	.	.	ENSG00000243232	ENST00000289269	T	0.47177	0.85	5.66	5.66	0.87406	.	0.000000	0.41823	D	0.000811	T	0.35307	0.0927	L	0.47190	1.495	0.80722	D	1	P;P	0.39624	0.681;0.491	B;B	0.36666	0.23;0.041	T	0.15607	-1.0431	10	0.25751	T	0.34	.	5.9244	0.19101	0.1867:0.6997:0.0:0.1136	.	736;736	Q9Y5I4-2;Q9Y5I4	.;PCDC2_HUMAN	V	736	ENSP00000289269:A736V	ENSP00000289269:A736V	A	+	2	0	PCDHAC2	140328742	0.994000	0.37717	0.957000	0.39632	0.990000	0.78478	2.547000	0.45786	2.680000	0.91292	0.561000	0.74099	GCG		0.418	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
PCDHB2	56133	broad.mit.edu	37	5	140475059	140475059	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140475059C>T	ENST00000194155.4	+	1	833	c.685C>T	c.(685-687)Ctg>Ttg	p.L229L		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	229	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.L229L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGCACGGCCCTGGTACGGAT	0.592																																					p.L229L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C685T	5						.						44.0	47.0	46.0					5																	140475059		2203	4300	6503	140455243	SO:0001819	synonymous_variant	56133	exon1			AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.685C>T	5.37:g.140475059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140455243	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																				0.592	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
PCDHB5	26167	broad.mit.edu	37	5	140517163	140517163	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140517163G>A	ENST00000231134.5	+	1	2364	c.2147G>A	c.(2146-2148)aGc>aAc	p.S716N		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	716					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.S716N(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGCAGGAGGAGCAGGGCGGCC	0.662																																					p.S716N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2147A	5						.						75.0	87.0	83.0					5																	140517163		2201	4296	6497	140497347	SO:0001583	missense	26167	exon1			AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2147G>A	5.37:g.140517163G>A	ENSP00000231134:p.Ser716Asn	Somatic		Capture	Illumina HiSeq	Phase_I	140497347	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	.	.	.	.	.	.	.	.	.	.	G	11.61	1.688557	0.29962	.	.	ENSG00000113209	ENST00000231134	T	0.14893	2.47	4.56	-5.55	0.02536	.	.	.	.	.	T	0.15955	0.0384	M	0.82517	2.595	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.42085	-0.9472	9	0.35671	T	0.21	.	0.8906	0.01253	0.2442:0.3026:0.2502:0.2029	.	716	Q9Y5E4	PCDB5_HUMAN	N	716	ENSP00000231134:S716N	ENSP00000231134:S716N	S	+	2	0	PCDHB5	140497347	0.000000	0.05858	0.000000	0.03702	0.118000	0.20060	-1.280000	0.02804	-1.051000	0.03226	-0.438000	0.05819	AGC		0.662	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
PCDHB16	57717	broad.mit.edu	37	5	140564086	140564086	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140564086C>T	ENST00000361016.2	+	1	3107	c.1952C>T	c.(1951-1953)cCg>cTg	p.P651L		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	651	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P651L(1)		breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCGAGCCTCCGCGCTCGGCC	0.716																																					p.P651L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1952T	5						.						17.0	19.0	18.0					5																	140564086		2096	4131	6227	140544270	SO:0001583	missense	57717	exon1			AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.1952C>T	5.37:g.140564086C>T	ENSP00000354293:p.Pro651Leu	Somatic		Capture	Illumina HiSeq	Phase_I	140544270	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	c	19.45	3.829274	0.71258	.	.	ENSG00000196963	ENST00000361016	T	0.56941	0.43	3.75	3.75	0.43078	Cadherin (4);Cadherin-like (1);	0.000000	0.34067	N	0.004300	T	0.71204	0.3312	M	0.86420	2.815	0.46437	D	0.999048	D	0.65815	0.995	D	0.63597	0.916	T	0.75728	-0.3216	10	0.62326	D	0.03	.	10.4827	0.44702	0.0:0.8987:0.0:0.1013	.	651	Q9NRJ7	PCDBG_HUMAN	L	651	ENSP00000354293:P651L	ENSP00000354293:P651L	P	+	2	0	PCDHB16	140544270	0.029000	0.19370	0.945000	0.38365	0.816000	0.46133	3.064000	0.49986	1.638000	0.50547	0.298000	0.19748	CCG		0.716	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
PCDHB14	56122	broad.mit.edu	37	5	140604458	140604458	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140604458C>A	ENST00000239449.4	+	1	1381	c.1381C>A	c.(1381-1383)Cgc>Agc	p.R461S	PCDHB14_ENST00000515856.2_Missense_Mutation_p.R308S	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	461	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.R461S(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCTGTTCGTCCGCGAGAACAA	0.607																																					p.R461S	Ovarian(141;50 1831 27899 33809 37648)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1381A	5						.						116.0	119.0	118.0					5																	140604458		2203	4297	6500	140584642	SO:0001583	missense	56122	exon1			AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1381C>A	5.37:g.140604458C>A	ENSP00000239449:p.Arg461Ser	Somatic		Capture	Illumina HiSeq	Phase_I	140584642	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	.	.	.	.	.	.	.	.	.	.	-	12.46	1.944732	0.34283	.	.	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.01584	4.75;4.75	4.5	2.52	0.30459	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01254	0.0041	N	0.12853	0.265	0.09310	N	1	P	0.37083	0.581	B	0.29353	0.101	T	0.52578	-0.8557	9	0.54805	T	0.06	.	10.5055	0.44832	0.0:0.7143:0.2052:0.0804	.	461	Q9Y5E9	PCDBE_HUMAN	S	308;461	ENSP00000444518:R308S;ENSP00000239449:R461S	ENSP00000239449:R461S	R	+	1	0	PCDHB14	140584642	0.000000	0.05858	0.150000	0.22450	0.584000	0.36387	-1.715000	0.01880	0.998000	0.38996	0.556000	0.70494	CGC		0.607	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PCDHB15	56121	broad.mit.edu	37	5	140626754	140626754	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140626754C>T	ENST00000231173.3	+	1	1608	c.1608C>T	c.(1606-1608)cgC>cgT	p.R536R		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	536	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.R536R(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCACAGACCGCGGCTTCCCGG	0.662																																					p.R536R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1608T	5						.						48.0	59.0	55.0					5																	140626754		2203	4300	6503	140606938	SO:0001819	synonymous_variant	56121	exon1			AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.1608C>T	5.37:g.140626754C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140606938	NM_018935	Q8IUX5	Silent	SNP	ENST00000231173.3	37	CCDS4257.1																																																																																				0.662	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
PCDHGA4	56111	broad.mit.edu	37	5	140737057	140737057	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140737057C>T	ENST00000571252.1	+	1	2290	c.2290C>T	c.(2290-2292)Cgg>Tgg	p.R764W	PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	764					homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCGGACTCGCGGAAGAGTCA	0.582																																					p.R764W												.	.	0			c.C2290T	5						.						84.0	91.0	89.0					5																	140737057		2203	4300	6503	140717241	SO:0001583	missense	56111	exon1			AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.2290C>T	5.37:g.140737057C>T	ENSP00000458570:p.Arg764Trp	Somatic		Capture	Illumina HiSeq	Phase_I	140717241	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																				0.582	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
PCDHGA5	56110	broad.mit.edu	37	5	140746055	140746055	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140746055C>T	ENST00000518069.1	+	1	2158	c.2158C>T	c.(2158-2160)Cac>Tac	p.H720Y	PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	720					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.H720Y(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|upper_aerodigestive_tract(3)	18			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGCGCTGGCACAAGTCACG	0.617																																					p.H720Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2158T	5						.						110.0	122.0	118.0					5																	140746055		2203	4300	6503	140726239	SO:0001583	missense	56110	exon1			AF152512	CCDS54925.1, CCDS75333.1	5q31	2010-01-26				ENSG00000253485		"""Cadherins / Protocadherins : Clustered"""	8703	other	protocadherin	"""cadherin ME3"""	606292				10380929	Standard	NM_018918		Approved	CDH-GAMMA-A5, ME3, PCDH-GAMMA-A5		Q9Y5G8		ENST00000518069.1:c.2158C>T	5.37:g.140746055C>T	ENSP00000429834:p.His720Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	140726239	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	11.68	1.710512	0.30322	.	.	ENSG00000253485	ENST00000518069	T	0.13538	2.58	5.17	1.14	0.20703	.	.	.	.	.	T	0.17023	0.0409	M	0.80746	2.51	0.23515	N	0.997511	B;B	0.14438	0.01;0.0	B;B	0.17979	0.02;0.013	T	0.24333	-1.0163	9	0.42905	T	0.14	.	5.422	0.16405	0.2267:0.5223:0.0:0.251	.	720;720	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	Y	720	ENSP00000429834:H720Y	ENSP00000429834:H720Y	H	+	1	0	PCDHGA5	140726239	1.000000	0.71417	0.918000	0.36340	0.848000	0.48234	1.217000	0.32455	0.282000	0.22254	0.563000	0.77884	CAC		0.617	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918	
PCDHGB3	56102	broad.mit.edu	37	5	140778767	140778767	+	Intron	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140778767C>T	ENST00000576222.1	+	1	2546				PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3						homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACGCGGTGCCTGGAACACTA	0.368																																					p.P358L												.	.	0			c.C1073T	5						.						76.0	76.0	76.0					5																	140778767		1874	4107	5981	140758951	SO:0001627	intron_variant	56101	exon1			AF152519	CCDS58980.1, CCDS75334.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8710	other	protocadherin		606301				10380929	Standard	NM_018924		Approved	PCDH-GAMMA-B3		Q9Y5G1		ENST00000576222.1:c.2415+26391C>T	5.37:g.140778767C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140758951	NM_032099	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																				0.368	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924	
PCDHGA12	26025	broad.mit.edu	37	5	140811041	140811041	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140811041G>A	ENST00000252085.3	+	1	857	c.715G>A	c.(715-717)Gca>Aca	p.A239T	PCDHGB6_ENST00000520790.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_003735.2|NM_032094.1	NP_003726.1|NP_115265.1	O60330	PCDGC_HUMAN	protocadherin gamma subfamily A, 12	239	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A239T(2)		breast(2)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(23)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	58			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAACGACAACGCACCAGCGTT	0.662																																					p.A239T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G715A	5						.						54.0	55.0	54.0					5																	140811041		2203	4300	6503	140791225	SO:0001583	missense	26025	exon1			AF152506	CCDS4260.1, CCDS75346.1	5q31	2010-01-26	2002-05-23		ENSG00000253159	ENSG00000253159		"""Cadherins / Protocadherins : Clustered"""	8699	other	protocadherin	"""fibroblast cadherin FIB3"""	603059	"""cadherin 21"""	CDH21		10380929	Standard	NM_003735		Approved	KIAA0588, FIB3, PCDH-GAMMA-A12		O60330	OTTHUMG00000129611	ENST00000252085.3:c.715G>A	5.37:g.140811041G>A	ENSP00000252085:p.Ala239Thr	Somatic		Capture	Illumina HiSeq	Phase_I	140791225	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	11.24	1.580342	0.28180	.	.	ENSG00000253159	ENST00000252085	T	0.03181	4.02	4.94	3.15	0.36227	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.05686	0.0149	M	0.80183	2.485	0.23180	N	0.998168	P;P	0.38992	0.653;0.522	B;B	0.32533	0.147;0.086	T	0.33240	-0.9876	9	0.51188	T	0.08	.	4.9751	0.14136	0.077:0.271:0.5127:0.1393	.	239;239	O60330-2;O60330	.;PCDGC_HUMAN	T	239	ENSP00000252085:A239T	ENSP00000252085:A239T	A	+	1	0	PCDHGA12	140791225	0.000000	0.05858	0.939000	0.37840	0.375000	0.29983	0.332000	0.19751	0.669000	0.31146	0.655000	0.94253	GCA		0.662	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735	
PCDHGC4	56098	broad.mit.edu	37	5	140866821	140866821	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:140866821C>T	ENST00000306593.1	+	1	2081	c.2081C>T	c.(2080-2082)gCt>gTt	p.A694V	PCDHGB6_ENST00000520790.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGC5_ENST00000252087.1_5'Flank|PCDHGA10_ENST00000398610.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	694					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A694V(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTACTTGGCTGTGTCCCTA	0.498																																					p.A694V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2081T	5						.						152.0	124.0	133.0					5																	140866821		2203	4300	6503	140847005	SO:0001583	missense	56098	exon1			AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"""Cadherins / Protocadherins : Clustered"""	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.2081C>T	5.37:g.140866821C>T	ENSP00000306918:p.Ala694Val	Somatic		Capture	Illumina HiSeq	Phase_I	140847005	NM_032406	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	37	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.519139	0.27211	.	.	ENSG00000242419	ENST00000306593	T	0.39056	1.1	5.67	4.79	0.61399	.	.	.	.	.	T	0.12987	0.0315	N	0.00608	-1.33	0.23966	N	0.996327	B;B	0.28880	0.068;0.226	B;B	0.22601	0.025;0.04	T	0.12682	-1.0538	9	0.21540	T	0.41	.	7.5079	0.27555	0.0:0.7198:0.0:0.2802	.	694;694	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	V	694	ENSP00000306918:A694V	ENSP00000306918:A694V	A	+	2	0	PCDHGC4	140847005	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.713000	0.54882	1.363000	0.46019	0.591000	0.81541	GCT		0.498	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928	
HDAC3	8841	broad.mit.edu	37	5	141004824	141004824	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:141004824T>C	ENST00000305264.3	-	14	1247	c.1168A>G	c.(1168-1170)Act>Gct	p.T390A	AC008781.7_ENST00000422040.2_RNA|HDAC3_ENST00000469207.1_5'UTR	NM_003883.3	NP_003874.2	O15379	HDAC3_HUMAN	histone deacetylase 3	390					cellular lipid metabolic process (GO:0044255)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle (GO:0045786)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|protein deacetylation (GO:0006476)|regulation of mitotic cell cycle (GO:0007346)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|cyclin binding (GO:0030332)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)	p.T390A(1)		endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Vorinostat(DB02546)	GCCTCATCAGTCCTGTCATAG	0.527																																					p.T390A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1168G	5						.						221.0	199.0	207.0					5																	141004824		2203	4300	6503	140985008	SO:0001583	missense	8841	exon14			AF059650	CCDS4264.1	5q31.1-q31.2	2008-07-18			ENSG00000171720	ENSG00000171720	3.5.1.98		4854	protein-coding gene	gene with protein product		605166				9501169, 9464271	Standard	NM_003883		Approved	RPD3, HD3, RPD3-2	uc003llf.2	O15379	OTTHUMG00000129629	ENST00000305264.3:c.1168A>G	5.37:g.141004824T>C	ENSP00000302967:p.Thr390Ala	Somatic		Capture	Illumina HiSeq	Phase_I	140985008	NM_003883	D3DQE1|O43268|Q9UEI5|Q9UEV0	Missense_Mutation	SNP	ENST00000305264.3	37	CCDS4264.1	.	.	.	.	.	.	.	.	.	.	T	11.31	1.599711	0.28534	.	.	ENSG00000171720	ENST00000305264	T	0.68331	-0.32	5.25	5.25	0.73442	.	0.101640	0.64402	D	0.000003	T	0.50616	0.1626	N	0.25245	0.725	0.43385	D	0.995492	B	0.02656	0.0	B	0.01281	0.0	T	0.47407	-0.9120	10	0.38643	T	0.18	-15.4001	10.2199	0.43190	0.0:0.0777:0.0:0.9223	.	390	O15379	HDAC3_HUMAN	A	390	ENSP00000302967:T390A	ENSP00000302967:T390A	T	-	1	0	HDAC3	140985008	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.014000	0.57145	2.200000	0.70718	0.460000	0.39030	ACT		0.527	HDAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251824.2	NM_003883	
RBM27	54439	broad.mit.edu	37	5	145616938	145616938	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:145616938G>A	ENST00000265271.5	+	8	1388	c.1222G>A	c.(1222-1224)Gtg>Atg	p.V408M	RBM27_ENST00000506502.1_Missense_Mutation_p.V408M	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	408	Pro-rich.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.V408M(1)		NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTTGCATCAGTGGGAACAAG	0.433																																					p.V408M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1222A	5						.						202.0	167.0	178.0					5																	145616938		1568	3582	5150	145597131	SO:0001583	missense	54439	exon8			AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1222G>A	5.37:g.145616938G>A	ENSP00000265271:p.Val408Met	Somatic		Capture	Illumina HiSeq	Phase_I	145597131	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	G	17.32	3.359621	0.61403	.	.	ENSG00000091009	ENST00000265271	T	0.46819	0.86	5.43	5.43	0.79202	.	0.266144	0.32120	N	0.006550	T	0.31451	0.0797	N	0.12182	0.205	0.36497	D	0.868774	P;B	0.44578	0.838;0.062	B;B	0.41813	0.367;0.01	T	0.34551	-0.9824	10	0.33940	T	0.23	-8.5729	12.5757	0.56362	0.0762:0.0:0.9238:0.0	.	408;408	Q9P2N5;B3KY61	RBM27_HUMAN;.	M	408	ENSP00000265271:V408M	ENSP00000265271:V408M	V	+	1	0	RBM27	145597131	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.883000	0.56168	2.535000	0.85469	0.591000	0.81541	GTG		0.433	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
TCERG1	10915	broad.mit.edu	37	5	145834701	145834701	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:145834701C>T	ENST00000296702.5	+	2	180	c.142C>T	c.(142-144)Cga>Tga	p.R48*	TCERG1_ENST00000394421.2_Nonsense_Mutation_p.R48*	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	48	Pro-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)	p.R48*(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACCTCTGATGCGACCTCCTCC	0.607																																					p.R48X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C142T	5						.						116.0	114.0	115.0					5																	145834701		2203	4300	6503	145814894	SO:0001587	stop_gained	10915	exon2			AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.142C>T	5.37:g.145834701C>T	ENSP00000296702:p.Arg48*	Somatic		Capture	Illumina HiSeq	Phase_I	145814894	NM_001040006	Q2NKN2|Q59EA1	Nonsense_Mutation	SNP	ENST00000296702.5	37	CCDS4282.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.951205	0.92660	.	.	ENSG00000113649	ENST00000296702;ENST00000394421	.	.	.	5.4	1.4	0.22301	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.0549	15.203	0.73157	0.4566:0.5434:0.0:0.0	.	.	.	.	X	48	.	ENSP00000296702:R48X	R	+	1	2	TCERG1	145814894	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	1.700000	0.37815	0.061000	0.16311	0.563000	0.77884	CGA		0.607	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
JAKMIP2	9832	broad.mit.edu	37	5	147040948	147040948	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:147040948G>A	ENST00000265272.5	-	3	657	c.190C>T	c.(190-192)Cgc>Tgc	p.R64C	JAKMIP2_ENST00000507386.1_Missense_Mutation_p.R64C|JAKMIP2_ENST00000333010.6_Missense_Mutation_p.R22C	NM_001270941.1|NM_014790.4	NP_001257870.1|NP_055605.2	Q96AA8	JKIP2_HUMAN	janus kinase and microtubule interacting protein 2	64						Golgi apparatus (GO:0005794)		p.R64C(1)		NS(1)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(22)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGTGCTTGCGCTGCTCCAGC	0.493																																					p.R64C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C190T	5						.						135.0	126.0	129.0					5																	147040948		2203	4300	6503	147021141	SO:0001583	missense	9832	exon3			AB011127	CCDS4285.1, CCDS59495.1, CCDS64284.1, CCDS75352.1	5q32	2009-08-13	2009-08-13		ENSG00000176049	ENSG00000176049			29067	protein-coding gene	gene with protein product		611197				9628581	Standard	NM_001270941		Approved	JAMIP2, KIAA0555	uc010jgo.2	Q96AA8	OTTHUMG00000129731	ENST00000265272.5:c.190C>T	5.37:g.147040948G>A	ENSP00000265272:p.Arg64Cys	Somatic		Capture	Illumina HiSeq	Phase_I	147021141	NM_014790	A4ZZA7|A8K5G5|B4DSG0|G5E9Y0|O60302|Q548S1	Missense_Mutation	SNP	ENST00000265272.5	37	CCDS4285.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962353	0.74016	.	.	ENSG00000176049	ENST00000507386;ENST00000265272;ENST00000333010;ENST00000539401	T;T;T	0.35605	1.3;1.3;1.3	4.53	4.53	0.55603	.	0.053264	0.85682	D	0.000000	T	0.32941	0.0846	L	0.29908	0.895	0.58432	D	0.999998	D;D;D;D	0.67145	0.987;0.996;0.996;0.993	B;P;P;P	0.44561	0.335;0.453;0.453;0.453	T	0.24261	-1.0165	10	0.56958	D	0.05	.	18.1501	0.89672	0.0:0.0:1.0:0.0	.	22;64;64;64	B4DSG0;Q96AA8-3;G5E9Y0;Q96AA8	.;.;.;JKIP2_HUMAN	C	64;64;22;64	ENSP00000421398:R64C;ENSP00000265272:R64C;ENSP00000328989:R22C	ENSP00000265272:R64C	R	-	1	0	JAKMIP2	147021141	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.420000	0.97426	2.460000	0.83146	0.462000	0.41574	CGC		0.493	JAKMIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251941.1	NM_014790	
SPINK5	11005	broad.mit.edu	37	5	147480074	147480074	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:147480074G>C	ENST00000256084.7	+	13	1192	c.1150G>C	c.(1150-1152)Gag>Cag	p.E384Q	SPINK5_ENST00000398454.1_Missense_Mutation_p.E384Q|SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.E384Q	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	384	Kazal-like 6. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.E384Q(2)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGCACCAGAGAGAACGATCC	0.488																																					p.E384Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1150C	5						.						156.0	151.0	153.0					5																	147480074		1960	4168	6128	147460267	SO:0001583	missense	11005	exon13			AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.1150G>C	5.37:g.147480074G>C	ENSP00000256084:p.Glu384Gln	Somatic		Capture	Illumina HiSeq	Phase_I	147460267	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.923208	0.52653	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	4.69	3.82	0.43975	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.000000	0.37483	N	0.002067	T	0.21718	0.0523	M	0.84846	2.72	0.26313	N	0.977794	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.986;0.999;0.999	T	0.11941	-1.0567	10	0.15066	T	0.55	-12.5245	8.5047	0.33179	0.1047:0.0:0.8953:0.0	.	365;384;384;384	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	Q	384;384;365;384	ENSP00000381472:E384Q;ENSP00000352936:E384Q;ENSP00000421519:E365Q;ENSP00000256084:E384Q	ENSP00000256084:E384Q	E	+	1	0	SPINK5	147460267	0.997000	0.39634	0.980000	0.43619	0.577000	0.36160	2.731000	0.47343	1.345000	0.45676	0.591000	0.81541	GAG		0.488	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
PDE6A	5145	broad.mit.edu	37	5	149313514	149313514	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:149313514G>T	ENST00000255266.5	-	3	815	c.696C>A	c.(694-696)aaC>aaA	p.N232K		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	232					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)	p.N232K(1)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GAGTTTCACAGTTGTGCAGGT	0.488																																					p.N232K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C696A	5						.						82.0	74.0	77.0					5																	149313514		2203	4300	6503	149293707	SO:0001583	missense	5145	exon3				CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.696C>A	5.37:g.149313514G>T	ENSP00000255266:p.Asn232Lys	Somatic		Capture	Illumina HiSeq	Phase_I	149293707	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.096845	0.37048	.	.	ENSG00000132915	ENST00000255266	T	0.69306	-0.39	5.68	3.92	0.45320	GAF (1);	0.048392	0.85682	D	0.000000	T	0.55273	0.1910	L	0.55481	1.735	0.46586	D	0.999117	B	0.10296	0.003	B	0.15484	0.013	T	0.46414	-0.9193	10	0.05959	T	0.93	.	10.7963	0.46461	0.1552:0.0:0.8448:0.0	.	232	P16499	PDE6A_HUMAN	K	232	ENSP00000255266:N232K	ENSP00000255266:N232K	N	-	3	2	PDE6A	149293707	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.665000	0.46791	0.880000	0.35969	-0.216000	0.12614	AAC		0.488	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
ANXA6	309	broad.mit.edu	37	5	150502564	150502564	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:150502564C>T	ENST00000354546.5	-	16	1374	c.1147G>A	c.(1147-1149)Gaa>Aaa	p.E383K	ANXA6_ENST00000523714.1_Missense_Mutation_p.E351K|ANXA6_ENST00000356496.5_Missense_Mutation_p.E383K|ANXA6_ENST00000377751.5_Intron|ANXA6_ENST00000521512.1_Missense_Mutation_p.E176K	NM_001155.4	NP_001146.2	P08133	ANXA6_HUMAN	annexin A6	383					calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|protein homooligomerization (GO:0051260)|regulation of muscle contraction (GO:0006937)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|cholesterol binding (GO:0015485)|GTP binding (GO:0005525)|ligand-gated ion channel activity (GO:0015276)|lipid binding (GO:0008289)|protein homodimerization activity (GO:0042803)	p.E383K(1)		endometrium(2)|kidney(1)|lung(9)	12		Medulloblastoma(196;0.0912)|all_hematologic(541;0.208)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ATTGTGTCTTCGTCAGTCCCT	0.572																																					p.E383K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1147A	5						.						140.0	146.0	144.0					5																	150502564		2134	4252	6386	150482757	SO:0001583	missense	309	exon16			J03578	CCDS47315.1, CCDS54941.1	5q33.1	2008-02-05			ENSG00000197043	ENSG00000197043		"""Annexins"""	544	protein-coding gene	gene with protein product		114070		ANX6		3258820	Standard	NM_001155		Approved		uc003ltl.2	P08133	OTTHUMG00000164179	ENST00000354546.5:c.1147G>A	5.37:g.150502564C>T	ENSP00000346550:p.Glu383Lys	Somatic		Capture	Illumina HiSeq	Phase_I	150482757	NM_001155	B7Z8A7|D3DQH4|E9PGK1|Q6ZT79	Missense_Mutation	SNP	ENST00000354546.5	37	CCDS47315.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623217	0.87460	.	.	ENSG00000197043	ENST00000354546;ENST00000523714;ENST00000356496;ENST00000521512;ENST00000540153	T;T;T;T	0.05081	3.5;3.5;3.5;3.5	5.48	4.6	0.57074	Annexin repeat, conserved site (1);	0.103749	0.64402	D	0.000005	T	0.14917	0.0360	L	0.50993	1.605	0.80722	D	1	P;D;D	0.59767	0.924;0.986;0.986	B;P;P	0.54759	0.295;0.705;0.76	T	0.00655	-1.1624	10	0.59425	D	0.04	.	15.1622	0.72793	0.0:0.8577:0.1422:0.0	.	176;383;383	E5RK69;A6NN80;P08133	.;.;ANXA6_HUMAN	K	383;351;383;176;257	ENSP00000346550:E383K;ENSP00000430517:E351K;ENSP00000348889:E383K;ENSP00000430420:E176K	ENSP00000346550:E383K	E	-	1	0	ANXA6	150482757	1.000000	0.71417	0.033000	0.17914	0.021000	0.10359	5.234000	0.65343	1.280000	0.44463	-0.175000	0.13238	GAA		0.572	ANXA6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377668.2	NM_001155	
FAT2	2196	broad.mit.edu	37	5	150917504	150917504	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:150917504G>T	ENST00000261800.5	-	11	9055	c.9043C>A	c.(9043-9045)Ctc>Atc	p.L3015I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3015	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.L3015I(1)		NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCAGTATAGAGAAGCTAGAGA	0.458																																					p.L3015I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C9043A	5						.						79.0	75.0	76.0					5																	150917504		2203	4300	6503	150897697	SO:0001583	missense	2196	exon11			AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.9043C>A	5.37:g.150917504G>T	ENSP00000261800:p.Leu3015Ile	Somatic		Capture	Illumina HiSeq	Phase_I	150897697	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	5.460	0.269952	0.10349	.	.	ENSG00000086570	ENST00000261800	T	0.01767	4.65	4.69	2.86	0.33363	Cadherin (2);Cadherin-like (1);	0.426666	0.19830	N	0.105108	T	0.01156	0.0038	N	0.16066	0.365	0.22552	N	0.998993	P	0.46621	0.881	B	0.37692	0.256	T	0.54009	-0.8357	10	0.17832	T	0.49	.	8.9299	0.35663	0.1364:0.236:0.6276:0.0	.	3015	Q9NYQ8	FAT2_HUMAN	I	3015	ENSP00000261800:L3015I	ENSP00000261800:L3015I	L	-	1	0	FAT2	150897697	0.970000	0.33590	0.999000	0.59377	0.069000	0.16628	0.858000	0.27845	0.074000	0.16767	-1.255000	0.01485	CTC		0.458	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
G3BP1	10146	broad.mit.edu	37	5	151183590	151183590	+	Missense_Mutation	SNP	C	C	T	rs187250945		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:151183590C>T	ENST00000394123.3	+	12	1484	c.1339C>T	c.(1339-1341)Cgt>Tgt	p.R447C	G3BP1_ENST00000543466.1_Missense_Mutation_p.R265C|G3BP1_ENST00000356245.3_Missense_Mutation_p.R447C			Q13283	G3BP1_HUMAN	GTPase activating protein (SH3 domain) binding protein 1	447	Gly-rich.				ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Ras protein signal transduction (GO:0007265)|transport (GO:0006810)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)	p.R447C(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(1)|skin(3)|urinary_tract(2)	29		all_hematologic(541;0.0338)|Medulloblastoma(196;0.091)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			AGGCCCTCCCCGTGGAGGCAT	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		17665	0.0		0.001	False		,,,				2504	0.0				p.R447C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1339T	5						.						83.0	88.0	86.0					5																	151183590		2203	4300	6503	151163783	SO:0001583	missense	10146	exon12			BC006997	CCDS4319.1	5q33.1	2013-02-12	2006-11-01		ENSG00000145907	ENSG00000145907		"""RNA binding motif (RRM) containing"""	30292	protein-coding gene	gene with protein product	"""Ras-GTPase-activating protein SH3-domain-binding protein"""	608431				8649363, 9889278	Standard	NM_005754		Approved	HDH-VIII, G3BP	uc003lum.3	Q13283	OTTHUMG00000130123	ENST00000394123.3:c.1339C>T	5.37:g.151183590C>T	ENSP00000377681:p.Arg447Cys	Somatic		Capture	Illumina HiSeq	Phase_I	151163783	NM_005754	Q5HYE9	Missense_Mutation	SNP	ENST00000394123.3	37	CCDS4319.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	14.86	2.662706	0.47572	.	.	ENSG00000145907	ENST00000394123;ENST00000543466;ENST00000356245;ENST00000274596	T;T;T	0.78246	-1.05;-1.16;-1.05	5.35	3.54	0.40534	.	0.000000	0.85682	D	0.000000	T	0.73297	0.3569	M	0.63843	1.955	0.80722	D	1	B	0.09022	0.002	B	0.04013	0.001	T	0.69793	-0.5049	10	0.72032	D	0.01	-1.1728	10.6212	0.45481	0.1325:0.7983:0.0:0.0693	.	447	Q13283	G3BP1_HUMAN	C	447;265;447;289	ENSP00000377681:R447C;ENSP00000445035:R265C;ENSP00000348578:R447C	ENSP00000274596:R289C	R	+	1	0	G3BP1	151163783	0.978000	0.34361	0.945000	0.38365	0.997000	0.91878	2.469000	0.45110	0.710000	0.31997	0.650000	0.86243	CGT		0.607	G3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252431.1	NM_005754	
GALNT10	55568	broad.mit.edu	37	5	153674418	153674418	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:153674418G>T	ENST00000297107.6	+	2	339	c.202G>T	c.(202-204)Ggg>Tgg	p.G68W	GALNT10_ENST00000425427.2_Missense_Mutation_p.G68W|GALNT10_ENST00000377661.2_Missense_Mutation_p.G68W	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	68					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.G68W(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			CTTGGGAGATGGGCAGAAGCT	0.502																																					p.G68W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G202T	5						.						105.0	96.0	99.0					5																	153674418		2203	4300	6503	153654611	SO:0001583	missense	55568	exon2			AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.202G>T	5.37:g.153674418G>T	ENSP00000297107:p.Gly68Trp	Somatic		Capture	Illumina HiSeq	Phase_I	153654611	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.308913	0.81247	.	.	ENSG00000164574	ENST00000425427;ENST00000297107;ENST00000377661	T;T;T	0.57107	0.65;0.42;0.51	5.64	4.78	0.61160	.	1.252890	0.05935	U	0.635940	T	0.73745	0.3626	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.997;0.999	P;D	0.71184	0.887;0.972	T	0.59423	-0.7457	10	0.66056	D	0.02	.	13.2442	0.60014	0.0735:0.0:0.9265:0.0	.	68;68	Q86SR1;Q86SR1-3	GLT10_HUMAN;.	W	68	ENSP00000415210:G68W;ENSP00000297107:G68W;ENSP00000366889:G68W	ENSP00000297107:G68W	G	+	1	0	GALNT10	153654611	1.000000	0.71417	0.844000	0.33320	0.950000	0.60333	5.202000	0.65169	1.530000	0.49136	0.650000	0.86243	GGG		0.502	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
GALNT10	55568	broad.mit.edu	37	5	153789116	153789116	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:153789116G>A	ENST00000297107.6	+	9	1317	c.1180G>A	c.(1180-1182)Gcc>Acc	p.A394T	GALNT10_ENST00000377657.3_Missense_Mutation_p.A67T|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377661.2_Missense_Mutation_p.A332T|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	394					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)	p.A394T(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TAAGCGGGTGGCCGAAGTGTG	0.572																																					p.A394T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1180A	5						.						118.0	129.0	125.0					5																	153789116		2203	4300	6503	153769309	SO:0001583	missense	55568	exon9			AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1180G>A	5.37:g.153789116G>A	ENSP00000297107:p.Ala394Thr	Somatic		Capture	Illumina HiSeq	Phase_I	153769309	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.676653	0.88445	.	.	ENSG00000164574	ENST00000297107;ENST00000377661;ENST00000377657	T;T;T	0.72051	-0.62;-0.62;-0.62	5.69	5.69	0.88448	.	0.047848	0.85682	D	0.000000	D	0.88883	0.6558	M	0.93763	3.455	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.80764	0.994;0.994;0.961	D	0.91088	0.4904	10	0.87932	D	0	.	19.8182	0.96579	0.0:0.0:1.0:0.0	.	332;65;394	Q86SR1-2;D6R8Y1;Q86SR1	.;.;GLT10_HUMAN	T	394;332;67	ENSP00000297107:A394T;ENSP00000366889:A332T;ENSP00000366885:A67T	ENSP00000297107:A394T	A	+	1	0	GALNT10	153769309	1.000000	0.71417	0.993000	0.49108	0.276000	0.26787	9.640000	0.98453	2.700000	0.92200	0.561000	0.74099	GCC		0.572	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
KIF4B	285643	broad.mit.edu	37	5	154394629	154394629	+	Missense_Mutation	SNP	C	C	T	rs534609073		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:154394629C>T	ENST00000435029.4	+	1	1370	c.1210C>T	c.(1210-1212)Cgt>Tgt	p.R404C		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	404					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|plus-end-directed microtubule motor activity (GO:0008574)	p.R404C(2)		breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(27)|ovary(2)|upper_aerodigestive_tract(1)	58	Renal(175;0.00488)	Medulloblastoma(196;0.0523)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			AAAATTAAGTCGTTGTCTGAG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		21094	0.001		0.0	False		,,,				2504	0.0				p.R404C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1210T	5						.						134.0	136.0	135.0					5																	154394629		2203	4300	6503	154374822	SO:0001583	missense	285643	exon1			AF241316	CCDS47324.1	5q33.2	2010-06-22			ENSG00000226650	ENSG00000226650		"""Kinesins"""	6322	protein-coding gene	gene with protein product		609184					Standard	NM_001099293		Approved		uc010jih.1	Q2VIQ3	OTTHUMG00000164143	ENST00000435029.4:c.1210C>T	5.37:g.154394629C>T	ENSP00000387875:p.Arg404Cys	Somatic		Capture	Illumina HiSeq	Phase_I	154374822	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	.	.	.	.	.	.	.	.	.	.	c	7.443	0.641103	0.14386	.	.	ENSG00000226650	ENST00000435029	T	0.57595	0.39	1.61	1.61	0.23674	.	.	.	.	.	T	0.41143	0.1146	L	0.59436	1.845	0.26060	N	0.98137	P	0.34462	0.454	B	0.26310	0.068	T	0.35025	-0.9805	9	0.46703	T	0.11	.	5.1786	0.15148	0.3436:0.6564:0.0:0.0	.	404	Q2VIQ3	KIF4B_HUMAN	C	404	ENSP00000387875:R404C	ENSP00000387875:R404C	R	+	1	0	KIF4B	154374822	0.091000	0.21658	0.777000	0.31699	0.393000	0.30537	-0.187000	0.09656	1.213000	0.43380	0.563000	0.77884	CGT		0.453	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1		
HAVCR2	84868	broad.mit.edu	37	5	156533811	156533811	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:156533811T>C	ENST00000307851.4	-	2	951	c.221A>G	c.(220-222)gAt>gGt	p.D74G	HAVCR2_ENST00000517358.1_5'UTR|HAVCR2_ENST00000522593.1_Missense_Mutation_p.D74G|CTB-120L21.1_ENST00000517708.1_RNA	NM_032782.4	NP_116171.3	Q8TDQ0	HAVR2_HUMAN	hepatitis A virus cellular receptor 2	74	Ig-like V-type.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.D74G(1)		cervix(1)|large_intestine(4)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	22	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATAATTCACATCCCTTTCATC	0.537																																					p.D74G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A221G	5						.						160.0	148.0	152.0					5																	156533811		2203	4300	6503	156466389	SO:0001583	missense	84868	exon2			AK027334	CCDS4333.1	5q34	2014-01-14			ENSG00000135077	ENSG00000135077		"""Immunoglobulin superfamily / V-set domain containing"""	18437	protein-coding gene	gene with protein product	"""T-cell immunoglobulin mucin family member 3"""	606652				11823861	Standard	NM_032782		Approved	Tim-3, TIM3, FLJ14428, TIMD3	uc003lwk.2	Q8TDQ0	OTTHUMG00000130249	ENST00000307851.4:c.221A>G	5.37:g.156533811T>C	ENSP00000312002:p.Asp74Gly	Somatic		Capture	Illumina HiSeq	Phase_I	156466389	NM_032782	B2RAY2|Q8WW60|Q96K94	Missense_Mutation	SNP	ENST00000307851.4	37	CCDS4333.1	.	.	.	.	.	.	.	.	.	.	T	10.81	1.455446	0.26161	.	.	ENSG00000135077	ENST00000307851;ENST00000522593	T;T	0.02606	4.23;4.23	5.48	-3.4	0.04853	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.944756	0.08849	N	0.884682	T	0.01905	0.0060	L	0.28192	0.835	0.09310	N	1	B;B	0.26775	0.07;0.159	B;B	0.24848	0.033;0.056	T	0.46938	-0.9155	10	0.29301	T	0.29	-1.2924	2.8581	0.05578	0.1134:0.3433:0.117:0.4263	.	74;74	Q8TDQ0-2;Q8TDQ0	.;HAVR2_HUMAN	G	74	ENSP00000312002:D74G;ENSP00000430873:D74G	ENSP00000312002:D74G	D	-	2	0	HAVCR2	156466389	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.141000	0.16076	-0.757000	0.04697	-0.250000	0.11733	GAT		0.537	HAVCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252574.2		
CLINT1	9685	broad.mit.edu	37	5	157232964	157232964	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:157232964G>T	ENST00000411809.2	-	7	1056	c.852C>A	c.(850-852)acC>acA	p.T284T	CLINT1_ENST00000523908.1_Silent_p.T284T|CLINT1_ENST00000523094.1_Silent_p.T266T|CLINT1_ENST00000296951.5_Silent_p.T266T|CLINT1_ENST00000530742.1_Silent_p.T266T	NM_014666.3	NP_055481.1	Q14677	EPN4_HUMAN	clathrin interactor 1	284					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin-coated vesicle (GO:0030136)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|lipid binding (GO:0008289)			breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|urinary_tract(1)	21	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CAAGATCAATGGTTTTGGAAG	0.478																																					p.T284T	Colon(22;427 587 2170 6147 14291)											.	.	0			c.C852A	5						.						276.0	276.0	276.0					5																	157232964		2138	4241	6379	157165542	SO:0001819	synonymous_variant	9685	exon7			AF434813	CCDS47330.1, CCDS56388.1, CCDS56389.1	5q33.3	2006-06-13			ENSG00000113282	ENSG00000113282			23186	protein-coding gene	gene with protein product		607265				12213833, 12429846	Standard	NM_014666		Approved	ENTH, KIAA0171, EPNR, CLINT	uc011ddv.2	Q14677	OTTHUMG00000163527	ENST00000411809.2:c.852C>A	5.37:g.157232964G>T		None		Capture	Illumina HiSeq	Phase_I	157165542	NM_014666	B7Z6F8|D3DQJ6|Q8NAF1|Q96E05	Silent	SNP	ENST00000411809.2	37	CCDS47330.1	.	.	.	.	.	.	.	.	.	.	G	9.036	0.988473	0.18966	.	.	ENSG00000113282	ENST00000521615	.	.	.	5.63	2.75	0.32379	.	.	.	.	.	T	0.53594	0.1806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45862	-0.9232	4	.	.	.	-14.8106	5.4662	0.16644	0.2158:0.0:0.6439:0.1403	.	.	.	.	N	1	.	.	H	-	1	0	CLINT1	157165542	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.752000	0.26362	0.752000	0.32923	-0.259000	0.10710	CAT		0.478	CLINT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374001.1	NM_014666	
CCNJL	79616	broad.mit.edu	37	5	159680741	159680741	+	Missense_Mutation	SNP	C	C	T	rs201691454		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:159680741C>T	ENST00000393977.3	-	7	1237	c.952G>A	c.(952-954)Ggc>Agc	p.G318S	CCNJL_ENST00000257536.7_Missense_Mutation_p.G270S|CCNJL_ENST00000377503.2_5'UTR	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	318						nucleus (GO:0005634)		p.G318S(1)		endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGGGTGTGCCGGGCACCATT	0.637																																					p.G318S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G952A	5						.						30.0	37.0	35.0					5																	159680741		2019	4158	6177	159613319	SO:0001583	missense	79616	exon7			BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.952G>A	5.37:g.159680741C>T	ENSP00000377547:p.Gly318Ser	Somatic		Capture	Illumina HiSeq	Phase_I	159613319	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	37	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.695494	0.00731	.	.	ENSG00000135083	ENST00000393977;ENST00000257536	T;T	0.27256	2.08;1.68	5.0	-4.07	0.03975	.	1.042630	0.07468	N	0.901765	T	0.08891	0.0220	N	0.03324	-0.35	0.09310	N	0.999999	B;B	0.23591	0.0;0.088	B;B	0.10450	0.001;0.005	T	0.34900	-0.9810	10	0.20046	T	0.44	-20.4251	6.7768	0.23624	0.1138:0.3902:0.0:0.496	.	270;318	B4DZA8;Q8IV13	.;CCNJL_HUMAN	S	318;270	ENSP00000377547:G318S;ENSP00000257536:G270S	ENSP00000257536:G270S	G	-	1	0	CCNJL	159613319	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.021000	0.12504	-0.720000	0.04935	-0.136000	0.14681	GGC		0.637	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
SPDL1	54908	broad.mit.edu	37	5	169021405	169021405	+	Missense_Mutation	SNP	G	G	A	rs201660793	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:169021405G>A	ENST00000265295.4	+	6	968	c.689G>A	c.(688-690)cGt>cAt	p.R230H	SPDL1_ENST00000510751.1_3'UTR	NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1									p.R230H(1)									TAGAAAGCTCGTGTAGCAAAT	0.358													G|||	2	0.000399361	0.0	0.0	5008	,	,		19747	0.001		0.0	False		,,,				2504	0.001				p.R230H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G689A	5						.						80.0	85.0	83.0					5																	169021405		2202	4300	6502	168953983	SO:0001583	missense	54908	exon6			BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"""spindly homolog (Drosophila)"""		"""coiled-coil domain containing 99"""	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.689G>A	5.37:g.169021405G>A	ENSP00000265295:p.Arg230His	Somatic		Capture	Illumina HiSeq	Phase_I	168953983	NM_017785		Missense_Mutation	SNP	ENST00000265295.4	37	CCDS4370.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	24.5	4.539715	0.85917	.	.	ENSG00000040275	ENST00000265295;ENST00000513941	T	0.53206	0.63	5.81	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.67183	0.2866	M	0.72894	2.215	0.58432	D	0.999999	D;P	0.89917	1.0;0.76	D;B	0.91635	0.999;0.191	T	0.68232	-0.5463	10	0.42905	T	0.14	-9.6157	15.0559	0.71912	0.068:0.0:0.932:0.0	.	152;230	B4E393;Q96EA4	.;SPDLY_HUMAN	H	230	ENSP00000265295:R230H	ENSP00000265295:R230H	R	+	2	0	CCDC99	168953983	1.000000	0.71417	0.986000	0.45419	0.967000	0.64934	4.731000	0.62022	1.453000	0.47775	-0.150000	0.13652	CGT		0.358	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785	
RGS14	10636	broad.mit.edu	37	5	176794499	176794499	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:176794499G>T	ENST00000408923.3	+	6	756	c.568G>T	c.(568-570)Gga>Tga	p.G190*		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	190					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)	p.G190*(1)		breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			CGAAGCCGAGGGACGCCCTCT	0.682																																					p.G190X	NSCLC(47;353 1896 28036)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G568T	5						.						20.0	22.0	22.0					5																	176794499		2024	4174	6198	176727105	SO:0001587	stop_gained	10636	exon6			AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"""Regulators of G-protein signaling"""	9996	protein-coding gene	gene with protein product		602513	"""regulator of G-protein signalling 14"""				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.568G>T	5.37:g.176794499G>T	ENSP00000386229:p.Gly190*	Somatic		Capture	Illumina HiSeq	Phase_I	176727105	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Nonsense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.0|28.0	4.884008|4.884008	0.91814|0.91814	.|.	.|.	ENSG00000169220|ENSG00000169220	ENST00000408923|ENST00000511890	.|.	.|.	.|.	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	0.064298|.	0.64402|.	D|.	0.000009|.	.|T	.|0.72301	.|0.3443	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74506	.|-0.3643	.|3	0.62326|.	D|.	0.03|.	-21.2226|-21.2226	17.3879|17.3879	0.87422|0.87422	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	X|S	190|59	.|.	ENSP00000386229:G190X|.	G|R	+|+	1|3	0|2	RGS14|RGS14	176727105|176727105	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.840000|0.840000	0.47671|0.47671	6.362000|6.362000	0.73077|0.73077	2.344000|2.344000	0.79699|0.79699	0.313000|0.313000	0.20887|0.20887	GGA|AGG		0.682	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480	
GRM6	2916	broad.mit.edu	37	5	178413416	178413416	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:178413416C>T	ENST00000517717.1	-	9	1877	c.1839G>A	c.(1837-1839)acG>acA	p.T613T	GRM6_ENST00000231188.5_Silent_p.T613T|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	613					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)			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)		GGACGATGGGCGTGTTGTTGT	0.677																																					p.T613T												.	.	0			c.G1839A	5						.						37.0	35.0	36.0					5																	178413416		2203	4300	6503	178346022	SO:0001819	synonymous_variant	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.1839G>A	5.37:g.178413416C>T		None		Capture	Illumina HiSeq	Phase_I	178346022	NM_000843		Silent	SNP	ENST00000517717.1	37	CCDS4442.1																																																																																				0.677	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
ZNF354C	30832	broad.mit.edu	37	5	178506334	178506334	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:178506334C>T	ENST00000315475.6	+	5	1207	c.901C>T	c.(901-903)Cga>Tga	p.R301*		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	301					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R301*(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GAAACCGTATCGATGTAGGGA	0.418																																					p.R301X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C901T	5						.						150.0	147.0	148.0					5																	178506334		2203	4300	6503	178438940	SO:0001587	stop_gained	30832	exon5				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.901C>T	5.37:g.178506334C>T	ENSP00000324064:p.Arg301*	Somatic		Capture	Illumina HiSeq	Phase_I	178438940	NM_014594	Q6P4P9|Q8NFX1	Nonsense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	C	18.17	3.563334	0.65651	.	.	ENSG00000177932	ENST00000315475	.	.	.	3.8	2.84	0.33178	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-5.9571	8.2791	0.31889	0.3551:0.6449:0.0:0.0	.	.	.	.	X	301	.	ENSP00000324064:R301X	R	+	1	2	ZNF354C	178438940	0.000000	0.05858	0.191000	0.23289	0.038000	0.13279	-2.135000	0.01306	2.108000	0.64289	0.591000	0.81541	CGA		0.418	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ZNF354C	30832	broad.mit.edu	37	5	178506423	178506423	+	Silent	SNP	C	C	T	rs373125160		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:178506423C>T	ENST00000315475.6	+	5	1296	c.990C>T	c.(988-990)tgC>tgT	p.C330C		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	330					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C330C(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TCTATAAATGCGGCGAATGTG	0.433																																					p.C330C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C990T	5						.	C		0,4406		0,0,2203	171.0	181.0	178.0		990	0.2	0.2	5		178	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF354C	NM_014594.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		330/555	178506423	1,13005	2203	4300	6503	178439029	SO:0001819	synonymous_variant	30832	exon5				CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.990C>T	5.37:g.178506423C>T		Somatic		Capture	Illumina HiSeq	Phase_I	178439029	NM_014594	Q6P4P9|Q8NFX1	Silent	SNP	ENST00000315475.6	37	CCDS4443.1																																																																																				0.433	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
TPPP	11076	broad.mit.edu	37	5	666222	666222	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:666222T>G	ENST00000360578.5	-	3	449	c.328A>C	c.(328-330)Acc>Ccc	p.T110P	CEP72_ENST00000514507.1_Intron|AC026740.1_ENST00000594226.1_5'Flank	NM_007030.2	NP_008961.1	O94811	TPPP_HUMAN	tubulin polymerization promoting protein	110	Mediates interaction with LIMK1.				microtubule bundle formation (GO:0001578)|microtubule polymerization (GO:0046785)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein polymerization (GO:0032273)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)	p.T110P(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5		Ovarian(839;0.0563)	Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)	GBM - Glioblastoma multiforme(108;0.0191)		AAGGTGATGGTCCGGCAAGAC	0.657																																					p.T110P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A328C	5						.						75.0	69.0	71.0					5																	666222		2203	4300	6503	719222	SO:0001583	missense	11076	exon3			AB017016	CCDS3856.1	5p15.33	2008-02-05			ENSG00000171368	ENSG00000171368			24164	protein-coding gene	gene with protein product	"""brain specific protein p25 alpha"""	608773				10083737, 12093283, 15590652, 17105200	Standard	NM_007030		Approved	p25alpha, TPPP1, p25, TPPP/p25	uc003jbh.4	O94811	OTTHUMG00000131011	ENST00000360578.5:c.328A>C	5.37:g.666222T>G	ENSP00000353785:p.Thr110Pro	Somatic		Capture	Illumina HiSeq	Phase_I	719222	NM_007030		Missense_Mutation	SNP	ENST00000360578.5	37	CCDS3856.1	.	.	.	.	.	.	.	.	.	.	t	13.63	2.295187	0.40594	.	.	ENSG00000171368	ENST00000360578	T	0.44083	0.93	4.54	2.01	0.26516	EF-hand-like domain (1);	0.107677	0.64402	N	0.000006	T	0.56337	0.1978	M	0.79475	2.455	0.42889	D	0.994199	D	0.69078	0.997	D	0.67231	0.95	T	0.51826	-0.8656	10	0.36615	T	0.2	-32.7042	6.3067	0.21143	0.0:0.0799:0.3092:0.6109	.	110	O94811	TPPP_HUMAN	P	110	ENSP00000353785:T110P	ENSP00000353785:T110P	T	-	1	0	TPPP	719222	0.001000	0.12720	0.989000	0.46669	0.135000	0.20990	0.485000	0.22324	0.193000	0.20303	-0.501000	0.04562	ACC		0.657	TPPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253645.3	NM_007030	
SLC6A18	348932	broad.mit.edu	37	5	1243834	1243834	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:1243834delG	ENST00000324642.3	+	9	1419	c.1296delG	c.(1294-1296)gtgfs	p.V432fs	SLC6A18_ENST00000296821.4_Intron	NM_182632.2	NP_872438.2	Q96N87	S6A18_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 18	432					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)	p.V434fs*11(1)		endometrium(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(4)|upper_aerodigestive_tract(1)	34	all_cancers(3;2.99e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.76e-10)		Epithelial(17;0.000356)|all cancers(22;0.00124)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			TGCTGGACGTGGGGGTCCTGC	0.652																																					p.V432fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1296delG	5						.						67.0	59.0	62.0					5																	1243834		2203	4300	6503	1296834	SO:0001589	frameshift_variant	348932	exon9			AK055798	CCDS3860.1	5p15	2013-07-19	2013-07-19		ENSG00000164363	ENSG00000164363		"""Solute carriers"""	26441	protein-coding gene	gene with protein product		610300	"""solute carrier family 6 (neurotransmitter transporter), member 18"", ""solute carrier family 6, member 18"""			19478081	Standard	NM_182632		Approved	FLJ31236, Xtrp2	uc003jby.2	Q96N87	OTTHUMG00000090356	ENST00000324642.3:c.1296delG	5.37:g.1243834delG	ENSP00000323549:p.Val432fs	Somatic		Capture	Illumina HiSeq	Phase_I	1296834	NM_182632		Frame_Shift_Del	DEL	ENST00000324642.3	37	CCDS3860.1																																																																																				0.652	SLC6A18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206728.3	NM_182632	
MTRR	4552	broad.mit.edu	37	5	7889311	7889311	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:7889311T>C	ENST00000264668.2	+	9	1361	c.1331T>C	c.(1330-1332)gTa>gCa	p.V444A	MTRR_ENST00000440940.2_Missense_Mutation_p.V417A	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	444	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)	p.V444A(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AGCCGCTTTGTACGAGATGCC	0.537																																					p.V417A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1250C	5						.						187.0	160.0	169.0					5																	7889311		2203	4300	6503	7942311	SO:0001583	missense	4552	exon9			AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1331T>C	5.37:g.7889311T>C	ENSP00000264668:p.Val444Ala	Somatic		Capture	Illumina HiSeq	Phase_I	7942311	NM_002454	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	T	16.69	3.194083	0.58017	.	.	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.35789	1.29;1.29	5.08	5.08	0.68730	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.471231	0.23095	N	0.051984	T	0.54615	0.1869	M	0.83223	2.63	0.80722	D	1	P	0.48834	0.916	P	0.51582	0.674	T	0.62789	-0.6780	10	0.66056	D	0.02	-10.3355	14.8678	0.70430	0.0:0.0:0.0:1.0	.	444	Q9UBK8	MTRR_HUMAN	A	444;417	ENSP00000264668:V444A;ENSP00000402510:V417A	ENSP00000264668:V444A	V	+	2	0	MTRR	7942311	0.967000	0.33354	0.033000	0.17914	0.016000	0.09150	7.556000	0.82233	1.909000	0.55274	0.533000	0.62120	GTA		0.537	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
FAM105A	54491	broad.mit.edu	37	5	14608915	14608915	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:14608915delT	ENST00000274217.3	+	7	806	c.686delT	c.(685-687)cttfs	p.L229fs		NM_019018.2	NP_061891.1	Q9NUU6	F105A_HUMAN	family with sequence similarity 105, member A	229	OTU.							p.S231fs*13(1)		large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11	Lung NSC(4;0.00592)					TGCAACACCCTTTTTTCAGAT	0.328																																					p.L229fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.686delT	5						.						77.0	77.0	77.0					5																	14608915		2203	4300	6503	14661915	SO:0001589	frameshift_variant	54491	exon7				CCDS3884.1	5p15.2	2014-02-24			ENSG00000145569	ENSG00000145569		"""OTU domain containing"""	25629	protein-coding gene	gene with protein product						12477932	Standard	NM_019018		Approved	FLJ11127, NET20	uc003jfj.3	Q9NUU6	OTTHUMG00000131056	ENST00000274217.3:c.686delT	5.37:g.14608915delT	ENSP00000274217:p.Leu229fs	Somatic		Capture	Illumina HiSeq	Phase_I	14661915	NM_019018	Q53H50|Q9H037	Frame_Shift_Del	DEL	ENST00000274217.3	37	CCDS3884.1																																																																																				0.328	FAM105A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253710.1	NM_019018	
CDH18	1016	broad.mit.edu	37	5	19483492	19483492	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:19483492G>A	ENST00000507958.1	-	14	2790	c.1800C>T	c.(1798-1800)tgC>tgT	p.C600C	CDH18_ENST00000502796.1_Missense_Mutation_p.A564V|CDH18_ENST00000506372.1_Missense_Mutation_p.A565V|CDH18_ENST00000382275.1_Silent_p.C600C|CDH18_ENST00000274170.4_Silent_p.C600C			Q13634	CAD18_HUMAN	cadherin 18, type 2	600	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.C600C(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(24)|lung(76)|ovary(5)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)	138	Lung NSC(1;0.00734)|all_lung(1;0.0197)					CTTCTGCATGGCAGGTCCGCA	0.527																																					p.A564V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1691T	5						.						75.0	67.0	70.0					5																	19483492		2203	4300	6503	19519249	SO:0001819	synonymous_variant	1016	exon12			U59325	CCDS3889.1, CCDS54835.1, CCDS75229.1	5p14.3	2010-01-26			ENSG00000145526	ENSG00000145526		"""Cadherins / Major cadherins"""	1757	protein-coding gene	gene with protein product		603019				9030594, 10191097	Standard	NM_004934		Approved	CDH14, EY-CADHERIN	uc003jgd.3	Q13634	OTTHUMG00000090578	ENST00000507958.1:c.1800C>T	5.37:g.19483492G>A		Somatic		Capture	Illumina HiSeq	Phase_I	19519249	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Missense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	G	18.05	3.535974	0.64972	.	.	ENSG00000145526	ENST00000506372;ENST00000502796;ENST00000515257	T;T;T	0.58797	0.31;0.31;0.51	5.54	5.54	0.83059	.	.	.	.	.	T	0.47040	0.1424	.	.	.	0.80722	D	1	B	0.19445	0.036	B	0.15052	0.012	T	0.33497	-0.9866	7	.	.	.	.	18.0513	0.89349	0.0:0.0:1.0:0.0	.	564	B4DHG6	.	V	565;564;431	ENSP00000424931:A565V;ENSP00000422138:A564V;ENSP00000427383:A431V	.	A	-	2	0	CDH18	19519249	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.537000	0.60643	2.615000	0.88500	0.655000	0.94253	GCC		0.527	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934	
PRDM9	56979	broad.mit.edu	37	5	23527757	23527757	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:23527757C>T	ENST00000296682.3	+	11	2742	c.2560C>T	c.(2560-2562)Cac>Tac	p.H854Y		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	854					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)	p.H854Y(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						CCAGAGGACACACACAGGGGA	0.592										HNSCC(3;0.000094)																											p.H854Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2560T	5						.						71.0	80.0	77.0					5																	23527757		2191	4295	6486	23563514	SO:0001583	missense	56979	exon11			AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2560C>T	5.37:g.23527757C>T	ENSP00000296682:p.His854Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	23563514	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927429	0.52759	.	.	ENSG00000164256	ENST00000296682	T	0.67523	-0.27	3.2	3.2	0.36748	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.84483	0.5482	H	0.95187	3.635	0.41644	D	0.989091	P	0.52061	0.95	P	0.61874	0.895	D	0.88858	0.3324	9	0.87932	D	0	-8.385	12.3711	0.55256	0.0:1.0:0.0:0.0	.	854	Q9NQV7	PRDM9_HUMAN	Y	854	ENSP00000296682:H854Y	ENSP00000296682:H854Y	H	+	1	0	PRDM9	23563514	1.000000	0.71417	1.000000	0.80357	0.341000	0.28922	5.955000	0.70306	1.837000	0.53436	0.472000	0.43445	CAC		0.592	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
CDH10	1008	broad.mit.edu	37	5	24488246	24488246	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:24488246A>G	ENST00000264463.4	-	12	2400	c.1893T>C	c.(1891-1893)ttT>ttC	p.F631F	CDH10_ENST00000502921.1_5'UTR	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	631					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.F631F(1)		NS(1)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(29)|lung(111)|ovary(6)|pancreas(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)	185				STAD - Stomach adenocarcinoma(35;0.0556)		TCAGAGCTGCAAACAGTACTA	0.363										HNSCC(23;0.051)																											p.F631F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1893C	5						.						37.0	38.0	38.0					5																	24488246		2200	4289	6489	24524003	SO:0001819	synonymous_variant	1008	exon12			AF039747	CCDS3892.1	5p14.2	2010-01-26			ENSG00000040731	ENSG00000040731		"""Cadherins / Major cadherins"""	1749	protein-coding gene	gene with protein product		604555				2059658	Standard	NM_006727		Approved		uc003jgr.2	Q9Y6N8	OTTHUMG00000090667	ENST00000264463.4:c.1893T>C	5.37:g.24488246A>G		Somatic		Capture	Illumina HiSeq	Phase_I	24524003	NM_006727	Q9ULB3	Silent	SNP	ENST00000264463.4	37	CCDS3892.1																																																																																				0.363	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727	
DROSHA	29102	broad.mit.edu	37	5	31472171	31472171	+	Splice_Site	SNP	G	G	A	rs202101007		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:31472171G>A	ENST00000511367.2	-	16	2484	c.2240C>T	c.(2239-2241)aCg>aTg	p.T747M	DROSHA_ENST00000344624.3_Splice_Site_p.T747M|DROSHA_ENST00000513349.1_Splice_Site_p.T710M|DROSHA_ENST00000442743.1_Splice_Site_p.T710M	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	747	Necessary for interaction with DGCR8 and pri-miRNA processing activity.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)	p.T747M(2)		breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AGAACATACCGTCCCAGGGTT	0.443																																					p.T747M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C2240T	5						.	G	MET/THR,MET/THR	0,3972		0,0,1986	140.0	136.0	138.0		2129,2240	4.8	1.0	5		138	1,8299		0,1,4149	no	missense-near-splice,missense-near-splice	DROSHA	NM_001100412.1,NM_013235.4	81,81	0,1,6135	AA,AG,GG		0.012,0.0,0.0081	benign,benign	710/1338,747/1375	31472171	1,12271	1986	4150	6136	31507928	SO:0001630	splice_region_variant	29102	exon16			AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.2241+1C>T	5.37:g.31472171G>A		Somatic		Capture	Illumina HiSeq	Phase_I	31507928	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	G	8.521	0.868785	0.17322	0.0	1.2E-4	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188	T;T;T;T	0.39592	1.65;1.65;1.07;1.07	5.81	4.84	0.62591	.	0.084366	0.85682	D	0.000000	T	0.12050	0.0293	N	0.00633	-1.31	0.45648	D	0.998571	B;B	0.14805	0.011;0.006	B;B	0.10450	0.004;0.005	T	0.17531	-1.0366	10	0.30854	T	0.27	-11.2848	3.8438	0.08926	0.3268:0.0:0.6732:0.0	.	710;747	E7EMP9;Q9NRR4	.;RNC_HUMAN	M	747;747;710;710;672;703	ENSP00000425979:T747M;ENSP00000339845:T747M;ENSP00000409335:T710M;ENSP00000424161:T710M	ENSP00000265075:T672M	T	-	2	0	DROSHA	31507928	1.000000	0.71417	0.994000	0.49952	0.831000	0.47069	6.044000	0.71012	2.746000	0.94184	0.655000	0.94253	ACG		0.443	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	Missense_Mutation
TARS	6897	broad.mit.edu	37	5	33453456	33453456	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:33453456G>A	ENST00000265112.3	+	4	703	c.392G>A	c.(391-393)cGc>cAc	p.R131H	TARS_ENST00000502553.1_Missense_Mutation_p.R131H|TARS_ENST00000414361.2_Intron|TARS_ENST00000455217.2_Missense_Mutation_p.R164H|TARS_ENST00000541634.1_Missense_Mutation_p.R27H	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	131					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)	p.R131H(2)		NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	GACCTGGACCGCCCTCTGGAA	0.393																																					p.R131H												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G392A	5						.						117.0	122.0	120.0					5																	33453456		2203	4300	6503	33489213	SO:0001583	missense	6897	exon4			AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	11572	protein-coding gene	gene with protein product	"""threonine tRNA ligase 1, cytoplasmic"""	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.392G>A	5.37:g.33453456G>A	ENSP00000265112:p.Arg131His	Somatic		Capture	Illumina HiSeq	Phase_I	33489213	NM_152295	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Missense_Mutation	SNP	ENST00000265112.3	37	CCDS3899.1	.	.	.	.	.	.	.	.	.	.	G	35	5.474492	0.96291	.	.	ENSG00000113407	ENST00000502553;ENST00000265112;ENST00000541634;ENST00000455217	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	5.9	5.02	0.67125	TGS-like (1);TGS (1);Beta-grasp fold, ferredoxin-type (1);	0.000000	0.85682	D	0.000000	T	0.38295	0.1035	M	0.93016	3.37	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.986;0.995	T	0.44559	-0.9320	10	0.72032	D	0.01	-15.6244	15.516	0.75826	0.0672:0.0:0.9328:0.0	.	164;27;131	B4DEG8;G3XAN9;P26639	.;.;SYTC_HUMAN	H	131;131;27;164	ENSP00000424387:R131H;ENSP00000265112:R131H;ENSP00000438469:R27H;ENSP00000387710:R164H	ENSP00000265112:R131H	R	+	2	0	TARS	33489213	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	8.013000	0.88655	2.810000	0.96702	0.585000	0.79938	CGC		0.393	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295	
RXFP3	51289	broad.mit.edu	37	5	33937182	33937182	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:33937182C>T	ENST00000330120.3	+	1	692	c.337C>T	c.(337-339)Cgc>Tgc	p.R113C		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	113					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)	p.R113C(2)		endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						GCAGGGCTGGCGCAAGTCCTC	0.592																																					p.R113C												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C337T	5						.						111.0	103.0	106.0					5																	33937182		2203	4300	6503	33972939	SO:0001583	missense	51289	exon1			D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"""GPCR / Class A : Relaxin family peptide receptors"""	24883	protein-coding gene	gene with protein product		609445	"""relaxin 3 receptor 1"", ""relaxin family peptide receptor 3"""	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.337C>T	5.37:g.33937182C>T	ENSP00000328708:p.Arg113Cys	Somatic		Capture	Illumina HiSeq	Phase_I	33972939	NM_016568	Q14DA5	Missense_Mutation	SNP	ENST00000330120.3	37	CCDS3900.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.685466	0.68157	.	.	ENSG00000182631	ENST00000330120	T	0.46063	0.88	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.153499	0.53938	D	0.000047	T	0.65606	0.2707	M	0.83223	2.63	0.54753	D	0.999988	D	0.89917	1.0	D	0.72625	0.978	T	0.69544	-0.5117	10	0.72032	D	0.01	-20.2284	12.6926	0.56982	0.2731:0.7269:0.0:0.0	.	113	Q9NSD7	RL3R1_HUMAN	C	113	ENSP00000328708:R113C	ENSP00000328708:R113C	R	+	1	0	RXFP3	33972939	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.411000	0.59781	2.700000	0.92200	0.650000	0.86243	CGC		0.592	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568	
NIPBL	25836	broad.mit.edu	37	5	37064770	37064770	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:37064770A>C	ENST00000282516.8	+	47	8690	c.8191A>C	c.(8191-8193)Acc>Ccc	p.T2731P		NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	2731					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)	p.T2731P(1)		autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			AGTGCAGAAAACCAGCAGTGG	0.512																																					p.T2731P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A8191C	5						.						160.0	145.0	150.0					5																	37064770		2203	4300	6503	37100527	SO:0001583	missense	25836	exon47			AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.8191A>C	5.37:g.37064770A>C	ENSP00000282516:p.Thr2731Pro	Somatic		Capture	Illumina HiSeq	Phase_I	37100527	NM_133433	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Missense_Mutation	SNP	ENST00000282516.8	37	CCDS3920.1	.	.	.	.	.	.	.	.	.	.	A	16.67	3.187183	0.57909	.	.	ENSG00000164190	ENST00000282516	D	0.94650	-3.48	5.84	5.84	0.93424	.	0.118550	0.56097	D	0.000038	D	0.93132	0.7813	L	0.29908	0.895	0.80722	D	1	D	0.61080	0.989	P	0.50708	0.648	D	0.94049	0.7316	10	0.72032	D	0.01	-5.8377	16.2167	0.82231	1.0:0.0:0.0:0.0	.	2731	Q6KC79	NIPBL_HUMAN	P	2731	ENSP00000282516:T2731P	ENSP00000282516:T2731P	T	+	1	0	NIPBL	37100527	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.962000	0.93254	2.231000	0.72958	0.533000	0.62120	ACC		0.512	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
RICTOR	253260	broad.mit.edu	37	5	38945041	38945041	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:38945041C>A	ENST00000357387.3	-	35	4793	c.4763G>T	c.(4762-4764)aGc>aTc	p.S1588I	RICTOR_ENST00000296782.5_Missense_Mutation_p.S1612I	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2									p.S1588I(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GCTTTTGGTGCTGCTAGCTGA	0.398																																					p.S1588I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G4763T	5						.						115.0	114.0	115.0					5																	38945041		2203	4300	6503	38980798	SO:0001583	missense	253260	exon35				CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.4763G>T	5.37:g.38945041C>A	ENSP00000349959:p.Ser1588Ile	Somatic		Capture	Illumina HiSeq	Phase_I	38980798	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.701333	0.88924	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.55052	0.55;0.54	5.34	5.34	0.76211	.	0.036042	0.85682	D	0.000000	T	0.70369	0.3216	M	0.68593	2.085	0.58432	D	0.999998	D;P	0.64830	0.994;0.904	P;P	0.62298	0.9;0.571	T	0.73062	-0.4101	10	0.87932	D	0	-11.6307	19.4047	0.94643	0.0:1.0:0.0:0.0	.	1588;1612	Q6R327;Q6R327-3	RICTR_HUMAN;.	I	1588;1612	ENSP00000349959:S1588I;ENSP00000296782:S1612I	ENSP00000296782:S1612I	S	-	2	0	RICTOR	38980798	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.591000	0.74090	2.660000	0.90430	0.563000	0.77884	AGC		0.398	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
OXCT1	5019	broad.mit.edu	37	5	41805770	41805770	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:41805770C>T	ENST00000196371.5	-	9	1014	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	OXCT1_ENST00000509987.1_Missense_Mutation_p.R99Q	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	285					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)	p.R285Q(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	TCCCTCTTTCCGGATTGATAA	0.383																																					p.R285Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G854A	5						.						104.0	106.0	105.0					5																	41805770		2203	4300	6503	41841527	SO:0001583	missense	5019	exon9			U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.854G>A	5.37:g.41805770C>T	ENSP00000196371:p.Arg285Gln	Somatic		Capture	Illumina HiSeq	Phase_I	41841527	NM_000436	B2R5V2|B7Z528	Missense_Mutation	SNP	ENST00000196371.5	37	CCDS3937.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.863757	0.51482	.	.	ENSG00000083720	ENST00000196371;ENST00000509987	T;T	0.78816	-1.21;-1.21	5.65	5.65	0.86999	.	0.202046	0.43919	D	0.000506	T	0.75451	0.3851	M	0.65498	2.005	0.33154	D	0.546049	B	0.23990	0.095	B	0.08055	0.003	T	0.74642	-0.3597	10	0.17832	T	0.49	-11.1818	18.8549	0.92247	0.0:1.0:0.0:0.0	.	285	P55809	SCOT1_HUMAN	Q	285;99	ENSP00000196371:R285Q;ENSP00000425348:R99Q	ENSP00000196371:R285Q	R	-	2	0	OXCT1	41841527	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	2.634000	0.46528	2.821000	0.97095	0.650000	0.86243	CGG		0.383	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436	
FST	10468	broad.mit.edu	37	5	52776663	52776663	+	Silent	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:52776663G>C	ENST00000256759.3	+	1	425	c.42G>C	c.(40-42)ctG>ctC	p.L14L	FST_ENST00000396947.3_Silent_p.L14L	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	14					BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)	p.L14L(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				TTTGCCTCCTGCTGCTGCTGC	0.731																																					p.L14L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G42C	5						.						20.0	15.0	17.0					5																	52776663		2000	3838	5838	52812420	SO:0001819	synonymous_variant	10468	exon1			M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.42G>C	5.37:g.52776663G>C		Somatic		Capture	Illumina HiSeq	Phase_I	52812420	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1																																																																																				0.731	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409	
ARL15	54622	broad.mit.edu	37	5	53409208	53409208	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:53409208A>G	ENST00000504924.1	-	4	379	c.286T>C	c.(286-288)Tac>Cac	p.Y96H	ARL15_ENST00000510591.2_5'UTR|ARL15_ENST00000502271.1_5'UTR|ARL15_ENST00000507646.2_Missense_Mutation_p.Y96H	NM_019087.2	NP_061960.1	Q9NXU5	ARL15_HUMAN	ADP-ribosylation factor-like 15	96					small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	GTP binding (GO:0005525)	p.Y84H(1)|p.Y96H(1)		endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	6		Lung NSC(810;0.000779)				CCTTGGTAGTAGCGGCTCCAG	0.408																																					p.Y96H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T286C	5						.						79.0	74.0	75.0					5																	53409208		1841	4090	5931	53444965	SO:0001583	missense	54622	exon4			BC026093	CCDS54850.1	5p15.2	2014-05-09	2005-11-03	2005-11-03		ENSG00000185305		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	25945	protein-coding gene	gene with protein product			"""ADP-ribosylation factor related protein 2"""	ARFRP2		12477932	Standard	NM_019087		Approved	FLJ20051	uc003jpg.1	Q9NXU5		ENST00000504924.1:c.286T>C	5.37:g.53409208A>G	ENSP00000433427:p.Tyr96His	Somatic		Capture	Illumina HiSeq	Phase_I	53444965	NM_019087	Q6IAD0	Missense_Mutation	SNP	ENST00000504924.1	37	CCDS54850.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.744215	0.89663	.	.	ENSG00000185305	ENST00000504924;ENST00000507646	T;T	0.79653	-1.29;-1.29	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.91026	0.7177	M	0.87617	2.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92455	0.5973	10	0.87932	D	0	-15.4941	16.3083	0.82859	1.0:0.0:0.0:0.0	.	96	Q9NXU5	ARL15_HUMAN	H	96	ENSP00000433427:Y96H;ENSP00000432680:Y96H	ENSP00000433427:Y96H	Y	-	1	0	ARL15	53444965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.250000	0.74265	0.455000	0.32223	TAC		0.408	ARL15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368432.2	NM_019087	
CDC20B	166979	broad.mit.edu	37	5	54420640	54420640	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:54420640C>T	ENST00000381375.2	-	9	1351	c.1206G>A	c.(1204-1206)acG>acA	p.T402T	CDC20B_ENST00000296733.1_Silent_p.T402T|CDC20B_ENST00000322374.6_Silent_p.T402T|CDC20B_ENST00000334206.5_3'UTR			Q86Y33	CD20B_HUMAN	cell division cycle 20B	402								p.T402T(1)		kidney(1)|large_intestine(5)|lung(7)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	19		Lung NSC(810;0.000744)|Breast(144;0.159)|Prostate(74;0.194)	LUSC - Lung squamous cell carcinoma(15;0.225)			CCTTGACTGCCGTAGACTGGG	0.473																																					p.T402T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1206A	5						.						63.0	58.0	59.0					5																	54420640		2203	4300	6503	54456397	SO:0001819	synonymous_variant	166979	exon9			AB086378	CCDS3966.1, CCDS47207.1, CCDS54852.1	5q11.2	2013-01-17	2013-01-17		ENSG00000164287	ENSG00000164287		"""WD repeat domain containing"""	24222	protein-coding gene	gene with protein product			"""CDC20 cell division cycle 20 homolog B (S. cerevisiae)"", ""cell division cycle 20 homolog B (S. cerevisiae)"""				Standard	NM_152623		Approved	FLJ37927	uc003jpo.2	Q86Y33	OTTHUMG00000131185	ENST00000381375.2:c.1206G>A	5.37:g.54420640C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54456397	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																				0.473	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623	
GPBP1	65056	broad.mit.edu	37	5	56526957	56526957	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:56526957C>T	ENST00000506184.2	+	5	1325	c.220C>T	c.(220-222)Cgt>Tgt	p.R74C	GPBP1_ENST00000424459.3_Missense_Mutation_p.R74C|GPBP1_ENST00000514387.2_5'UTR|GPBP1_ENST00000538707.1_Missense_Mutation_p.R81C|GPBP1_ENST00000264779.6_Missense_Mutation_p.R81C|GPBP1_ENST00000511209.1_Missense_Mutation_p.R81C|GPBP1_ENST00000454432.2_Missense_Mutation_p.R74C			Q86WP2	GPBP1_HUMAN	GC-rich promoter binding protein 1	74					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R74C(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	19		Lung NSC(810;0.000861)|Prostate(74;0.0305)|Breast(144;0.222)		OV - Ovarian serous cystadenocarcinoma(10;7.64e-39)		AAATGGATGGCGTACACATGG	0.348																																					p.R74C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C220T	5						.						83.0	75.0	78.0					5																	56526957		2203	4300	6503	56562714	SO:0001583	missense	65056	exon5				CCDS34162.1, CCDS47211.1, CCDS47212.1, CCDS47212.2, CCDS56368.1	5q11.2	2008-02-05				ENSG00000062194			29520	protein-coding gene	gene with protein product		608412				12842993	Standard	NM_022913		Approved	DKFZp761C169, vasculin	uc003jrk.4	Q86WP2		ENST00000506184.2:c.220C>T	5.37:g.56526957C>T	ENSP00000421202:p.Arg74Cys	Somatic		Capture	Illumina HiSeq	Phase_I	56562714	NM_022913	A6NKW3|Q6NSH6|Q9H0D4|Q9H785|Q9NSN4	Missense_Mutation	SNP	ENST00000506184.2	37	CCDS34162.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.260274	0.39995	.	.	ENSG00000062194	ENST00000424459;ENST00000506184;ENST00000454432;ENST00000511209;ENST00000264779;ENST00000538707	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.76	3.97	0.46021	.	0.052272	0.85682	D	0.000000	T	0.27241	0.0668	N	0.22421	0.69	0.58432	D	0.999996	B;B;B;B	0.31640	0.134;0.333;0.163;0.333	B;B;B;B	0.25506	0.031;0.061;0.042;0.061	T	0.07888	-1.0749	10	0.35671	T	0.21	-11.4601	12.6511	0.56761	0.0:0.8641:0.0:0.1359	.	74;81;81;74	D4PHA4;Q86WP2-2;Q86WP2-3;Q86WP2	.;.;.;GPBP1_HUMAN	C	74;74;74;81;81;81	ENSP00000401596:R74C;ENSP00000421202:R74C;ENSP00000403522:R74C;ENSP00000422337:R81C;ENSP00000264779:R81C;ENSP00000440090:R81C	ENSP00000264779:R81C	R	+	1	0	GPBP1	56562714	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.924000	0.48876	1.444000	0.47605	0.591000	0.81541	CGT		0.348	GPBP1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000374496.1	NM_022913	
ACTBL2	345651	broad.mit.edu	37	5	56777684	56777684	+	Missense_Mutation	SNP	A	A	G	rs368870319		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:56777684A>G	ENST00000423391.1	-	1	952	c.851T>C	c.(850-852)aTg>aCg	p.M284T	AC025470.1_ENST00000584598.1_RNA|CTD-2023N9.1_ENST00000506106.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	284						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)	p.M284T(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		ATCGCACTTCATGATAGAGTT	0.493																																					p.M284T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T851C	5						.	A	THR/MET	0,4406		0,0,2203	111.0	102.0	105.0		851	4.9	1.0	5		105	2,8598	2.2+/-6.3	0,2,4298	no	missense	ACTBL2	NM_001017992.2	81	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign	284/377	56777684	2,13004	2203	4300	6503	56813441	SO:0001583	missense	345651	exon1				CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.851T>C	5.37:g.56777684A>G	ENSP00000416706:p.Met284Thr	Somatic		Capture	Illumina HiSeq	Phase_I	56813441	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348672	0.41599	0.0	2.33E-4	ENSG00000169067	ENST00000423391	D	0.94280	-3.39	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.96225	0.8769	M	0.83774	2.66	0.47949	D	0.999552	P	0.34743	0.466	P	0.54174	0.744	D	0.96661	0.9489	10	0.87932	D	0	.	12.5346	0.56135	1.0:0.0:0.0:0.0	.	284	Q562R1	ACTBL_HUMAN	T	284	ENSP00000416706:M284T	ENSP00000416706:M284T	M	-	2	0	ACTBL2	56813441	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.332000	0.79203	2.057000	0.61298	0.533000	0.62120	ATG		0.493	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992	
SMIM15	643155	broad.mit.edu	37	5	60455859	60455859	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:60455859A>G	ENST00000339020.3	-	3	565	c.140T>C	c.(139-141)aTg>aCg	p.M47T	CTC-436P18.1_ENST00000506902.1_RNA|SMIM15_ENST00000507416.1_Missense_Mutation_p.M47T	NM_001048249.3	NP_001041714.1	Q7Z3B0	SIM15_HUMAN	small integral membrane protein 15	47						integral component of membrane (GO:0016021)		p.M47T(1)									GGCCTCAATCATCTTGGCCAA	0.453																																					p.M47T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T140C	5						.						167.0	152.0	157.0					5																	60455859		2203	4300	6503	60491616	SO:0001583	missense	643155	exon3				CCDS34165.1	5q12	2013-06-21	2012-12-03	2012-12-03	ENSG00000188725	ENSG00000188725			33861	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 43"""	C5orf43			Standard	NM_001048249		Approved	DKFZP686E2158	uc010iwm.1	Q7Z3B0	OTTHUMG00000162241	ENST00000339020.3:c.140T>C	5.37:g.60455859A>G	ENSP00000339324:p.Met47Thr	Somatic		Capture	Illumina HiSeq	Phase_I	60491616	NM_001048249	B9EJC4	Missense_Mutation	SNP	ENST00000339020.3	37	CCDS34165.1	.	.	.	.	.	.	.	.	.	.	A	10.58	1.390575	0.25118	.	.	ENSG00000188725	ENST00000339020;ENST00000507416	T;T	0.42513	0.97;0.97	5.23	5.23	0.72850	.	0.041383	0.85682	D	0.000000	T	0.35158	0.0922	.	.	.	0.80722	D	1	B	0.17667	0.023	B	0.17098	0.017	T	0.09314	-1.0680	9	0.30854	T	0.27	-10.7279	15.1104	0.72351	1.0:0.0:0.0:0.0	.	47	Q7Z3B0	CE043_HUMAN	T	47	ENSP00000339324:M47T;ENSP00000421336:M47T	ENSP00000339324:M47T	M	-	2	0	C5orf43	60491616	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.848000	0.92172	1.983000	0.57843	0.533000	0.62120	ATG		0.453	SMIM15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368078.1	NM_001048249	
CARTPT	9607	broad.mit.edu	37	5	71015749	71015749	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:71015749C>T	ENST00000296777.4	+	2	333	c.202C>T	c.(202-204)Cgt>Tgt	p.R68C	CARTPT_ENST00000513096.1_3'UTR	NM_004291.3	NP_004282.1	Q16568	CART_HUMAN	CART prepropeptide	68					activation of MAPKK activity (GO:0000186)|adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|circadian regulation of gene expression (GO:0032922)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of appetite (GO:0032099)|negative regulation of bone resorption (GO:0045779)|negative regulation of glucagon secretion (GO:0070093)|negative regulation of osteoclast differentiation (GO:0045671)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of epinephrine secretion (GO:0032812)|positive regulation of transmission of nerve impulse (GO:0051971)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|somatostatin secretion (GO:0070253)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|secretory granule (GO:0030141)		p.R68C(1)		large_intestine(1)|lung(2)|ovary(1)	4		Lung NSC(167;0.00153)|Ovarian(174;0.0175)|Prostate(74;0.11)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;8.4e-56)	Amphetamine(DB00182)	CAAGAGTAAACGTGTTCCCAT	0.527																																					p.R68C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C202T	5						.						172.0	153.0	159.0					5																	71015749		2203	4300	6503	71051505	SO:0001583	missense	9607	exon2			U16826	CCDS4011.1	5q13.2	2008-02-05			ENSG00000164326	ENSG00000164326			24323	protein-coding gene	gene with protein product	"""cocaine and amphetamine regulated transcript"""	602606				9590691, 8647455	Standard	NM_004291		Approved	CART	uc003kbv.2	Q16568	OTTHUMG00000131261	ENST00000296777.4:c.202C>T	5.37:g.71015749C>T	ENSP00000296777:p.Arg68Cys	Somatic		Capture	Illumina HiSeq	Phase_I	71051505	NM_004291	Q6FG92	Missense_Mutation	SNP	ENST00000296777.4	37	CCDS4011.1	.	.	.	.	.	.	.	.	.	.	C	18.33	3.599335	0.66332	.	.	ENSG00000164326	ENST00000296777	T	0.59772	0.24	5.02	4.13	0.48395	.	0.184559	0.46145	D	0.000301	T	0.61311	0.2337	L	0.55990	1.75	0.58432	D	0.999991	D	0.54397	0.966	P	0.51487	0.671	T	0.64748	-0.6334	10	0.87932	D	0	.	11.5773	0.50869	0.3434:0.6566:0.0:0.0	.	68	Q16568	CART_HUMAN	C	68	ENSP00000296777:R68C	ENSP00000296777:R68C	R	+	1	0	CARTPT	71051505	0.989000	0.36119	0.997000	0.53966	0.883000	0.51084	0.259000	0.18405	1.075000	0.40932	0.655000	0.94253	CGT		0.527	CARTPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254029.2	NM_004291	
PTCD2	79810	broad.mit.edu	37	5	71627179	71627179	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:71627179G>T	ENST00000380639.5	+	4	461	c.445G>T	c.(445-447)Gca>Tca	p.A149S	PTCD2_ENST00000503868.1_Intron|PTCD2_ENST00000536805.1_Intron|PTCD2_ENST00000543322.1_Missense_Mutation_p.A149S	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	149					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)	p.A149S(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		CGAGGAATCTGCAGTGGAGCT	0.408																																					p.A149S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G445T	5						.						280.0	251.0	261.0					5																	71627179		2203	4300	6503	71662935	SO:0001583	missense	79810	exon4			BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.445G>T	5.37:g.71627179G>T	ENSP00000370013:p.Ala149Ser	Somatic		Capture	Illumina HiSeq	Phase_I	71662935	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Missense_Mutation	SNP	ENST00000380639.5	37	CCDS4014.2	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354889	0.61293	.	.	ENSG00000049883	ENST00000380639;ENST00000543322	T;T	0.61392	0.11;0.11	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.76856	0.4046	M	0.76002	2.32	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77360	-0.2617	10	0.59425	D	0.04	.	18.3504	0.90336	0.0:0.0:1.0:0.0	.	149	Q8WV60	PTCD2_HUMAN	S	149	ENSP00000370013:A149S;ENSP00000438810:A149S	ENSP00000308948:A149S	A	+	1	0	PTCD2	71662935	1.000000	0.71417	0.852000	0.33557	0.008000	0.06430	7.154000	0.77437	2.868000	0.98415	0.557000	0.71058	GCA		0.408	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754	
ZNF366	167465	broad.mit.edu	37	5	71739686	71739686	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:71739686C>T	ENST00000318442.5	-	5	2622	c.2132G>A	c.(2131-2133)gGc>gAc	p.G711D	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	711	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)	p.G711D(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		AAAAGAGGGGCCCCGCCGGGT	0.502																																					p.G711D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2132A	5						.						67.0	77.0	74.0					5																	71739686		2203	4300	6503	71775442	SO:0001583	missense	167465	exon5			AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.2132G>A	5.37:g.71739686C>T	ENSP00000313158:p.Gly711Asp	Somatic		Capture	Illumina HiSeq	Phase_I	71775442	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.935049	0.52866	.	.	ENSG00000178175	ENST00000318442	T	0.09911	2.93	5.87	4.06	0.47325	.	0.083505	0.51477	D	0.000083	T	0.08935	0.0221	L	0.29908	0.895	0.38759	D	0.954296	P	0.49635	0.926	B	0.41571	0.36	T	0.13845	-1.0494	10	0.66056	D	0.02	-30.6779	10.3722	0.44060	0.0:0.6752:0.2549:0.0699	.	711	Q8N895	ZN366_HUMAN	D	711	ENSP00000313158:G711D	ENSP00000313158:G711D	G	-	2	0	ZNF366	71775442	0.284000	0.24287	1.000000	0.80357	0.944000	0.59088	0.894000	0.28350	1.615000	0.50252	0.655000	0.94253	GGC		0.502	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
HEXB	3074	broad.mit.edu	37	5	74009374	74009374	+	Missense_Mutation	SNP	G	G	A	rs533645939		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:74009374G>A	ENST00000261416.7	+	7	932	c.815G>A	c.(814-816)cGt>cAt	p.R272H	HEXB_ENST00000511181.1_Missense_Mutation_p.R47H	NM_000521.3	NP_000512	P07686	HEXB_HUMAN	hexosaminidase B (beta polypeptide)	272					astrocyte cell migration (GO:0043615)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular calcium ion homeostasis (GO:0006874)|cellular protein metabolic process (GO:0044267)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|ganglioside catabolic process (GO:0006689)|glycosaminoglycan metabolic process (GO:0030203)|glycosphingolipid metabolic process (GO:0006687)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|lipid storage (GO:0019915)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|male courtship behavior (GO:0008049)|myelination (GO:0042552)|neuromuscular process controlling balance (GO:0050885)|oligosaccharide catabolic process (GO:0009313)|oogenesis (GO:0048477)|penetration of zona pellucida (GO:0007341)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	acrosomal vesicle (GO:0001669)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	beta-N-acetylhexosaminidase activity (GO:0004563)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R272H(1)		endometrium(2)|kidney(3)|large_intestine(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.72e-57)		AATGATGTCCGTATGGTGATT	0.383																																					p.R272H	Melanoma(66;841 1270 13391 18706 27225)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G815A	5						.						163.0	160.0	161.0					5																	74009374		2203	4300	6503	74045130	SO:0001583	missense	3074	exon7			M13519	CCDS4022.1	5q13.3	2012-10-02			ENSG00000049860	ENSG00000049860	3.2.1.52		4879	protein-coding gene	gene with protein product		606873				2579389, 3013851	Standard	NM_000521		Approved		uc003kdf.4	P07686	OTTHUMG00000102057	ENST00000261416.7:c.815G>A	5.37:g.74009374G>A	ENSP00000261416:p.Arg272His	Somatic		Capture	Illumina HiSeq	Phase_I	74045130	NM_000521		Missense_Mutation	SNP	ENST00000261416.7	37	CCDS4022.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138251	0.37728	.	.	ENSG00000049860	ENST00000511181;ENST00000261416	D;D	0.96232	-3.95;-3.95	5.59	-7.03	0.01584	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.688740	0.15012	N	0.285520	D	0.94155	0.8125	M	0.82923	2.615	0.18873	N	0.999987	B	0.14805	0.011	B	0.17098	0.017	T	0.81439	-0.0932	10	0.40728	T	0.16	-0.8178	11.1409	0.48402	0.5263:0.0806:0.3932:0.0	.	272	P07686	HEXB_HUMAN	H	47;272	ENSP00000426285:R47H;ENSP00000261416:R272H	ENSP00000261416:R272H	R	+	2	0	HEXB	74045130	0.000000	0.05858	0.000000	0.03702	0.971000	0.66376	-0.013000	0.12678	-1.665000	0.01477	-0.474000	0.04947	CGT		0.383	HEXB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219859.6	NM_000521	
TMEM161B	153396	broad.mit.edu	37	5	87501637	87501637	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:87501637A>T	ENST00000296595.6	-	8	918	c.794T>A	c.(793-795)aTt>aAt	p.I265N	TMEM161B_ENST00000506536.1_Missense_Mutation_p.I83N|TMEM161B_ENST00000511218.1_Missense_Mutation_p.I83N|TMEM161B_ENST00000509387.1_Missense_Mutation_p.I138N|TMEM161B_ENST00000514135.1_Missense_Mutation_p.I265N|TMEM161B_ENST00000512429.1_Missense_Mutation_p.I254N	NM_153354.3	NP_699185.1	Q8NDZ6	T161B_HUMAN	transmembrane protein 161B	265						integral component of membrane (GO:0016021)		p.I265N(1)		endometrium(4)|large_intestine(3)|lung(9)|skin(3)|upper_aerodigestive_tract(1)	20		all_cancers(142;0.000275)|Lung NSC(167;0.00901)|all_lung(232;0.0111)|Colorectal(57;0.0959)|Ovarian(174;0.1)		OV - Ovarian serous cystadenocarcinoma(54;6.24e-36)|Epithelial(54;6.8e-31)|all cancers(79;1.07e-26)		TTACTGTGTAATTTTTTCTGT	0.333																																					p.I265N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T794A	5						.						88.0	88.0	88.0					5																	87501637		2203	4300	6503	87537393	SO:0001583	missense	153396	exon8			BC037287	CCDS4065.1, CCDS75269.1, CCDS75270.1	5q14.3	2008-02-05			ENSG00000164180	ENSG00000164180			28483	protein-coding gene	gene with protein product						12477932	Standard	NM_001289008		Approved	MGC33214	uc003kjc.3	Q8NDZ6	OTTHUMG00000131323	ENST00000296595.6:c.794T>A	5.37:g.87501637A>T	ENSP00000296595:p.Ile265Asn	Somatic		Capture	Illumina HiSeq	Phase_I	87537393	NM_153354	Q5CZH7|Q6UWQ6	Missense_Mutation	SNP	ENST00000296595.6	37	CCDS4065.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.612907	0.87258	.	.	ENSG00000164180	ENST00000514135;ENST00000296595;ENST00000506536;ENST00000511218;ENST00000512429;ENST00000443393;ENST00000509387	.	.	.	5.94	5.94	0.96194	.	0.246313	0.45606	D	0.000342	T	0.47838	0.1467	N	0.19112	0.55	0.58432	D	0.999996	P;P	0.47191	0.891;0.82	P;P	0.49192	0.602;0.602	T	0.40251	-0.9573	9	0.27785	T	0.31	-0.7316	16.3908	0.83537	1.0:0.0:0.0:0.0	.	83;265	B7Z6A5;Q8NDZ6	.;T161B_HUMAN	N	265;265;83;83;254;265;138	.	ENSP00000296595:I265N	I	-	2	0	TMEM161B	87537393	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.932000	0.92897	2.269000	0.75478	0.455000	0.32223	ATT		0.333	TMEM161B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254094.1	NM_153354	
TTC37	9652	broad.mit.edu	37	5	94877607	94877607	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:94877607A>C	ENST00000358746.2	-	6	536	c.238T>G	c.(238-240)Tta>Gta	p.L80V		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	80						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)		p.L80V(1)		breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						AAGTTTGCTAACCCCTAAAAG	0.303																																					p.L80V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T238G	5						.						69.0	69.0	69.0					5																	94877607		2203	4297	6500	94903363	SO:0001583	missense	9652	exon6			AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.238T>G	5.37:g.94877607A>C	ENSP00000351596:p.Leu80Val	Somatic		Capture	Illumina HiSeq	Phase_I	94903363	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513516	0.64522	.	.	ENSG00000198677	ENST00000358746;ENST00000514952;ENST00000513823	T;T;T	0.80653	-1.4;0.22;-1.4	5.44	4.29	0.51040	Tetratricopeptide-like helical (1);	0.174861	0.36066	N	0.002815	D	0.90017	0.6883	M	0.91768	3.24	0.42460	D	0.99278	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89713	0.3913	10	0.66056	D	0.02	.	7.5407	0.27737	0.7634:0.0:0.2366:0.0	.	32;80	D6RCE2;Q6PGP7	.;TTC37_HUMAN	V	80;32;80	ENSP00000351596:L80V;ENSP00000423742:L32V;ENSP00000425403:L80V	ENSP00000351596:L80V	L	-	1	2	TTC37	94903363	0.840000	0.29493	0.998000	0.56505	0.973000	0.67179	1.741000	0.38238	1.023000	0.39654	0.529000	0.55759	TTA		0.303	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
ELL2	22936	broad.mit.edu	37	5	95233946	95233946	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:95233946C>G	ENST00000237853.4	-	8	1872	c.1523G>C	c.(1522-1524)gGa>gCa	p.G508A	ELL2_ENST00000431061.2_Missense_Mutation_p.G258A	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	508					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.G508A(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TAAAATACCTCCACTGGAATT	0.338																																					p.G508A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1523C	5						.						85.0	91.0	89.0					5																	95233946		2201	4300	6501	95259702	SO:0001583	missense	22936	exon8			U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1523G>C	5.37:g.95233946C>G	ENSP00000237853:p.Gly508Ala	Somatic		Capture	Illumina HiSeq	Phase_I	95259702	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.532|4.532	0.098710|0.098710	0.08681|0.08681	.|.	.|.	ENSG00000118985|ENSG00000118985	ENST00000508757|ENST00000237853;ENST00000431061	.|T	.|0.21543	.|2.0	5.69|5.69	3.33|3.33	0.38152|0.38152	.|.	.|0.763965	.|0.13104	.|N	.|0.413565	T|T	0.08802|0.08802	0.0218|0.0218	N|N	0.08118|0.08118	0|0	0.39001|0.39001	D|D	0.959342|0.959342	.|B	.|0.02656	.|0.0	.|B	.|0.01281	.|0.0	T|T	0.19614|0.19614	-1.0300|-1.0300	5|10	.|0.10377	.|T	.|0.69	-0.0075|-0.0075	5.4954|5.4954	0.16799|0.16799	0.0:0.1731:0.1602:0.6667|0.0:0.1731:0.1602:0.6667	.|.	.|508	.|O00472	.|ELL2_HUMAN	Q|A	26|508;258	.|ENSP00000237853:G508A	.|ENSP00000237853:G508A	E|G	-|-	1|2	0|0	ELL2|ELL2	95259702|95259702	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.990000|0.990000	0.78478|0.78478	1.654000|1.654000	0.37334|0.37334	0.418000|0.418000	0.25898|0.25898	0.591000|0.591000	0.81541|0.81541	GAG|GGA		0.338	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
CHD1	1105	broad.mit.edu	37	5	98212165	98212165	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:98212165C>T	ENST00000284049.3	-	23	3484	c.3335G>A	c.(3334-3336)cGt>cAt	p.R1112H		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	1112					chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|methylated histone binding (GO:0035064)	p.R1112H(1)		NS(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(2)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	49		all_cancers(142;5.36e-08)|all_epithelial(76;6.97e-11)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|all_lung(232;0.00119)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0717)	Epirubicin(DB00445)	TGGTCTTCCACGTTTCTTTGG	0.423																																					p.R1112H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3335A	5						.						197.0	195.0	195.0					5																	98212165		2203	4300	6503	98240065	SO:0001583	missense	1105	exon23			AF006513	CCDS34204.1	5q15-q21	2008-07-18			ENSG00000153922	ENSG00000153922			1915	protein-coding gene	gene with protein product		602118				8460153, 9326634	Standard	XM_005271866		Approved		uc003knf.3	O14646	OTTHUMG00000162744	ENST00000284049.3:c.3335G>A	5.37:g.98212165C>T	ENSP00000284049:p.Arg1112His	Somatic		Capture	Illumina HiSeq	Phase_I	98240065	NM_001270	Q17RZ3	Missense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.952982	0.73902	.	.	ENSG00000153922	ENST00000284049	D	0.91011	-2.77	5.14	5.14	0.70334	.	0.000000	0.34484	U	0.003926	D	0.91573	0.7338	M	0.79011	2.435	0.80722	D	1	D	0.56746	0.977	B	0.43623	0.425	D	0.93148	0.6547	10	0.87932	D	0	.	18.981	0.92755	0.0:1.0:0.0:0.0	.	1112	O14646	CHD1_HUMAN	H	1112	ENSP00000284049:R1112H	ENSP00000284049:R1112H	R	-	2	0	CHD1	98240065	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	7.480000	0.81109	2.546000	0.85860	0.650000	0.86243	CGT		0.423	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270	
SLCO6A1	133482	broad.mit.edu	37	5	101834481	101834481	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:101834481delT	ENST00000506729.1	-	1	239	c.68delA	c.(67-69)gagfs	p.E23fs	SLCO6A1_ENST00000379807.3_Frame_Shift_Del_p.E23fs|SLCO6A1_ENST00000513675.1_Frame_Shift_Del_p.E23fs|SLCO6A1_ENST00000379810.1_Frame_Shift_Del_p.E23fs|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000389019.3_Frame_Shift_Del_p.E23fs|SLCO6A1_ENST00000514551.1_5'Flank			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	23				E -> D (in Ref. 3; BAD18590). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.E23fs*29(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(17)|lung(22)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	60		all_cancers(142;8e-09)|all_epithelial(76;2.83e-12)|Prostate(80;0.00125)|Colorectal(57;0.00342)|Ovarian(225;0.024)|Lung NSC(167;0.0259)|all_lung(232;0.0323)		Epithelial(69;1.47e-15)|COAD - Colon adenocarcinoma(37;0.0113)		CCGCGCGGCCTCCAGCGGCTC	0.657																																					p.E23fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.68delA	5						.						79.0	93.0	88.0					5																	101834481		2203	4298	6501	101862380	SO:0001589	frameshift_variant	133482	exon1			AF505657	CCDS34206.1, CCDS75282.1	5q21.2	2013-05-22			ENSG00000205359	ENSG00000205359		"""Solute carriers"""	23613	protein-coding gene	gene with protein product	"""cancer/testis antigen 48"""	613365					Standard	XM_005271874		Approved	OATP6A1, OATPY, MGC26949, CT48	uc003knp.3	Q86UG4	OTTHUMG00000162759	ENST00000506729.1:c.68delA	5.37:g.101834481delT	ENSP00000421339:p.Glu23fs	Somatic		Capture	Illumina HiSeq	Phase_I	101862380	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Frame_Shift_Del	DEL	ENST00000506729.1	37	CCDS34206.1																																																																																				0.657	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488	
APC	324	broad.mit.edu	37	5	112173831	112173831	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:112173831delA	ENST00000457016.1	+	16	2920	c.2540delA	c.(2539-2541)gaafs	p.E847fs	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Frame_Shift_Del_p.E847fs|APC_ENST00000508376.2_Frame_Shift_Del_p.E847fs			P25054	APC_HUMAN	adenomatous polyposis coli	847	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.D849fs*12(2)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TCTCGTTCTGAAAAAGATAGA	0.418		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.E829fs	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	3	Deletion - Frameshift(2)|Unknown(1)	large_intestine(2)|skin(1)	c.2486delA	5						.						59.0	60.0	60.0					5																	112173831		2202	4300	6502	112201730	SO:0001589	frameshift_variant	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.2540delA	5.37:g.112173831delA	ENSP00000413133:p.Glu847fs	Somatic		Capture	Illumina HiSeq	Phase_I	112201730	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Frame_Shift_Del	DEL	ENST00000457016.1	37	CCDS4107.1																																																																																				0.418	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
RMND5B	64777	broad.mit.edu	37	5	177565142	177565143	+	Frame_Shift_Del	DEL	GA	GA	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GA	GA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:177565142_177565143delGA	ENST00000515098.1	+	4	373_374	c.22_23delGA	c.(22-24)gagfs	p.E8fs	RMND5B_ENST00000313386.4_Frame_Shift_Del_p.E8fs|RMND5B_ENST00000542098.1_Intron			Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog B (S. cerevisiae)	8								p.E10fs*16(1)		endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	17	all_cancers(89;0.00294)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGCGTGCGTGGAGAGAGAGCTG	0.668																																					p.8_8del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.22_23del	5						.																																			177497749	SO:0001589	frameshift_variant	64777	exon3			BC009911	CCDS4431.1, CCDS75382.1	5q35.3	2012-07-20			ENSG00000145916	ENSG00000145916			26181	protein-coding gene	gene with protein product	"""GID complex subunit 2 homolog B"""					12975309	Standard	NM_022762		Approved	FLJ22318, GID2, GID2B	uc003mim.3	Q96G75	OTTHUMG00000130897	ENST00000515098.1:c.22_23delGA	5.37:g.177565148_177565149delGA	ENSP00000420875:p.Glu8fs	Somatic		Capture	Illumina HiSeq	Phase_I	177497748	NM_022762	Q1HE27|Q6UVY7|Q9H6F6	Frame_Shift_Del	DEL	ENST00000515098.1	37	CCDS4431.1																																																																																				0.668	RMND5B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373542.1	NM_022762	
TBC1D9B	23061	broad.mit.edu	37	5	179331747	179331747	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:179331747G>T	ENST00000356834.3	-	2	221	c.184C>A	c.(184-186)Ctg>Atg	p.L62M	TBC1D9B_ENST00000355235.3_Missense_Mutation_p.L62M	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	62						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)	p.L62M(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GTCTGGTGCAGGATGCGGTAA	0.662																																					p.L62M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C184A	5						.						60.0	49.0	53.0					5																	179331747		2193	4291	6484	179264353	SO:0001583	missense	23061	exon2			AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.184C>A	5.37:g.179331747G>T	ENSP00000349291:p.Leu62Met	Somatic		Capture	Illumina HiSeq	Phase_I	179264353	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Missense_Mutation	SNP	ENST00000356834.3	37	CCDS43408.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017593	0.75161	.	.	ENSG00000197226	ENST00000356834;ENST00000355235	T;T	0.29142	1.58;1.58	5.07	5.07	0.68467	.	0.099826	0.43747	D	0.000531	T	0.58921	0.2156	M	0.87456	2.885	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.65561	-0.6138	10	0.87932	D	0	-15.0175	11.5152	0.50518	0.1308:0.0:0.8692:0.0	.	62;62;62	A1L3A9;Q66K14-2;Q66K14	.;.;TBC9B_HUMAN	M	62	ENSP00000349291:L62M;ENSP00000347375:L62M	ENSP00000347375:L62M	L	-	1	2	TBC1D9B	179264353	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.476000	0.60216	2.345000	0.79718	0.561000	0.74099	CTG		0.662	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
FLT4	2324	broad.mit.edu	37	5	180058748	180058748	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:180058748delG	ENST00000261937.6	-	2	167	c.89delC	c.(88-90)ccgfs	p.P30fs	FLT4_ENST00000393347.3_Frame_Shift_Del_p.P30fs|FLT4_ENST00000502649.1_Frame_Shift_Del_p.P30fs|FLT4_ENST00000424276.2_5'UTR	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	30	Ig-like C2-type 1.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.P30fs*3(2)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	GTTCAAGGTCGGGGGGGTCAT	0.632																																					p.P30fs	Colon(97;1075 1466 27033 27547 35871)											.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.89delC	5						.						71.0	60.0	64.0					5																	180058748		2203	4300	6503	179991354	SO:0001589	frameshift_variant	2324	exon2			X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.89delC	5.37:g.180058748delG	ENSP00000261937:p.Pro30fs	Somatic		Capture	Illumina HiSeq	Phase_I	179991354	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Frame_Shift_Del	DEL	ENST00000261937.6	37	CCDS4457.1																																																																																				0.632	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
CWC27	10283	broad.mit.edu	37	5	64181359	64181359	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:64181359delA	ENST00000381070.3	+	11	1245	c.1028delA	c.(1027-1029)gaafs	p.E343fs	CWC27_ENST00000545000.1_3'UTR	NM_005869.2	NP_005860.2	Q6UX04	CWC27_HUMAN	CWC27 spliceosome-associated protein homolog (S. cerevisiae)	343					mRNA splicing, via spliceosome (GO:0000398)|protein folding (GO:0006457)	catalytic step 2 spliceosome (GO:0071013)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)	p.R345fs*26(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(5)|prostate(1)	21						AAACAAGCAGAAAAAAGAAGT	0.388																																					p.E343fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1028delA	5						.						72.0	70.0	70.0					5																	64181359		2203	4299	6502	64217115	SO:0001589	frameshift_variant	10283	exon11			AF039692	CCDS3982.2, CCDS75252.1	5q12.3	2010-01-26	2010-01-26	2010-01-26	ENSG00000153015	ENSG00000153015			10664	protein-coding gene	gene with protein product			"""serologically defined colon cancer antigen 10"""	SDCCAG10		9610721, 19941820	Standard	XM_005248399		Approved	NY-CO-10	uc003jtn.1	Q6UX04	OTTHUMG00000074069	ENST00000381070.3:c.1028delA	5.37:g.64181359delA	ENSP00000370460:p.Glu343fs	Somatic		Capture	Illumina HiSeq	Phase_I	64217115	NM_005869	O60529|O60530|Q96EM3	Frame_Shift_Del	DEL	ENST00000381070.3	37	CCDS3982.2																																																																																				0.388	CWC27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157247.4	NM_005869	
TBCA	6902	broad.mit.edu	37	5	77004108	77004108	+	Frame_Shift_Del	DEL	T	T	-	rs148477021		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:77004108delT	ENST00000380377.4	-	2	221	c.118delA	c.(118-120)atgfs	p.M40fs	TBCA_ENST00000517679.1_Frame_Shift_Del_p.M51fs|TBCA_ENST00000520039.1_Intron|TBCA_ENST00000306388.6_Frame_Shift_Del_p.M40fs|TBCA_ENST00000522370.1_Frame_Shift_Del_p.M16fs|TBCA_ENST00000518338.2_Frame_Shift_Del_p.M40fs|TBCA_ENST00000520361.1_Frame_Shift_Del_p.M40fs	NM_004607.2	NP_004598.1	O75347	TBCA_HUMAN	tubulin folding cofactor A	40					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tubulin complex assembly (GO:0007021)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)	chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)	p.M40fs*1(1)		kidney(1)|large_intestine(2)|lung(1)|ovary(1)	5		all_lung(232;0.000511)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;1.02e-49)|Epithelial(54;1.05e-44)|all cancers(79;4.08e-40)		TCAGCTCTCATTTTTTCAATC	0.274																																					p.M40X												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.118delA	5						.						127.0	117.0	121.0					5																	77004108		2203	4297	6500	77039864	SO:0001589	frameshift_variant	6902	exon2			AF038952	CCDS4040.1, CCDS75263.1	5q14.1	2008-02-05	2006-11-21		ENSG00000171530	ENSG00000171530			11579	protein-coding gene	gene with protein product		610058	"""tubulin-specific chaperone a"""			9653160, 8706133	Standard	XM_005248586		Approved		uc003kfh.1	O75347	OTTHUMG00000102173	ENST00000380377.4:c.118delA	5.37:g.77004108delT	ENSP00000369736:p.Met40fs	Somatic		Capture	Illumina HiSeq	Phase_I	77039864	NM_004607	B4DT30	Frame_Shift_Del	DEL	ENST00000380377.4	37	CCDS4040.1																																																																																				0.274	TBCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220021.3	NM_004607	
PAPD4	167153	broad.mit.edu	37	5	78919076	78919076	+	Splice_Site	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr5:78919076delA	ENST00000296783.3	+	5	528	c.229delA	c.(229-231)aga>ga	p.R77fs	PAPD4_ENST00000428308.2_Splice_Site_p.R77fs|PAPD4_ENST00000504233.1_Splice_Site_p.R77fs|PAPD4_ENST00000453514.1_Splice_Site_p.R77fs|PAPD4_ENST00000423041.2_Splice_Site_p.R77fs			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	77					hematopoietic progenitor cell differentiation (GO:0002244)|histone mRNA catabolic process (GO:0071044)|mRNA processing (GO:0006397)|RNA polyadenylation (GO:0043631)	cytoplasm (GO:0005737)|nuclear RNA-directed RNA polymerase complex (GO:0031380)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|polynucleotide adenylyltransferase activity (GO:0004652)	p.R77fs*2(1)		biliary_tract(1)|breast(2)|endometrium(4)|kidney(3)|large_intestine(9)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Lung NSC(167;0.00293)|all_lung(232;0.00323)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;8.61e-47)|Epithelial(54;1.32e-41)|all cancers(79;2.45e-36)		TGTTTTCAGGAGATTAAGCGA	0.328																																					p.R77fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.229delA	5						.						67.0	64.0	65.0					5																	78919076		2203	4300	6503	78954832	SO:0001630	splice_region_variant	167153	exon4			AL833136	CCDS4048.1, CCDS75265.1, CCDS75266.1	5q14.1	2014-03-21			ENSG00000164329	ENSG00000164329			26776	protein-coding gene	gene with protein product	"""TUTase2"""	614121				12477932	Standard	NM_173797		Approved	FLJ38499, GLD2, TUT2	uc003kgb.2	Q6PIY7	OTTHUMG00000108163	ENST00000296783.3:c.228-1A>-	5.37:g.78919076delA		Somatic		Capture	Illumina HiSeq	Phase_I	78954832	NM_001114394	Q86WZ2|Q8N927	Frame_Shift_Del	DEL	ENST00000296783.3	37	CCDS4048.1																																																																																				0.328	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797	Frame_Shift_Del
MBOAT1	154141	broad.mit.edu	37	6	20152886	20152887	+	Frame_Shift_Ins	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:20152886_20152887insA	ENST00000324607.7	-	2	377_378	c.213_214insT	c.(211-216)tttggcfs	p.G72fs	MBOAT1_ENST00000536798.1_Frame_Shift_Ins_p.G72fs|MBOAT1_ENST00000541730.1_5'UTR	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	72					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)	p.G72fs*31(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			AAATAGATGCCAAAAATGGTGG	0.441																																					p.G72fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.214_215insT	6						.																																			20260866	SO:0001589	frameshift_variant	154141	exon2			AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.214dupT	6.37:g.20152891_20152891dupA	ENSP00000324944:p.Gly72fs	Somatic		Capture	Illumina HiSeq	Phase_I	20260865	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Frame_Shift_Ins	INS	ENST00000324607.7	37	CCDS34346.1																																																																																				0.441	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
PKHD1	5314	broad.mit.edu	37	6	51619701	51619702	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	G	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:51619701_51619702insG	ENST00000371117.3	-	56	8952_8953	c.8677_8678insC	c.(8677-8679)catfs	p.H2893fs	PKHD1_ENST00000340994.4_Frame_Shift_Ins_p.H2893fs	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2893					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.H2893fs*2(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TATTTTGTCATGGGGGCGCCAA	0.441																																					p.H2893fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.8678_8679insC	6						.																																			51727661	SO:0001589	frameshift_variant	5314	exon56			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8678dupC	6.37:g.51619706_51619706dupG	ENSP00000360158:p.His2893fs	Somatic		Capture	Illumina HiSeq	Phase_I	51727660	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Frame_Shift_Ins	INS	ENST00000371117.3	37	CCDS4935.1																																																																																				0.441	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PHF3	23469	broad.mit.edu	37	6	64408416	64408417	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	T	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:64408416_64408417insT	ENST00000262043.3	+	8	3243_3244	c.2903_2904insT	c.(2902-2907)tcttttfs	p.SF968fs	PHF3_ENST00000393387.1_Frame_Shift_Ins_p.SF968fs			Q92576	PHF3_HUMAN	PHD finger protein 3	968	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.R971fs*6(1)		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)			GAGCTTTTCTCTTTTTTTCGGG	0.302																																					p.S968fs	GBM(135;136 1820 29512 34071 46235)											.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2903_2904insT	6						.																																			64466376	SO:0001589	frameshift_variant	23469	exon7			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.2910dupT	6.37:g.64408423_64408423dupT	ENSP00000262043:p.Ser968fs	Somatic		Capture	Illumina HiSeq	Phase_I	64466375	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Frame_Shift_Ins	INS	ENST00000262043.3	37	CCDS4966.1																																																																																				0.302	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
SIM1	6492	broad.mit.edu	37	6	100896039	100896039	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:100896039C>T	ENST00000369208.3	-	8	1615	c.833G>A	c.(832-834)cGc>cAc	p.R278H	SIM1_ENST00000262901.4_Missense_Mutation_p.R278H			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	278	PAS 2. {ECO:0000255|PROSITE- ProRule:PRU00140}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.R278H(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GTGCGCGCAGCGCAGGTGGAA	0.622																																					p.R278H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G833A	6						.						105.0	78.0	87.0					6																	100896039		2203	4300	6503	101002760	SO:0001583	missense	6492	exon7			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.833G>A	6.37:g.100896039C>T	ENSP00000358210:p.Arg278His	Somatic		Capture	Illumina HiSeq	Phase_I	101002760	NM_005068	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	19.44	3.827558	0.71143	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.26660	1.72;1.72	5.29	4.43	0.53597	PAS fold-3 (1);PAS (1);	0.146472	0.64402	D	0.000005	T	0.50069	0.1594	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.64170	-0.6470	10	0.72032	D	0.01	.	13.9725	0.64250	0.0:0.9273:0.0:0.0727	.	278	P81133	SIM1_HUMAN	H	278	ENSP00000358210:R278H;ENSP00000262901:R278H	ENSP00000262901:R278H	R	-	2	0	SIM1	101002760	1.000000	0.71417	1.000000	0.80357	0.193000	0.23685	7.487000	0.81328	1.240000	0.43803	0.655000	0.94253	CGC		0.622	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3	NM_005068	
GCNT2	2651	broad.mit.edu	37	6	10529706	10529706	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:10529706A>G	ENST00000379597.3	+	1	1118	c.562A>G	c.(562-564)Atc>Gtc	p.I188V	GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000495262.1_Missense_Mutation_p.I188V|GCNT2_ENST00000397423.2_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	188					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.I188V(1)		endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		GAAGTATGTCATCAACACCTG	0.517																																					p.I188V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A562G	6						.						42.0	44.0	43.0					6																	10529706		2203	4300	6503	10637692	SO:0001583	missense	2651	exon3			L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.562A>G	6.37:g.10529706A>G	ENSP00000368917:p.Ile188Val	Somatic		Capture	Illumina HiSeq	Phase_I	10637692	NM_145649		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.252070	0.39797	.	.	ENSG00000111846	ENST00000495262;ENST00000379597	T;T	0.09817	2.94;2.94	5.61	-4.09	0.03951	.	0.396294	0.25732	N	0.028665	T	0.10981	0.0268	M	0.84326	2.69	0.80722	D	1	P;P	0.40230	0.708;0.708	P;P	0.46452	0.517;0.517	T	0.04767	-1.0928	10	0.49607	T	0.09	-10.1831	14.5684	0.68194	0.2841:0.6548:0.0611:0.0	.	188;187	Q8N0V5;Q08M29	GNT2A_HUMAN;.	V	188	ENSP00000419411:I188V;ENSP00000368917:I188V	ENSP00000368917:I188V	I	+	1	0	GCNT2	10637692	0.003000	0.15002	0.018000	0.16275	0.772000	0.43724	0.100000	0.15231	-0.982000	0.03515	-0.290000	0.09829	ATC		0.517	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
ASCC3	10973	broad.mit.edu	37	6	101248237	101248237	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:101248237C>A	ENST00000369162.2	-	6	1410	c.1066G>T	c.(1066-1068)Gaa>Taa	p.E356*	ASCC3_ENST00000522650.1_Nonsense_Mutation_p.E356*	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	356					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.E356*(1)		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)		TCTAAATCTTCTCCAGCCTTT	0.368																																					p.E356X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G1066T	6						.						175.0	164.0	168.0					6																	101248237		2203	4300	6503	101354958	SO:0001587	stop_gained	10973	exon6			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.1066G>T	6.37:g.101248237C>A	ENSP00000358159:p.Glu356*	Somatic		Capture	Illumina HiSeq	Phase_I	101354958	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Nonsense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	C	41	9.132437	0.99077	.	.	ENSG00000112249	ENST00000369162;ENST00000522650	.	.	.	5.51	5.51	0.81932	.	0.200887	0.46145	D	0.000307	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	19.4189	0.94712	0.0:1.0:0.0:0.0	.	.	.	.	X	356	.	ENSP00000358159:E356X	E	-	1	0	ASCC3	101354958	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.439000	0.73430	2.587000	0.87381	0.561000	0.74099	GAA		0.368	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
PRDM1	639	broad.mit.edu	37	6	106553334	106553334	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:106553334C>T	ENST00000369096.4	+	5	1533	c.1299C>T	c.(1297-1299)ggC>ggT	p.G433G	PRDM1_ENST00000369089.3_Silent_p.G299G|PRDM1_ENST00000369091.2_Silent_p.G397G	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	433					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.G397G(1)		NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		GCATGAATGGCATCAACAACT	0.582			"""D, N, Mis, F, S"""		DLBCL																																p.G433G			Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1299T	6						.						72.0	62.0	66.0					6																	106553334		2203	4300	6503	106660027	SO:0001819	synonymous_variant	639	exon5				CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1299C>T	6.37:g.106553334C>T		Somatic		Capture	Illumina HiSeq	Phase_I	106660027	NM_001198	B2REA6|E1P5E0|Q86WM7	Silent	SNP	ENST00000369096.4	37	CCDS5054.2																																																																																				0.582	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
ERVFRD-1	405754	broad.mit.edu	37	6	11105450	11105450	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:11105450G>A	ENST00000472091.1	-	2	469	c.94C>T	c.(94-96)Ctc>Ttc	p.L32F	ERVFRD-1_ENST00000542862.1_Missense_Mutation_p.L32F|SMIM13_ENST00000416247.2_Intron	NM_207582.2	NP_997465.1	P60508	SYCY2_HUMAN	endogenous retrovirus group FRD, member 1	32					syncytium formation (GO:0006949)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|viral envelope (GO:0019031)		p.L32F(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(4)|stomach(1)	15						GTACTTTGGAGCAGTTGCTGA	0.522																																					p.L32F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C94T	6						.						71.0	70.0	70.0					6																	11105450		2203	4300	6503	11213436	SO:0001583	missense	405754	exon2			AK075092, AK123938, AY358244	CCDS4519.1	6p24.2	2014-05-02			ENSG00000244476	ENSG00000244476			33823	other	endogenous retrovirus		610524				12970426, 14557543, 15476554, 21542922	Standard	NM_207582		Approved	HERV-W/FRD, HERV-FRD, envFRD, ERVFRDE1, syncytin-2	uc003mzt.3	P60508	OTTHUMG00000159193	ENST00000472091.1:c.94C>T	6.37:g.11105450G>A	ENSP00000420174:p.Leu32Phe	Somatic		Capture	Illumina HiSeq	Phase_I	11213436	NM_207582		Missense_Mutation	SNP	ENST00000472091.1	37	CCDS4519.1	.	.	.	.	.	.	.	.	.	.	G	17.60	3.430609	0.62844	.	.	ENSG00000244476	ENST00000472091;ENST00000542862	T;T	0.33865	1.39;1.39	0.235	0.235	0.15431	.	.	.	.	.	T	0.28200	0.0696	L	0.32530	0.975	0.24819	N	0.992592	D	0.64830	0.994	D	0.80764	0.994	T	0.06661	-1.0814	8	0.72032	D	0.01	.	.	.	.	.	32	P60508	EFRD1_HUMAN	F	32	ENSP00000420174:L32F;ENSP00000444461:L32F	ENSP00000420174:L32F	L	-	1	0	ERVFRD-1	11213436	0.958000	0.32768	0.885000	0.34714	0.889000	0.51656	0.364000	0.20325	0.308000	0.22923	0.313000	0.20887	CTC		0.522	ERVFRD-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353776.1	NM_207582	
GPR6	2830	broad.mit.edu	37	6	110300981	110300982	+	Missense_Mutation	DNP	GG	GG	AC			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GG	GG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:110300981_110300982GG>AC	ENST00000275169.3	+	1	684_685	c.666_667GG>AC	c.(664-669)ctGGcg>ctACcg	p.A223P	GPR6_ENST00000414000.2_Missense_Mutation_p.A238P	NM_005284.3	NP_005275.1	P46095	GPR6_HUMAN	G protein-coupled receptor 6	223					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.L222>?(1)		breast(1)|endometrium(1)|large_intestine(7)|lung(7)|prostate(1)|skin(1)	18		all_cancers(87;1.64e-05)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;2.83e-05)|all_lung(197;0.00016)|Lung NSC(302;0.000318)|Colorectal(196;0.0488)		BRCA - Breast invasive adenocarcinoma(108;8.01e-05)|Epithelial(106;8.76e-05)|all cancers(137;0.000197)|OV - Ovarian serous cystadenocarcinoma(136;0.0307)		TGCGCCCGCTGGCGCGCAGCCA	0.698																																					.												.	.	1	Complex(1)	large_intestine(1)	c.666_667AC	6						.																																			110407675	SO:0001583	missense	2830	exon1				CCDS5079.1, CCDS69172.1	6q21	2012-08-21				ENSG00000146360		"""GPCR / Class A : Orphans"""	4515	protein-coding gene	gene with protein product		600553				8530049	Standard	NM_001286099		Approved		uc003ptu.3	P46095	OTTHUMG00000015354	Exception_encountered	6.37:g.110300981_110300982delinsAC	ENSP00000275169:p.Ala223Pro	Somatic		Capture	Illumina HiSeq	Phase_I	110407674	NM_005284	B4DHS9|J3KQR3|Q17RJ7|Q5SYL0	Missense_Mutation	DNP	ENST00000275169.3	37	CCDS5079.1																																																																																				0.698	GPR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041774.1		
RWDD1	51389	broad.mit.edu	37	6	116901505	116901505	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:116901505G>A	ENST00000466444.2	+	2	337	c.121G>A	c.(121-123)Gct>Act	p.A41T	RWDD1_ENST00000392526.1_De_novo_Start_OutOfFrame|RWDD1_ENST00000517800.1_3'UTR|RWDD1_ENST00000487832.2_De_novo_Start_OutOfFrame	NM_015952.2	NP_057036.2	Q9H446	RWDD1_HUMAN	RWD domain containing 1	41	RWD. {ECO:0000255|PROSITE- ProRule:PRU00179}.							p.A41T(1)		NS(1)|breast(2)|central_nervous_system(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)	12		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.026)|all cancers(137;0.0312)|OV - Ovarian serous cystadenocarcinoma(136;0.0689)|Epithelial(106;0.161)		GACGTCTGAGGCTGGAGAAAA	0.353																																					p.A41T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G121A	6						.						52.0	49.0	50.0					6																	116901505		2203	4300	6503	117008198	SO:0001583	missense	51389	exon2			AF092134	CCDS34520.1, CCDS43496.1	6q13-q22.33	2012-12-07			ENSG00000111832	ENSG00000111832			20993	protein-coding gene	gene with protein product						10810093	Standard	NM_016104		Approved	PTD013	uc003pxd.3	Q9H446	OTTHUMG00000015441	ENST00000466444.2:c.121G>A	6.37:g.116901505G>A	ENSP00000420357:p.Ala41Thr	Somatic		Capture	Illumina HiSeq	Phase_I	117008198	NM_015952	A8K3W2|A8MT24|Q9Y313|Q9Y6B3	Missense_Mutation	SNP	ENST00000466444.2	37	CCDS34520.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990942	0.54041	.	.	ENSG00000111832	ENST00000466444	T	0.42513	0.97	5.95	5.95	0.96441	Ubiquitin-conjugating enzyme/RWD-like (2);RWD domain (3);	0.226038	0.45606	D	0.000349	T	0.18257	0.0438	N	0.16567	0.415	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.06391	-1.0829	10	0.22109	T	0.4	-2.6286	20.3812	0.98933	0.0:0.0:1.0:0.0	.	41	Q9H446	RWDD1_HUMAN	T	41	ENSP00000420357:A41T	ENSP00000420357:A41T	A	+	1	0	RWDD1	117008198	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.006000	0.70724	2.821000	0.97095	0.650000	0.86243	GCT		0.353	RWDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041952.2	NM_015952	
GOPC	57120	broad.mit.edu	37	6	117890768	117890768	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:117890768C>A	ENST00000368498.2	-	7	1119	c.1044G>T	c.(1042-1044)aaG>aaT	p.K348N	DCBLD1_ENST00000296955.8_Intron|GOPC_ENST00000535237.1_Missense_Mutation_p.K348N|GOPC_ENST00000052569.6_Missense_Mutation_p.K340N|GOPC_ENST00000467125.1_5'UTR	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	348	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)	p.K348N(1)	GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		CTTCTTTATGCTTTGTGTCCC	0.428			O	ROS1	glioblastoma																																p.K348N			Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1044T	6						.						206.0	202.0	204.0					6																	117890768		2203	4300	6503	117997461	SO:0001583	missense	57120	exon7			AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.1044G>T	6.37:g.117890768C>A	ENSP00000357484:p.Lys348Asn	Somatic		Capture	Illumina HiSeq	Phase_I	117997461	NM_020399	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	37	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823889	0.71143	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.50813	0.73;0.73;0.73	5.75	3.98	0.46160	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.44993	0.1320	L	0.37697	1.125	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.72625	0.963;0.978;0.963	T	0.48885	-0.8995	10	0.59425	D	0.04	1.4217	11.4423	0.50105	0.0:0.7993:0.0:0.2007	.	340;348;348	Q9HD26-2;Q9HD26;F5H1Y4	.;GOPC_HUMAN;.	N	340;348;348	ENSP00000052569:K340N;ENSP00000357484:K348N;ENSP00000445690:K348N	ENSP00000052569:K340N	K	-	3	2	GOPC	117997461	0.991000	0.36638	1.000000	0.80357	0.998000	0.95712	0.312000	0.19397	0.785000	0.33685	0.563000	0.77884	AAG		0.428	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399	
GJA1	2697	broad.mit.edu	37	6	121768709	121768709	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:121768709G>A	ENST00000282561.3	+	2	873	c.716G>A	c.(715-717)cGg>cAg	p.R239Q		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	239			R -> Q (in CMDR). {ECO:0000269|PubMed:23951358}.|R -> W (in congenital heart malformations; dbSNP:rs2227887). {ECO:0000269|PubMed:15978203}.		adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.R239Q(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	GTTAAGGATCGGGTTAAGGGA	0.478																																					p.R239Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G716A	6						.						107.0	106.0	106.0					6																	121768709		2203	4300	6503	121810408	SO:0001583	missense	2697	exon2			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"""Ion channels / Gap junction proteins (connexins)"""	4274	protein-coding gene	gene with protein product	"""oculodentodigital dysplasia (syndactyly type III)"", ""connexin 43"""	121014	"""gap junction protein, alpha-like"", ""gap junction protein, alpha 1, 43kDa (connexin 43)"""	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.716G>A	6.37:g.121768709G>A	ENSP00000282561:p.Arg239Gln	Somatic		Capture	Illumina HiSeq	Phase_I	121810408	NM_000165	B2R5U9|Q6FHU1|Q9Y5I8	Missense_Mutation	SNP	ENST00000282561.3	37	CCDS5123.1	.	.	.	.	.	.	.	.	.	.	G	7.571	0.666701	0.14710	.	.	ENSG00000152661	ENST00000440608;ENST00000282561	D	0.97279	-4.32	5.54	5.54	0.83059	.	0.063974	0.64402	D	0.000006	D	0.91050	0.7184	L	0.32530	0.975	0.58432	D	0.999997	B	0.23058	0.079	B	0.08055	0.003	D	0.88955	0.3389	10	0.12430	T	0.62	.	19.4987	0.95085	0.0:0.0:1.0:0.0	.	239	P17302	CXA1_HUMAN	Q	223;239	ENSP00000282561:R239Q	ENSP00000282561:R239Q	R	+	2	0	GJA1	121810408	1.000000	0.71417	0.961000	0.40146	0.161000	0.22273	9.420000	0.97426	2.609000	0.88269	0.460000	0.39030	CGG		0.478	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165	
GJA1	2697	broad.mit.edu	37	6	121769082	121769082	+	Silent	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:121769082T>G	ENST00000282561.3	+	2	1246	c.1089T>G	c.(1087-1089)ccT>ccG	p.P363P		NM_000165.3	NP_000156.1	P17302	CXA1_HUMAN	gap junction protein, alpha 1, 43kDa	363					adult heart development (GO:0007512)|apoptotic process (GO:0006915)|ATP transport (GO:0015867)|atrial cardiac muscle cell action potential (GO:0086014)|atrial ventricular junction remodeling (GO:0003294)|blood vessel morphogenesis (GO:0048514)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|cell-cell signaling (GO:0007267)|cellular response to mechanical stimulus (GO:0071260)|chronic inflammatory response (GO:0002544)|embryonic digit morphogenesis (GO:0042733)|endothelium development (GO:0003158)|epithelial cell maturation (GO:0002070)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lens development in camera-type eye (GO:0002088)|membrane organization (GO:0061024)|milk ejection (GO:0060156)|muscle contraction (GO:0006936)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of gene expression (GO:0010629)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|osteoblast differentiation (GO:0001649)|positive regulation of behavioral fear response (GO:2000987)|positive regulation of cell communication by chemical coupling (GO:0010652)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of striated muscle tissue development (GO:0045844)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein oligomerization (GO:0051259)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of bone mineralization (GO:0030500)|regulation of bone remodeling (GO:0046850)|regulation of calcium ion transport (GO:0051924)|regulation of tight junction assembly (GO:2000810)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to fluid shear stress (GO:0034405)|response to peptide hormone (GO:0043434)|response to pH (GO:0009268)|signal transduction (GO:0007165)|skeletal muscle tissue regeneration (GO:0043403)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vascular transport (GO:0010232)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|contractile fiber (GO:0043292)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gap junction (GO:0005921)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle membrane (GO:0030660)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|membrane raft (GO:0045121)|mitochondrial outer membrane (GO:0005741)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)	gap junction channel activity (GO:0005243)|ion transmembrane transporter activity (GO:0015075)|signal transducer activity (GO:0004871)	p.P363P(1)		autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(2)|large_intestine(10)|liver(2)|lung(13)|ovary(2)	33				GBM - Glioblastoma multiforme(226;0.00252)	Carvedilol(DB01136)	ACCAGCGACCTTCAAGCAGAG	0.493																																					p.P363P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1089G	6						.						65.0	70.0	68.0					6																	121769082		2201	4295	6496	121810781	SO:0001819	synonymous_variant	2697	exon2			BC026329	CCDS5123.1	6q22.31	2013-05-10	2007-01-16		ENSG00000152661	ENSG00000152661		"""Ion channels / Gap junction proteins (connexins)"""	4274	protein-coding gene	gene with protein product	"""oculodentodigital dysplasia (syndactyly type III)"", ""connexin 43"""	121014	"""gap junction protein, alpha-like"", ""gap junction protein, alpha 1, 43kDa (connexin 43)"""	ODDD, GJAL		10331943, 1646158	Standard	NM_000165		Approved	CX43, ODD, ODOD, SDTY3	uc003pyr.3	P17302	OTTHUMG00000015479	ENST00000282561.3:c.1089T>G	6.37:g.121769082T>G		Somatic		Capture	Illumina HiSeq	Phase_I	121810781	NM_000165	B2R5U9|Q6FHU1|Q9Y5I8	Silent	SNP	ENST00000282561.3	37	CCDS5123.1																																																																																				0.493	GJA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042023.1	NM_000165	
HEY2	23493	broad.mit.edu	37	6	126080274	126080274	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:126080274G>A	ENST00000368364.3	+	5	537	c.340G>A	c.(340-342)Gca>Aca	p.A114T	HEY2_ENST00000368365.1_Missense_Mutation_p.A68T	NM_012259.2	NP_036391.1	Q9UBP5	HEY2_HUMAN	hes-related family bHLH transcription factor with YRPW motif 2	114	Transcriptional repression and interaction with NCOR1 and SIN3A. {ECO:0000250}.				anterior/posterior axis specification (GO:0009948)|arterial endothelial cell differentiation (GO:0060842)|ascending aorta morphogenesis (GO:0035910)|atrial septum morphogenesis (GO:0060413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate commitment (GO:0045165)|cochlea development (GO:0090102)|coronary vasculature morphogenesis (GO:0060977)|dorsal aorta morphogenesis (GO:0035912)|endocardial cushion to mesenchymal transition involved in heart valve formation (GO:0003199)|heart trabecula formation (GO:0060347)|labyrinthine layer blood vessel development (GO:0060716)|mesenchymal cell development (GO:0014031)|muscular septum morphogenesis (GO:0003150)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of cardiac vascular smooth muscle cell differentiation (GO:2000723)|negative regulation of gene expression (GO:0010629)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription by transcription factor localization (GO:0010621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000820)|negative regulation of transcription initiation from RNA polymerase II promoter (GO:0060633)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of heart rate (GO:0010460)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of auditory receptor cell differentiation (GO:0045607)|regulation of vasculogenesis (GO:2001212)|smooth muscle cell differentiation (GO:0051145)|tricuspid valve formation (GO:0003195)|tricuspid valve morphogenesis (GO:0003186)|umbilical cord morphogenesis (GO:0036304)|vascular smooth muscle cell development (GO:0097084)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	histone deacetylase binding (GO:0042826)|microsatellite binding (GO:0035939)|protein binding transcription factor activity (GO:0000988)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.A114P(1)|p.A114T(1)		breast(1)|large_intestine(7)|lung(5)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (4;0.0608)|GBM - Glioblastoma multiforme(226;0.0361)|all cancers(137;0.193)		CTACTTTGACGCACACGCTCT	0.527																																					p.A114T												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G340A	6						.						127.0	119.0	122.0					6																	126080274		2203	4300	6503	126121967	SO:0001583	missense	23493	exon5			AJ249545	CCDS5131.1	6q	2013-10-17	2013-10-17		ENSG00000135547	ENSG00000135547		"""Basic helix-loop-helix proteins"""	4881	protein-coding gene	gene with protein product		604674	"""hairy/enhancer-of-split related with YRPW motif 2"""			10415358	Standard	NM_012259		Approved	bHLHb32, HERP1, HESR2	uc003qad.3	Q9UBP5	OTTHUMG00000015512	ENST00000368364.3:c.340G>A	6.37:g.126080274G>A	ENSP00000357348:p.Ala114Thr	Somatic		Capture	Illumina HiSeq	Phase_I	126121967	NM_012259		Missense_Mutation	SNP	ENST00000368364.3	37	CCDS5131.1	.	.	.	.	.	.	.	.	.	.	G	36	5.789287	0.96945	.	.	ENSG00000135547	ENST00000368365;ENST00000368364	T;T	0.41400	1.0;1.0	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	T	0.23727	0.0574	L	0.42581	1.335	0.80722	D	1	B	0.28584	0.216	B	0.26517	0.07	T	0.06427	-1.0827	10	0.18276	T	0.48	-8.2687	19.5573	0.95357	0.0:0.0:1.0:0.0	.	114	Q9UBP5	HEY2_HUMAN	T	68;114	ENSP00000357349:A68T;ENSP00000357348:A114T	ENSP00000357348:A114T	A	+	1	0	HEY2	126121967	1.000000	0.71417	0.872000	0.34217	0.948000	0.59901	7.917000	0.87498	2.629000	0.89072	0.561000	0.74099	GCA		0.527	HEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042077.1		
KIAA0408	9729	broad.mit.edu	37	6	127767923	127767923	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:127767923T>C	ENST00000483725.3	-	5	1877	c.1541A>G	c.(1540-1542)aAg>aGg	p.K514R	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	514								p.K514R(1)		endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		TGTGGATTTCTTGGTGGGATT	0.468																																					p.K514R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1541G	6						.						139.0	132.0	134.0					6																	127767923		2203	4300	6503	127809616	SO:0001583	missense	9729	exon5			AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1541A>G	6.37:g.127767923T>C	ENSP00000435150:p.Lys514Arg	Somatic		Capture	Illumina HiSeq	Phase_I	127809616	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Missense_Mutation	SNP	ENST00000483725.3	37	CCDS34531.1	.	.	.	.	.	.	.	.	.	.	T	9.587	1.125169	0.20959	.	.	ENSG00000189367	ENST00000483725	T	0.37411	1.2	5.08	3.92	0.45320	.	0.165679	0.26927	U	0.021786	T	0.27098	0.0664	L	0.53249	1.67	0.09310	N	1	D	0.56746	0.977	P	0.53593	0.73	T	0.08597	-1.0714	10	0.59425	D	0.04	-1.1151	7.9279	0.29885	0.0:0.1586:0.0:0.8414	.	514	Q6ZU52	K0408_HUMAN	R	514	ENSP00000435150:K514R	ENSP00000435150:K514R	K	-	2	0	KIAA0408	127809616	0.392000	0.25229	0.004000	0.12327	0.294000	0.27393	1.888000	0.39708	0.795000	0.33922	0.533000	0.62120	AAG		0.468	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702	
SOGA3	387104	broad.mit.edu	37	6	127796640	127796640	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:127796640C>T	ENST00000525778.1	-	6	3276	c.2531G>A	c.(2530-2532)cGc>cAc	p.R844H	SOGA3_ENST00000368268.2_Missense_Mutation_p.R844H|SOGA3_ENST00000474293.2_5'UTR|SOGA3_ENST00000465909.2_Missense_Mutation_p.R844H|SOGA3_ENST00000556132.1_Missense_Mutation_p.R844H|SOGA3_ENST00000481848.2_Missense_Mutation_p.R844H			Q5TF21	SOGA3_HUMAN	SOGA family member 3	844					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.R844H(1)									CACGTAGATGCGCGCCTCGGT	0.652																																					p.R844H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2531A	6						.						90.0	103.0	98.0					6																	127796640		2187	4284	6471	127838333	SO:0001583	missense	387104	exon6			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.2531G>A	6.37:g.127796640C>T	ENSP00000434570:p.Arg844His	Somatic		Capture	Illumina HiSeq	Phase_I	127838333	NM_001012279		Missense_Mutation	SNP	ENST00000525778.1	37	CCDS43505.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087600	0.94100	.	.	ENSG00000214338	ENST00000556132;ENST00000368268;ENST00000525778;ENST00000465909	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.43942	0.1270	L	0.56769	1.78	0.80722	D	1	D	0.71674	0.998	P	0.61592	0.891	T	0.33214	-0.9877	10	0.62326	D	0.03	-14.0363	19.6185	0.95645	0.0:1.0:0.0:0.0	.	844	Q5TF21	CF174_HUMAN	H	844	ENSP00000451768:R844H;ENSP00000357251:R844H;ENSP00000434570:R844H;ENSP00000435559:R844H	ENSP00000435559:R844H	R	-	2	0	C6orf174	127838333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.089000	0.71384	2.641000	0.89580	0.462000	0.41574	CGC		0.652	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
SOGA3	387104	broad.mit.edu	37	6	127836755	127836755	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:127836755C>T	ENST00000525778.1	-	2	1750	c.1005G>A	c.(1003-1005)gcG>gcA	p.A335A	SOGA3_ENST00000368268.2_Silent_p.A335A|SOGA3_ENST00000465909.2_Silent_p.A335A|SOGA3_ENST00000556132.1_Silent_p.A335A|SOGA3_ENST00000481848.2_Silent_p.A335A			Q5TF21	SOGA3_HUMAN	SOGA family member 3	335					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)		p.A335A(1)									ACGAAGGGGGCGCTGCCGCCT	0.697																																					p.A335A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1005A	6						.						8.0	9.0	8.0					6																	127836755		1806	3967	5773	127878448	SO:0001819	synonymous_variant	387104	exon2			AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1005G>A	6.37:g.127836755C>T		Somatic		Capture	Illumina HiSeq	Phase_I	127878448	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																				0.697	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
PTPRK	5796	broad.mit.edu	37	6	128540178	128540178	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:128540178C>T	ENST00000368215.3	-	6	756	c.757G>A	c.(757-759)Gct>Act	p.A253T	PTPRK_ENST00000368207.3_Missense_Mutation_p.A253T|PTPRK_ENST00000532331.1_Missense_Mutation_p.A253T|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000368227.3_Missense_Mutation_p.A253T|PTPRK_ENST00000368213.5_Missense_Mutation_p.A253T|PTPRK_ENST00000368210.3_Missense_Mutation_p.A253T|PTPRK_ENST00000368226.4_Missense_Mutation_p.A253T			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	253	Ig-like C2-type.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.A253T(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		CTGAAGGAAGCGGCAAACCTT	0.413																																					p.A253T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G757A	6						.						154.0	137.0	143.0					6																	128540178		2203	4300	6503	128581871	SO:0001583	missense	5796	exon6			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.757G>A	6.37:g.128540178C>T	ENSP00000357198:p.Ala253Thr	Somatic		Capture	Illumina HiSeq	Phase_I	128581871	NM_002844	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.	.	.	.	.	.	.	.	.	.	C	29.1	4.973795	0.92919	.	.	ENSG00000152894	ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	4.78	4.78	0.61160	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.41465	0.1160	L	0.58810	1.83	0.45066	D	0.998089	D;D;D;D;D;D	0.76494	0.997;0.993;0.985;0.999;0.972;0.965	P;P;P;P;B;B	0.62298	0.536;0.827;0.513;0.9;0.262;0.17	T	0.34030	-0.9845	10	0.52906	T	0.07	.	17.8323	0.88686	0.0:1.0:0.0:0.0	.	253;253;253;110;253;253	B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.;.;.;.;PTPRK_HUMAN;.	T	253;253;253;253;253;253;253;110	ENSP00000357209:A253T;ENSP00000357210:A253T;ENSP00000432973:A253T;ENSP00000357196:A253T;ENSP00000357193:A253T;ENSP00000357198:A253T;ENSP00000357190:A253T	ENSP00000357190:A253T	A	-	1	0	PTPRK	128581871	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	5.697000	0.68295	2.189000	0.69895	0.455000	0.32223	GCT		0.413	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
TAAR5	9038	broad.mit.edu	37	6	132910784	132910784	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:132910784C>T	ENST00000258034.2	-	1	93	c.42G>A	c.(40-42)gcG>gcA	p.A14A		NM_003967.2	NP_003958.2	O14804	TAAR5_HUMAN	trace amine associated receptor 5	14					G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|trimethylamine receptor activity (GO:1990081)	p.A14A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	32	Breast(56;0.112)			OV - Ovarian serous cystadenocarcinoma(155;0.00604)|GBM - Glioblastoma multiforme(226;0.015)		AGCAGAATGCCGCAGGGTGCT	0.522																																					p.A14A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G42A	6						.						80.0	77.0	78.0					6																	132910784		2203	4300	6503	132952477	SO:0001819	synonymous_variant	9038	exon1			AF021818	CCDS5156.1	6q23.2	2012-08-08			ENSG00000135569	ENSG00000135569		"""GPCR / Class A : Trace amine associated receptors"""	30236	protein-coding gene	gene with protein product		607405				9464258, 15718104	Standard	NM_003967		Approved	PNR	uc003qdk.2	O14804	OTTHUMG00000015581	ENST00000258034.2:c.42G>A	6.37:g.132910784C>T		Somatic		Capture	Illumina HiSeq	Phase_I	132952477	NM_003967	D8KZS1|Q2M1V1|Q4VBL1|Q5VUQ3|Q6NTA8	Silent	SNP	ENST00000258034.2	37	CCDS5156.1																																																																																				0.522	TAAR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042257.1	NM_003967	
VNN1	8876	broad.mit.edu	37	6	133013660	133013660	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:133013660C>A	ENST00000367928.4	-	5	903	c.890G>T	c.(889-891)gGa>gTa	p.G297V		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	297	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)	p.G297V(1)		NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		GAGGAGTTTTCCCTCTTCTGT	0.438																																					p.G297V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G890T	6						.						59.0	58.0	58.0					6																	133013660		2203	4300	6503	133055353	SO:0001583	missense	8876	exon5			AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.890G>T	6.37:g.133013660C>A	ENSP00000356905:p.Gly297Val	Somatic		Capture	Illumina HiSeq	Phase_I	133055353	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	.	.	.	.	.	.	.	.	.	.	C	19.72	3.879904	0.72294	.	.	ENSG00000112299	ENST00000367928	D	0.85339	-1.97	5.97	5.97	0.96955	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (3);	0.000000	0.85682	D	0.000000	D	0.92506	0.7620	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92039	0.5639	10	0.66056	D	0.02	-14.9626	20.4388	0.99107	0.0:1.0:0.0:0.0	.	297	O95497	VNN1_HUMAN	V	297	ENSP00000356905:G297V	ENSP00000356905:G297V	G	-	2	0	VNN1	133055353	0.989000	0.36119	1.000000	0.80357	0.590000	0.36582	5.114000	0.64648	2.836000	0.97738	0.655000	0.94253	GGA		0.438	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
GFOD1	54438	broad.mit.edu	37	6	13365113	13365113	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:13365113G>A	ENST00000379287.3	-	2	1699	c.1035C>T	c.(1033-1035)tgC>tgT	p.C345C	GFOD1_ENST00000379284.1_Silent_p.C242C	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1	345						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)	p.C345C(1)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			TGTCCACCACGCACAAGGCAT	0.667																																					p.C345C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1035T	6						.						58.0	54.0	56.0					6																	13365113		2203	4300	6503	13473092	SO:0001819	synonymous_variant	54438	exon2			AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 114"""	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.1035C>T	6.37:g.13365113G>A		Somatic		Capture	Illumina HiSeq	Phase_I	13473092	NM_018988	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Silent	SNP	ENST00000379287.3	37	CCDS4524.1																																																																																				0.667	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988	
EYA4	2070	broad.mit.edu	37	6	133836572	133836572	+	Splice_Site	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:133836572A>G	ENST00000367895.5	+	17	2079	c.1615A>G	c.(1615-1617)Agg>Ggg	p.R539G	EYA4_ENST00000355286.6_Splice_Site_p.R516G|EYA4_ENST00000355167.3_Splice_Site_p.R539G|EYA4_ENST00000430974.2_Splice_Site_p.R491G|EYA4_ENST00000525849.1_Splice_Site_p.R516G|RP3-323P13.2_ENST00000607033.1_RNA|EYA4_ENST00000452339.2_Splice_Site_p.R485G|EYA4_ENST00000431403.2_Splice_Site_p.R539G|EYA4_ENST00000531901.1_Splice_Site_p.R545G	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	539					anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA repair (GO:0006281)|inner ear development (GO:0048839)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)	p.R539G(1)		breast(1)|central_nervous_system(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|skin(1)	48	Colorectal(23;0.221)			GBM - Glioblastoma multiforme(68;0.00457)|OV - Ovarian serous cystadenocarcinoma(155;0.0152)		TATTAGCACTAGGTAAGTGGA	0.358																																					p.R516G	Melanoma(57;398 1237 3528 4702 7415)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1546G	6						.						146.0	142.0	143.0					6																	133836572		2203	4300	6503	133878265	SO:0001630	splice_region_variant	2070	exon16			Y17114	CCDS5165.1, CCDS5166.1, CCDS43506.1, CCDS75521.1, CCDS75523.1	6q23	2014-09-17	2014-06-19		ENSG00000112319	ENSG00000112319		"""Protein tyrosine phosphatases / Asp-based PTPs"""	3522	protein-coding gene	gene with protein product		603550	"""eyes absent (Drosophila) homolog 4"", ""eyes absent homolog 4 (Drosophila)"""	DFNA10, CMD1J		9887327, 11159937	Standard	NM_004100		Approved		uc003qed.4	O95677	OTTHUMG00000015602	ENST00000367895.5:c.1616+1A>G	6.37:g.133836572A>G		Somatic		Capture	Illumina HiSeq	Phase_I	133878265	NM_172103	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Missense_Mutation	SNP	ENST00000367895.5	37	CCDS5165.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.183620	0.78677	.	.	ENSG00000112319	ENST00000452339;ENST00000430974;ENST00000367895;ENST00000355167;ENST00000355286;ENST00000531901;ENST00000525849;ENST00000431403	D;D;D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.73	5.73	0.89815	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.000000	0.85682	D	0.000000	D	0.91192	0.7225	M	0.78456	2.415	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;1.0;0.999	D	0.92383	0.5915	10	0.87932	D	0	-19.653	16.3123	0.82883	1.0:0.0:0.0:0.0	.	545;491;485;516;539;539	F2Z2Y1;E7ESD5;E7EN58;O95677-2;O95677-4;O95677	.;.;.;.;.;EYA4_HUMAN	G	485;491;539;539;516;545;516;539	ENSP00000395916:R485G;ENSP00000388670:R491G;ENSP00000356870:R539G;ENSP00000347294:R539G;ENSP00000347434:R516G;ENSP00000432770:R545G;ENSP00000433219:R516G;ENSP00000404558:R539G	ENSP00000347294:R539G	R	+	1	2	EYA4	133878265	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	7.256000	0.78350	2.308000	0.77769	0.533000	0.62120	AGG		0.358	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100	Missense_Mutation
GPR126	57211	broad.mit.edu	37	6	142691838	142691838	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:142691838G>A	ENST00000230173.6	+	4	1453	c.977G>A	c.(976-978)aGc>aAc	p.S326N	GPR126_ENST00000296932.8_Missense_Mutation_p.S326N|GPR126_ENST00000367609.3_Missense_Mutation_p.S326N|GPR126_ENST00000545477.1_Intron|GPR126_ENST00000367608.2_Missense_Mutation_p.S326N	NM_020455.5	NP_065188	Q86SQ4	GP126_HUMAN	G protein-coupled receptor 126	326	Pentaxin.				G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S325N(1)|p.S326N(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(12)|lung(10)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	36	Breast(32;0.176)			OV - Ovarian serous cystadenocarcinoma(155;9.33e-06)|GBM - Glioblastoma multiforme(68;0.00121)		TCCAACCTCAGCTGTAATGTG	0.403																																					p.S326N												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G977A	6						.						115.0	114.0	115.0					6																	142691838		1846	4103	5949	142733531	SO:0001583	missense	57211	exon4			AK027843	CCDS47489.1, CCDS47490.1, CCDS47491.1, CCDS55064.1	6q23.1-q24.3	2014-08-08			ENSG00000112414	ENSG00000112414		"""-"", ""GPCR / Class B : Orphans"""	13841	protein-coding gene	gene with protein product		612243				12565841	Standard	NM_001032395		Approved	FLJ14937	uc010khe.3	Q86SQ4	OTTHUMG00000015709	ENST00000230173.6:c.977G>A	6.37:g.142691838G>A	ENSP00000230173:p.Ser326Asn	Somatic		Capture	Illumina HiSeq	Phase_I	142733531	NM_001032394	Q5TGN7|Q6DHZ4|Q6F3F5|Q6F3F6|Q6F3F7|Q6F3F8|Q6MZU7|Q8IXA4|Q8NC14|Q96JW0	Missense_Mutation	SNP	ENST00000230173.6	37	CCDS47490.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406918	0.62399	.	.	ENSG00000112414	ENST00000230173;ENST00000367608;ENST00000296932;ENST00000367609	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	6.07	5.19	0.71726	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.064530	0.64402	D	0.000003	T	0.69305	0.3096	M	0.69823	2.125	0.34448	D	0.700402	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.77557	0.983;0.983;0.983;0.99	T	0.76556	-0.2916	10	0.72032	D	0.01	.	17.3592	0.87345	0.0:0.125:0.8749:0.0	.	326;326;326;326	Q86SQ4-4;Q86SQ4-3;Q86SQ4-2;Q86SQ4	.;.;.;GP126_HUMAN	N	326	ENSP00000230173:S326N;ENSP00000356580:S326N;ENSP00000296932:S326N;ENSP00000356581:S326N	ENSP00000230173:S326N	S	+	2	0	GPR126	142733531	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	2.819000	0.48049	1.557000	0.49525	-0.291000	0.09656	AGC		0.403	GPR126-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042487.2		
PEX3	8504	broad.mit.edu	37	6	143793319	143793319	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:143793319T>C	ENST00000367591.4	+	8	664	c.601T>C	c.(601-603)Tcc>Ccc	p.S201P		NM_003630.2	NP_003621.1	P56589	PEX3_HUMAN	peroxisomal biogenesis factor 3	201					peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of peroxisomal membrane (GO:0005779)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)|protein-lipid complex (GO:0032994)	lipid binding (GO:0008289)|protein dimerization activity (GO:0046983)	p.S201P(1)		endometrium(1)|large_intestine(9)|lung(4)|ovary(2)|skin(2)	18				OV - Ovarian serous cystadenocarcinoma(155;5.73e-06)|GBM - Glioblastoma multiforme(68;0.0117)		ACATTCTTTGTCCCTTTTGGA	0.333																																					p.S201P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T601C	6						.						70.0	76.0	74.0					6																	143793319		2202	4299	6501	143835012	SO:0001583	missense	8504	exon8			AJ001625	CCDS5199.1	6q24.2	2008-05-15			ENSG00000034693	ENSG00000034693			8858	protein-coding gene	gene with protein product		603164				9657383	Standard	NM_003630		Approved		uc003qjl.3	P56589	OTTHUMG00000015730	ENST00000367591.4:c.601T>C	6.37:g.143793319T>C	ENSP00000356563:p.Ser201Pro	Somatic		Capture	Illumina HiSeq	Phase_I	143835012	NM_003630	Q6FGP5	Missense_Mutation	SNP	ENST00000367591.4	37	CCDS5199.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.773415	0.90108	.	.	ENSG00000034693	ENST00000344281;ENST00000367592;ENST00000367591	T;T	0.57107	0.42;0.42	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	T	0.68348	0.2991	M	0.77820	2.39	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77557	0.988;0.99	T	0.73272	-0.4035	10	0.72032	D	0.01	-9.928	16.3736	0.83374	0.0:0.0:0.0:1.0	.	201;201	B4DV31;P56589	.;PEX3_HUMAN	P	157;157;201	ENSP00000356564:S157P;ENSP00000356563:S201P	ENSP00000344195:S157P	S	+	1	0	PEX3	143835012	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.916000	0.75776	2.273000	0.75805	0.482000	0.46254	TCC		0.333	PEX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042525.1		
UTRN	7402	broad.mit.edu	37	6	145073037	145073037	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:145073037A>G	ENST00000367545.3	+	55	8304	c.8304A>G	c.(8302-8304)ctA>ctG	p.L2768L	UTRN_ENST00000367526.4_Silent_p.L323L	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2768					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.L2768L(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		ATCCCTCTCTAAAGATGTCTC	0.418																																					p.L2768L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A8304G	6						.						101.0	92.0	95.0					6																	145073037		2203	4300	6503	145114730	SO:0001819	synonymous_variant	7402	exon55			AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.8304A>G	6.37:g.145073037A>G		Somatic		Capture	Illumina HiSeq	Phase_I	145114730	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1																																																																																				0.418	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
SHPRH	257218	broad.mit.edu	37	6	146264843	146264843	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:146264843A>G	ENST00000367505.2	-	9	1938	c.1674T>C	c.(1672-1674)gaT>gaC	p.D558D	SHPRH_ENST00000367503.3_Silent_p.D558D|SHPRH_ENST00000438092.2_Silent_p.D558D|SHPRH_ENST00000275233.7_Silent_p.D558D			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	558					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.D558D(1)		breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		GATCATCATCATCATCAGAGG	0.373																																					p.D558D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1674C	6						.						134.0	123.0	127.0					6																	146264843		1836	4093	5929	146306536	SO:0001819	synonymous_variant	257218	exon9			AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.1674T>C	6.37:g.146264843A>G		Somatic		Capture	Illumina HiSeq	Phase_I	146306536	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	37	CCDS43513.2																																																																																				0.373	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
LATS1	9113	broad.mit.edu	37	6	150016224	150016224	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:150016224G>A	ENST00000543571.1	-	3	1029	c.482C>T	c.(481-483)gCc>gTc	p.A161V	LATS1_ENST00000392273.3_Missense_Mutation_p.A161V|LATS1_ENST00000542747.1_5'UTR|LATS1_ENST00000253339.5_Missense_Mutation_p.A161V	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		TTTCATGCTGGCATTAATAGG	0.358																																					p.A161V												.	.	0			c.C482T	6						.						144.0	143.0	144.0					6																	150016224		2203	4300	6503	150057917	SO:0001583	missense	9113	exon3			AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000543571.1:c.482C>T	6.37:g.150016224G>A	ENSP00000437550:p.Ala161Val	None		Capture	Illumina HiSeq	Phase_I	150057917	NM_004690		Missense_Mutation	SNP	ENST00000543571.1	37	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.931864	0.92389	.	.	ENSG00000131023	ENST00000543571;ENST00000253339;ENST00000392273;ENST00000458696	T;T;T;T	0.22336	1.96;1.96;1.96;1.96	5.08	5.08	0.68730	.	0.000000	0.56097	D	0.000030	T	0.17662	0.0424	L	0.47716	1.5	0.41812	D	0.98997	P;P;P	0.52463	0.941;0.592;0.953	P;B;B	0.46917	0.531;0.169;0.388	T	0.01036	-1.1473	9	.	.	.	.	18.8208	0.92096	0.0:0.0:1.0:0.0	.	13;161;161	Q59FN4;O95835-2;O95835	.;.;LATS1_HUMAN	V	161;161;161;107	ENSP00000437550:A161V;ENSP00000253339:A161V;ENSP00000444678:A161V;ENSP00000441265:A107V	.	A	-	2	0	LATS1	150057917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.090000	0.89526	2.532000	0.85374	0.557000	0.71058	GCC		0.358	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	NM_004690	
AKAP12	9590	broad.mit.edu	37	6	151673193	151673193	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:151673193G>T	ENST00000253332.1	+	3	3856	c.3667G>T	c.(3667-3669)Gca>Tca	p.A1223S	AKAP12_ENST00000402676.2_Missense_Mutation_p.A1223S|AKAP12_ENST00000354675.6_Missense_Mutation_p.A1125S|AKAP12_ENST00000359755.5_Missense_Mutation_p.A1118S			Q02952	AKA12_HUMAN	A kinase (PRKA) anchor protein 12	1223					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of protein kinase C signaling (GO:0090036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)	p.A1223S(1)		breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	68		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.175)	OV - Ovarian serous cystadenocarcinoma(155;2.98e-11)		GAGGCCTCCAGCACCTTCCAG	0.478																																					p.A1223S	Melanoma(141;1616 1805 10049 24534 51979)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3667T	6						.						52.0	54.0	53.0					6																	151673193		2203	4300	6503	151714886	SO:0001583	missense	9590	exon4			U81607	CCDS5229.1, CCDS5230.1	6q24-q25	2011-07-01	2008-08-29		ENSG00000131016	ENSG00000131016		"""A-kinase anchor proteins"""	370	protein-coding gene	gene with protein product	"""gravin"", ""Src-Suppressed C Kinase Substrate"""	604698	"""A kinase (PRKA) anchor protein (gravin) 12"""			9000000	Standard	NM_144497		Approved	AKAP250, SSeCKS	uc011eep.2	Q02952	OTTHUMG00000015833	ENST00000253332.1:c.3667G>T	6.37:g.151673193G>T	ENSP00000253332:p.Ala1223Ser	Somatic		Capture	Illumina HiSeq	Phase_I	151714886	NM_005100	O00310|O00498|Q4LE68|Q5SZ80|Q5TGN1|Q68D82|Q99970	Missense_Mutation	SNP	ENST00000253332.1	37	CCDS5229.1	.	.	.	.	.	.	.	.	.	.	G	16.02	3.004203	0.54254	.	.	ENSG00000131016	ENST00000402676;ENST00000253332;ENST00000354675;ENST00000359755	T;T;T;T	0.07688	3.17;3.17;3.17;3.17	5.08	-0.523	0.11924	.	1.719500	0.03638	N	0.238972	T	0.01320	0.0043	L	0.27053	0.805	0.09310	N	1	B;B;B	0.24368	0.102;0.102;0.062	B;B;B	0.21151	0.033;0.033;0.014	T	0.42599	-0.9442	10	0.12103	T	0.63	.	2.4605	0.04540	0.1495:0.117:0.4507:0.2828	.	1118;1125;1223	Q02952-3;Q02952-2;Q02952	.;.;AKA12_HUMAN	S	1223;1223;1125;1118	ENSP00000384537:A1223S;ENSP00000253332:A1223S;ENSP00000346702:A1125S;ENSP00000352794:A1118S	ENSP00000253332:A1223S	A	+	1	0	AKAP12	151714886	0.000000	0.05858	0.000000	0.03702	0.520000	0.34377	0.259000	0.18405	-0.117000	0.11872	0.455000	0.32223	GCA		0.478	AKAP12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042712.1		
RMND1	55005	broad.mit.edu	37	6	151743691	151743691	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:151743691A>G	ENST00000367303.4	-	8	1109	c.987T>C	c.(985-987)atT>atC	p.I329I	RMND1_ENST00000336451.3_Silent_p.I118I	NM_017909.2	NP_060379.2	Q9NWS8	RMND1_HUMAN	required for meiotic nuclear division 1 homolog (S. cerevisiae)	329					translation (GO:0006412)	mitochondrion (GO:0005739)		p.I329I(1)		central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		Ovarian(120;0.125)	BRCA - Breast invasive adenocarcinoma(37;0.146)	OV - Ovarian serous cystadenocarcinoma(155;6.8e-11)		GAATTGACTGAATAGATTCAA	0.254																																					p.I329I												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T987C	6						.						25.0	24.0	24.0					6																	151743691		2189	4273	6462	151785384	SO:0001819	synonymous_variant	55005	exon8			AK000634	CCDS5232.1, CCDS75539.1	6q25.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000155906	ENSG00000155906			21176	protein-coding gene	gene with protein product		614917	"""chromosome 6 open reading frame 96"""	C6orf96			Standard	NM_001271937		Approved	bA351K16.3, FLJ20627, RMD1	uc003qoi.3	Q9NWS8	OTTHUMG00000015837	ENST00000367303.4:c.987T>C	6.37:g.151743691A>G		Somatic		Capture	Illumina HiSeq	Phase_I	151785384	NM_017909	A8K8H4|Q0VDG6|Q5SZ48|Q5SZ83|Q6NSC5|Q96EN7	Silent	SNP	ENST00000367303.4	37	CCDS5232.1																																																																																				0.254	RMND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042718.2	NM_017909	
CCDC170	80129	broad.mit.edu	37	6	151914413	151914413	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:151914413A>C	ENST00000239374.7	+	8	1564	c.1465A>C	c.(1465-1467)Aag>Cag	p.K489Q	CCDC170_ENST00000367290.5_Missense_Mutation_p.K489Q	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	489								p.K489Q(1)									TTTGCAGAGAAAGGTAGGAGA	0.423																																					p.K489Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1465C	6						.						64.0	61.0	62.0					6																	151914413		1878	4100	5978	151956106	SO:0001583	missense	80129	exon8			AK026958	CCDS43515.1	6q25.1	2012-03-26	2012-03-26	2012-03-26	ENSG00000120262	ENSG00000120262			21177	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 97"""	C6orf97			Standard	NM_025059		Approved	FLJ23305, bA282P11.1	uc003qol.3	Q8IYT3	OTTHUMG00000015839	ENST00000239374.7:c.1465A>C	6.37:g.151914413A>C	ENSP00000239374:p.Lys489Gln	Somatic		Capture	Illumina HiSeq	Phase_I	151956106	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Missense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.349458	0.82132	.	.	ENSG00000120262	ENST00000239374;ENST00000367290	T;T	0.10668	2.85;2.85	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.28366	0.0701	M	0.79805	2.47	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	T	0.03051	-1.1078	10	0.59425	D	0.04	-28.6266	16.5764	0.84681	1.0:0.0:0.0:0.0	.	489	Q8IYT3	CF097_HUMAN	Q	489	ENSP00000239374:K489Q;ENSP00000356259:K489Q	ENSP00000239374:K489Q	K	+	1	0	C6orf97	151956106	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	7.575000	0.82447	2.371000	0.80710	0.533000	0.62120	AAG		0.423	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059	
ESR1	2099	broad.mit.edu	37	6	152129201	152129201	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:152129201T>C	ENST00000206249.3	+	1	516	c.154T>C	c.(154-156)Tac>Cac	p.Y52H	ESR1_ENST00000427531.2_5'Flank|ESR1_ENST00000456483.2_Missense_Mutation_p.Y52H|ESR1_ENST00000338799.5_Missense_Mutation_p.Y52H|ESR1_ENST00000406599.1_Missense_Mutation_p.Y52H|ESR1_ENST00000440973.1_Missense_Mutation_p.Y52H|ESR1_ENST00000443427.1_Missense_Mutation_p.Y52H	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	52	Interaction with DDX5; self-association.|Modulating (transactivation AF-1); mediates interaction with MACROD1.				androgen metabolic process (GO:0008209)|antral ovarian follicle growth (GO:0001547)|cellular response to estradiol stimulus (GO:0071392)|chromatin remodeling (GO:0006338)|epithelial cell development (GO:0002064)|epithelial cell proliferation involved in mammary gland duct elongation (GO:0060750)|gene expression (GO:0010467)|intracellular estrogen receptor signaling pathway (GO:0030520)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|male gonad development (GO:0008584)|mammary gland alveolus development (GO:0060749)|mammary gland branching involved in pregnancy (GO:0060745)|negative regulation of gene expression (GO:0010629)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|regulation of apoptotic process (GO:0042981)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of transcription, DNA-templated (GO:0006355)|response to estradiol (GO:0032355)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|uterus development (GO:0060065)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcriptionally active chromatin (GO:0035327)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|enzyme binding (GO:0019899)|estrogen receptor activity (GO:0030284)|estrogen response element binding (GO:0034056)|estrogen-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0038052)|identical protein binding (GO:0042802)|nitric-oxide synthase regulator activity (GO:0030235)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.Y52H(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(11)|lung(19)|ovary(1)|prostate(2)|skin(1)	49		Ovarian(120;0.0448)	BRCA - Breast invasive adenocarcinoma(37;0.0841)	OV - Ovarian serous cystadenocarcinoma(155;4.55e-10)	Allylestrenol(DB01431)|Clomifene(DB00882)|Conjugated Estrogens(DB00286)|Danazol(DB01406)|Desogestrel(DB00304)|Dienestrol(DB00890)|Diethylstilbestrol(DB00255)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Estropipate(DB04574)|Ethinyl Estradiol(DB00977)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluoxymesterone(DB01185)|Fulvestrant(DB00947)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Melatonin(DB01065)|Mestranol(DB01357)|Naloxone(DB01183)|Norgestimate(DB00957)|Ospemifene(DB04938)|Progesterone(DB00396)|Quinestrol(DB04575)|Raloxifene(DB00481)|Tamoxifen(DB00675)|Toremifene(DB00539)|Trilostane(DB01108)	GCCCGCCGTGTACAACTACCC	0.701																																					p.Y52H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T154C	6						.						20.0	24.0	23.0					6																	152129201		2201	4300	6501	152170894	SO:0001583	missense	2099	exon2			X03635	CCDS5234.1	6q24-q27	2013-01-16			ENSG00000091831	ENSG00000091831		"""Nuclear hormone receptors"""	3467	protein-coding gene	gene with protein product		133430		ESR		3754034	Standard	NM_000125		Approved	NR3A1, Era	uc003qon.4	P03372	OTTHUMG00000016103	ENST00000206249.3:c.154T>C	6.37:g.152129201T>C	ENSP00000206249:p.Tyr52His	Somatic		Capture	Illumina HiSeq	Phase_I	152170894	NM_001122740	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Missense_Mutation	SNP	ENST00000206249.3	37	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.289442	0.59976	.	.	ENSG00000091831	ENST00000404742;ENST00000440973;ENST00000338799;ENST00000456483;ENST00000446550;ENST00000443427;ENST00000206249;ENST00000406599	T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.06	3.86	0.44501	.	0.493330	0.21148	N	0.079364	T	0.24275	0.0588	L	0.34521	1.04	0.80722	D	1	D;P;P;P	0.76494	0.999;0.942;0.928;0.942	D;P;P;P	0.71184	0.972;0.815;0.795;0.87	T	0.02813	-1.1107	10	0.16896	T	0.51	.	10.9907	0.47547	0.14:0.0:0.0:0.86	.	52;52;52;52	Q9H2M1;A8KAF4;G4XH65;P03372	.;.;.;ESR1_HUMAN	H	52	ENSP00000385373:Y52H;ENSP00000405330:Y52H;ENSP00000342630:Y52H;ENSP00000415934:Y52H;ENSP00000411105:Y52H;ENSP00000387500:Y52H;ENSP00000206249:Y52H;ENSP00000384064:Y52H	ENSP00000206249:Y52H	Y	+	1	0	ESR1	152170894	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	5.673000	0.68109	0.731000	0.32448	0.460000	0.39030	TAC		0.701	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1		
TIAM2	26230	broad.mit.edu	37	6	155450713	155450713	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:155450713T>A	ENST00000461783.3	+	6	1629	c.356T>A	c.(355-357)gTt>gAt	p.V119D	TIAM2_ENST00000360366.4_Missense_Mutation_p.V119D|TIAM2_ENST00000529824.2_Missense_Mutation_p.V119D|TIAM2_ENST00000456144.1_Missense_Mutation_p.V119D|TIAM2_ENST00000318981.5_Missense_Mutation_p.V119D|TIAM2_ENST00000367174.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	119					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.V119D(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		TTCCACTCTGTTGGCCACGAG	0.557																																					p.V119D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T356A	6						.						74.0	62.0	66.0					6																	155450713		2203	4300	6503	155492405	SO:0001583	missense	26230	exon3				CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.356T>A	6.37:g.155450713T>A	ENSP00000437188:p.Val119Asp	Somatic		Capture	Illumina HiSeq	Phase_I	155492405	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	T	6.295	0.422511	0.11928	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000535583;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.07327	3.31;3.2;3.25;3.31;3.32;3.25	4.88	0.855	0.19013	.	0.620573	0.16729	N	0.201960	T	0.02418	0.0074	L	0.54323	1.7	0.22185	N	0.999307	B	0.09022	0.002	B	0.04013	0.001	T	0.40905	-0.9538	10	0.87932	D	0	.	3.0081	0.06035	0.1412:0.0778:0.1475:0.6336	.	119	Q8IVF5	TIAM2_HUMAN	D	119;365;119;119;119;119;119;119	ENSP00000437188:V119D;ENSP00000434901:V119D;ENSP00000407746:V119D;ENSP00000327315:V119D;ENSP00000353528:V119D;ENSP00000433348:V119D	ENSP00000327315:V119D	V	+	2	0	TIAM2	155492405	0.035000	0.19736	0.001000	0.08648	0.035000	0.12851	1.348000	0.33987	-0.031000	0.13781	0.260000	0.18958	GTT		0.557	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
JARID2	3720	broad.mit.edu	37	6	15520318	15520318	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:15520318G>A	ENST00000341776.2	+	18	3821	c.3577G>A	c.(3577-3579)Gtc>Atc	p.V1193I	JARID2_ENST00000397311.3_Missense_Mutation_p.V1021I	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1193					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.V1193I(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				TATCAGTCTGGTCAATCAGAT	0.483																																					p.V1193I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3577A	6						.						73.0	64.0	67.0					6																	15520318		2203	4300	6503	15628297	SO:0001583	missense	3720	exon18			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.3577G>A	6.37:g.15520318G>A	ENSP00000341280:p.Val1193Ile	Somatic		Capture	Illumina HiSeq	Phase_I	15628297	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370178	0.61624	.	.	ENSG00000008083	ENST00000341776;ENST00000397311	D;D	0.90385	-2.66;-2.66	5.71	5.71	0.89125	Zinc finger, C5HC2-type (1);	0.000000	0.85682	D	0.000000	D	0.89560	0.6750	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.85781	0.1361	10	0.13108	T	0.6	-17.7037	19.8484	0.96730	0.0:0.0:1.0:0.0	.	1193	Q92833	JARD2_HUMAN	I	1193;1021	ENSP00000341280:V1193I;ENSP00000380478:V1021I	ENSP00000341280:V1193I	V	+	1	0	JARID2	15628297	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.901000	0.92560	2.684000	0.91462	0.655000	0.94253	GTC		0.483	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
NOX3	50508	broad.mit.edu	37	6	155757594	155757594	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:155757594C>A	ENST00000159060.2	-	7	858	c.756G>T	c.(754-756)gtG>gtT	p.V252V		NM_015718.2	NP_056533.1	Q9HBY0	NOX3_HUMAN	NADPH oxidase 3	252	Ferric oxidoreductase.				detection of gravity (GO:0009590)|otolith development (GO:0048840)|superoxide anion generation (GO:0042554)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NADPH oxidase complex (GO:0043020)	superoxide-generating NADPH oxidase activity (GO:0016175)	p.V252V(1)		cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	45		Breast(66;0.0183)		OV - Ovarian serous cystadenocarcinoma(155;2.18e-12)|BRCA - Breast invasive adenocarcinoma(81;0.00815)		GGCATTGGGCCACTGTCTGCC	0.458																																					p.V252V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G756T	6						.						135.0	114.0	121.0					6																	155757594		2203	4300	6503	155799286	SO:0001819	synonymous_variant	50508	exon7			AF190122	CCDS5250.1	6q25.3	2008-05-15			ENSG00000074771	ENSG00000074771			7890	protein-coding gene	gene with protein product		607105				11376945	Standard	NM_015718		Approved	GP91-3	uc003qqm.3	Q9HBY0	OTTHUMG00000015883	ENST00000159060.2:c.756G>T	6.37:g.155757594C>A		Somatic		Capture	Illumina HiSeq	Phase_I	155799286	NM_015718	Q9HBJ9	Silent	SNP	ENST00000159060.2	37	CCDS5250.1																																																																																				0.458	NOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042819.1		
TULP4	56995	broad.mit.edu	37	6	158923870	158923870	+	Missense_Mutation	SNP	G	G	A	rs143651023		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:158923870G>A	ENST00000367097.3	+	13	4532	c.3175G>A	c.(3175-3177)Gcc>Acc	p.A1059T	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	1059					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1059T(1)		endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TACCGCCAGCGCCTCCCCGTT	0.706																																					p.A1059T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3175A	6						.	G	,THR/ALA	4,4400	8.1+/-20.4	0,4,2198	29.0	31.0	30.0		,3175	-3.9	0.8	6	dbSNP_134	30	4,8588	3.7+/-12.6	0,4,4292	yes	intron,missense	TULP4	NM_001007466.1,NM_020245.3	,58	0,8,6490	AA,AG,GG		0.0466,0.0908,0.0616	,benign	,1059/1544	158923870	8,12988	2202	4296	6498	158843858	SO:0001583	missense	56995	exon13				CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.3175G>A	6.37:g.158923870G>A	ENSP00000356064:p.Ala1059Thr	Somatic		Capture	Illumina HiSeq	Phase_I	158843858	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.048085	0.00398	9.08E-4	4.66E-4	ENSG00000130338	ENST00000367097	T	0.60299	0.2	5.06	-3.94	0.04130	.	0.420838	0.27932	N	0.017264	T	0.05593	0.0147	N	0.01417	-0.88	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.30179	-0.9987	10	0.02654	T	1	-11.9351	6.1848	0.20491	0.5519:0.0:0.3358:0.1123	.	1059	Q9NRJ4	TULP4_HUMAN	T	1059	ENSP00000356064:A1059T	ENSP00000356064:A1059T	A	+	1	0	TULP4	158843858	0.146000	0.22672	0.770000	0.31555	0.038000	0.13279	0.539000	0.23175	-0.727000	0.04888	-2.069000	0.00389	GCC		0.706	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
FNDC1	84624	broad.mit.edu	37	6	159636082	159636082	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:159636082G>A	ENST00000297267.9	+	5	766	c.566G>A	c.(565-567)cGc>cAc	p.R189H	FNDC1_ENST00000340366.6_Missense_Mutation_p.R189H	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	189	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R189H(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AAGAGTCCACGCAGATCACGG	0.552																																					p.R189H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G566A	6						.						77.0	80.0	79.0					6																	159636082		1969	4158	6127	159556070	SO:0001583	missense	84624	exon5			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.566G>A	6.37:g.159636082G>A	ENSP00000297267:p.Arg189His	Somatic		Capture	Illumina HiSeq	Phase_I	159556070	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.134827	0.77662	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.08546	3.08;4.0	6.17	6.17	0.99709	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.10294	0.0252	N	0.08118	0	0.42767	D	0.993827	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.974	T	0.46414	-0.9193	10	0.72032	D	0.01	-30.1272	20.4745	0.99168	0.0:0.0:1.0:0.0	.	189;189	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	H	189	ENSP00000297267:R189H;ENSP00000342460:R189H	ENSP00000297267:R189H	R	+	2	0	FNDC1	159556070	1.000000	0.71417	0.993000	0.49108	0.997000	0.91878	4.661000	0.61518	2.941000	0.99782	0.655000	0.94253	CGC		0.552	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
FNDC1	84624	broad.mit.edu	37	6	159654306	159654306	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:159654306G>A	ENST00000297267.9	+	11	2962	c.2762G>A	c.(2761-2763)cGg>cAg	p.R921Q	FNDC1_ENST00000340366.6_Missense_Mutation_p.R858Q	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	921					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R921Q(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		AGCCTGCATCGGAAGGAACCC	0.602																																					p.R921Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2762A	6						.						66.0	76.0	72.0					6																	159654306		1971	4154	6125	159574296	SO:0001583	missense	84624	exon11			AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2762G>A	6.37:g.159654306G>A	ENSP00000297267:p.Arg921Gln	Somatic		Capture	Illumina HiSeq	Phase_I	159574296	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.811076	0.32053	.	.	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.18657	2.2;2.81	5.33	-0.659	0.11424	.	0.921751	0.09236	N	0.829883	T	0.03564	0.0102	N	0.24115	0.695	0.09310	N	1	B;B	0.27117	0.168;0.105	B;B	0.19946	0.027;0.012	T	0.42361	-0.9456	10	0.36615	T	0.2	-5.173	5.1953	0.15233	0.4093:0.14:0.4507:0.0	.	858;921	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	Q	921;858	ENSP00000297267:R921Q;ENSP00000342460:R858Q	ENSP00000297267:R921Q	R	+	2	0	FNDC1	159574296	0.044000	0.20184	0.017000	0.16124	0.535000	0.34838	0.042000	0.13949	-0.500000	0.06614	-0.749000	0.03505	CGG		0.602	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
IGF2R	3482	broad.mit.edu	37	6	160448246	160448246	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:160448246C>T	ENST00000356956.1	+	6	824	c.676C>T	c.(676-678)Cgg>Tgg	p.R226W		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	226					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)	p.R226W(1)		breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	TTCACAGCTGCGGGCCTGTCC	0.552																																					p.R226W												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C676T	6						.						38.0	39.0	39.0					6																	160448246		2203	4300	6503	160368236	SO:0001583	missense	3482	exon6			J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.676C>T	6.37:g.160448246C>T	ENSP00000349437:p.Arg226Trp	Somatic		Capture	Illumina HiSeq	Phase_I	160368236	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129298	0.77549	.	.	ENSG00000197081	ENST00000356956	T	0.02345	4.33	5.22	2.24	0.28232	Mannose-6-phosphate receptor, binding (1);	0.389135	0.28057	N	0.016766	T	0.02455	0.0075	M	0.67397	2.05	0.09310	N	1	D	0.69078	0.997	P	0.47162	0.54	T	0.30592	-0.9973	10	0.72032	D	0.01	-11.7411	12.7316	0.57201	0.6225:0.3775:0.0:0.0	.	226	P11717	MPRI_HUMAN	W	226	ENSP00000349437:R226W	ENSP00000349437:R226W	R	+	1	2	IGF2R	160368236	0.860000	0.29831	0.005000	0.12908	0.590000	0.36582	1.142000	0.31540	0.205000	0.20568	0.655000	0.94253	CGG		0.552	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
LPA	4018	broad.mit.edu	37	6	161006078	161006078	+	Splice_Site	SNP	G	G	A	rs370793685		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:161006078G>A	ENST00000316300.5	-	26	4333	c.4289C>T	c.(4288-4290)gCt>gTt	p.A1430V	LPA_ENST00000447678.1_Splice_Site_p.A1430V			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3938	Kringle 13. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)	p.A1430V(1)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	ATAGACATACGCATTTGGATA	0.433																																					p.A1430V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C4289T	6						.						187.0	181.0	183.0					6																	161006078		2119	4268	6387	160926068	SO:0001630	splice_region_variant	4018	exon27			X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4289+1C>T	6.37:g.161006078G>A		Somatic		Capture	Illumina HiSeq	Phase_I	160926068	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	g	10.47	1.359209	0.24598	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.66995	-0.24;-0.24	2.56	1.63	0.23807	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.68393	0.2996	M	0.77406	2.37	0.21220	N	0.999755	D	0.71674	0.998	D	0.73380	0.98	T	0.56823	-0.7915	8	.	.	.	.	7.0905	0.25282	0.0:0.2839:0.7161:0.0	.	3938	P08519	APOA_HUMAN	V	1430	ENSP00000321334:A1430V;ENSP00000395608:A1430V	.	A	-	2	0	LPA	160926068	1.000000	0.71417	0.946000	0.38457	0.049000	0.14656	3.561000	0.53770	0.362000	0.24319	-0.662000	0.03851	GCT		0.433	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	Missense_Mutation
MAP3K4	4216	broad.mit.edu	37	6	161514053	161514053	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:161514053G>A	ENST00000392142.4	+	14	3461	c.3313G>A	c.(3313-3315)Gcc>Acc	p.A1105T	MAP3K4_ENST00000366920.2_Missense_Mutation_p.A1105T|MAP3K4_ENST00000366919.2_Missense_Mutation_p.A1105T|MAP3K4_ENST00000348824.7_Missense_Mutation_p.A1105T	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	1105					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)	p.A1105T(2)		breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		AATTGAACCTGCCTTTATTTC	0.358																																					p.A1105T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G3313A	6						.						157.0	141.0	146.0					6																	161514053		2203	4300	6503	161434043	SO:0001583	missense	4216	exon14			AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.3313G>A	6.37:g.161514053G>A	ENSP00000375986:p.Ala1105Thr	Somatic		Capture	Illumina HiSeq	Phase_I	161434043	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	.	.	.	.	.	.	.	.	.	.	G	18.70	3.680929	0.68042	.	.	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53	5.84	4.97	0.65823	.	0.132156	0.50627	D	0.000104	T	0.45677	0.1354	L	0.41236	1.265	0.54753	D	0.999983	B;B;B;B	0.32160	0.029;0.358;0.161;0.236	B;B;B;B	0.30495	0.096;0.07;0.116;0.11	T	0.48822	-0.9001	10	0.15066	T	0.55	-10.4272	16.3119	0.82874	0.0:0.0:0.8666:0.1334	.	1105;95;1105;1105	F5H538;Q9P1M2;Q9Y6R4-2;Q9Y6R4	.;.;.;M3K4_HUMAN	T	1105	ENSP00000355886:A1105T;ENSP00000375986:A1105T;ENSP00000355887:A1105T;ENSP00000297332:A1105T	ENSP00000297332:A1105T	A	+	1	0	MAP3K4	161434043	1.000000	0.71417	0.973000	0.42090	0.997000	0.91878	7.622000	0.83099	1.462000	0.47948	0.655000	0.94253	GCC		0.358	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
FAM217A	222826	broad.mit.edu	37	6	4070051	4070051	+	Nonsense_Mutation	SNP	G	G	A	rs371728702		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:4070051G>A	ENST00000274673.3	-	7	809	c.406C>T	c.(406-408)Caa>Taa	p.Q136*	FAM217A_ENST00000380188.2_5'UTR	NM_173563.2	NP_775834.2	Q8IXS0	F217A_HUMAN	family with sequence similarity 217, member A	136								p.Q136*(1)									GGACCAACTTGCTTATCAACT	0.398																																					p.Q136X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C406T	6						.	G	stop/GLN	0,4406		0,0,2203	80.0	74.0	76.0		406	4.5	0.0	6		76	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	C6orf146	NM_173563.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		136/509	4070051	1,13005	2203	4300	6503	4015050	SO:0001587	stop_gained	222826	exon7			BC039349	CCDS4489.1	6p25.1	2012-02-07	2012-02-07	2012-02-07	ENSG00000145975	ENSG00000145975			21362	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 146"""	C6orf146			Standard	NM_173563		Approved	MGC43581	uc003mvx.3	Q8IXS0	OTTHUMG00000014159	ENST00000274673.3:c.406C>T	6.37:g.4070051G>A	ENSP00000274673:p.Gln136*	Somatic		Capture	Illumina HiSeq	Phase_I	4015050	NM_173563	Q5JYK1	Nonsense_Mutation	SNP	ENST00000274673.3	37	CCDS4489.1	.	.	.	.	.	.	.	.	.	.	G	16.70	3.195954	0.58126	0.0	1.16E-4	ENSG00000145975	ENST00000274673;ENST00000470599	.	.	.	5.34	4.46	0.54185	.	0.696198	0.13681	N	0.370204	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-0.0756	11.4754	0.50295	0.0:0.0:0.8205:0.1794	.	.	.	.	X	136;264	.	ENSP00000274673:Q136X	Q	-	1	0	C6orf146	4015050	0.015000	0.18098	0.007000	0.13788	0.007000	0.05969	1.911000	0.39937	1.597000	0.50072	0.650000	0.86243	CAA		0.398	FAM217A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352577.2	NM_173563	
GMPR	2766	broad.mit.edu	37	6	16295324	16295324	+	Silent	SNP	G	G	A	rs368447687		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:16295324G>A	ENST00000259727.4	+	9	1059	c.945G>A	c.(943-945)acG>acA	p.T315T	GMPR_ENST00000544145.1_3'UTR	NM_006877.3	NP_006868.3	P36959	GMPR1_HUMAN	guanosine monophosphate reductase	315					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|response to cold (GO:0009409)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|GMP reductase complex (GO:1902560)	GMP reductase activity (GO:0003920)|metal ion binding (GO:0046872)	p.T315T(1)		NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	20	Breast(50;0.0427)|Ovarian(93;0.103)	all_hematologic(90;0.0895)				TGAGGTCCACGTGCACCTACG	0.552																																					p.T315T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G945A	6						.	G		0,4406		0,0,2203	87.0	78.0	81.0		945	1.0	1.0	6		81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GMPR	NM_006877.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		315/346	16295324	2,13004	2203	4300	6503	16403303	SO:0001819	synonymous_variant	2766	exon9				CCDS4537.1	6p23	2009-07-10			ENSG00000137198	ENSG00000137198	1.7.1.7		4376	protein-coding gene	gene with protein product		139265				2194676	Standard	NM_006877		Approved		uc003nbs.3	P36959	OTTHUMG00000014302	ENST00000259727.4:c.945G>A	6.37:g.16295324G>A		Somatic		Capture	Illumina HiSeq	Phase_I	16403303	NM_006877	Q96HQ6	Silent	SNP	ENST00000259727.4	37	CCDS4537.1																																																																																				0.552	GMPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039942.2		
ATXN1	6310	broad.mit.edu	37	6	16327508	16327508	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:16327508C>A	ENST00000244769.4	-	8	1970	c.1034G>T	c.(1033-1035)gGc>gTc	p.G345V	ATXN1_ENST00000436367.1_Missense_Mutation_p.G345V	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	345					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.G345V(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				GCCTGCCTTGCCCAGGCCCAG	0.677																																					p.G345V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1034T	6						.						48.0	56.0	54.0					6																	16327508		2203	4299	6502	16435487	SO:0001583	missense	6310	exon8			X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.1034G>T	6.37:g.16327508C>A	ENSP00000244769:p.Gly345Val	Somatic		Capture	Illumina HiSeq	Phase_I	16435487	NM_000332	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	C	3.627	-0.076413	0.07184	.	.	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.75589	-0.95;-0.95	5.07	1.85	0.25348	.	0.917094	0.09500	N	0.793712	T	0.23289	0.0563	N	0.01576	-0.805	0.34504	D	0.706429	B	0.02656	0.0	B	0.01281	0.0	T	0.01810	-1.1269	10	0.27082	T	0.32	-5.2425	5.948	0.19229	0.5958:0.2211:0.1831:0.0	.	345	P54253	ATX1_HUMAN	V	345	ENSP00000244769:G345V;ENSP00000416360:G345V	ENSP00000244769:G345V	G	-	2	0	ATXN1	16435487	0.251000	0.23961	0.996000	0.52242	0.792000	0.44763	2.052000	0.41316	0.405000	0.25532	0.561000	0.74099	GGC		0.677	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
CAP2	10486	broad.mit.edu	37	6	17543330	17543330	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:17543330G>A	ENST00000229922.2	+	11	1697	c.1165G>A	c.(1165-1167)Gtg>Atg	p.V389M	CAP2_ENST00000489374.1_Missense_Mutation_p.V277M|CAP2_ENST00000493172.1_Missense_Mutation_p.V129M|CAP2_ENST00000378990.2_Missense_Mutation_p.V363M|CAP2_ENST00000465994.1_Missense_Mutation_p.V325M	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	389	C-CAP/cofactor C-like. {ECO:0000255|PROSITE-ProRule:PRU00659}.				activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)		p.V389M(1)		breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TGACAATGTGGTGGGCATTGT	0.433																																					p.V389M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1165A	6						.						168.0	166.0	167.0					6																	17543330		2203	4300	6503	17651309	SO:0001583	missense	10486	exon11			BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.1165G>A	6.37:g.17543330G>A	ENSP00000229922:p.Val389Met	Somatic		Capture	Illumina HiSeq	Phase_I	17651309	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Missense_Mutation	SNP	ENST00000229922.2	37	CCDS4539.1	.	.	.	.	.	.	.	.	.	.	g	32	5.144989	0.94603	.	.	ENSG00000112186	ENST00000229922;ENST00000378994;ENST00000489374;ENST00000378990;ENST00000493172;ENST00000465994	T;T;T;T	0.19105	2.17;2.21;2.17;2.18	5.55	5.55	0.83447	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	M	0.93638	3.44	0.80722	D	1	D;D;D;D;D	0.89917	0.986;1.0;0.971;0.999;1.0	P;D;P;D;D	0.91635	0.709;0.998;0.823;0.963;0.999	T	0.66610	-0.5880	10	0.87932	D	0	-21.5742	19.8519	0.96744	0.0:0.0:1.0:0.0	.	129;277;325;363;389	B7Z214;B7Z385;B7Z1C4;E9PDI2;P40123	.;.;.;.;CAP2_HUMAN	M	389;306;277;363;129;325	ENSP00000229922:V389M;ENSP00000417705:V277M;ENSP00000368275:V363M;ENSP00000418604:V325M	ENSP00000229922:V389M	V	+	1	0	CAP2	17651309	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.813000	0.99286	2.774000	0.95407	0.561000	0.74099	GTG		0.433	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
KIF13A	63971	broad.mit.edu	37	6	17781486	17781486	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:17781486G>T	ENST00000259711.6	-	30	3696	c.3591C>A	c.(3589-3591)tcC>tcA	p.S1197S	KIF13A_ENST00000378826.2_Silent_p.S1197S|KIF13A_ENST00000378814.5_Silent_p.S1184S|KIF13A_ENST00000378816.5_Silent_p.S1197S|KIF13A_ENST00000378843.2_Silent_p.S1184S	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1197					ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.S1197S(1)		breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			AGTTCACGCCGGATGCATGGG	0.498																																					p.S1197S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C3591A	6						.						76.0	76.0	76.0					6																	17781486		1972	4162	6134	17889465	SO:0001819	synonymous_variant	63971	exon30			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313	ENST00000259711.6:c.3591C>A	6.37:g.17781486G>T		Somatic		Capture	Illumina HiSeq	Phase_I	17889465	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Silent	SNP	ENST00000259711.6	37	CCDS47381.1	.	.	.	.	.	.	.	.	.	.	g	0.028	-1.355514	0.01256	.	.	ENSG00000137177	ENST00000358380	.	.	.	5.14	-9.39	0.00619	.	.	.	.	.	T	0.17408	0.0418	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39396	-0.9616	4	.	.	.	.	3.2161	0.06699	0.1672:0.1322:0.1742:0.5264	.	.	.	.	Q	591	.	.	P	-	2	0	KIF13A	17889465	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-5.586000	0.00111	-2.326000	0.00637	-2.077000	0.00380	CCG		0.498	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4		
DEK	7913	broad.mit.edu	37	6	18236733	18236733	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:18236733G>A	ENST00000397239.3	-	9	1444	c.997C>T	c.(997-999)Ctg>Ttg	p.L333L	DEK_ENST00000244776.7_Silent_p.L299L	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	333					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)	p.L333L(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			GCACTGGCCAGTAATTTCTTT	0.318			T	NUP214	AML																																p.L333L			Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C997T	6						.						101.0	106.0	104.0					6																	18236733		2201	4296	6497	18344712	SO:0001819	synonymous_variant	7913	exon9			X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"""DEK oncogene (DNA binding)"", ""DEK oncogene"""			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.997C>T	6.37:g.18236733G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18344712	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																				0.318	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4		
KIAA0319	9856	broad.mit.edu	37	6	24556935	24556935	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:24556935G>T	ENST00000378214.3	-	18	3281	c.2757C>A	c.(2755-2757)ggC>ggA	p.G919G	KIAA0319_ENST00000543707.1_Silent_p.G919G|KIAA0319_ENST00000535378.1_Silent_p.G910G|KIAA0319_ENST00000537886.1_Silent_p.G919G|KIAA0319_ENST00000430948.2_Silent_p.G874G	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	919			G -> A (in dbSNP:rs10946705).		negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G919G(1)		breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						AGTGACCATGGCCAGAACACT	0.498																																					p.G919G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2757A	6						.						87.0	78.0	81.0					6																	24556935		2203	4300	6503	24664914	SO:0001819	synonymous_variant	9856	exon18			AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.2757C>A	6.37:g.24556935G>T		Somatic		Capture	Illumina HiSeq	Phase_I	24664914	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Silent	SNP	ENST00000378214.3	37	CCDS34348.1																																																																																				0.498	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
LRRC16A	55604	broad.mit.edu	37	6	25495385	25495385	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:25495385T>G	ENST00000329474.6	+	16	1635	c.1267T>G	c.(1267-1269)Tct>Gct	p.S423A		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	423					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)	p.S423A(1)		breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						TTTTAGTAGTTCTCTGGCTTT	0.378																																					p.S423A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1267G	6						.						133.0	125.0	128.0					6																	25495385		1843	4085	5928	25603364	SO:0001583	missense	55604	exon16			AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.1267T>G	6.37:g.25495385T>G	ENSP00000331983:p.Ser423Ala	Somatic		Capture	Illumina HiSeq	Phase_I	25603364	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	T	7.266	0.606149	0.14002	.	.	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.53423	0.62	5.4	5.4	0.78164	.	0.211384	0.50627	D	0.000102	T	0.11537	0.0281	N	0.05574	-0.02	0.80722	D	1	B;B;B	0.20550	0.015;0.027;0.046	B;B;B	0.19946	0.012;0.008;0.027	T	0.12760	-1.0535	10	0.02654	T	1	.	15.7249	0.77747	0.0:0.0:0.0:1.0	.	423;423;423	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	A	423	ENSP00000331983:S423A	ENSP00000331983:S423A	S	+	1	0	LRRC16A	25603364	1.000000	0.71417	0.996000	0.52242	0.985000	0.73830	3.444000	0.52914	2.177000	0.69029	0.459000	0.35465	TCT		0.378	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
MAS1L	116511	broad.mit.edu	37	6	29454802	29454802	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:29454802A>G	ENST00000377127.3	-	1	936	c.878T>C	c.(877-879)gTc>gCc	p.V293A		NM_052967.1	NP_443199.1	P35410	MAS1L_HUMAN	MAS1 proto-oncogene like, G protein-coupled receptor	293					G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.V293A(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(7)|pancreas(1)|prostate(2)|skin(2)	28						GGAGGTGGTGACAAACATTTT	0.488																																					p.V293A	NSCLC(153;755 1987 3859 11251 32945)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T878C	6						.						41.0	45.0	43.0					6																	29454802		2203	4300	6503	29562781	SO:0001583	missense	116511	exon1			S78653	CCDS4661.1	6p22.1	2014-06-26	2014-06-26		ENSG00000204687	ENSG00000204687		"""GPCR / Class A : Orphans"""	13961	protein-coding gene	gene with protein product		607235	"""MAS1 oncogene-like"""				Standard	NM_052967		Approved	MAS-L, MRG, dJ994E9.2	uc011dlq.2	P35410	OTTHUMG00000031089	ENST00000377127.3:c.878T>C	6.37:g.29454802A>G	ENSP00000366331:p.Val293Ala	Somatic		Capture	Illumina HiSeq	Phase_I	29562781	NM_052967	Q5SUN5	Missense_Mutation	SNP	ENST00000377127.3	37	CCDS4661.1	.	.	.	.	.	.	.	.	.	.	A	0.088	-1.172012	0.01646	.	.	ENSG00000204687	ENST00000377127	T	0.70749	-0.51	2.0	-4.0	0.04057	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.16257	0.0391	N	0.11201	0.11	0.09310	N	1	B	0.15141	0.012	B	0.18871	0.023	T	0.10222	-1.0639	9	0.16896	T	0.51	.	1.0473	0.01572	0.2893:0.1344:0.3729:0.2034	.	293	P35410	MAS1L_HUMAN	A	293	ENSP00000366331:V293A	ENSP00000366331:V293A	V	-	2	0	MAS1L	29562781	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.427000	0.06999	-2.096000	0.00852	-0.513000	0.04457	GTC		0.488	MAS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076126.2	NM_052967	
TRIM26	7726	broad.mit.edu	37	6	30154075	30154075	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:30154075C>T	ENST00000454678.2	-	10	1634	c.1198G>A	c.(1198-1200)Gag>Aag	p.E400K	TRIM26_ENST00000453195.1_Missense_Mutation_p.E400K|TRIM26_ENST00000437089.1_Missense_Mutation_p.E400K	NM_003449.4	NP_003440.1	Q12899	TRI26_HUMAN	tripartite motif containing 26	400	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.|Poly-Glu.				innate immune response (GO:0045087)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)	p.E400K(1)		lung(1)|ovary(2)	3						TAGCCGGcctcctcttcctcc	0.557																																					p.E400K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1198A	6						.						128.0	75.0	94.0					6																	30154075		1511	2709	4220	30262054	SO:0001583	missense	7726	exon10			AB088090	CCDS4678.1	6p21.3	2013-01-09	2011-01-25	2001-11-23	ENSG00000234127	ENSG00000234127		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	12962	protein-coding gene	gene with protein product		600830	"""tripartite motif-containing 26"""	ZNF173		8530076	Standard	NM_003449		Approved	RNF95	uc003npt.3	Q12899	OTTHUMG00000031041	ENST00000454678.2:c.1198G>A	6.37:g.30154075C>T	ENSP00000410446:p.Glu400Lys	Somatic		Capture	Illumina HiSeq	Phase_I	30262054	NM_003449	A6NG96|Q5SRL2	Missense_Mutation	SNP	ENST00000454678.2	37	CCDS4678.1	.	.	.	.	.	.	.	.	.	.	C	0.106	-1.145163	0.01714	.	.	ENSG00000234127	ENST00000453195;ENST00000454678;ENST00000437089	T;T;T	0.61980	0.06;0.06;0.06	5.1	3.3	0.37823	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.160627	0.29940	N	0.010816	T	0.21631	0.0521	N	0.22421	0.69	0.09310	N	1	B;B	0.14438	0.01;0.0	B;B	0.10450	0.005;0.001	T	0.14364	-1.0475	10	0.28530	T	0.3	.	6.064	0.19854	0.1867:0.7186:0.0:0.0947	.	400;400	Q5SRL2;Q12899	.;TRI26_HUMAN	K	400	ENSP00000391879:E400K;ENSP00000410446:E400K;ENSP00000395491:E400K	ENSP00000395491:E400K	E	-	1	0	TRIM26	30262054	0.998000	0.40836	0.005000	0.12908	0.002000	0.02628	4.655000	0.61476	0.715000	0.32103	-0.343000	0.07986	GAG		0.557	TRIM26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253442.1	NM_003449	
TUBB	203068	broad.mit.edu	37	6	30691260	30691260	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:30691260delG	ENST00000327892.8	+	4	727	c.421delG	c.(421-423)gggfs	p.G142fs	XXbac-BPG252P9.9_ENST00000607476.1_RNA|TUBB_ENST00000396384.1_Frame_Shift_Del_p.G70fs|TUBB_ENST00000435534.1_Intron|TUBB_ENST00000396389.1_Frame_Shift_Del_p.G124fs|TUBB_ENST00000330914.3_Frame_Shift_Del_p.G70fs	NM_178014.2	NP_821133.1	P07437	TBB5_HUMAN	tubulin, beta class I	142					cell division (GO:0051301)|cellular component movement (GO:0006928)|cellular process (GO:0009987)|cytoskeleton-dependent intracellular transport (GO:0030705)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|natural killer cell mediated cytotoxicity (GO:0042267)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cell body (GO:0044297)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nuclear envelope lumen (GO:0005641)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|MHC class I protein binding (GO:0042288)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.G142fs*23(1)		breast(1)|endometrium(1)|kidney(8)|large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	16					Colchicine(DB01394)|Podofilox(DB01179)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)	CTCACTGGGCGGGGGCACAGG	0.572																																					p.G141fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.421delG	6						.						65.0	64.0	65.0					6																	30691260		2203	4300	6503	30799239	SO:0001589	frameshift_variant	203068	exon4			AB062393	CCDS4687.1	6p21.33	2011-10-10	2011-10-10		ENSG00000196230	ENSG00000196230		"""Tubulins"""	20778	protein-coding gene	gene with protein product	"""class I beta-tubulin"", ""beta1-tubulin"""	191130	"""tubulin, beta polypeptide"", ""tubulin, beta"""			11504633, 8270253	Standard	NM_001293212		Approved	OK/SW-cl.56, MGC16435, M40, Tubb5	uc003nrl.3	P07437	OTTHUMG00000031059	ENST00000327892.8:c.421delG	6.37:g.30691260delG	ENSP00000339001:p.Gly142fs	Somatic		Capture	Illumina HiSeq	Phase_I	30799239	NM_178014	P05218|Q8WUC1|Q9CY33	Frame_Shift_Del	DEL	ENST00000327892.8	37	CCDS4687.1																																																																																				0.572	TUBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076074.2	NM_178014	
VARS2	57176	broad.mit.edu	37	6	30889394	30889394	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:30889394G>A	ENST00000321897.5	+	17	2293	c.1661G>A	c.(1660-1662)cGg>cAg	p.R554Q	VARS2_ENST00000542001.1_Missense_Mutation_p.R414Q|VARS2_ENST00000541562.1_Missense_Mutation_p.R584Q|VARS2_ENST00000416670.2_Missense_Mutation_p.R554Q|VARS2_ENST00000476162.1_3'UTR			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	554					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.R554Q(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						GTGGTTGGGCGGTCAGAGGCT	0.587																																					p.R414Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1241A	6						.						34.0	30.0	31.0					6																	30889394		1510	2708	4218	30997373	SO:0001583	missense	57176	exon17			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.1661G>A	6.37:g.30889394G>A	ENSP00000316092:p.Arg554Gln	Somatic		Capture	Illumina HiSeq	Phase_I	30997373	NM_001167733	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.881504	0.72294	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	5.35	5.35	0.76521	Rossmann-like alpha/beta/alpha sandwich fold (1);Aminoacyl-tRNA synthetase, class Ia (1);	0.115026	0.56097	D	0.000022	T	0.26159	0.0638	M	0.75264	2.295	0.22996	N	0.998455	P;P;D	0.69078	0.911;0.892;0.997	B;B;P	0.51777	0.41;0.247;0.679	T	0.16867	-1.0388	10	0.87932	D	0	-31.2577	10.0731	0.42345	0.0912:0.0:0.9088:0.0	.	552;584;554	B7ZL25;F5GXJ0;Q5ST30	.;.;SYVM_HUMAN	Q	554;554;414;584	ENSP00000316092:R554Q;ENSP00000394802:R554Q;ENSP00000438200:R414Q;ENSP00000441000:R584Q	ENSP00000316092:R554Q	R	+	2	0	VARS2	30997373	0.895000	0.30542	0.997000	0.53966	0.979000	0.70002	5.218000	0.65257	2.509000	0.84616	0.555000	0.69702	CGG		0.587	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442	
LY6G5C	80741	broad.mit.edu	37	6	31644797	31644797	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:31644797G>T	ENST00000383237.4	-	3	393	c.390C>A	c.(388-390)ttC>ttA	p.F130L	LY6G5C_ENST00000474395.1_5'UTR|LY6G5C_ENST00000375860.2_Missense_Mutation_p.F128L|LY6G5C_ENST00000375858.3_Missense_Mutation_p.F127L			Q5SRR4	LY65C_HUMAN	lymphocyte antigen 6 complex, locus G5C	130	UPAR/Ly6.					extracellular region (GO:0005576)		p.F127L(1)		endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	7						AGTATTGAGAGAATATCCAGA	0.473																																					p.F130L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C390A	6						.						127.0	137.0	133.0					6																	31644797		1511	2709	4220	31752776	SO:0001583	missense	80741	exon3				CCDS34401.1, CCDS34401.2	6p21	2010-02-17	2002-07-29	2002-08-01	ENSG00000204428	ENSG00000204428			13932	protein-coding gene	gene with protein product		610434	"""chromosome 6 open reading frame 20"""	C6orf20		12079290	Standard	NM_025262		Approved	G5c, NG33	uc003nvu.2	Q5SRR4	OTTHUMG00000031228	ENST00000383237.4:c.390C>A	6.37:g.31644797G>T	ENSP00000372724:p.Phe130Leu	Somatic		Capture	Illumina HiSeq	Phase_I	31752776	NM_025262	A6NCW4|B0UXB3|B0UXB4|B0UZ69|B0UZQ0|B1B0L9|O95871|Q5SQ59|Q8NDY0|Q8NDY1	Missense_Mutation	SNP	ENST00000383237.4	37	CCDS34401.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.08|15.08	2.727747|2.727747	0.48833|0.48833	.|.	.|.	ENSG00000204428|ENSG00000204428	ENST00000375860;ENST00000375858;ENST00000383237|ENST00000375863	D;D;D|.	0.85411|.	-1.98;-1.98;-1.98|.	3.54|3.54	-1.73|-1.73	0.08081|0.08081	.|.	0.823363|.	0.10205|.	N|.	0.702790|.	T|T	0.13586|0.13586	0.0329|0.0329	L|L	0.32530|0.32530	0.975|0.975	0.20563|0.20563	N|N	0.999888|0.999888	P|.	0.36909|.	0.573|.	B|.	0.32090|.	0.14|.	T|T	0.34204|0.34204	-0.9838|-0.9838	10|5	0.02654|.	T|.	1|.	-18.0515|-18.0515	7.6888|7.6888	0.28557|0.28557	0.6467:0.0:0.3533:0.0|0.6467:0.0:0.3533:0.0	.|.	130|.	Q5SRR4|.	LY65C_HUMAN|.	L|Y	128;127;130|205	ENSP00000365020:F128L;ENSP00000365018:F127L;ENSP00000372724:F130L|.	ENSP00000365018:F127L|.	F|S	-|-	3|2	2|0	LY6G5C|LY6G5C	31752776|31752776	0.019000|0.019000	0.18553|0.18553	0.173000|0.173000	0.22940|0.22940	0.926000|0.926000	0.56050|0.56050	-0.032000|-0.032000	0.12266|0.12266	-0.405000|-0.405000	0.07599|0.07599	0.313000|0.313000	0.20887|0.20887	TTC|TCT		0.473	LY6G5C-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076473.4		
TNXB	7148	broad.mit.edu	37	6	32020477	32020477	+	Missense_Mutation	SNP	C	C	T	rs543265032		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:32020477C>T	ENST00000375244.3	-	26	9286	c.9085G>A	c.(9085-9087)Gtg>Atg	p.V3029M	TNXB_ENST00000375247.2_Missense_Mutation_p.V3027M			P22105	TENX_HUMAN	tenascin XB	3074	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.V3105M(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						ACTGGGCCCACGCGCTGCCCC	0.647													c|||	1	0.000199681	0.0	0.0	5008	,	,		14953	0.0		0.0	False		,,,				2504	0.001				p.V3027M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G9079A	6						.						55.0	62.0	59.0					6																	32020477		1390	2616	4006	32128455	SO:0001583	missense	7148	exon26			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9085G>A	6.37:g.32020477C>T	ENSP00000364393:p.Val3029Met	Somatic		Capture	Illumina HiSeq	Phase_I	32128455	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	c	11.76	1.735094	0.30774	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.04454	3.62;3.62	4.42	3.55	0.40652	.	0.284575	0.19181	U	0.120664	T	0.03390	0.0098	M	0.76170	2.325	0.23232	N	0.998076	P	0.45283	0.855	B	0.42462	0.388	T	0.31833	-0.9929	10	0.35671	T	0.21	.	11.2008	0.48741	0.0:0.6407:0.3593:0.0	.	3027	P22105-3	.	M	3029;3027	ENSP00000364393:V3029M;ENSP00000364396:V3027M	ENSP00000364393:V3029M	V	-	1	0	TNXB	32128455	0.000000	0.05858	0.714000	0.30535	0.035000	0.12851	-0.170000	0.09897	0.829000	0.34733	-0.218000	0.12543	GTG		0.647	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	broad.mit.edu	37	6	32036719	32036719	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:32036719C>A	ENST00000375244.3	-	16	5983	c.5782G>T	c.(5782-5784)Gga>Tga	p.G1928*	TNXB_ENST00000375247.2_Nonsense_Mutation_p.G1928*			P22105	TENX_HUMAN	tenascin XB	2010	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.G2015*(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGGTCACCTCCTATGCGGACC	0.522																																					p.G1928X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G5782T	6						.						128.0	146.0	140.0					6																	32036719		1346	2595	3941	32144697	SO:0001587	stop_gained	7148	exon16			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.5782G>T	6.37:g.32036719C>A	ENSP00000364393:p.Gly1928*	Somatic		Capture	Illumina HiSeq	Phase_I	32144697	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Nonsense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	46	12.939950	0.99707	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	.	.	.	5.16	5.16	0.70880	.	0.990719	0.08200	N	0.982495	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22109	T	0.4	.	15.9306	0.79656	0.0:1.0:0.0:0.0	.	.	.	.	X	1928	.	ENSP00000364393:G1928X	G	-	1	0	TNXB	32144697	0.010000	0.17322	0.009000	0.14445	0.001000	0.01503	2.584000	0.46102	2.587000	0.87381	0.655000	0.94253	GGA		0.522	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
TNXB	7148	broad.mit.edu	37	6	32063797	32063797	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:32063797G>A	ENST00000479795.1	-	3	1973	c.1833C>T	c.(1831-1833)taC>taT	p.Y611Y	TNXB_ENST00000375244.3_Silent_p.Y611Y|TNXB_ENST00000375247.2_Silent_p.Y611Y			P22105	TENX_HUMAN	tenascin XB	611	EGF-like 15. {ECO:0000255|PROSITE- ProRule:PRU00076}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)	p.Y611Y(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CCTCACTCACGTAGCCTTCCC	0.662																																					p.Y611Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1833T	6						.						36.0	37.0	37.0					6																	32063797		2198	4282	6480	32171775	SO:0001819	synonymous_variant	7148	exon3			X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000479795.1:c.1833C>T	6.37:g.32063797G>A		Somatic		Capture	Illumina HiSeq	Phase_I	32171775	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000479795.1	37																																																																																					0.662	TNXB-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000357059.1	NM_019105	
GPSM3	63940	broad.mit.edu	37	6	32159152	32159152	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:32159152G>C	ENST00000375040.3	-	4	866	c.474C>G	c.(472-474)caC>caG	p.H158Q	GPSM3_ENST00000375043.3_Missense_Mutation_p.H158Q|GPSM3_ENST00000487761.1_Missense_Mutation_p.H155Q|PBX2_ENST00000375050.4_5'Flank	NM_001276501.1	NP_001263430.1	Q9Y4H4	GPSM3_HUMAN	G-protein signaling modulator 3	158					regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	cytoplasm (GO:0005737)	GDP-dissociation inhibitor activity (GO:0005092)	p.H158Q(1)		large_intestine(1)	1						CTCAGCAGGTGTGTGTGGGGG	0.627																																					p.H158Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C474G	6						.						105.0	114.0	111.0					6																	32159152		2203	4300	6503	32267130	SO:0001583	missense	63940	exon8			AF155657	CCDS34419.1	6p21.3	2010-06-24	2010-06-24	2004-02-04	ENSG00000213654	ENSG00000213654			13945	protein-coding gene	gene with protein product	"""activator of G-protein signaling 4"""		"""chromosome 6 open reading frame 9"", ""G-protein signalling modulator 3 (AGS3-like, C. elegans)"""	C6orf9		2259622, 15096500	Standard	NM_022107		Approved	NG1, G18, G18.1a, G18.1b, G18.2, AGS4	uc003oaz.3	Q9Y4H4	OTTHUMG00000031244	ENST00000375040.3:c.474C>G	6.37:g.32159152G>C	ENSP00000364180:p.His158Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32267130	NM_022107	A2BFJ3	Missense_Mutation	SNP	ENST00000375040.3	37	CCDS34419.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.196269	0.38806	.	.	ENSG00000213654	ENST00000487761;ENST00000375040;ENST00000375043	.	.	.	4.51	1.35	0.21983	.	0.145425	0.28560	U	0.014919	T	0.10208	0.0250	N	0.08118	0	0.38998	D	0.959287	P;P	0.38195	0.622;0.622	B;B	0.33568	0.137;0.166	T	0.05801	-1.0863	9	0.62326	D	0.03	-12.2988	5.6273	0.17490	0.392:0.0:0.608:0.0	.	158;158	Q9Y4H4;A2BFJ3	GPSM3_HUMAN;.	Q	155;158;158	.	ENSP00000364180:H158Q	H	-	3	2	GPSM3	32267130	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	0.852000	0.27764	0.479000	0.27511	0.563000	0.77884	CAC		0.627	GPSM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076509.1	NM_022107	
BTNL2	56244	broad.mit.edu	37	6	32372927	32372927	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:32372927T>C	ENST00000374993.1	-	2	215	c.216A>G	c.(214-216)acA>acG	p.T72T	BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000454136.3_Silent_p.T72T|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000544175.1_Intron|BTNL2_ENST00000429232.2_Silent_p.T72T|BTNL2_ENST00000374995.3_Silent_p.T72T	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	72	Ig-like V-type 1.					integral component of membrane (GO:0016021)		p.T72T(1)		central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						CAAACACAGGTGTGCTGGGCT	0.567																																					p.T72T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A216G	6						.						230.0	218.0	222.0					6																	32372927		1511	2709	4220	32480905	SO:0001819	synonymous_variant	56244	exon2			AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.216A>G	6.37:g.32372927T>C		Somatic		Capture	Illumina HiSeq	Phase_I	32480905	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Silent	SNP	ENST00000374993.1	37																																																																																					0.567	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
HLA-DPB1	3115	broad.mit.edu	37	6	33043899	33043899	+	Silent	SNP	C	C	A	rs139072161	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:33043899C>A	ENST00000418931.2	+	1	197	c.81C>A	c.(79-81)gtC>gtA	p.V27V	HLA-DPA1_ENST00000419277.1_Intron|HLA-DPB1_ENST00000535465.1_Silent_p.V27V|HLA-DPA1_ENST00000463066.1_5'Flank|HLA-DPA1_ENST00000428995.1_5'Flank	NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1	27					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						CATCTGTGGTCCAGGGCAGGG	0.557																																					p.V27V												.	.	0			c.C81A	6						.						42.0	37.0	39.0					6																	33043899		1509	2709	4218	33151877	SO:0001819	synonymous_variant	3115	exon1				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	ENST00000418931.2:c.81C>A	6.37:g.33043899C>A		None		Capture	Illumina HiSeq	Phase_I	33151877	NM_002121	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Silent	SNP	ENST00000418931.2	37	CCDS4765.1																																																																																				0.557	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2	NM_002121	
FGD2	221472	broad.mit.edu	37	6	36983627	36983627	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:36983627C>T	ENST00000274963.8	+	9	1284	c.1113C>T	c.(1111-1113)gcC>gcT	p.A371A		NM_173558.3	NP_775829.2	Q7Z6J4	FGD2_HUMAN	FYVE, RhoGEF and PH domain containing 2	371	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.A371A(1)		central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	25						TCGATGTGGCCGGGATGAAGG	0.587																																					p.A371A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1113T	6						.																																			37091605	SO:0001819	synonymous_variant	221472	exon9			AK097230	CCDS4829.1	6p21.2	2013-01-10	2004-08-24		ENSG00000146192	ENSG00000146192		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3664	protein-coding gene	gene with protein product		605091	"""FGD1 family, member 2"""			10458911	Standard	NM_173558		Approved	ZFYVE4	uc010jwp.1	Q7Z6J4	OTTHUMG00000014616	ENST00000274963.8:c.1113C>T	6.37:g.36983627C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37091605	NM_173558	Q5T8I1|Q6P6A8|Q6ZNL5|Q8IZ32|Q8N868|Q9H7M2	Silent	SNP	ENST00000274963.8	37	CCDS4829.1																																																																																				0.587	FGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040398.2	NM_173558	
DNAH8	1769	broad.mit.edu	37	6	38854775	38854775	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:38854775delT	ENST00000359357.3	+	55	8071	c.7817delT	c.(7816-7818)attfs	p.I2606fs	DNAH8_ENST00000441566.1_Frame_Shift_Del_p.I2570fs|DNAH8_ENST00000449981.2_Frame_Shift_Del_p.I2823fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2606	AAA 3. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.F2607fs*22(2)		NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ATAGACAAAATTTTTGGTATG	0.313																																					p.I2606fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.7817delT	6						.						80.0	80.0	80.0					6																	38854775		2203	4300	6503	38962753	SO:0001589	frameshift_variant	1769	exon55			Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.7817delT	6.37:g.38854775delT	ENSP00000352312:p.Ile2606fs	Somatic		Capture	Illumina HiSeq	Phase_I	38962753	NM_001371	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37																																																																																					0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
GUCA1B	2979	broad.mit.edu	37	6	42152575	42152575	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:42152575C>A	ENST00000230361.3	-	4	676	c.581G>T	c.(580-582)aGa>aTa	p.R194I		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	194					body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)	p.R194I(1)		large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			ACTTTTCCGTCTCTGCTGAGC	0.587																																					p.R194I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G581T	6						.						118.0	99.0	106.0					6																	42152575		2203	4300	6503	42260553	SO:0001583	missense	2979	exon4			AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"""EF-hand domain containing"""	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.581G>T	6.37:g.42152575C>A	ENSP00000230361:p.Arg194Ile	Somatic		Capture	Illumina HiSeq	Phase_I	42260553	NM_002098	Q9NU15	Missense_Mutation	SNP	ENST00000230361.3	37	CCDS4865.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.632565	0.87660	.	.	ENSG00000112599	ENST00000230361	T	0.76448	-1.02	3.7	3.7	0.42460	.	0.101732	0.64402	D	0.000006	T	0.59128	0.2171	N	0.08118	0	0.80722	D	1	P	0.51351	0.944	P	0.50490	0.642	T	0.71048	-0.4705	10	0.87932	D	0	.	13.7464	0.62879	0.0:1.0:0.0:0.0	.	194	Q9UMX6	GUC1B_HUMAN	I	194	ENSP00000230361:R194I	ENSP00000230361:R194I	R	-	2	0	GUCA1B	42260553	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.083000	0.57643	2.361000	0.80049	0.655000	0.94253	AGA		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098	
PRPH2	5961	broad.mit.edu	37	6	42690068	42690068	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:42690068G>A	ENST00000230381.5	-	1	244	c.5C>T	c.(4-6)gCg>gTg	p.A2V		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	2					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)		p.A2V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			TTTCAGTAGCGCCATGCTTGC	0.552																																					p.A2V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5T	6						.						55.0	53.0	54.0					6																	42690068		2203	4300	6503	42798046	SO:0001583	missense	5961	exon1				CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.5C>T	6.37:g.42690068G>A	ENSP00000230381:p.Ala2Val	Somatic		Capture	Illumina HiSeq	Phase_I	42798046	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.791036	0.50102	.	.	ENSG00000112619	ENST00000230381	T	0.03413	3.94	5.61	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.05364	0.0142	L	0.39898	1.24	0.58432	D	0.999999	D	0.89917	1.0	D	0.64595	0.927	T	0.50083	-0.8869	10	0.33940	T	0.23	.	14.594	0.68392	0.0703:0.0:0.9297:0.0	.	2	P23942	PRPH2_HUMAN	V	2	ENSP00000230381:A2V	ENSP00000230381:A2V	A	-	2	0	PRPH2	42798046	1.000000	0.71417	1.000000	0.80357	0.451000	0.32288	5.258000	0.65479	1.360000	0.45960	0.655000	0.94253	GCG		0.552	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	
RRP36	88745	broad.mit.edu	37	6	42995125	42995125	+	Nonsense_Mutation	SNP	C	C	T	rs575586322		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:42995125C>T	ENST00000244496.5	+	6	563	c.553C>T	c.(553-555)Cga>Tga	p.R185*		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	185					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.R185*(1)		NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						ACAGCAGGAACGAAAGCAACA	0.532													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18408	0.0		0.0	False		,,,				2504	0.0				p.R185X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C553T	6						.						66.0	62.0	64.0					6																	42995125		2203	4300	6503	43103103	SO:0001587	stop_gained	88745	exon6			BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.553C>T	6.37:g.42995125C>T	ENSP00000244496:p.Arg185*	Somatic		Capture	Illumina HiSeq	Phase_I	43103103	NM_033112	Q9BRF6|Q9P0C8	Nonsense_Mutation	SNP	ENST00000244496.5	37	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	C	10.09	1.256271	0.22965	.	.	ENSG00000124541	ENST00000244496	.	.	.	5.57	2.75	0.32379	.	0.450953	0.20205	N	0.097011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.9473	0.29993	0.2741:0.6517:0.0:0.0742	.	.	.	.	X	185	.	ENSP00000244496:R185X	R	+	1	2	RRP36	43103103	0.015000	0.18098	0.008000	0.14137	0.022000	0.10575	0.869000	0.27996	0.270000	0.21984	-0.251000	0.11542	CGA		0.532	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
PTK7	5754	broad.mit.edu	37	6	43097528	43097528	+	Missense_Mutation	SNP	C	C	T	rs376958481		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:43097528C>T	ENST00000230419.4	+	3	652	c.431C>T	c.(430-432)aCc>aTc	p.T144I	PTK7_ENST00000471863.1_Missense_Mutation_p.T144I|PTK7_ENST00000352931.2_Missense_Mutation_p.T144I|PTK7_ENST00000481273.1_Missense_Mutation_p.T152I|PTK7_ENST00000345201.2_Missense_Mutation_p.T144I|PTK7_ENST00000349241.2_Missense_Mutation_p.T144I	NM_002821.4	NP_002812.2	Q13308	PTK7_HUMAN	protein tyrosine kinase 7	144	Ig-like C2-type 2.				actin cytoskeleton reorganization (GO:0031532)|axis elongation (GO:0003401)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|cochlea morphogenesis (GO:0090103)|convergent extension (GO:0060026)|establishment of epithelial cell apical/basal polarity (GO:0045198)|establishment of planar polarity (GO:0001736)|lung-associated mesenchyme development (GO:0060484)|neural tube closure (GO:0001843)|peptidyl-tyrosine phosphorylation (GO:0018108)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of neuron projection development (GO:0010976)|signal transduction (GO:0007165)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T144I(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(12)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.00784)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			CAGCCACAGACCCAGGTCACA	0.587											OREG0017449	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T144I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C431T	6						.						105.0	85.0	92.0					6																	43097528		2203	4300	6503	43205506	SO:0001583	missense	5754	exon3			AF447176	CCDS4884.1, CCDS4885.1, CCDS4886.1, CCDS4887.1, CCDS59021.1	6p21.1-p12.2	2013-02-18	2013-02-18		ENSG00000112655	ENSG00000112655	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9618	protein-coding gene	gene with protein product		601890	"""PTK7 protein tyrosine kinase 7"""			7478540	Standard	NM_002821		Approved	CCK4	uc011dve.2	Q13308	OTTHUMG00000014721	ENST00000230419.4:c.431C>T	6.37:g.43097528C>T	ENSP00000230419:p.Thr144Ile	Somatic	913	Capture	Illumina HiSeq	Phase_I	43205506	NM_152880	A8K974|B7Z477|E9PFZ5|Q13417|Q5T650|Q6IQ54|Q8NFA5|Q8NFA6|Q8NFA7|Q8NFA8	Missense_Mutation	SNP	ENST00000230419.4	37	CCDS4884.1	.	.	.	.	.	.	.	.	.	.	C	14.50	2.554754	0.45487	.	.	ENSG00000112655	ENST00000230419;ENST00000471863;ENST00000349241;ENST00000352931;ENST00000345201;ENST00000481273;ENST00000419972	T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25	5.66	3.53	0.40419	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.330379	0.35903	N	0.002918	T	0.15739	0.0379	L	0.49256	1.55	0.32163	N	0.582648	B;B;B;B;B;B	0.24092	0.0;0.097;0.0;0.002;0.0;0.003	B;B;B;B;B;B	0.25506	0.005;0.061;0.004;0.008;0.003;0.012	T	0.06698	-1.0812	10	0.38643	T	0.18	.	10.479	0.44682	0.0:0.8215:0.0:0.1785	.	152;144;144;144;144;144	E9PFZ5;Q13308-3;Q13308-2;Q13308-4;Q13308;Q86X91	.;.;.;.;PTK7_HUMAN;.	I	144;144;144;144;144;152;152	ENSP00000230419:T144I;ENSP00000419037:T144I;ENSP00000325462:T144I;ENSP00000326029:T144I;ENSP00000325992:T144I;ENSP00000418754:T152I	ENSP00000230418:T144I	T	+	2	0	PTK7	43205506	0.997000	0.39634	1.000000	0.80357	0.979000	0.70002	2.066000	0.41452	0.648000	0.30732	0.563000	0.77884	ACC		0.587	PTK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040580.2		
CUL9	23113	broad.mit.edu	37	6	43188319	43188319	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:43188319G>A	ENST00000252050.4	+	32	6489	c.6405G>A	c.(6403-6405)tcG>tcA	p.S2135S	CUL9_ENST00000372647.2_Silent_p.S2107S|CUL9_ENST00000354495.3_Silent_p.S2025S|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	2135					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)	p.S2135S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TCGTCTCCTCGCCAGAGGTCA	0.607																																					p.S2135S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G6405A	6						.						106.0	108.0	107.0					6																	43188319		2203	4300	6503	43296297	SO:0001819	synonymous_variant	23113	exon32			AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.6405G>A	6.37:g.43188319G>A		Somatic		Capture	Illumina HiSeq	Phase_I	43296297	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																				0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
ABCC10	89845	broad.mit.edu	37	6	43412601	43412601	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:43412601C>T	ENST00000372530.4	+	13	2980	c.2765C>T	c.(2764-2766)gCg>gTg	p.A922V	ABCC10_ENST00000244533.3_Missense_Mutation_p.A894V	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	922	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)	p.A894V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	TCCCAGGAGGCGCAACCCTCC	0.612																																					p.A922V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2765T	6						.						69.0	66.0	67.0					6																	43412601		2203	4300	6503	43520579	SO:0001583	missense	89845	exon13			U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2765C>T	6.37:g.43412601C>T	ENSP00000361608:p.Ala922Val	Somatic		Capture	Illumina HiSeq	Phase_I	43520579	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	0.411	-0.913232	0.02415	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.45668	0.89;0.89	4.69	-6.57	0.01842	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	1.208730	0.05791	N	0.610289	T	0.04092	0.0114	N	0.02802	-0.49	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.19910	-1.0291	10	0.24483	T	0.36	-30.6781	4.02	0.09662	0.0834:0.2969:0.1656:0.4541	.	894;922	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	922;894	ENSP00000361608:A922V;ENSP00000244533:A894V	ENSP00000244533:A894V	A	+	2	0	ABCC10	43520579	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-2.024000	0.01436	-1.899000	0.01098	-1.119000	0.02030	GCG		0.612	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
XPO5	57510	broad.mit.edu	37	6	43538651	43538651	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:43538651C>T	ENST00000265351.7	-	4	591	c.381G>A	c.(379-381)gaG>gaA	p.E127E		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	127					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.E127E(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			GCTGTGGCCACTCTCGCTTGA	0.398																																					p.E127E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G381A	6						.						130.0	127.0	128.0					6																	43538651		1910	4139	6049	43646629	SO:0001819	synonymous_variant	57510	exon4			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.381G>A	6.37:g.43538651C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43646629	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																				0.398	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750	
GPR110	266977	broad.mit.edu	37	6	46977647	46977647	+	Silent	SNP	C	C	T	rs571038697		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:46977647C>T	ENST00000371253.2	-	11	1739	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.T311T	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	508					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.T508T(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						TTTGAATAACCGTGGATATCA	0.398																																					p.T508T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1524A	6						.						69.0	71.0	71.0					6																	46977647		2203	4300	6503	47085606	SO:0001819	synonymous_variant	266977	exon11			AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1524G>A	6.37:g.46977647C>T		Somatic		Capture	Illumina HiSeq	Phase_I	47085606	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																				0.398	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
CD2AP	23607	broad.mit.edu	37	6	47567086	47567086	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:47567086G>A	ENST00000359314.5	+	13	1780	c.1324G>A	c.(1324-1326)Gta>Ata	p.V442I		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	442					mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)	p.V442I(1)		kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			AACTGAGCCAGTATCAAAACT	0.358																																					p.V442I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1324A	6						.						59.0	58.0	58.0					6																	47567086		2203	4300	6503	47675045	SO:0001583	missense	23607	exon13			AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1324G>A	6.37:g.47567086G>A	ENSP00000352264:p.Val442Ile	Somatic		Capture	Illumina HiSeq	Phase_I	47675045	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.436297	0.25813	.	.	ENSG00000198087	ENST00000359314	T	0.26373	1.74	5.75	-0.614	0.11590	.	2.644200	0.01839	N	0.035189	T	0.05502	0.0145	L	0.31294	0.92	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.24368	-1.0162	10	0.34782	T	0.22	-4.8974	1.9009	0.03267	0.1893:0.1043:0.2794:0.4269	.	442	Q9Y5K6	CD2AP_HUMAN	I	442	ENSP00000352264:V442I	ENSP00000352264:V442I	V	+	1	0	CD2AP	47675045	0.937000	0.31787	0.556000	0.28293	0.611000	0.37282	0.311000	0.19380	-0.132000	0.11557	0.650000	0.86243	GTA		0.358	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2		
GPR115	221393	broad.mit.edu	37	6	47682676	47682676	+	Silent	SNP	G	G	A	rs528737219		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:47682676G>A	ENST00000283303.2	+	6	1953	c.1695G>A	c.(1693-1695)ccG>ccA	p.P565P	GPR115_ENST00000371220.1_Silent_p.P622P|RN7SKP116_ENST00000516902.1_RNA|GPR115_ENST00000327753.3_Silent_p.P565P	NM_153838.3	NP_722580.3	Q8IZF3	GP115_HUMAN	G protein-coupled receptor 115	565					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.P565P(1)		NS(1)|breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	52						TTGCCATCCCGGCGTTCGTCA	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		20712	0.0		0.0	False		,,,				2504	0.001				p.P565P	GBM(22;431 510 9010 26644 32828)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1695A	6						.						127.0	127.0	127.0					6																	47682676		2203	4300	6503	47790635	SO:0001819	synonymous_variant	221393	exon6			AK095395	CCDS4922.2	6p12.3	2014-08-08			ENSG00000153294	ENSG00000153294		"""-"", ""GPCR / Class B : Orphans"""	19011	protein-coding gene	gene with protein product		614268				12435584	Standard	NM_153838		Approved	FLJ38076, PGR18	uc003oza.1	Q8IZF3	OTTHUMG00000014800	ENST00000283303.2:c.1695G>A	6.37:g.47682676G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47790635	NM_153838	B3KTD0|Q2PNZ0|Q5T5B5|Q5T5B6|Q86SN9|Q8IXE6	Silent	SNP	ENST00000283303.2	37	CCDS4922.2																																																																																				0.488	GPR115-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040819.2	NM_153838	
OPN5	221391	broad.mit.edu	37	6	47763066	47763066	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:47763066G>A	ENST00000371211.2	+	4	551	c.523G>A	c.(523-525)Gta>Ata	p.V175I	OPN5_ENST00000244799.4_3'UTR|OPN5_ENST00000489301.2_Missense_Mutation_p.V175I|OPN5_ENST00000393699.2_Missense_Mutation_p.V175I	NM_181744.3	NP_859528.1	Q6U736	OPN5_HUMAN	opsin 5	175					phototransduction (GO:0007602)|protein-chromophore linkage (GO:0018298)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)	p.V175I(1)		endometrium(1)|large_intestine(3)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(2)	29						GGGGGACTACGTACCTGAGCC	0.592																																					p.V175I	Melanoma(28;740 973 10870 42660 45347)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G523A	6						.						82.0	71.0	75.0					6																	47763066		2203	4300	6503	47871025	SO:0001583	missense	221391	exon4			AY288419	CCDS4923.1	6p12.3	2012-08-08	2004-01-23		ENSG00000124818	ENSG00000124818		"""GPCR / Class A : Opsin receptors"""	19992	protein-coding gene	gene with protein product	"""neuropsin"""	609042	"""transmembrane protein 13"""	TMEM13		14623103, 14623098	Standard	NR_033806		Approved	neuropsin, dJ402H5.1	uc003ozc.3	Q6U736	OTTHUMG00000014803	ENST00000371211.2:c.523G>A	6.37:g.47763066G>A	ENSP00000360255:p.Val175Ile	Somatic		Capture	Illumina HiSeq	Phase_I	47871025	NM_181744	A0AV33|Q5T5B9|Q5T886|Q7Z603|Q86SL5	Missense_Mutation	SNP	ENST00000371211.2	37	CCDS4923.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.165444	0.78339	.	.	ENSG00000124818	ENST00000489301;ENST00000371211;ENST00000393699	T;T;T	0.71934	-0.61;-0.61;-0.61	5.91	5.91	0.95273	GPCR, rhodopsin-like superfamily (1);	0.285555	0.44285	D	0.000472	T	0.44561	0.1299	L	0.28344	0.845	0.27159	N	0.961206	B	0.17038	0.02	B	0.18263	0.021	T	0.15983	-1.0418	10	0.17369	T	0.5	.	20.2857	0.98533	0.0:0.0:1.0:0.0	.	175	Q6U736	OPN5_HUMAN	I	175	ENSP00000426991:V175I;ENSP00000360255:V175I;ENSP00000377302:V175I	ENSP00000360255:V175I	V	+	1	0	OPN5	47871025	1.000000	0.71417	0.960000	0.40013	0.958000	0.62258	9.476000	0.97823	2.803000	0.96430	0.650000	0.86243	GTA		0.592	OPN5-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359451.1	NM_181744	
PTCHD4	442213	broad.mit.edu	37	6	47846983	47846983	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:47846983T>A	ENST00000339488.4	-	3	1630	c.1597A>T	c.(1597-1599)Agc>Tgc	p.S533C		NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	533						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)	p.S533C(1)|p.S533R(1)									TCCTGGACGCTGCTGTTCCAG	0.488																																					p.S533C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.A1597T	6						.						54.0	48.0	50.0					6																	47846983		2203	4300	6503	47954942	SO:0001583	missense	442213	exon3				CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.1597A>T	6.37:g.47846983T>A	ENSP00000341914:p.Ser533Cys	Somatic		Capture	Illumina HiSeq	Phase_I	47954942	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	CCDS34473.2	.	.	.	.	.	.	.	.	.	.	T	15.89	2.965362	0.53507	.	.	ENSG00000244694	ENST00000339488	D	0.86164	-2.08	5.48	4.32	0.51571	.	0.097108	0.64402	D	0.000001	T	0.81403	0.4815	L	0.27053	0.805	0.80722	D	1	B	0.33266	0.404	P	0.49637	0.617	T	0.82849	-0.0254	10	0.72032	D	0.01	.	11.1172	0.48266	0.0:0.0724:0.0:0.9276	.	533	Q6ZW05	CF138_HUMAN	C	533	ENSP00000341914:S533C	ENSP00000341914:S533C	S	-	1	0	C6orf138	47954942	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.698000	0.84413	0.933000	0.37291	0.528000	0.53228	AGC		0.488	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732	
PKHD1	5314	broad.mit.edu	37	6	51618009	51618009	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:51618009T>G	ENST00000371117.3	-	57	9215	c.8940A>C	c.(8938-8940)gaA>gaC	p.E2980D	PKHD1_ENST00000340994.4_Missense_Mutation_p.E2980D	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2980					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CTGAAAATTCTTCTCGGCTGG	0.433																																					p.E2980D												.	.	0			c.A8940C	6						.						82.0	84.0	83.0					6																	51618009		2203	4300	6503	51725968	SO:0001583	missense	5314	exon57			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.8940A>C	6.37:g.51618009T>G	ENSP00000360158:p.Glu2980Asp	None		Capture	Illumina HiSeq	Phase_I	51725968	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	10.70	1.424302	0.25639	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.83163	-1.69;-1.69	5.97	3.63	0.41609	.	0.389019	0.26855	N	0.022142	T	0.37348	0.1000	N	0.05608	-0.01	0.27181	N	0.960651	B;B;B	0.20671	0.017;0.013;0.047	B;B;B	0.14578	0.007;0.011;0.008	T	0.28681	-1.0036	10	0.12766	T	0.61	.	4.6459	0.12572	0.1311:0.2146:0.0:0.6543	.	2980;2980;2980	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	D	2980	ENSP00000360158:E2980D;ENSP00000341097:E2980D	ENSP00000341097:E2980D	E	-	3	2	PKHD1	51725968	0.129000	0.22400	0.983000	0.44433	0.735000	0.41995	0.143000	0.16115	0.532000	0.28657	0.533000	0.62120	GAA		0.433	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
PKHD1	5314	broad.mit.edu	37	6	51927423	51927423	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:51927423C>T	ENST00000371117.3	-	14	1287	c.1012G>A	c.(1012-1014)Gtt>Att	p.V338I	AL590391.1_ENST00000408630.2_RNA|PKHD1_ENST00000340994.4_Missense_Mutation_p.V338I	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	338					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.V338I(1)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGTCCCTCAACAGCATCTCCA	0.483																																					p.V338I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1012A	6						.						169.0	159.0	162.0					6																	51927423		2203	4300	6503	52035382	SO:0001583	missense	5314	exon14			AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.1012G>A	6.37:g.51927423C>T	ENSP00000360158:p.Val338Ile	Somatic		Capture	Illumina HiSeq	Phase_I	52035382	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	8.458	0.854698	0.17106	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.86865	-1.97;-2.18	5.65	-3.14	0.05250	Cell surface receptor IPT/TIG (1);	1.967350	0.02245	N	0.066176	T	0.60170	0.2248	L	0.36672	1.1	0.09310	N	1	B;B	0.26708	0.157;0.156	B;B	0.21917	0.037;0.023	T	0.51725	-0.8669	10	0.34782	T	0.22	.	1.4974	0.02469	0.3522:0.331:0.117:0.1998	.	338;338	P08F94-2;P08F94	.;PKHD1_HUMAN	I	338	ENSP00000360158:V338I;ENSP00000341097:V338I	ENSP00000341097:V338I	V	-	1	0	PKHD1	52035382	0.000000	0.05858	0.002000	0.10522	0.293000	0.27360	-0.886000	0.04157	-0.527000	0.06374	0.655000	0.94253	GTT		0.483	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
LGSN	51557	broad.mit.edu	37	6	63990353	63990353	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:63990353C>T	ENST00000370657.4	-	4	1136	c.1103G>A	c.(1102-1104)cGt>cAt	p.R368H	LGSN_ENST00000370658.5_3'UTR			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	368					glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)	p.R368H(1)		NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTGGAATAACGCTTTCGGCA	0.473																																					p.R368H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1103A	6						.						145.0	145.0	145.0					6																	63990353		2203	4300	6503	64048312	SO:0001583	missense	51557	exon4			AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"""glutamate-ammonia ligase (glutamine synthetase) domain containing 1"""	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.1103G>A	6.37:g.63990353C>T	ENSP00000359691:p.Arg368His	Somatic		Capture	Illumina HiSeq	Phase_I	64048312	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	37	CCDS4964.1	.	.	.	.	.	.	.	.	.	.	C	11.67	1.708930	0.30322	.	.	ENSG00000146166	ENST00000370657	D	0.99023	-5.34	5.77	4.9	0.64082	Glutamine synthetase, catalytic domain (1);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.189111	0.64402	N	0.000017	D	0.96555	0.8876	L	0.42581	1.335	0.80722	D	1	D	0.55800	0.973	P	0.47470	0.548	D	0.96207	0.9150	10	0.87932	D	0	-12.9163	6.5664	0.22515	0.0:0.6793:0.1609:0.1598	.	368	Q5TDP6	LGSN_HUMAN	H	368	ENSP00000359691:R368H	ENSP00000359691:R368H	R	-	2	0	LGSN	64048312	0.992000	0.36948	0.863000	0.33907	0.026000	0.11368	2.604000	0.46274	1.434000	0.47414	0.655000	0.94253	CGT		0.473	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571	
PHF3	23469	broad.mit.edu	37	6	64422953	64422953	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:64422953T>C	ENST00000262043.3	+	16	5809	c.5469T>C	c.(5467-5469)ttT>ttC	p.F1823F	PHF3_ENST00000393387.1_Silent_p.F1823F			Q92576	PHF3_HUMAN	PHD finger protein 3	1823	Pro-rich.				multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.F1823F(1)		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)			CTCCTAATTTTCCCCCACAAA	0.507																																					p.F1823F	GBM(135;136 1820 29512 34071 46235)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T5469C	6						.						135.0	142.0	140.0					6																	64422953		2203	4300	6503	64480912	SO:0001819	synonymous_variant	23469	exon15			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.5469T>C	6.37:g.64422953T>C		Somatic		Capture	Illumina HiSeq	Phase_I	64480912	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1																																																																																				0.507	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2		
BAI3	577	broad.mit.edu	37	6	69758199	69758199	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:69758199A>C	ENST00000370598.1	+	14	3051	c.2230A>C	c.(2230-2232)Agc>Cgc	p.S744R		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	744					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.S744R(1)		NS(2)|breast(4)|central_nervous_system(5)|endometrium(5)|kidney(2)|large_intestine(28)|liver(1)|lung(111)|ovary(10)|pancreas(4)|prostate(7)|skin(22)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	210		all_lung(197;0.212)				AATTCCAAAAAGCATTTTCAC	0.358																																					p.S744R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2230C	6						.						72.0	76.0	74.0					6																	69758199		2203	4300	6503	69814920	SO:0001583	missense	577	exon14			AB005299	CCDS4968.1	6q12	2014-08-08			ENSG00000135298	ENSG00000135298		"""-"", ""GPCR / Class B : Orphans"""	945	protein-coding gene	gene with protein product		602684				9533023	Standard	NM_001704		Approved	KIAA0550	uc003pev.4	O60242	OTTHUMG00000014982	ENST00000370598.1:c.2230A>C	6.37:g.69758199A>C	ENSP00000359630:p.Ser744Arg	Somatic		Capture	Illumina HiSeq	Phase_I	69814920	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.978952	0.53827	.	.	ENSG00000135298	ENST00000370598	T	0.10763	2.84	5.12	5.12	0.69794	Domain of unknown function DUF3497 (1);	0.154253	0.56097	D	0.000023	T	0.06234	0.0161	L	0.46157	1.445	0.80722	D	1	B	0.15719	0.014	B	0.18871	0.023	T	0.07347	-1.0777	10	0.52906	T	0.07	.	15.2069	0.73186	1.0:0.0:0.0:0.0	.	744	O60242	BAI3_HUMAN	R	744	ENSP00000359630:S744R	ENSP00000359630:S744R	S	+	1	0	BAI3	69814920	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.124000	0.77185	2.060000	0.61445	0.533000	0.62120	AGC		0.358	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1		
RIMS1	22999	broad.mit.edu	37	6	72943543	72943543	+	Splice_Site	SNP	G	G	A	rs369457976		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:72943543G>A	ENST00000521978.1	+	7	1746	c.1746G>A	c.(1744-1746)tcG>tcA	p.S582S	RIMS1_ENST00000348717.5_Splice_Site_p.S582S|RIMS1_ENST00000518273.1_Splice_Site_p.S582S|RIMS1_ENST00000517827.1_Splice_Site_p.S41S|RIMS1_ENST00000401910.3_Splice_Site_p.S56S|RIMS1_ENST00000522291.1_Splice_Site_p.S582S|RIMS1_ENST00000425662.2_5'UTR|RIMS1_ENST00000523963.1_Splice_Site_p.S56S|RIMS1_ENST00000264839.7_Splice_Site_p.S582S|RIMS1_ENST00000517960.1_Splice_Site_p.S582S|RIMS1_ENST00000491071.2_Splice_Site_p.S582S|RIMS1_ENST00000520567.1_Splice_Site_p.S582S	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	582					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)	p.S582S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CTATTAGTTCGGTAAGTTTTC	0.393																																					p.S41S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G123A	6						.	G	,,,,	0,3786		0,0,1893	136.0	139.0	138.0		168,168,,123,1746	4.3	1.0	6		138	1,8229		0,1,4114	no	coding-synonymous-near-splice,coding-synonymous-near-splice,utr-5,coding-synonymous-near-splice,coding-synonymous-near-splice	RIMS1	NM_001168407.1,NM_001168408.1,NM_001168409.1,NM_001168410.1,NM_014989.4	,,,,	0,1,6007	AA,AG,GG		0.0122,0.0,0.0083	,,,,	56/1013,56/818,,41/827,582/1693	72943543	1,12015	1893	4115	6008	73000264	SO:0001630	splice_region_variant	22999	exon2			AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.1746+1G>A	6.37:g.72943543G>A		Somatic		Capture	Illumina HiSeq	Phase_I	73000264	NM_001168410	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Silent	SNP	ENST00000521978.1	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.211912	0.39102	0.0	1.22E-4	ENSG00000079841	ENST00000517433	.	.	.	6.08	4.31	0.51392	.	.	.	.	.	T	0.49729	0.1574	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49652	-0.8917	4	.	.	.	-8.9532	11.1147	0.48254	0.198:0.0:0.802:0.0	.	.	.	.	T	156	.	.	A	+	1	0	RIMS1	73000264	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	3.791000	0.55469	0.904000	0.36572	0.591000	0.81541	GCA		0.393	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		Silent
CD109	135228	broad.mit.edu	37	6	74440112	74440112	+	Missense_Mutation	SNP	G	G	A	rs201515057		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:74440112G>A	ENST00000287097.5	+	4	434	c.322G>A	c.(322-324)Gga>Aga	p.G108R	CD109_ENST00000437994.2_Missense_Mutation_p.G108R|CD109_ENST00000422508.2_Intron			Q6YHK3	CD109_HUMAN	CD109 molecule	108					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)	p.G108R(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						ACGTGTAACCGGACGTACCCA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		18803	0.001		0.0	False		,,,				2504	0.0				p.G108R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G322A	6						.						141.0	136.0	138.0					6																	74440112		2203	4300	6503	74496833	SO:0001583	missense	135228	exon4			AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.322G>A	6.37:g.74440112G>A	ENSP00000287097:p.Gly108Arg	Somatic		Capture	Illumina HiSeq	Phase_I	74496833	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.38	1.919492	0.33908	.	.	ENSG00000156535	ENST00000437994;ENST00000287097	T;T	0.27402	1.69;1.67	4.35	3.48	0.39840	.	0.272209	0.35096	N	0.003451	T	0.28566	0.0707	L	0.27053	0.805	0.41486	D	0.988195	D;P;D	0.89917	1.0;0.936;0.963	D;P;P	0.91635	0.999;0.56;0.579	T	0.14671	-1.0464	10	0.87932	D	0	.	11.1832	0.48640	0.0913:0.0:0.9087:0.0	.	108;108;108	Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	R	108	ENSP00000388062:G108R;ENSP00000287097:G108R	ENSP00000287097:G108R	G	+	1	0	CD109	74496833	1.000000	0.71417	0.009000	0.14445	0.087000	0.18053	4.653000	0.61462	1.178000	0.42870	0.655000	0.94253	GGA		0.398	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
COL12A1	1303	broad.mit.edu	37	6	75833783	75833783	+	Missense_Mutation	SNP	C	C	T	rs151324784		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:75833783C>T	ENST00000322507.8	-	42	7061	c.6752G>A	c.(6751-6753)cGt>cAt	p.R2251H	COL12A1_ENST00000483888.2_Missense_Mutation_p.R2251H|COL12A1_ENST00000345356.6_Missense_Mutation_p.R1087H|COL12A1_ENST00000416123.2_Missense_Mutation_p.R2251H	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2251	Fibronectin type-III 18. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)	p.R2251H(1)		breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TTCTGATCCACGCACTGTAAT	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		18950	0.0		0.001	False		,,,				2504	0.0				p.R2251H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6752A	6						.	C	HIS/ARG,HIS/ARG	0,3848		0,0,1924	117.0	112.0	114.0		6752,3260	5.3	1.0	6	dbSNP_134	114	4,8246		0,4,4121	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	29,29	0,4,6045	TT,TC,CC		0.0485,0.0,0.0331	probably-damaging,probably-damaging	2251/3064,1087/1900	75833783	4,12094	1924	4125	6049	75890503	SO:0001583	missense	1303	exon42			U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.6752G>A	6.37:g.75833783C>T	ENSP00000325146:p.Arg2251His	Somatic		Capture	Illumina HiSeq	Phase_I	75890503	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.95	3.513510	0.64522	0.0	4.85E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.34	5.34	0.76211	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.067890	0.53938	D	0.000059	T	0.08223	0.0205	L	0.44542	1.39	0.35907	D	0.830793	D;D	0.69078	0.996;0.997	P;D	0.63877	0.868;0.919	T	0.07065	-1.0792	10	0.51188	T	0.08	.	14.9563	0.71116	0.0:0.8575:0.1425:0.0	.	1087;2251	Q99715-2;Q99715	.;COCA1_HUMAN	H	2251;2251;1087;2251;2251	ENSP00000325146:R2251H;ENSP00000305147:R1087H;ENSP00000412864:R2251H;ENSP00000421216:R2251H	ENSP00000325146:R2251H	R	-	2	0	COL12A1	75890503	0.620000	0.27068	1.000000	0.80357	0.689000	0.40095	1.733000	0.38156	2.673000	0.90976	0.591000	0.81541	CGT		0.418	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
HTR1B	3351	broad.mit.edu	37	6	78172445	78172445	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:78172445C>T	ENST00000369947.2	-	1	1045	c.676G>A	c.(676-678)Gcc>Acc	p.A226T		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	226					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|bone remodeling (GO:0046849)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to temperature stimulus (GO:0071502)|drinking behavior (GO:0042756)|G-protein coupled receptor internalization (GO:0002031)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of serotonin secretion (GO:0014063)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of behavior (GO:0050795)|regulation of dopamine secretion (GO:0014059)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to mineralocorticoid (GO:0051385)|synaptic transmission (GO:0007268)|vasoconstriction (GO:0042310)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(9)|prostate(2)|upper_aerodigestive_tract(2)	25		all_cancers(76;0.0867)|Acute lymphoblastic leukemia(125;0.00119)|all_hematologic(105;0.0332)		BRCA - Breast invasive adenocarcinoma(397;0.205)	Almotriptan(DB00918)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Clozapine(DB00363)|Dihydroergotamine(DB00320)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Frovatriptan(DB00998)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Methysergide(DB00247)|Naratriptan(DB00952)|Olanzapine(DB00334)|Ondansetron(DB00904)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Sumatriptan(DB00669)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	CCATAGAGGGCGATGAGGAGC	0.592																																					p.A226T												.	.	0			c.G676A	6						.						59.0	62.0	61.0					6																	78172445		2203	4300	6503	78229164	SO:0001583	missense	3351	exon1			BC069065	CCDS4986.1	6q13	2012-08-08	2012-02-03		ENSG00000135312	ENSG00000135312		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5287	protein-coding gene	gene with protein product		182131	"""5-hydroxytryptamine (serotonin) receptor 1B"""			1348246, 11247661	Standard	NM_000863		Approved	S12, 5-HT1B, HTR1D2, 5-HT1DB	uc003pil.1	P28222	OTTHUMG00000015066	ENST00000369947.2:c.676G>A	6.37:g.78172445C>T	ENSP00000358963:p.Ala226Thr	None		Capture	Illumina HiSeq	Phase_I	78229164	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145301	0.77888	.	.	ENSG00000135312	ENST00000369947	T	0.37058	1.22	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.122489	0.53938	D	0.000047	T	0.19005	0.0456	N	0.21373	0.66	0.58432	D	0.999999	P	0.52061	0.95	B	0.44163	0.443	T	0.01165	-1.1431	9	.	.	.	.	17.9819	0.89144	0.0:1.0:0.0:0.0	.	226	P28222	5HT1B_HUMAN	T	226	ENSP00000358963:A226T	.	A	-	1	0	HTR1B	78229164	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.048000	0.49862	2.728000	0.93425	0.555000	0.69702	GCC		0.592	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863	
DOPEY1	23033	broad.mit.edu	37	6	83840090	83840090	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:83840090A>G	ENST00000349129.2	+	17	2850	c.2590A>G	c.(2590-2592)Ata>Gta	p.I864V	DOPEY1_ENST00000369739.3_Missense_Mutation_p.I855V|DOPEY1_ENST00000237163.5_Missense_Mutation_p.I845V	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	864					protein transport (GO:0015031)			p.I864V(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		TCTGAGGTACATAGCTGAGAA	0.403																																					p.I864V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2590G	6						.						103.0	98.0	100.0					6																	83840090		2203	4300	6503	83896809	SO:0001583	missense	23033	exon17			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.2590A>G	6.37:g.83840090A>G	ENSP00000195654:p.Ile864Val	Somatic		Capture	Illumina HiSeq	Phase_I	83896809	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763787	0.49574	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T	0.26660	1.72;1.73	5.58	5.58	0.84498	.	0.095508	0.64402	D	0.000002	T	0.15089	0.0364	L	0.48642	1.525	0.80722	D	1	B;B;B	0.18741	0.03;0.025;0.025	B;B;B	0.20767	0.031;0.019;0.019	T	0.02654	-1.1128	10	0.54805	T	0.06	.	15.7532	0.78005	1.0:0.0:0.0:0.0	.	755;855;864	E1P545;B2RWN9;Q5JWR5	.;.;DOP1_HUMAN	V	864;845;845	ENSP00000195654:I864V;ENSP00000237163:I845V	ENSP00000237163:I845V	I	+	1	0	DOPEY1	83896809	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.112000	0.77086	2.117000	0.64856	0.460000	0.39030	ATA		0.403	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018	
ME1	4199	broad.mit.edu	37	6	84025059	84025059	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:84025059delA	ENST00000369705.3	-	6	790	c.674delT	c.(673-675)ttgfs	p.L225fs	ME1_ENST00000543031.1_Frame_Shift_Del_p.L150fs|ME1_ENST00000541327.1_Frame_Shift_Del_p.L59fs	NM_002395.4	NP_002386.1	P48163	MAOX_HUMAN	malic enzyme 1, NADP(+)-dependent, cytosolic	225					carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|malate metabolic process (GO:0006108)|NADP biosynthetic process (GO:0006741)|protein tetramerization (GO:0051262)|response to carbohydrate (GO:0009743)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|electron carrier activity (GO:0009055)|malate dehydrogenase (decarboxylating) (NAD+) activity (GO:0004471)|malate dehydrogenase (decarboxylating) (NADP+) activity (GO:0004473)|malic enzyme activity (GO:0004470)|manganese ion binding (GO:0030145)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|oxaloacetate decarboxylase activity (GO:0008948)	p.L225fs*14(1)		NS(2)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36		all_cancers(76;1.28e-06)|Acute lymphoblastic leukemia(125;5.03e-07)|all_hematologic(105;0.000238)|all_epithelial(107;0.00218)		BRCA - Breast invasive adenocarcinoma(397;0.0641)		GAATTCGTCCAAAAAATCATC	0.303																																					p.L225fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.674delT	6						.						109.0	111.0	110.0					6																	84025059		2203	4299	6502	84081778	SO:0001589	frameshift_variant	4199	exon6			X77244	CCDS34492.1	6q12	2012-10-02			ENSG00000065833	ENSG00000065833	1.1.1.40		6983	protein-coding gene	gene with protein product		154250				8187880	Standard	NM_002395		Approved		uc003pjy.3	P48163	OTTHUMG00000015111	ENST00000369705.3:c.674delT	6.37:g.84025059delA	ENSP00000358719:p.Leu225fs	Somatic		Capture	Illumina HiSeq	Phase_I	84081778	NM_002395	B4DZ70|Q16797|Q16855|Q53F72|Q5VWA2|Q9BWX8|Q9H1W3|Q9UIY4	Frame_Shift_Del	DEL	ENST00000369705.3	37	CCDS34492.1																																																																																				0.303	ME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041350.1		
SRSF12	135295	broad.mit.edu	37	6	89827549	89827549	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:89827549C>T	ENST00000452027.2	-	1	251	c.58G>A	c.(58-60)Gcc>Acc	p.A20T		NM_080743.4	NP_542781.3	Q8WXF0	SRS12_HUMAN	serine/arginine-rich splicing factor 12	20	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cytoplasmic transport (GO:0016482)|mRNA 5'-splice site recognition (GO:0000395)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|spliceosomal tri-snRNP complex assembly (GO:0000244)	nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RS domain binding (GO:0050733)|unfolded protein binding (GO:0051082)	p.A20T(1)		autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)	8						CACCTGGTGGCGTCCGCGACG	0.741																																					p.A20T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G58A	6						.						16.0	22.0	20.0					6																	89827549		1947	4123	6070	89884268	SO:0001583	missense	135295	exon1			AF449428	CCDS47459.1	6q16.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000154548	ENSG00000154548		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	21220	protein-coding gene	gene with protein product	"""splicing factor, arginine/serine-rich 19"", ""SR splicing factor 12"""		"""splicing factor, arginine/serine-rich 13B"""	SFRS13B		11684676, 20516191	Standard	NM_080743		Approved	SRrp35, SFRS19	uc021zcq.1	Q8WXF0	OTTHUMG00000015192	ENST00000452027.2:c.58G>A	6.37:g.89827549C>T	ENSP00000414302:p.Ala20Thr	Somatic		Capture	Illumina HiSeq	Phase_I	89884268	NM_080743	B2RA22|Q5T7K0|Q8WW25	Missense_Mutation	SNP	ENST00000452027.2	37	CCDS47459.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.089896	0.36855	.	.	ENSG00000154548	ENST00000452027	T	0.34472	1.36	3.8	1.98	0.26296	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.333187	0.19315	U	0.117296	T	0.03739	0.0106	N	0.02708	-0.52	0.29364	N	0.864464	B	0.15141	0.012	B	0.13407	0.009	T	0.44360	-0.9333	10	0.14252	T	0.57	.	5.6826	0.17784	0.1923:0.7018:0.0:0.1058	.	20	Q8WXF0	SRS12_HUMAN	T	20	ENSP00000414302:A20T	ENSP00000414302:A20T	A	-	1	0	SRSF12	89884268	1.000000	0.71417	0.997000	0.53966	0.667000	0.39255	2.677000	0.46892	0.259000	0.21709	0.555000	0.69702	GCC		0.741	SRSF12-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041474.2	NM_080743	
MDN1	23195	broad.mit.edu	37	6	90392965	90392965	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:90392965T>G	ENST00000369393.3	-	73	12103	c.11988A>C	c.(11986-11988)gaA>gaC	p.E3996D	MDN1_ENST00000428876.1_Missense_Mutation_p.E3996D			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3996					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.E3996D(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		AGTCAGGCTGTTCTTCCTTGT	0.502																																					p.E3996D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A11988C	6						.						99.0	85.0	90.0					6																	90392965		2203	4300	6503	90449686	SO:0001583	missense	23195	exon73			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.11988A>C	6.37:g.90392965T>G	ENSP00000358400:p.Glu3996Asp	Somatic		Capture	Illumina HiSeq	Phase_I	90449686	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	12.15	1.851600	0.32699	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03358	3.96;3.96	5.7	-1.95	0.07548	.	0.355876	0.28859	N	0.013902	T	0.01421	0.0046	M	0.62723	1.935	0.30966	N	0.723055	P	0.50443	0.935	B	0.39971	0.315	T	0.47911	-0.9080	10	0.15952	T	0.53	.	12.0868	0.53702	0.0:0.5378:0.0:0.4622	.	3996	Q9NU22	MDN1_HUMAN	D	3996	ENSP00000358400:E3996D;ENSP00000413970:E3996D	ENSP00000358400:E3996D	E	-	3	2	MDN1	90449686	0.451000	0.25705	0.933000	0.37362	0.715000	0.41141	-0.346000	0.07760	-0.196000	0.10366	0.459000	0.35465	GAA		0.502	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	broad.mit.edu	37	6	90504337	90504337	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:90504337C>T	ENST00000369393.3	-	3	628	c.513G>A	c.(511-513)gtG>gtA	p.V171V	MDN1_ENST00000428876.1_Silent_p.V171V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	171					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)	p.V171V(1)		NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAGGGACACACACACTCCAGT	0.542																																					p.V171V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G513A	6						.						127.0	103.0	111.0					6																	90504337		2203	4300	6503	90561058	SO:0001819	synonymous_variant	23195	exon3			AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.513G>A	6.37:g.90504337C>T		Somatic		Capture	Illumina HiSeq	Phase_I	90561058	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																				0.542	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
CASP8AP2	9994	broad.mit.edu	37	6	90578312	90578312	+	RNA	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:90578312A>C	ENST00000551025.1	+	0	6740									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		GGGGTGATACAGGTAGATGAA	0.408																																					p.Q1768P	Colon(187;1656 2025 17045 31481 39901)											.	.	0			c.A5303C	6						.						80.0	74.0	76.0					6																	90578312		1925	4143	6068	90635033			9994	exon8			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90578312A>C		Somatic		Capture	Illumina HiSeq	Phase_I	90635033	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																					0.408	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
CASP8AP2	9994	broad.mit.edu	37	6	90578430	90578430	+	RNA	DEL	A	A	-	rs371166110		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:90578430delA	ENST00000551025.1	+	0	6858									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		CATGTGAAGTAAAAAAAGATG	0.388																																					p.V1807fs	Colon(187;1656 2025 17045 31481 39901)											.	.	0			c.5421delA	6						.						51.0	49.0	50.0					6																	90578430		1844	4095	5939	90635151			9994	exon8			AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90578430delA		Somatic		Capture	Illumina HiSeq	Phase_I	90635151	NM_001137667		Frame_Shift_Del	DEL	ENST00000551025.1	37																																																																																					0.388	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
PNISR	25957	broad.mit.edu	37	6	99853925	99853925	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:99853925C>A	ENST00000369239.5	-	8	1188	c.984G>T	c.(982-984)gaG>gaT	p.E328D	PNISR_ENST00000438806.1_Missense_Mutation_p.E328D	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	328						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.E328D(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						ACTCTTTCTCCTCTTCAGTCA	0.383																																					p.E328D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G984T	6						.						206.0	183.0	191.0					6																	99853925		2203	4300	6503	99960646	SO:0001583	missense	25957	exon7			AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.984G>T	6.37:g.99853925C>A	ENSP00000358242:p.Glu328Asp	Somatic		Capture	Illumina HiSeq	Phase_I	99960646	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Missense_Mutation	SNP	ENST00000369239.5	37	CCDS5043.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.853938	0.51270	.	.	ENSG00000132424	ENST00000369239;ENST00000438806	T;T	0.42513	0.97;0.97	5.68	0.647	0.17796	.	0.044712	0.85682	D	0.000000	T	0.19886	0.0478	M	0.72353	2.195	0.53688	D	0.999979	P	0.35507	0.506	B	0.28553	0.091	T	0.04723	-1.0931	10	0.45353	T	0.12	.	9.167	0.37058	0.0:0.2859:0.0:0.7141	.	328	Q8TF01	PNISR_HUMAN	D	328	ENSP00000358242:E328D;ENSP00000387997:E328D	ENSP00000358242:E328D	E	-	3	2	PNISR	99960646	1.000000	0.71417	0.997000	0.53966	0.871000	0.50021	0.797000	0.26999	-0.046000	0.13446	-0.302000	0.09304	GAG		0.383	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870	
USP45	85015	broad.mit.edu	37	6	99893708	99893708	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:99893708delT	ENST00000327681.6	-	14	2472	c.1940delA	c.(1939-1941)aacfs	p.N647fs	USP45_ENST00000392738.2_Frame_Shift_Del_p.N327fs|USP45_ENST00000539675.1_Intron|USP45_ENST00000500704.2_Frame_Shift_Del_p.N647fs|USP45_ENST00000369233.2_Frame_Shift_Del_p.N599fs	NM_001080481.1	NP_001073950.1	Q70EL2	UBP45_HUMAN	ubiquitin specific peptidase 45	647	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.N647fs*16(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(2)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	22		all_cancers(76;0.000208)|Acute lymphoblastic leukemia(125;8.41e-11)|all_hematologic(75;2.56e-07)|all_epithelial(107;0.122)|Colorectal(196;0.133)		BRCA - Breast invasive adenocarcinoma(108;0.0718)		CTTCTGTTTGTTTTTAGTACA	0.303																																					p.N647fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1940delA	6						.						46.0	47.0	47.0					6																	99893708		2203	4294	6497	100000429	SO:0001589	frameshift_variant	85015	exon14			AL832030	CCDS34501.1	6q16.2	2008-02-05	2005-08-08		ENSG00000123552	ENSG00000123552		"""Ubiquitin-specific peptidases"""	20080	protein-coding gene	gene with protein product			"""ubiquitin specific protease 45"""			12838346	Standard	NM_001080481		Approved	MGC14793	uc003ppx.2	Q70EL2	OTTHUMG00000015267	ENST00000327681.6:c.1940delA	6.37:g.99893708delT	ENSP00000333376:p.Asn647fs	Somatic		Capture	Illumina HiSeq	Phase_I	100000429	NM_001080481	B2RXG0|Q5T062|Q86T44|Q86TC0|Q9BRU1	Frame_Shift_Del	DEL	ENST00000327681.6	37	CCDS34501.1																																																																																				0.303	USP45-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041609.2	NM_032929	
REV3L	5980	broad.mit.edu	37	6	111694685	111694685	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:111694685delA	ENST00000358835.3	-	14	5327	c.4873delT	c.(4873-4875)tcafs	p.S1625fs	REV3L_ENST00000368802.3_Frame_Shift_Del_p.S1625fs|REV3L_ENST00000368805.1_Frame_Shift_Del_p.S1625fs|REV3L_ENST00000435970.1_Frame_Shift_Del_p.S1547fs			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1625					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)	p.S1547fs*28(1)		NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		CCTGGATCTGAAAAAAAGATG	0.318								DNA polymerases (catalytic subunits)																													p.S1625fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.4873delT	6						.						58.0	64.0	62.0					6																	111694685		2193	4298	6491	111801378	SO:0001589	frameshift_variant	5980	exon13			AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4873delT	6.37:g.111694685delA	ENSP00000351697:p.Ser1625fs	Somatic		Capture	Illumina HiSeq	Phase_I	111801378	NM_002912	O43214|Q5TC33	Frame_Shift_Del	DEL	ENST00000358835.3	37	CCDS5091.2																																																																																				0.318	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
TRDN	10345	broad.mit.edu	37	6	123594495	123594495	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:123594495delT	ENST00000398178.3	-	28	1632	c.1611delA	c.(1609-1611)aaafs	p.K537fs	TRDN_ENST00000334268.4_Frame_Shift_Del_p.K537fs	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	537					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)	p.V538fs*8(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		GTATTTGCACTTTTTCAGATA	0.239																																					p.K537fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1611delA	6						.						7.0	8.0	7.0					6																	123594495		1229	2729	3958	123636194	SO:0001589	frameshift_variant	10345	exon28			U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1611delA	6.37:g.123594495delT	ENSP00000381240:p.Lys537fs	Somatic		Capture	Illumina HiSeq	Phase_I	123636194	NM_006073	A5D6W5|F5H2W7|Q6NSB8	Frame_Shift_Del	DEL	ENST00000398178.3	37	CCDS55053.1																																																																																				0.239	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PTPRK	5796	broad.mit.edu	37	6	128318089	128318089	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:128318089delT	ENST00000368215.3	-	17	2720	c.2721delA	c.(2719-2721)aaafs	p.K907fs	PTPRK_ENST00000368207.3_Frame_Shift_Del_p.K934fs|PTPRK_ENST00000532331.1_Frame_Shift_Del_p.K924fs|PTPRK_ENST00000368227.3_Frame_Shift_Del_p.K920fs|PTPRK_ENST00000368213.5_Frame_Shift_Del_p.K908fs|PTPRK_ENST00000368210.3_Frame_Shift_Del_p.K920fs|PTPRK_ENST00000368226.4_Frame_Shift_Del_p.K908fs			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	907	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to reactive oxygen species (GO:0034614)|cellular response to UV (GO:0034644)|focal adhesion assembly (GO:0048041)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|protein localization to cell surface (GO:0034394)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D909fs*13(1)|p.D909fs*4(1)	PTPRK/RSPO3(10)	autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(14)|lung(24)|ovary(3)|pancreas(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	72				all cancers(137;0.0118)|GBM - Glioblastoma multiforme(226;0.0372)|OV - Ovarian serous cystadenocarcinoma(136;0.24)		TATTTTGATCTTTTTTAGCTA	0.308																																					p.K908fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(1)|lung(1)	c.2724delA	6						.						96.0	89.0	91.0					6																	128318089		2203	4300	6503	128359782	SO:0001589	frameshift_variant	5796	exon17			L77886	CCDS5137.1, CCDS47473.1, CCDS75517.1	6q22.2-q22.3	2013-02-11			ENSG00000152894	ENSG00000152894		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9674	protein-coding gene	gene with protein product		602545				9047348, 8663237	Standard	NM_002844		Approved	R-PTP-kappa	uc010kfc.3	Q15262	OTTHUMG00000015536	ENST00000368215.3:c.2721delA	6.37:g.128318089delT	ENSP00000357198:p.Lys907fs	Somatic		Capture	Illumina HiSeq	Phase_I	128359782	NM_002844	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Frame_Shift_Del	DEL	ENST00000368215.3	37																																																																																					0.308	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1		
QKI	9444	broad.mit.edu	37	6	163836318	163836318	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr6:163836318G>T	ENST00000361752.3	+	1	644	c.93G>T	c.(91-93)ctG>ctT	p.L31L	QKI_ENST00000453779.2_Silent_p.L31L|QKI_ENST00000424802.3_Silent_p.L31L|CAHM_ENST00000604200.1_lincRNA|QKI_ENST00000275262.7_Silent_p.L31L|QKI_ENST00000392127.2_Silent_p.L31L|QKI_ENST00000361195.2_Silent_p.L31L	NM_006775.2|NM_206853.2|NM_206854.2|NM_206855.2	NP_006766.1|NP_996735.1|NP_996736.1|NP_996737.1	Q96PU8	QKI_HUMAN	QKI, KH domain containing, RNA binding	31					long-chain fatty acid biosynthetic process (GO:0042759)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|muscle cell differentiation (GO:0042692)|myelination (GO:0042552)|positive regulation of gene expression (GO:0010628)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|spermatid development (GO:0007286)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.L31L(1)		central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(5)|ovary(1)|prostate(3)|urinary_tract(2)	27		Breast(66;5e-05)|Prostate(117;0.0235)|all_neural(5;0.0416)|Ovarian(120;0.0448)|Glioma(2;0.203)		all cancers(1;4.4e-46)|OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|GBM - Glioblastoma multiforme(1;2.94e-19)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|Kidney(3;0.000199)|KIRC - Kidney renal clear cell carcinoma(3;0.000234)		TGAGCAGCCTGCCCAACTTCT	0.642																																					p.L31L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G93T	6						.						93.0	91.0	92.0					6																	163836318		2203	4300	6503	163756308	SO:0001819	synonymous_variant	9444	exon1			AB067798	CCDS5285.1, CCDS5286.1, CCDS5287.1, CCDS43525.1, CCDS75546.1	6q26	2011-09-12	2011-09-12		ENSG00000112531	ENSG00000112531			21100	protein-coding gene	gene with protein product		609590	"""quaking homolog, KH domain RNA binding (mouse)"""			10535969	Standard	NM_006775		Approved	QK3	uc003qui.3	Q96PU8	OTTHUMG00000015977	ENST00000361752.3:c.93G>T	6.37:g.163836318G>T		Somatic		Capture	Illumina HiSeq	Phase_I	163756308	NM_206855	Q2I375|Q5MJQ1|Q969L9|Q96EJ3|Q96KA3|Q96PU6|Q96PU7|Q9P0X6|Q9P0X7|Q9P0X8|Q9P0X9|Q9P0Y0|Q9P0Y1	Silent	SNP	ENST00000361752.3	37	CCDS5285.1																																																																																				0.642	QKI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043016.2	NM_006775	
DAGLB	221955	broad.mit.edu	37	7	6449896	6449897	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:6449896_6449897insC	ENST00000297056.6	-	14	1853_1854	c.1684_1685insG	c.(1684-1686)gagfs	p.E562fs	DAGLB_ENST00000436575.1_Frame_Shift_Ins_p.E521fs|DAGLB_ENST00000428902.2_3'UTR|DAGLB_ENST00000425398.2_Frame_Shift_Ins_p.E433fs	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	562					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.E562fs*56(1)		breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		TAGGCTCTGCTCCCCCAGAAGA	0.629																																					p.E562fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1685_1686insG	7						.																																			6416422	SO:0001589	frameshift_variant	221955	exon14			AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.1685dupG	7.37:g.6449901_6449901dupC	ENSP00000297056:p.Glu562fs	Somatic		Capture	Illumina HiSeq	Phase_I	6416421	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Frame_Shift_Ins	INS	ENST00000297056.6	37	CCDS5350.1																																																																																				0.629	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
MOSPD3	64598	broad.mit.edu	37	7	100212577	100212577	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100212577C>T	ENST00000393950.2	+	4	881	c.599C>T	c.(598-600)cCg>cTg	p.P200L	MOSPD3_ENST00000223054.4_Missense_Mutation_p.P200L|MOSPD3_ENST00000424091.2_Missense_Mutation_p.P190L|MOSPD3_ENST00000379527.2_Missense_Mutation_p.P200L	NM_023948.4	NP_076438.1	O75425	MSPD3_HUMAN	motile sperm domain containing 3	200					heart development (GO:0007507)	integral component of membrane (GO:0016021)	structural molecule activity (GO:0005198)	p.P200L(1)		breast(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CTCCCACTCCCGGACGAACTC	0.612																																					p.P200L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C599T	7						.						90.0	97.0	94.0					7																	100212577		2203	4300	6503	100050513	SO:0001583	missense	64598	exon5			BC011653	CCDS5701.1, CCDS47662.1	7q22	2009-11-06			ENSG00000106330	ENSG00000106330			25078	protein-coding gene	gene with protein product		609125				15533722	Standard	XM_005250531		Approved	CDS3, NET30	uc003uvs.3	O75425	OTTHUMG00000159599	ENST00000393950.2:c.599C>T	7.37:g.100212577C>T	ENSP00000377522:p.Pro200Leu	Somatic		Capture	Illumina HiSeq	Phase_I	100050513	NM_001040098	A4D2D1|A6NG17|C9JE89|D6W5W1|O75423|O75424	Missense_Mutation	SNP	ENST00000393950.2	37	CCDS5701.1	.	.	.	.	.	.	.	.	.	.	A	14.95	2.688132	0.48097	.	.	ENSG00000106330	ENST00000223054;ENST00000493970;ENST00000379527;ENST00000393950;ENST00000424091;ENST00000393953	.	.	.	4.58	4.58	0.56647	.	0.239737	0.28109	N	0.016572	T	0.14270	0.0345	N	0.01874	-0.695	0.24301	N	0.995126	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16217	-1.0410	9	0.34782	T	0.22	-1.4353	8.5031	0.33170	0.8031:0.1969:0.0:0.0	.	190;200	C9JE89;O75425	.;MSPD3_HUMAN	L	200;200;200;200;190;186	.	ENSP00000223054:P200L	P	+	2	0	MOSPD3	100050513	1.000000	0.71417	0.999000	0.59377	0.074000	0.17049	1.438000	0.35002	0.902000	0.36520	-0.256000	0.11100	CCG		0.612	MOSPD3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356395.1	NM_023948	
SLC12A9	56996	broad.mit.edu	37	7	100457600	100457600	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100457600G>A	ENST00000354161.3	+	8	1196	c.1071G>A	c.(1069-1071)gcG>gcA	p.A357A	SLC12A9_ENST00000275729.3_Silent_p.A268A|SLC12A9_ENST00000428758.1_Silent_p.A357A|SLC12A9_ENST00000415287.1_Silent_p.A268A|SLC12A9_ENST00000540482.1_Silent_p.A357A|SLC12A9_ENST00000475623.1_3'UTR	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	357					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)	p.A357A(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CGCTCTCAGCGTCCATGAGCT	0.612																																					p.A357A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1071A	7						.						136.0	120.0	126.0					7																	100457600		2203	4300	6503	100295536	SO:0001819	synonymous_variant	56996	exon8			AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.1071G>A	7.37:g.100457600G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100295536	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																				0.612	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
SRRT	51593	broad.mit.edu	37	7	100482840	100482840	+	Missense_Mutation	SNP	C	C	T	rs113298167		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100482840C>T	ENST00000347433.4	+	10	1324	c.1166C>T	c.(1165-1167)gCg>gTg	p.A389V	SRRT_ENST00000388793.4_Missense_Mutation_p.A388V|SRRT_ENST00000457580.2_Missense_Mutation_p.A389V|SRRT_ENST00000432932.1_Missense_Mutation_p.A388V			Q9BXP5	SRRT_HUMAN	serrate, RNA effector molecule	389	Glu-rich.				cell proliferation (GO:0008283)|neuronal stem cell maintenance (GO:0097150)|primary miRNA processing (GO:0031053)|regulation of transcription, DNA-templated (GO:0006355)|response to arsenic-containing substance (GO:0046685)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)	p.A389V(1)		breast(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(5)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						CTAGAAGAAGCGCTCAAGGAG	0.567																																					p.A388V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1163T	7						.						57.0	65.0	62.0					7																	100482840		2203	4300	6503	100320776	SO:0001583	missense	51593	exon10				CCDS34709.1, CCDS47665.1, CCDS47666.1, CCDS47667.1	7q21	2014-04-14	2014-04-14		ENSG00000087087	ENSG00000087087			24101	protein-coding gene	gene with protein product	"""arsenite resistance protein"""	614469	"""serrate RNA effector molecule homolog (Arabidopsis)"""			11239002, 11230166	Standard	NM_015908		Approved	Asr2, serrate, ARS2	uc003uwy.2	Q9BXP5	OTTHUMG00000157031	ENST00000347433.4:c.1166C>T	7.37:g.100482840C>T	ENSP00000314491:p.Ala389Val	Somatic		Capture	Illumina HiSeq	Phase_I	100320776	NM_001128852	A4D2E5|A4D2E6|A6NK22|B4DJL4|B4DZA6|O95808|Q32MI4|Q6NT74|Q8TDQ5|Q9BWP6|Q9BXP4|Q9Y4S4	Missense_Mutation	SNP	ENST00000347433.4	37	CCDS34709.1	.	.	.	.	.	.	.	.	.	.	C	8.879	0.951163	0.18431	.	.	ENSG00000087087	ENST00000457580;ENST00000388793;ENST00000432932;ENST00000347433;ENST00000448764	T;T	0.17054	2.3;2.3	4.99	2.98	0.34508	.	0.738433	0.13211	N	0.405154	T	0.11196	0.0273	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.26052	-1.0114	10	0.41790	T	0.15	.	9.0526	0.36385	0.0:0.8039:0.0:0.1961	.	388;388;389;389	Q9BXP5-3;Q9BXP5-4;Q9BXP5-2;Q9BXP5	.;.;.;SRRT_HUMAN	V	389;388;388;389;19	ENSP00000416553:A389V;ENSP00000314491:A389V	ENSP00000314491:A389V	A	+	2	0	SRRT	100320776	0.140000	0.22579	0.311000	0.25182	0.603000	0.37013	0.665000	0.25083	0.567000	0.29293	0.655000	0.94253	GCG		0.567	SRRT-004	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347168.1	NM_015908	
AP1S1	1174	broad.mit.edu	37	7	100800029	100800029	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100800029G>T	ENST00000337619.5	+	2	276	c.158G>T	c.(157-159)aGg>aTg	p.R53M	MIR4653_ENST00000585107.1_RNA	NM_001283.3	NP_001274.1	P61966	AP1S1_HUMAN	adaptor-related protein complex 1, sigma 1 subunit	53					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor-mediated endocytosis (GO:0006898)|regulation of defense response to virus by virus (GO:0050690)|response to virus (GO:0009615)|viral process (GO:0016032)	AP-1 adaptor complex (GO:0030121)|coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)	p.R53M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)	8	Lung NSC(181;0.168)|all_lung(186;0.215)					CTGGAGTGGAGGGACCTCAAA	0.522																																					p.R53M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G158T	7						.						40.0	45.0	43.0					7																	100800029		2009	4170	6179	100586749	SO:0001583	missense	1174	exon2			AB015319	CCDS47669.1	7q22.1	2014-02-04			ENSG00000106367	ENSG00000106367			559	protein-coding gene	gene with protein product	"""clathrin-associated/assembly/adaptor protein, small 1 (19kD)"", ""clathrin coat assembly protein AP19"", ""sigma1A subunit of AP-1 clathrin adaptor complex"", ""AP-1 complex subunit sigma-1A"", ""sigma1A-adaptin"", ""golgi adaptor HA1/AP1 adaptin sigma-1A subunit"", ""clathrin assembly protein complex 1 sigma-1A small chain"", ""HA1 19 kDa subunit"""	603531	"""erythrokeratodermia variabilis 3 (Kamouraska type)"""	CLAPS1, EKV3		9653655, 9733768, 19057675	Standard	NM_001283		Approved	AP19, SIGMA1A, WUGSC:H_DJ0747G18.2	uc003uxv.4	P61966	OTTHUMG00000157103	ENST00000337619.5:c.158G>T	7.37:g.100800029G>T	ENSP00000336666:p.Arg53Met	Somatic		Capture	Illumina HiSeq	Phase_I	100586749	NM_001283	B2R5D8|P82267|Q00382|Q53YA7|Q9BTN4|Q9UDW9	Missense_Mutation	SNP	ENST00000337619.5	37	CCDS47669.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.37|17.37	3.373109|3.373109	0.61624|0.61624	.|.	.|.	ENSG00000106367|ENSG00000106367	ENST00000429457|ENST00000337619	.|.	.|.	.|.	5.84|5.84	5.84|5.84	0.93424|0.93424	.|Longin-like (1);AP complex, mu/sigma subunit (1);	.|0.106561	.|0.64402	.|D	.|0.000007	T|T	0.75347|0.75347	0.3837|0.3837	M|M	0.81497|0.81497	2.545|2.545	0.44736|0.44736	D|D	0.997735|0.997735	.|B	.|0.24768	.|0.111	.|B	.|0.36719	.|0.231	T|T	0.74748|0.74748	-0.3560|-0.3560	5|9	.|0.87932	.|D	.|0	0.0033|0.0033	17.6324|17.6324	0.88113|0.88113	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|53	.|P61966	.|AP1S1_HUMAN	W|M	95|53	.|.	.|ENSP00000336666:R53M	G|R	+|+	1|2	0|0	AP1S1|AP1S1	100586749|100586749	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.316000|4.316000	0.59178|0.59178	2.767000|2.767000	0.95098|0.95098	0.561000|0.561000	0.74099|0.74099	GGG|AGG		0.522	AP1S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347439.1	NM_001283	
CUX1	1523	broad.mit.edu	37	7	101842125	101842125	+	Silent	SNP	G	G	A	rs556348394		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:101842125G>A	ENST00000292535.7	+	16	1976	c.1938G>A	c.(1936-1938)ccG>ccA	p.P646P	CUX1_ENST00000560541.1_Intron|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000549414.2_Intron|CUX1_ENST00000550008.2_Intron|CUX1_ENST00000546411.2_Silent_p.P544P|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000360264.3_Silent_p.P657P|CUX1_ENST00000556210.1_Intron|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000425244.2_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	646					auditory receptor cell differentiation (GO:0042491)|kidney development (GO:0001822)|lung development (GO:0030324)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|retrograde transport, vesicle recycling within Golgi (GO:0000301)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)	p.P646P(1)		breast(2)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(8)|lung(26)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|stomach(1)|urinary_tract(5)	70						AGGAAGTACCGAAACGAAGAA	0.458																																					p.P646P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1938A	7						.						135.0	118.0	124.0					7																	101842125		2203	4300	6503	101628845	SO:0001819	synonymous_variant	1523	exon16			M74099	CCDS5720.1, CCDS5721.1, CCDS47672.1, CCDS56498.1, CCDS56499.1, CCDS56500.1, CCDS59071.1	7q22.1	2012-10-03	2007-11-07	2007-11-07	ENSG00000257923	ENSG00000257923		"""Homeoboxes / CUT class"""	2557	protein-coding gene	gene with protein product	"""golgi integral membrane protein 6"""	116896	"""cut (Drosophila)-like 1 (CCAAT displacement protein)"", ""cut-like 1, CCAAT displacement protein (Drosophila)"""	CUTL1		8468066, 9799793, 15004235	Standard	NM_001202543		Approved	CDP, CDP1, CUX, CUT, Clox, CDP/Cut, CDP/Cux, Cux/CDP, CASP, GOLIM6	uc003uyx.4	P39880	OTTHUMG00000157129	ENST00000292535.7:c.1938G>A	7.37:g.101842125G>A		Somatic		Capture	Illumina HiSeq	Phase_I	101628845	NM_181552	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																				0.458	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913	
Unknown	0	broad.mit.edu	37	Unknown	0	0	+	IGR	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrUnknown:0C>G								None (None upstream) : None (None downstream)																								0.0																																					p.E102Q												.	.	0			c.G304C	7						.																																			101995574	SO:0001628	intergenic_variant	548644	exon3																															Unknown.37:g.0C>G		Somatic		Capture	Illumina HiSeq	Phase_I	101995574	NM_001097615		Missense_Mutation	SNP		37																																																																																				0	0								
RELN	5649	broad.mit.edu	37	7	103276025	103276025	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:103276025T>C	ENST00000428762.1	-	19	2471	c.2312A>G	c.(2311-2313)cAg>cGg	p.Q771R	RELN_ENST00000424685.2_Missense_Mutation_p.Q771R|RELN_ENST00000343529.5_Missense_Mutation_p.Q771R	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	771					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.Q771R(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CAGTGTGAACTGGAGAAACCT	0.363																																					p.Q771R	NSCLC(146;835 1944 15585 22231 52158)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2312G	7						.						77.0	82.0	80.0					7																	103276025		2203	4300	6503	103063261	SO:0001583	missense	5649	exon19				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.2312A>G	7.37:g.103276025T>C	ENSP00000392423:p.Gln771Arg	Somatic		Capture	Illumina HiSeq	Phase_I	103063261	NM_005045	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.872776	0.72180	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.23950	1.88;1.88;1.88	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.61703	1.905	0.58432	D	0.99999	D;P	0.64830	0.994;0.936	D;P	0.75020	0.985;0.885	T	0.30765	-0.9967	10	0.33940	T	0.23	.	16.6512	0.85203	0.0:0.0:0.0:1.0	.	771;771	P78509-2;P78509	.;RELN_HUMAN	R	771	ENSP00000392423:Q771R;ENSP00000345694:Q771R;ENSP00000388446:Q771R	ENSP00000345694:Q771R	Q	-	2	0	RELN	103063261	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	7.222000	0.78025	2.333000	0.79357	0.482000	0.46254	CAG		0.363	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
KMT2E	55904	broad.mit.edu	37	7	104749513	104749513	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:104749513G>A	ENST00000311117.3	+	23	4138	c.3593G>A	c.(3592-3594)gGc>gAc	p.G1198D	KMT2E_ENST00000334914.7_Missense_Mutation_p.G253D|SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000334877.4_Missense_Mutation_p.G1198D|KMT2E_ENST00000257745.4_Missense_Mutation_p.G1198D	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1198					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.G1198D(1)									AATGGTGATGGCTGTGCCAGC	0.468																																					p.G1198D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3593A	7						.						111.0	95.0	100.0					7																	104749513		2203	4300	6503	104536749	SO:0001583	missense	55904	exon23			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3593G>A	7.37:g.104749513G>A	ENSP00000312379:p.Gly1198Asp	Somatic		Capture	Illumina HiSeq	Phase_I	104536749	NM_182931	B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.67|14.67	2.604930|2.604930	0.46423|0.46423	.|.	.|.	ENSG00000005483|ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914|ENST00000473063	D;D;D;T|.	0.91577|.	-2.87;-2.5;-2.87;0.86|.	5.65|5.65	4.76|4.76	0.60689|0.60689	.|.	0.105638|.	0.42964|.	D|.	0.000639|.	T|.	0.52837|.	0.1759|.	L|L	0.27053|0.27053	0.805|0.805	0.43054|0.43054	D|D	0.994669|0.994669	D|.	0.54047|.	0.964|.	B|.	0.44224|.	0.444|.	T|.	0.49744|.	-0.8907|.	10|.	0.07030|.	T|.	0.85|.	.|.	14.8534|14.8534	0.70316|0.70316	0.0:0.1433:0.8567:0.0|0.0:0.1433:0.8567:0.0	.|.	1198|.	Q8IZD2|.	MLL5_HUMAN|.	D|X	1198;1198;1198;1118;1198;253|9	ENSP00000312379:G1198D;ENSP00000335599:G1198D;ENSP00000257745:G1198D;ENSP00000333986:G253D|.	ENSP00000257745:G1198D|.	G|W	+|+	2|3	0|0	MLL5|MLL5	104536749|104536749	0.994000|0.994000	0.37717|0.37717	0.115000|0.115000	0.21578|0.21578	0.532000|0.532000	0.34746|0.34746	2.486000|2.486000	0.45259|0.45259	1.353000|1.353000	0.45828|0.45828	0.467000|0.467000	0.42956|0.42956	GGC|TGG		0.468	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1		
PIK3CG	5294	broad.mit.edu	37	7	106508334	106508334	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:106508334T>C	ENST00000359195.3	+	2	638	c.328T>C	c.(328-330)Tac>Cac	p.Y110H	PIK3CG_ENST00000496166.1_Missense_Mutation_p.Y110H|PIK3CG_ENST00000440650.2_Missense_Mutation_p.Y110H	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	110	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cytokine production (GO:0001816)|dendritic cell chemotaxis (GO:0002407)|endocytosis (GO:0006897)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte apoptotic process (GO:0097284)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|natural killer cell chemotaxis (GO:0035747)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of triglyceride catabolic process (GO:0010897)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion mediated by integrin (GO:0033628)|respiratory burst involved in defense response (GO:0002679)|secretory granule localization (GO:0032252)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|T cell chemotaxis (GO:0010818)|T cell proliferation (GO:0042098)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|ephrin receptor binding (GO:0046875)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.Y110H(1)		breast(7)|central_nervous_system(9)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(16)|liver(4)|lung(59)|ovary(4)|pancreas(4)|prostate(3)|skin(6)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	132						GTACGAGATCTACGACAAGTA	0.652																																					p.Y110H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T328C	7						.						25.0	26.0	26.0					7																	106508334		2203	4300	6503	106295570	SO:0001583	missense	5294	exon2				CCDS5739.1	7q22	2012-07-13	2012-07-13		ENSG00000105851	ENSG00000105851	2.7.1.153		8978	protein-coding gene	gene with protein product		601232	"""phosphoinositide-3-kinase, catalytic, gamma polypeptide"""				Standard	XM_005250443		Approved		uc003vdw.3	P48736	OTTHUMG00000157641	ENST00000359195.3:c.328T>C	7.37:g.106508334T>C	ENSP00000352121:p.Tyr110His	Somatic		Capture	Illumina HiSeq	Phase_I	106295570	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	T	19.22	3.784895	0.70222	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000359195	T;T;T	0.72394	-0.65;-0.65;-0.65	5.64	5.64	0.86602	.	0.105878	0.64402	D	0.000003	T	0.80319	0.4601	M	0.62723	1.935	0.80722	D	1	D	0.71674	0.998	D	0.65573	0.936	T	0.76873	-0.2798	10	0.22109	T	0.4	-23.3779	16.1449	0.81559	0.0:0.0:0.0:1.0	.	110	P48736	PK3CG_HUMAN	H	110	ENSP00000392258:Y110H;ENSP00000419260:Y110H;ENSP00000352121:Y110H	ENSP00000352121:Y110H	Y	+	1	0	PIK3CG	106295570	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.929000	0.87595	2.269000	0.75478	0.455000	0.32223	TAC		0.652	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1		
PRKAR2B	5577	broad.mit.edu	37	7	106797673	106797673	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:106797673C>T	ENST00000265717.4	+	10	1286	c.1027C>T	c.(1027-1029)Cga>Tga	p.R343*		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	343					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)	p.R343*(1)		breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						AGAAATCGCTCGATGCTCGCG	0.448																																					p.R343X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1027T	7						.						116.0	110.0	112.0					7																	106797673		2203	4300	6503	106584909	SO:0001587	stop_gained	5577	exon10				CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.1027C>T	7.37:g.106797673C>T	ENSP00000265717:p.Arg343*	Somatic		Capture	Illumina HiSeq	Phase_I	106584909	NM_002736	A4D0R9	Nonsense_Mutation	SNP	ENST00000265717.4	37	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037250	0.93630	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	.	.	.	5.97	5.06	0.68205	.	0.113417	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.5495	16.6476	0.85180	0.1303:0.8697:0.0:0.0	.	.	.	.	X	343;343;330	.	ENSP00000265717:R343X	R	+	1	2	PRKAR2B	106584909	0.996000	0.38824	0.987000	0.45799	0.948000	0.59901	3.330000	0.52068	2.828000	0.97474	0.655000	0.94253	CGA		0.448	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
ZNF277	11179	broad.mit.edu	37	7	111977817	111977817	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:111977817C>A	ENST00000361822.3	+	9	1031	c.902C>A	c.(901-903)tCt>tAt	p.S301Y	AC004112.4_ENST00000431064.1_RNA|AC004112.4_ENST00000411413.1_RNA	NM_021994.2	NP_068834.2	Q9NRM2	ZN277_HUMAN	zinc finger protein 277	301					cellular response to hydrogen peroxide (GO:0070301)|regulation of cellular senescence (GO:2000772)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)	p.S301Y(1)		breast(4)|endometrium(1)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	15						CACCCTGCCTCTGCAGTCTGC	0.368																																					p.S301Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C902A	7						.						129.0	130.0	130.0					7																	111977817		2203	4300	6503	111765053	SO:0001583	missense	11179	exon9			AF209198	CCDS5755.2	7q31.1	2012-10-05	2007-10-23	2007-10-23	ENSG00000198839	ENSG00000198839			13070	protein-coding gene	gene with protein product		605465	"""zinc finger protein (C2H2 type) 277"", ""zinc finger protein 277 pseudogene"""	ZNF277P		10860669, 16213364, 16395595	Standard	NM_021994		Approved	NRIF4	uc003vge.2	Q9NRM2	OTTHUMG00000150209	ENST00000361822.3:c.902C>A	7.37:g.111977817C>A	ENSP00000354501:p.Ser301Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	111765053	NM_021994	Q75MZ2|Q75MZ3|Q8WY14	Missense_Mutation	SNP	ENST00000361822.3	37	CCDS5755.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.047088	0.75846	.	.	ENSG00000198839	ENST00000361822;ENST00000421864	T;T	0.47528	0.84;0.84	5.83	4.93	0.64822	.	0.155147	0.64402	D	0.000018	T	0.52025	0.1709	L	0.36672	1.1	0.80722	D	1	D	0.53885	0.963	P	0.54629	0.757	T	0.51857	-0.8652	10	0.56958	D	0.05	-18.806	15.0015	0.71476	0.0:0.7716:0.2284:0.0	.	301	Q9NRM2	ZN277_HUMAN	Y	301;12	ENSP00000354501:S301Y;ENSP00000415735:S12Y	ENSP00000354501:S301Y	S	+	2	0	ZNF277	111765053	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.748000	0.38308	2.756000	0.94617	0.655000	0.94253	TCT		0.368	ZNF277-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316843.2	NM_021994	
FOXP2	93986	broad.mit.edu	37	7	114292323	114292323	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:114292323T>C	ENST00000393494.2	+	9	1439	c.1160T>C	c.(1159-1161)gTg>gCg	p.V387A	FOXP2_ENST00000393498.2_Missense_Mutation_p.V366A|FOXP2_ENST00000390668.3_Missense_Mutation_p.V411A|FOXP2_ENST00000403559.4_Missense_Mutation_p.V404A|FOXP2_ENST00000393491.3_Missense_Mutation_p.V295A|MIR3666_ENST00000607845.1_RNA|FOXP2_ENST00000350908.4_Missense_Mutation_p.V387A|FOXP2_ENST00000360232.4_Missense_Mutation_p.V387A|FOXP2_ENST00000393489.3_Missense_Mutation_p.V295A|FOXP2_ENST00000408937.3_Missense_Mutation_p.V412A|FOXP2_ENST00000393500.3_Missense_Mutation_p.V312A			O15409	FOXP2_HUMAN	forkhead box P2	387					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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 involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V412A(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						CAAATGCAGGTGGTGCAACAG	0.413																																					p.V387A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1160C	7						.						168.0	149.0	155.0					7																	114292323		2203	4300	6503	114079559	SO:0001583	missense	93986	exon8			U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.1160T>C	7.37:g.114292323T>C	ENSP00000377132:p.Val387Ala	Somatic		Capture	Illumina HiSeq	Phase_I	114079559	NM_148899	A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.990380	0.93106	.	.	ENSG00000128573	ENST00000393500;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000393489;ENST00000360232;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08;2.08	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.50137	0.1598	M	0.81112	2.525	0.80722	D	1	P;P;B;D;D;P;P	0.71674	0.924;0.924;0.012;0.998;0.998;0.924;0.954	P;P;B;D;D;P;D	0.77557	0.857;0.857;0.008;0.99;0.99;0.857;0.954	T	0.55283	-0.8165	10	0.87932	D	0	.	16.1502	0.81611	0.0:0.0:0.0:1.0	.	386;404;295;387;411;387;412	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4	.;.;.;.;.;FOXP2_HUMAN;.	A	312;387;412;404;387;364;295;387;411;295	ENSP00000377137:V312A;ENSP00000377132:V387A;ENSP00000386200:V412A;ENSP00000385069:V404A;ENSP00000265436:V387A;ENSP00000377129:V295A;ENSP00000353367:V387A;ENSP00000375084:V411A;ENSP00000377130:V295A	ENSP00000265436:V387A	V	+	2	0	FOXP2	114079559	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.933000	0.87642	2.203000	0.70933	0.460000	0.39030	GTG		0.413	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	
CTTNBP2	83992	broad.mit.edu	37	7	117431903	117431903	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:117431903T>C	ENST00000160373.3	-	4	1438	c.1347A>G	c.(1345-1347)agA>agG	p.R449R	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	449	Pro-rich.				brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)		p.R449R(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		GAAATCTAAATCTAGCTGCTT	0.478																																					p.R449R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1347G	7						.						228.0	217.0	221.0					7																	117431903		2203	4300	6503	117219139	SO:0001819	synonymous_variant	83992	exon4				CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1347A>G	7.37:g.117431903T>C		Somatic		Capture	Illumina HiSeq	Phase_I	117219139	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1																																																																																				0.478	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
RBM28	55131	broad.mit.edu	37	7	127973347	127973347	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:127973347A>G	ENST00000223073.2	-	9	1130	c.1016T>C	c.(1015-1017)aTc>aCc	p.I339T	RBM28_ENST00000415472.2_Missense_Mutation_p.I198T	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	339	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.I339T(1)		breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						GACATACCTGATAAAAACAGT	0.383																																					p.I198T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T593C	7						.						141.0	122.0	128.0					7																	127973347		2203	4300	6503	127760583	SO:0001583	missense	55131	exon5			AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"""RNA binding motif (RRM) containing"""	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1016T>C	7.37:g.127973347A>G	ENSP00000223073:p.Ile339Thr	Somatic		Capture	Illumina HiSeq	Phase_I	127760583	NM_001166135	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	Missense_Mutation	SNP	ENST00000223073.2	37	CCDS5801.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.160894	0.78226	.	.	ENSG00000106344	ENST00000223073;ENST00000415472	T;T	0.22134	1.97;1.97	5.44	5.44	0.79542	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.57272	0.2042	H	0.94964	3.605	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.80764	0.994;0.994	T	0.69917	-0.5015	10	0.87932	D	0	.	13.4661	0.61254	1.0:0.0:0.0:0.0	.	198;339	E9PDD9;Q9NW13	.;RBM28_HUMAN	T	339;198	ENSP00000223073:I339T;ENSP00000390517:I198T	ENSP00000223073:I339T	I	-	2	0	RBM28	127760583	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.359000	0.79477	2.077000	0.62373	0.533000	0.62120	ATC		0.383	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077	
ZC3HC1	51530	broad.mit.edu	37	7	129664189	129664189	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:129664189G>A	ENST00000358303.4	-	7	1018	c.934C>T	c.(934-936)Cca>Tca	p.P312S	RP11-306G20.1_ENST00000587038.1_RNA|RNA5SP245_ENST00000364239.1_RNA|ZC3HC1_ENST00000360708.5_Missense_Mutation_p.P312S|ZC3HC1_ENST00000311873.5_Missense_Mutation_p.P291S|RP11-306G20.1_ENST00000480018.1_RNA|ZC3HC1_ENST00000481503.1_Missense_Mutation_p.P269S	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	312					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)	p.P312S(1)		endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					AAGCGCTCTGGTCGCCCCTCA	0.592																																					p.P312S	Melanoma(115;540 1606 16325 28853 48167)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C934T	7						.						70.0	65.0	67.0					7																	129664189		2203	4300	6503	129451425	SO:0001583	missense	51530	exon7			AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.934C>T	7.37:g.129664189G>A	ENSP00000351052:p.Pro312Ser	Somatic		Capture	Illumina HiSeq	Phase_I	129451425	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Missense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.955609	0.34471	.	.	ENSG00000091732	ENST00000358303;ENST00000360708;ENST00000311873;ENST00000481503	T;T;T;T	0.41758	1.06;1.06;1.06;0.99	5.48	4.6	0.57074	Nuclear-interacting partner of ALK/Rsm1-like (1);	0.602264	0.16487	N	0.212293	T	0.25269	0.0614	N	0.25426	0.745	0.33147	D	0.545181	B;B;B	0.15141	0.012;0.0;0.0	B;B;B	0.18871	0.023;0.003;0.001	T	0.21518	-1.0243	10	0.07482	T	0.82	-5.328	8.1753	0.31278	0.0858:0.1575:0.7566:0.0	.	312;312;269	Q86WB0-3;Q86WB0;C9J0I9	.;NIPA_HUMAN;.	S	312;312;291;269	ENSP00000351052:P312S;ENSP00000353933:P312S;ENSP00000309301:P291S;ENSP00000418533:P269S	ENSP00000309301:P291S	P	-	1	0	ZC3HC1	129451425	0.002000	0.14202	0.992000	0.48379	0.850000	0.48378	0.350000	0.20079	2.584000	0.87258	0.563000	0.77884	CCA		0.592	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
PLXNA4	91584	broad.mit.edu	37	7	131883382	131883382	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:131883382G>A	ENST00000359827.3	-	13	3562	c.2600C>T	c.(2599-2601)aCa>aTa	p.T867I	PLXNA4_ENST00000321063.4_Missense_Mutation_p.T867I			Q9HCM2	PLXA4_HUMAN	plexin A4	867	IPT/TIG 1.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)	p.T867I(1)		NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCGGGGGCCTGTCACCGGGAT	0.567																																					p.T867I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2600T	7						.						53.0	56.0	55.0					7																	131883382		1861	4089	5950	131533922	SO:0001583	missense	91584	exon13			AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2600C>T	7.37:g.131883382G>A	ENSP00000352882:p.Thr867Ile	Somatic		Capture	Illumina HiSeq	Phase_I	131533922	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541151	0.65085	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.78707	-1.2;-1.2	5.94	5.94	0.96194	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.054645	0.64402	D	0.000001	T	0.74076	0.3669	L	0.45352	1.415	0.48288	D	0.999627	B	0.22604	0.072	B	0.28553	0.091	T	0.68934	-0.5278	10	0.45353	T	0.12	.	16.5939	0.84791	0.0:0.13:0.87:0.0	.	867	Q9HCM2	PLXA4_HUMAN	I	867	ENSP00000323194:T867I;ENSP00000352882:T867I	ENSP00000323194:T867I	T	-	2	0	PLXNA4	131533922	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.699000	0.61796	2.820000	0.97059	0.650000	0.86243	ACA		0.567	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
WDR91	29062	broad.mit.edu	37	7	134870950	134870950	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:134870950T>C	ENST00000354475.4	-	15	2228	c.2197A>G	c.(2197-2199)Atg>Gtg	p.M733V	WDR91_ENST00000344400.5_3'UTR|WDR91_ENST00000423565.1_Missense_Mutation_p.M698V	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	733								p.M733V(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						TTGCCATCCATGGAGGCGGTG	0.622																																					p.M733V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2197G	7						.						100.0	86.0	91.0					7																	134870950		2203	4300	6503	134521490	SO:0001583	missense	29062	exon15			AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.2197A>G	7.37:g.134870950T>C	ENSP00000346466:p.Met733Val	Somatic		Capture	Illumina HiSeq	Phase_I	134521490	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.853594	0.71719	.	.	ENSG00000105875	ENST00000354475;ENST00000423565	T;T	0.59906	0.23;0.23	5.54	5.54	0.83059	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.51381	0.1671	L	0.44542	1.39	0.80722	D	1	B	0.32302	0.363	B	0.34452	0.183	T	0.47100	-0.9143	10	0.22706	T	0.39	-37.9487	15.6802	0.77360	0.0:0.0:0.0:1.0	.	733	A4D1P6	WDR91_HUMAN	V	733;698	ENSP00000346466:M733V;ENSP00000392555:M698V	ENSP00000346466:M733V	M	-	1	0	WDR91	134521490	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.040000	0.89188	2.103000	0.63969	0.533000	0.62120	ATG		0.622	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
WDR91	29062	broad.mit.edu	37	7	134882846	134882846	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:134882846C>T	ENST00000354475.4	-	7	980	c.949G>A	c.(949-951)Ggg>Agg	p.G317R	AC009542.2_ENST00000595902.1_RNA|AC009542.2_ENST00000412549.2_RNA|WDR91_ENST00000344400.5_Missense_Mutation_p.G317R|WDR91_ENST00000423565.1_Missense_Mutation_p.G282R|WDR91_ENST00000485942.1_5'UTR	NM_014149.3	NP_054868.3	A4D1P6	WDR91_HUMAN	WD repeat domain 91	317								p.G317R(1)		breast(3)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	40						GTGGCCAGCCCGCTGAGGAGG	0.617																																					p.G317R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G949A	7						.						57.0	57.0	57.0					7																	134882846		2203	4300	6503	134533386	SO:0001583	missense	29062	exon7			AF161534	CCDS34758.1	7q33	2013-01-09			ENSG00000105875	ENSG00000105875		"""WD repeat domain containing"""	24997	protein-coding gene	gene with protein product						11042152, 11230166	Standard	NM_014149		Approved	HSPC049	uc003vsp.2	A4D1P6	OTTHUMG00000155414	ENST00000354475.4:c.949G>A	7.37:g.134882846C>T	ENSP00000346466:p.Gly317Arg	Somatic		Capture	Illumina HiSeq	Phase_I	134533386	NM_014149	A6NK54|C9JMI4|Q6FI65|Q6MZQ1|Q6P4I1|Q96AE5|Q96G63|Q9H062|Q9H9B6|Q9NVG7|Q9NZY6	Missense_Mutation	SNP	ENST00000354475.4	37	CCDS34758.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998294	0.54147	.	.	ENSG00000105875	ENST00000344400;ENST00000354475;ENST00000423565	T;T;T	0.63580	1.51;-0.05;0.53	5.65	3.71	0.42584	.	0.394114	0.31347	N	0.007813	T	0.44891	0.1315	L	0.29908	0.895	0.09310	N	1	D	0.53312	0.959	B	0.40410	0.328	T	0.45264	-0.9273	10	0.66056	D	0.02	-17.7023	6.3898	0.21581	0.1382:0.6558:0.1335:0.0725	.	317	A4D1P6	WDR91_HUMAN	R	317;317;282	ENSP00000340877:G317R;ENSP00000346466:G317R;ENSP00000392555:G282R	ENSP00000340877:G317R	G	-	1	0	WDR91	134533386	0.013000	0.17824	0.545000	0.28153	0.793000	0.44817	1.165000	0.31822	1.365000	0.46057	0.561000	0.74099	GGG		0.617	WDR91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340019.1	NM_014149	
NUP205	23165	broad.mit.edu	37	7	135323372	135323372	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:135323372C>G	ENST00000285968.6	+	38	5359	c.5333C>G	c.(5332-5334)gCt>gGt	p.A1778G		NM_015135.2	NP_055950	Q92621	NU205_HUMAN	nucleoporin 205kDa	1778					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)|nuclear pore complex assembly (GO:0051292)|nucleocytoplasmic transport (GO:0006913)|protein import into nucleus, docking (GO:0000059)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)	p.A1778G(1)		breast(4)|central_nervous_system(2)|endometrium(9)|kidney(7)|large_intestine(17)|liver(4)|lung(36)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	93						TTCCAGCATGCTGTGTGTCTC	0.393																																					p.A1778G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5333G	7						.						212.0	194.0	200.0					7																	135323372		2203	4300	6503	134973912	SO:0001583	missense	23165	exon38			D86978	CCDS34759.1	7q31.32	2007-03-26	2004-01-06	2004-01-07	ENSG00000155561	ENSG00000155561			18658	protein-coding gene	gene with protein product		614352	"""chromosome 7 open reading frame 14"""	C7orf14		9039502, 9348540	Standard	NM_015135		Approved	KIAA0225	uc003vsw.3	Q92621	OTTHUMG00000155497	ENST00000285968.6:c.5333C>G	7.37:g.135323372C>G	ENSP00000285968:p.Ala1778Gly	Somatic		Capture	Illumina HiSeq	Phase_I	134973912	NM_015135	A6H8X3|Q86YC1	Missense_Mutation	SNP	ENST00000285968.6	37	CCDS34759.1	.	.	.	.	.	.	.	.	.	.	c	13.30	2.196154	0.38806	.	.	ENSG00000155561	ENST00000285968	T	0.30981	1.51	5.26	4.38	0.52667	.	0.391778	0.30410	N	0.009691	T	0.19287	0.0463	N	0.19112	0.55	0.53688	D	0.999974	B	0.17038	0.02	B	0.11329	0.006	T	0.04440	-1.0951	10	0.13108	T	0.6	-6.055	13.6424	0.62260	0.0:0.9252:0.0:0.0748	.	1778	Q92621	NU205_HUMAN	G	1778	ENSP00000285968:A1778G	ENSP00000285968:A1778G	A	+	2	0	NUP205	134973912	0.950000	0.32346	0.118000	0.21660	0.986000	0.74619	2.390000	0.44416	1.219000	0.43474	0.460000	0.39030	GCT		0.393	NUP205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340358.1		
FAM180A	389558	broad.mit.edu	37	7	135418799	135418799	+	Missense_Mutation	SNP	G	G	A	rs368814924		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:135418799G>A	ENST00000338588.3	-	3	711	c.446C>T	c.(445-447)gCg>gTg	p.A149V	FAM180A_ENST00000435869.1_Intron|FAM180A_ENST00000415751.1_Missense_Mutation_p.A149V	NM_205855.3	NP_995327.1	Q6UWF9	F180A_HUMAN	family with sequence similarity 180, member A	149						extracellular region (GO:0005576)				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)	14						GAGGGACTGCGCCCAGATGTC	0.607																																					p.A149V												.	.	0			c.C446T	7						.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	103.0	87.0	92.0		446	5.7	1.0	7		92	0,8600		0,0,4300	no	missense	FAM180A	NM_205855.3	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	149/174	135418799	2,13004	2203	4300	6503	135069339	SO:0001583	missense	389558	exon3			AC091736, AK290250, AK310180, AY358803	CCDS5841.1	7q33	2008-07-25			ENSG00000189320	ENSG00000189320			33773	protein-coding gene	gene with protein product						12975309, 12690205	Standard	NM_205855		Approved	HWKM1940, UNQ1940	uc003vtd.3	Q6UWF9	OTTHUMG00000155537	ENST00000338588.3:c.446C>T	7.37:g.135418799G>A	ENSP00000342336:p.Ala149Val	None		Capture	Illumina HiSeq	Phase_I	135069339	NM_205855	B2RP85	Missense_Mutation	SNP	ENST00000338588.3	37	CCDS5841.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520493	0.85495	4.54E-4	0.0	ENSG00000189320	ENST00000338588;ENST00000415751	T;T	0.34667	1.35;1.35	5.65	5.65	0.86999	.	0.279462	0.40554	N	0.001062	T	0.47340	0.1440	M	0.65975	2.015	0.36364	D	0.860897	D	0.71674	0.998	P	0.52957	0.714	T	0.59873	-0.7372	10	0.72032	D	0.01	-2.3193	10.6221	0.45487	0.0865:0.0:0.9135:0.0	.	149	Q6UWF9	F180A_HUMAN	V	149	ENSP00000342336:A149V;ENSP00000395467:A149V	ENSP00000342336:A149V	A	-	2	0	FAM180A	135069339	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	3.756000	0.55205	2.677000	0.91161	0.561000	0.74099	GCG		0.607	FAM180A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340554.2	NM_205855	
KIAA1549	57670	broad.mit.edu	37	7	138602326	138602326	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:138602326C>T	ENST00000422774.1	-	2	2094	c.2046G>A	c.(2044-2046)caG>caA	p.Q682Q	KIAA1549_ENST00000242365.4_Silent_p.Q632Q|KIAA1549_ENST00000440172.1_Silent_p.Q682Q			Q9HCM3	K1549_HUMAN	KIAA1549	682	Ser-rich.					integral component of membrane (GO:0016021)		p.Q682Q(1)|p.Q632Q(1)	KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						GAAGAGACAGCTGAGATGACT	0.478			O	BRAF	pilocytic astrocytoma																																p.Q682Q	NSCLC(119;1534 1718 44213 46230 50068)		Dom	yes		7	7q34	57670	KIAA1549		O	.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G2046A	7						.						62.0	61.0	61.0					7																	138602326		1969	4167	6136	138252866	SO:0001819	synonymous_variant	57670	exon2				CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.2046G>A	7.37:g.138602326C>T		Somatic		Capture	Illumina HiSeq	Phase_I	138252866	NM_001164665	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																				0.478	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
HIPK2	28996	broad.mit.edu	37	7	139316026	139316026	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:139316026C>T	ENST00000406875.3	-	4	1326	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	HIPK2_ENST00000342645.6_Missense_Mutation_p.R411Q|HIPK2_ENST00000428878.2_Missense_Mutation_p.R411Q	NM_022740.4	NP_073577.3	Q9H2X6	HIPK2_HUMAN	homeodomain interacting protein kinase 2	411	Interaction with DAXX.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adult walking behavior (GO:0007628)|anterior/posterior pattern specification (GO:0009952)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|erythrocyte differentiation (GO:0030218)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|PML body organization (GO:0030578)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA binding (GO:0043388)|positive regulation of JNK cascade (GO:0046330)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|retina layer formation (GO:0010842)|SMAD protein signal transduction (GO:0060395)|smoothened signaling pathway (GO:0007224)|transforming growth factor beta receptor signaling pathway (GO:0007179)|voluntary musculoskeletal movement (GO:0050882)	cytoplasm (GO:0005737)|nuclear body (GO:0016604)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription coactivator activity (GO:0001105)|SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)|virion binding (GO:0046790)	p.R411Q(1)		breast(4)|central_nervous_system(4)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Melanoma(164;0.205)					TGAAATATACCGAATCTGCAA	0.408																																					p.R411Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1232A	7						.						48.0	47.0	47.0					7																	139316026		1847	4117	5964	138966566	SO:0001583	missense	28996	exon4			AF208291	CCDS75666.1, CCDS75667.1	7q32-q34	2004-01-29	2001-11-29		ENSG00000064393	ENSG00000064393			14402	protein-coding gene	gene with protein product		606868	"""homeodomain-interacting protein kinase 2"""			11120354	Standard	NM_001113239		Approved		uc003vvf.4	Q9H2X6	OTTHUMG00000157704	ENST00000406875.3:c.1232G>A	7.37:g.139316026C>T	ENSP00000385571:p.Arg411Gln	Somatic		Capture	Illumina HiSeq	Phase_I	138966566	NM_022740	Q75MR7|Q8WWI4|Q9H2Y1	Missense_Mutation	SNP	ENST00000406875.3	37		.	.	.	.	.	.	.	.	.	.	C	35	5.592015	0.96590	.	.	ENSG00000064393	ENST00000406875;ENST00000428878;ENST00000342645	T;T;T	0.63744	-0.06;-0.06;-0.06	5.43	5.43	0.79202	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.81182	0.4769	.	.	.	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.80764	0.994;0.986	T	0.83308	-0.0024	8	0.72032	D	0.01	.	19.2573	0.93951	0.0:1.0:0.0:0.0	.	411;411	Q9H2X6;Q9H2X6-3	HIPK2_HUMAN;.	Q	411	ENSP00000385571:R411Q;ENSP00000413724:R411Q;ENSP00000343108:R411Q	ENSP00000343108:R411Q	R	-	2	0	HIPK2	138966566	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.675000	0.84002	2.546000	0.85860	0.460000	0.39030	CGG		0.408	HIPK2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349430.3	NM_022740	
RAB19	401409	broad.mit.edu	37	7	140111746	140111746	+	Missense_Mutation	SNP	G	G	A	rs189143966		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:140111746G>A	ENST00000356407.3	+	2	342	c.274G>A	c.(274-276)Gca>Aca	p.A92T	RAB19_ENST00000275874.5_Missense_Mutation_p.A139T|RAB19_ENST00000537763.1_Missense_Mutation_p.A92T			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	92					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)	p.A139T(1)		breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					CAGTGCCCACGCAGCCATCAT	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		16874	0.001		0.0	False		,,,				2504	0.0				p.A92T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G274A	7						.						146.0	119.0	128.0					7																	140111746		2203	4300	6503	139758215	SO:0001583	missense	401409	exon3				CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"""RAB, member RAS oncogene"""	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.274G>A	7.37:g.140111746G>A	ENSP00000348778:p.Ala92Thr	Somatic		Capture	Illumina HiSeq	Phase_I	139758215	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Missense_Mutation	SNP	ENST00000356407.3	37	CCDS34762.2	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	27.4	4.832015	0.91036	.	.	ENSG00000146955	ENST00000495590;ENST00000275874;ENST00000537763;ENST00000356407	T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49	5.59	5.59	0.84812	Small GTP-binding protein domain (1);	0.046599	0.85682	D	0.000000	D	0.88599	0.6480	M	0.86651	2.83	0.51233	D	0.999912	D	0.65815	0.995	P	0.52672	0.706	D	0.90550	0.4508	10	0.87932	D	0	.	18.5797	0.91166	0.0:0.0:1.0:0.0	.	92	A4D1S5	RAB19_HUMAN	T	92;139;92;92	ENSP00000420782:A92T;ENSP00000275874:A139T;ENSP00000440167:A92T;ENSP00000348778:A92T	ENSP00000275874:A139T	A	+	1	0	RAB19	139758215	1.000000	0.71417	0.988000	0.46212	0.332000	0.28634	9.751000	0.98889	2.636000	0.89361	0.491000	0.48974	GCA		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1		
MKRN1	23608	broad.mit.edu	37	7	140159573	140159573	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:140159573C>A	ENST00000255977.2	-	3	702	c.478G>T	c.(478-480)Gga>Tga	p.G160*	MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000443720.2_Nonsense_Mutation_p.G160*|MKRN1_ENST00000474576.1_Nonsense_Mutation_p.G96*|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000437223.2_Intron	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	160					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.G160*(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					GAACCTGCTCCTACAGTTGCA	0.438																																					p.G160X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G478T	7						.						104.0	101.0	102.0					7																	140159573		2203	4300	6503	139806042	SO:0001587	stop_gained	23608	exon3			AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.478G>T	7.37:g.140159573C>A	ENSP00000255977:p.Gly160*	Somatic		Capture	Illumina HiSeq	Phase_I	139806042	NM_001145125	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Nonsense_Mutation	SNP	ENST00000255977.2	37	CCDS5860.1	.	.	.	.	.	.	.	.	.	.	C	35	5.470041	0.96274	.	.	ENSG00000133606	ENST00000255977;ENST00000539898;ENST00000474576;ENST00000443720;ENST00000471104;ENST00000467513;ENST00000494939	.	.	.	5.45	4.51	0.55191	.	0.130864	0.49916	D	0.000135	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	15.678	0.77344	0.0:0.8629:0.1371:0.0	.	.	.	.	X	160;96;96;160;96;96;96	.	ENSP00000255977:G160X	G	-	1	0	MKRN1	139806042	.	.	0.979000	0.43373	0.860000	0.49131	.	.	2.575000	0.86900	0.455000	0.32223	GGA		0.438	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.V600E	Colon(40;35 892 2973 5743 27438)		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,pituitary,NS,Substitution - Missense,0 	.	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	c.T1799A	7						.						112.0	104.0	107.0					7																	140453136		2203	4300	6503	140099605	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu	Somatic		Capture	Illumina HiSeq	Phase_I	140099605	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
KEL	3792	broad.mit.edu	37	7	142651288	142651288	+	Missense_Mutation	SNP	T	T	G	rs373642084		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:142651288T>G	ENST00000355265.2	-	8	1381	c.907A>C	c.(907-909)Act>Cct	p.T303P	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	303					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)	p.T303P(1)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					TGGTCGATAGTGACCATCTGG	0.552																																					p.T303P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A907C	7						.						38.0	42.0	41.0					7																	142651288		2203	4300	6503	142361410	SO:0001583	missense	3792	exon8			BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.907A>C	7.37:g.142651288T>G	ENSP00000347409:p.Thr303Pro	Somatic		Capture	Illumina HiSeq	Phase_I	142361410	NM_000420	B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.918195	0.33815	.	.	ENSG00000197993	ENST00000355265	D	0.84070	-1.8	6.07	4.91	0.64330	Peptidase M13 (1);	0.000000	0.64402	D	0.000011	D	0.90061	0.6896	M	0.80183	2.485	0.20196	N	0.999923	D	0.89917	1.0	D	0.97110	1.0	T	0.83050	-0.0153	10	0.72032	D	0.01	-8.7299	9.5742	0.39447	0.1562:0.0:0.0:0.8438	.	303	P23276	KELL_HUMAN	P	303	ENSP00000347409:T303P	ENSP00000347409:T303P	T	-	1	0	KEL	142361410	1.000000	0.71417	0.056000	0.19401	0.003000	0.03518	4.157000	0.58144	1.096000	0.41439	-0.481000	0.04817	ACT		0.552	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
OR2A5	393046	broad.mit.edu	37	7	143747769	143747769	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:143747769T>A	ENST00000408906.2	+	1	309	c.275T>A	c.(274-276)aTc>aAc	p.I92N		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.I92N(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					AGAAAAACAATCTCCTTTGTC	0.428																																					p.I92N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T275A	7						.						136.0	137.0	137.0					7																	143747769		2156	4276	6432	143378702	SO:0001583	missense	393046	exon1			U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.275T>A	7.37:g.143747769T>A	ENSP00000386208:p.Ile92Asn	Somatic		Capture	Illumina HiSeq	Phase_I	143378702	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	T	15.07	2.723217	0.48728	.	.	ENSG00000221836	ENST00000408906	T	0.00484	7.08	5.37	5.37	0.77165	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.02533	0.0077	H	0.96301	3.8	0.40324	D	0.978858	D	0.65815	0.995	D	0.75484	0.986	T	0.02683	-1.1124	9	0.87932	D	0	.	13.3761	0.60739	0.0:0.0:0.0:1.0	.	92	Q96R48	OR2A5_HUMAN	N	92	ENSP00000386208:I92N	ENSP00000386208:I92N	I	+	2	0	OR2A5	143378702	0.997000	0.39634	0.506000	0.27664	0.201000	0.24016	5.905000	0.69893	2.256000	0.74724	0.528000	0.53228	ATC		0.428	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
C7orf33	202865	broad.mit.edu	37	7	148311209	148311209	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:148311209G>A	ENST00000307003.2	+	2	641	c.280G>A	c.(280-282)Gcc>Acc	p.A94T		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	94								p.A94T(1)		central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			CAAATCTGGTGCCCCGTGGCA	0.507																																					p.A94T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G280A	7						.						86.0	80.0	82.0					7																	148311209		2203	4300	6503	147942142	SO:0001583	missense	202865	exon2			BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.280G>A	7.37:g.148311209G>A	ENSP00000304071:p.Ala94Thr	Somatic		Capture	Illumina HiSeq	Phase_I	147942142	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	37	CCDS5890.1	.	.	.	.	.	.	.	.	.	.	G	7.890	0.732174	0.15507	.	.	ENSG00000170279	ENST00000307003	.	.	.	1.08	-2.16	0.07080	.	.	.	.	.	T	0.15696	0.0378	N	0.08118	0	0.09310	N	1	B	0.23490	0.086	B	0.12837	0.008	T	0.15867	-1.0422	8	0.87932	D	0	.	4.5076	0.11896	0.5935:0.0:0.4065:0.0	.	94	Q8WU49	CG033_HUMAN	T	94	.	ENSP00000304071:A94T	A	+	1	0	C7orf33	147942142	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.574000	0.05868	-0.764000	0.04651	-0.448000	0.05591	GCC		0.507	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	
CUL1	8454	broad.mit.edu	37	7	148486905	148486905	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:148486905C>T	ENST00000325222.4	+	15	1940	c.1661C>T	c.(1660-1662)gCc>gTc	p.A554V	CUL1_ENST00000409469.1_Missense_Mutation_p.A554V|CUL1_ENST00000602748.1_Missense_Mutation_p.A554V	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	554					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein monoubiquitination (GO:0006513)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|SCF ubiquitin ligase complex (GO:0019005)		p.A554V(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(10)|liver(2)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	40	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGTACATTTGCCTTGCCGTCA	0.567																																					p.A554V												.	.	1	Substitution - Missense(1)	kidney(1)	c.C1661T	7						.						156.0	151.0	153.0					7																	148486905		2203	4300	6503	148117838	SO:0001583	missense	8454	exon15			U58087	CCDS34772.1	7q36.1	2011-05-24			ENSG00000055130	ENSG00000055130			2551	protein-coding gene	gene with protein product		603134				8681378	Standard	NM_003592		Approved		uc003wey.3	Q13616	OTTHUMG00000152776	ENST00000325222.4:c.1661C>T	7.37:g.148486905C>T	ENSP00000326804:p.Ala554Val	None		Capture	Illumina HiSeq	Phase_I	148117838	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.790071	0.31685	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000543583;ENST00000433865	T;T	0.73897	-0.79;-0.79	5.08	5.08	0.68730	Cullin, N-terminal (1);Cullin homology (3);	0.107917	0.64402	D	0.000007	T	0.64571	0.2610	L	0.28649	0.875	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.09377	0.001;0.004	T	0.58978	-0.7540	10	0.19147	T	0.46	-28.3459	18.4804	0.90809	0.0:1.0:0.0:0.0	.	481;554	E7EWR0;Q13616	.;CUL1_HUMAN	V	554;554;512;481	ENSP00000387160:A554V;ENSP00000326804:A554V	ENSP00000326804:A554V	A	+	2	0	CUL1	148117838	1.000000	0.71417	0.986000	0.45419	0.142000	0.21351	7.354000	0.79424	2.359000	0.80004	0.591000	0.81541	GCC		0.567	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592	
SSPO	23145	broad.mit.edu	37	7	149483303	149483303	+	RNA	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:149483303G>T	ENST00000378016.2	+	0	3371							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)	p.W374L(1)				Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACCCTGCTCTGGGATGGAGAT	0.637																																					p.L1125L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3375T	7						.						29.0	34.0	33.0					7																	149483303		2133	4222	6355	149114236			23145	exon21			AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149483303G>T		Somatic		Capture	Illumina HiSeq	Phase_I	149114236	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																					0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GIMAP8	155038	broad.mit.edu	37	7	150174635	150174635	+	Missense_Mutation	SNP	C	C	T	rs139453539	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:150174635C>T	ENST00000307271.3	+	5	2339	c.1765C>T	c.(1765-1767)Cgc>Tgc	p.R589C		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	589	AIG1-type G 3.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)	p.R589C(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		AGCCCTTCGGCGCATTTTTAA	0.463																																					p.R589C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1765T	7						.	C	CYS/ARG	0,4406		0,0,2203	71.0	82.0	79.0		1765	-2.4	0.0	7	dbSNP_134	79	2,8598	2.2+/-6.3	0,2,4298	no	missense	GIMAP8	NM_175571.2	180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	589/666	150174635	2,13004	2203	4300	6503	149805568	SO:0001583	missense	155038	exon5			AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.1765C>T	7.37:g.150174635C>T	ENSP00000305107:p.Arg589Cys	Somatic		Capture	Illumina HiSeq	Phase_I	149805568	NM_175571		Missense_Mutation	SNP	ENST00000307271.3	37	CCDS34777.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.321059	0.23994	0.0	2.33E-4	ENSG00000171115	ENST00000307271	T	0.06142	3.34	4.44	-2.36	0.06663	AIG1 (1);	2.070020	0.02112	N	0.054914	T	0.08891	0.0220	L	0.46157	1.445	0.09310	N	1	P	0.46327	0.876	P	0.45138	0.471	T	0.32508	-0.9904	10	0.59425	D	0.04	.	5.262	0.15578	0.4635:0.1613:0.3752:0.0	.	589	Q8ND71	GIMA8_HUMAN	C	589	ENSP00000305107:R589C	ENSP00000305107:R589C	R	+	1	0	GIMAP8	149805568	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.608000	0.05641	-0.282000	0.09128	-0.986000	0.02555	CGC		0.463	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
GIMAP4	55303	broad.mit.edu	37	7	150269720	150269720	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:150269720G>A	ENST00000255945.2	+	3	737	c.562G>A	c.(562-564)Gcg>Acg	p.A188T	GIMAP4_ENST00000461940.1_Missense_Mutation_p.A202T|GIMAP4_ENST00000494750.1_3'UTR	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	188	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)	p.A188T(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCGCTACTGTGCGTTAAACAA	0.527																																					p.A188T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G562A	7						.						99.0	99.0	99.0					7																	150269720		2203	4300	6503	149900653	SO:0001583	missense	55303	exon3			AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"""GTPases, IMAP"""	21872	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 1"""	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.562G>A	7.37:g.150269720G>A	ENSP00000255945:p.Ala188Thr	Somatic		Capture	Illumina HiSeq	Phase_I	149900653	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	37	CCDS5904.1	.	.	.	.	.	.	.	.	.	.	G	14.00	2.406120	0.42715	.	.	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000466938	T;T	0.60424	0.19;0.19	4.72	0.499	0.16914	AIG1 (1);	0.740336	0.12910	N	0.429025	T	0.58652	0.2137	M	0.66560	2.04	0.09310	N	1	P;P	0.43352	0.804;0.603	B;P	0.48368	0.415;0.575	T	0.49293	-0.8955	10	0.39692	T	0.17	.	7.0809	0.25231	0.0:0.3028:0.3648:0.3324	.	202;188	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	T	188;202;120	ENSP00000255945:A188T;ENSP00000419545:A202T	ENSP00000255945:A188T	A	+	1	0	GIMAP4	149900653	0.104000	0.21937	0.001000	0.08648	0.001000	0.01503	2.648000	0.46647	-0.080000	0.12685	0.655000	0.94253	GCG		0.527	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326	
ABCB8	11194	broad.mit.edu	37	7	150737669	150737669	+	Missense_Mutation	SNP	G	G	A	rs370506479		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:150737669G>A	ENST00000297504.6	+	12	1453	c.1387G>A	c.(1387-1389)Gtc>Atc	p.V463I	ABCB8_ENST00000498578.1_Missense_Mutation_p.V446I|ABCB8_ENST00000358849.4_Missense_Mutation_p.V446I|ABCB8_ENST00000542328.1_Missense_Mutation_p.V358I|ABCB8_ENST00000356058.4_3'UTR			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	463					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)	p.V446I(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGGCTGCTGCGTCCCCAAAGA	0.652																																					p.V446I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1336A	7						.	G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	71.0	77.0	75.0		1336	-1.0	0.1	7		75	0,8600		0,0,4300	no	missense	ABCB8	NM_007188.3	29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	446/719	150737669	2,13004	2203	4300	6503	150368602	SO:0001583	missense	11194	exon11			AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.1387G>A	7.37:g.150737669G>A	ENSP00000297504:p.Val463Ile	Somatic		Capture	Illumina HiSeq	Phase_I	150368602	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		.	.	.	.	.	.	.	.	.	.	G	0.034	-1.316344	0.01331	4.54E-4	0.0	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578	D;D;D;D	0.90004	-2.49;-2.49;-2.45;-2.6	4.53	-1.01	0.10169	.	0.316324	0.33272	N	0.005088	T	0.72128	0.3422	N	0.21282	0.65	0.80722	D	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.59392	-0.7463	10	0.02654	T	1	-0.0138	4.5614	0.12161	0.3966:0.3148:0.2886:0.0	.	358;446;463;446	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2	.;.;ABCB8_HUMAN;.	I	446;429;463;358;446	ENSP00000351717:V446I;ENSP00000297504:V463I;ENSP00000438776:V358I;ENSP00000418271:V446I	ENSP00000297504:V463I	V	+	1	0	ABCB8	150368602	0.038000	0.19896	0.053000	0.19242	0.388000	0.30384	0.508000	0.22692	-0.323000	0.08602	-0.340000	0.08031	GTC		0.652	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
CYP2W1	54905	broad.mit.edu	37	7	1026290	1026290	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:1026290C>A	ENST00000308919.7	+	5	689	c.676C>A	c.(676-678)Ctg>Atg	p.L226M	CYP2W1_ENST00000340150.6_Missense_Mutation_p.L170M	NM_017781.2	NP_060251.2	Q8TAV3	CP2W1_HUMAN	cytochrome P450, family 2, subfamily W, polypeptide 1	226					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)	p.L226M(1)		breast(1)|large_intestine(1)|lung(4)|urinary_tract(1)	7		Ovarian(82;0.0112)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		GCTCGGGGCCCTGCTCCAGCT	0.697																																					p.L226M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C676A	7						.						40.0	46.0	44.0					7																	1026290		2199	4297	6496	992816	SO:0001583	missense	54905	exon5			AK000366	CCDS5319.2	7p22.3	2004-07-05			ENSG00000073067	ENSG00000073067		"""Cytochrome P450s"""	20243	protein-coding gene	gene with protein product		615967					Standard	XM_005249792		Approved	FLJ20359, MGC34287	uc003sjq.1	Q8TAV3	OTTHUMG00000074071	ENST00000308919.7:c.676C>A	7.37:g.1026290C>A	ENSP00000310149:p.Leu226Met	Somatic		Capture	Illumina HiSeq	Phase_I	992816	NM_017781		Missense_Mutation	SNP	ENST00000308919.7	37	CCDS5319.2	.	.	.	.	.	.	.	.	.	.	C	11.75	1.731988	0.30684	.	.	ENSG00000073067	ENST00000308919;ENST00000340150	T;T	0.71461	-0.57;-0.57	4.05	2.18	0.27775	.	0.870661	0.10196	N	0.703993	T	0.80259	0.4590	M	0.83603	2.65	0.09310	N	1	P;P	0.49559	0.767;0.925	P;P	0.56648	0.685;0.803	T	0.66019	-0.6027	10	0.62326	D	0.03	.	7.2388	0.26084	0.0:0.708:0.0:0.292	.	170;226	A6NJ10;Q8TAV3	.;CP2W1_HUMAN	M	226;170	ENSP00000310149:L226M;ENSP00000344178:L170M	ENSP00000310149:L226M	L	+	1	2	CYP2W1	992816	0.000000	0.05858	0.435000	0.26784	0.744000	0.42396	-0.002000	0.12924	0.428000	0.26173	0.561000	0.74099	CTG		0.697	CYP2W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157249.1	NM_017781	
AMZ1	155185	broad.mit.edu	37	7	2748296	2748296	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:2748296C>A	ENST00000312371.4	+	4	915	c.547C>A	c.(547-549)Ctg>Atg	p.L183M	AMZ1_ENST00000489665.1_3'UTR|AMZ1_ENST00000407112.1_Missense_Mutation_p.L183M	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	183							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.L183M(1)		breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		ACTGTCTGACCTGTACCCCCA	0.642																																					p.L183M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C547A	7						.						99.0	82.0	87.0					7																	2748296		2203	4300	6503	2714822	SO:0001583	missense	155185	exon4			AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.547C>A	7.37:g.2748296C>A	ENSP00000308149:p.Leu183Met	Somatic		Capture	Illumina HiSeq	Phase_I	2714822	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	37	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.776620	0.49786	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.70749	-0.51;-0.51	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000020	D	0.82779	0.5111	M	0.81802	2.56	0.39096	D	0.961187	D;D	0.89917	1.0;0.994	D;P	0.91635	0.999;0.844	D	0.85659	0.1287	10	0.72032	D	0.01	-13.2483	10.771	0.46323	0.0:0.9109:0.0:0.0891	.	183;183	B3KRS0;Q400G9	.;AMZ1_HUMAN	M	183	ENSP00000308149:L183M;ENSP00000386020:L183M	ENSP00000308149:L183M	L	+	1	2	AMZ1	2714822	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	2.608000	0.46308	2.078000	0.62432	0.462000	0.41574	CTG		0.642	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
SDK1	221935	broad.mit.edu	37	7	4277392	4277392	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:4277392A>G	ENST00000404826.2	+	42	6245	c.6106A>G	c.(6106-6108)Aag>Gag	p.K2036E	SDK1_ENST00000389531.3_Missense_Mutation_p.K2016E|SDK1_ENST00000466611.1_3'UTR	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	2036					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.K2036E(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CGGGCAGAATAAGAAGTATAA	0.572																																					p.K2036E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A6106G	7						.						140.0	129.0	133.0					7																	4277392		2203	4300	6503	4243918	SO:0001583	missense	221935	exon42			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.6106A>G	7.37:g.4277392A>G	ENSP00000385899:p.Lys2036Glu	Somatic		Capture	Illumina HiSeq	Phase_I	4243918	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	A	11.27	1.588259	0.28357	.	.	ENSG00000146555	ENST00000404826;ENST00000446104;ENST00000389531	T;T	0.61859	0.07;0.09	5.27	4.1	0.47936	.	0.072732	0.52532	D	0.000065	T	0.64091	0.2567	M	0.74258	2.255	0.25148	N	0.990441	P;P;P;B	0.45283	0.855;0.726;0.774;0.393	P;B;P;B	0.48368	0.575;0.214;0.493;0.05	T	0.58301	-0.7660	10	0.42905	T	0.14	.	12.3033	0.54887	0.8583:0.1417:0.0:0.0	.	2016;96;523;2036	F8W6X9;Q7Z5N4-2;F2Z3E9;Q7Z5N4	.;.;.;SDK1_HUMAN	E	2036;284;2016	ENSP00000385899:K2036E;ENSP00000374182:K2016E	ENSP00000374182:K2016E	K	+	1	0	SDK1	4243918	0.984000	0.35163	0.007000	0.13788	0.727000	0.41649	2.727000	0.47311	0.815000	0.34398	0.496000	0.49642	AAG		0.572	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
FOXK1	221937	broad.mit.edu	37	7	4798841	4798841	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:4798841C>T	ENST00000328914.4	+	6	1404	c.1404C>T	c.(1402-1404)agC>agT	p.S468S	FOXK1_ENST00000446823.1_Silent_p.S305S	NM_001037165.1	NP_001032242.1			forkhead box K1									p.S446S(1)|p.S468S(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		ATTCCCAAAGCGCACCCGGTA	0.687																																					p.S468S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1404T	7						.						69.0	72.0	71.0					7																	4798841		2203	4300	6503	4765367	SO:0001819	synonymous_variant	221937	exon6			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1404C>T	7.37:g.4798841C>T		Somatic		Capture	Illumina HiSeq	Phase_I	4765367	NM_001037165		Silent	SNP	ENST00000328914.4	37	CCDS34591.1																																																																																				0.687	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
FOXK1	221937	broad.mit.edu	37	7	4800857	4800857	+	Missense_Mutation	SNP	G	G	A	rs373966273		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:4800857G>A	ENST00000328914.4	+	8	1859	c.1859G>A	c.(1858-1860)cGg>cAg	p.R620Q	FOXK1_ENST00000446823.1_Missense_Mutation_p.R457Q	NM_001037165.1	NP_001032242.1			forkhead box K1									p.R598Q(1)|p.R620Q(1)		breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;7.43e-15)		CTTCCAGTCCGGGCCGTGACC	0.667																																					p.R620Q												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1859A	7						.	G	GLN/ARG	0,4406		0,0,2203	47.0	46.0	46.0		1859	5.5	1.0	7		46	1,8599	1.2+/-3.3	0,1,4299	no	missense	FOXK1	NM_001037165.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	620/734	4800857	1,13005	2203	4300	6503	4767383	SO:0001583	missense	221937	exon8			BK004104	CCDS34591.1	7p22	2006-12-15			ENSG00000164916	ENSG00000164916		"""Forkhead boxes"""	23480	protein-coding gene	gene with protein product						15202027	Standard	NM_001037165		Approved	IMAGE:5164497	uc003snc.1	P85037	OTTHUMG00000151739	ENST00000328914.4:c.1859G>A	7.37:g.4800857G>A	ENSP00000328720:p.Arg620Gln	Somatic		Capture	Illumina HiSeq	Phase_I	4767383	NM_001037165		Missense_Mutation	SNP	ENST00000328914.4	37	CCDS34591.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.728290	0.48833	0.0	1.16E-4	ENSG00000164916	ENST00000446823;ENST00000450194;ENST00000328914;ENST00000545598	D;D	0.96427	-3.56;-4.01	5.46	5.46	0.80206	.	0.062738	0.64402	D	0.000005	D	0.93605	0.7958	N	0.25647	0.755	0.35830	D	0.825249	D;P	0.59357	0.985;0.812	P;B	0.45794	0.493;0.072	D	0.95247	0.8356	10	0.41790	T	0.15	.	16.4776	0.84136	0.0:0.0:1.0:0.0	.	620;457	P85037;P85037-2	FOXK1_HUMAN;.	Q	457;376;620;503	ENSP00000394442:R457Q;ENSP00000328720:R620Q	ENSP00000328720:R620Q	R	+	2	0	FOXK1	4767383	0.999000	0.42202	0.998000	0.56505	0.364000	0.29643	4.740000	0.62087	2.573000	0.86826	0.655000	0.94253	CGG		0.667	FOXK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323729.2		
FBXL18	80028	broad.mit.edu	37	7	5541433	5541433	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:5541433C>T	ENST00000382368.3	-	3	590	c.467G>A	c.(466-468)gGc>gAc	p.G156D	FBXL18_ENST00000453700.3_Missense_Mutation_p.G156D	NM_024963.4	NP_079239.3	Q96ME1	FXL18_HUMAN	F-box and leucine-rich repeat protein 18	156								p.G156D(1)	FBXL18/RNF216(2)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)	21		Ovarian(82;0.0607)		UCEC - Uterine corpus endometrioid carcinoma (126;0.181)|OV - Ovarian serous cystadenocarcinoma(56;3.64e-13)		GGCGTCGAAGCCGGGGCTCAC	0.677																																					p.G156D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G467A	7						.						9.0	12.0	11.0					7																	5541433		2104	4191	6295	5507959	SO:0001583	missense	80028	exon3			AK057042	CCDS43546.1	7p22.2	2011-06-09			ENSG00000155034	ENSG00000155034		"""F-boxes / Leucine-rich repeats"""	21874	protein-coding gene	gene with protein product		609084					Standard	NM_024963		Approved	FLJ11467, Fbl18	uc003son.4	Q96ME1	OTTHUMG00000151832	ENST00000382368.3:c.467G>A	7.37:g.5541433C>T	ENSP00000371805:p.Gly156Asp	Somatic		Capture	Illumina HiSeq	Phase_I	5507959	NM_024963	Q9BR90|Q9BTC7|Q9HAK7	Missense_Mutation	SNP	ENST00000382368.3	37	CCDS43546.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.0|23.0	4.365474|4.365474	0.82463|0.82463	.|.	.|.	ENSG00000155034|ENSG00000155034	ENST00000458142|ENST00000382368;ENST00000312577;ENST00000453700	.|T;T	.|0.61859	.|0.13;0.07	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.048273	.|0.85682	.|D	.|0.000000	T|T	0.66963|0.66963	0.2843|0.2843	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.79784	.|0.993;0.993	T|T	0.67639|0.67639	-0.5619|-0.5619	5|10	.|0.48119	.|T	.|0.1	.|.	18.1629|18.1629	0.89716|0.89716	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|156;156	.|F5H4Z4;Q96ME1-4	.|.;.	T|D	40|156	.|ENSP00000371805:G156D;ENSP00000444797:G156D	.|ENSP00000311990:G156D	A|G	-|-	1|2	0|0	FBXL18|FBXL18	5507959|5507959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.945000|0.945000	0.59286|0.59286	4.920000|4.920000	0.63390|0.63390	2.528000|2.528000	0.85240|0.85240	0.655000|0.655000	0.94253|0.94253	GCT|GGC		0.677	FBXL18-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324093.1	NM_024963	
CYTH3	9265	broad.mit.edu	37	7	6210575	6210575	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:6210575C>T	ENST00000350796.3	-	8	733	c.597G>A	c.(595-597)atG>atA	p.M199I	CYTH3_ENST00000396741.2_Missense_Mutation_p.M114I|CYTH3_ENST00000488964.1_5'UTR	NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	199	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				establishment of epithelial cell polarity (GO:0090162)|Golgi vesicle transport (GO:0048193)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)	p.M199I(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(7)|urinary_tract(1)	19						TGGTGTTGAGCATGATGATGG	0.627																																					p.M199I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G597A	7						.						178.0	127.0	144.0					7																	6210575		2203	4300	6503	6177100	SO:0001583	missense	9265	exon8			AJ223957	CCDS5346.1	7p22.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000008256	ENSG00000008256		"""Pleckstrin homology (PH) domain containing"""	9504	protein-coding gene	gene with protein product		605081	"""pleckstrin homology, Sec7 and coiled-coil domains 3"""	PSCD3		9072969	Standard	NM_004227		Approved	GRP1, ARNO3, cytohesin-3	uc003spt.3	O43739	OTTHUMG00000023440	ENST00000350796.3:c.597G>A	7.37:g.6210575C>T	ENSP00000297044:p.Met199Ile	Somatic		Capture	Illumina HiSeq	Phase_I	6177100	NM_004227	A4D2N8	Missense_Mutation	SNP	ENST00000350796.3	37	CCDS5346.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.629313	0.87560	.	.	ENSG00000008256	ENST00000350796;ENST00000396741	T;T	0.60797	0.16;0.16	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.68824	0.3043	M	0.76002	2.32	0.80722	D	1	P;D	0.54397	0.726;0.966	P;P	0.50082	0.515;0.63	T	0.74097	-0.3775	10	0.66056	D	0.02	.	18.8792	0.92350	0.0:1.0:0.0:0.0	.	114;199	B7Z2V9;O43739-2	.;.	I	199;114	ENSP00000297044:M199I;ENSP00000379967:M114I	ENSP00000297044:M199I	M	-	3	0	CYTH3	6177100	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.618000	0.83043	2.468000	0.83385	0.655000	0.94253	ATG		0.627	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227	
FAM220A	84792	broad.mit.edu	37	7	6370579	6370579	+	Silent	SNP	C	C	T	rs375783206		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:6370579C>T	ENST00000313324.4	-	2	674	c.207G>A	c.(205-207)ccG>ccA	p.P69P	FAM220A_ENST00000533877.1_5'Flank	NM_001037163.1	NP_001032240.1	Q7Z4H9	F220A_HUMAN	family with sequence similarity 220, member A	69						nucleus (GO:0005634)		p.P69P(1)									CAGCCCCGCTCGGATCCTTTC	0.537													C|||	1	0.000199681	0.0	0.0	5008	,	,		18403	0.0		0.0	False		,,,				2504	0.001				p.P69P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G207A	7						.	C		0,4406		0,0,2203	36.0	37.0	37.0		207	2.3	0.0	7		37	1,8595		0,1,4297	no	coding-synonymous	C7orf70	NM_001037163.1		0,1,6500	TT,TC,CC		0.0116,0.0,0.0077		69/260	6370579	1,13001	2203	4298	6501	6337104	SO:0001819	synonymous_variant	84792	exon2			BC006110	CCDS34599.1	7p22.1	2012-03-19	2012-03-19	2012-03-19	ENSG00000178397	ENSG00000178397			22422	protein-coding gene	gene with protein product	"""STAT3-interacting protein as a repressor"""		"""chromosome 7 open reading frame 70"""	C7orf70			Standard	NM_001037163		Approved	SIPAR, MGC12966	uc003spu.3	Q7Z4H9	OTTHUMG00000122091	ENST00000313324.4:c.207G>A	7.37:g.6370579C>T		Somatic		Capture	Illumina HiSeq	Phase_I	6337104	NM_001037163	Q75ML2|Q8NA52|Q9BRR7	Silent	SNP	ENST00000313324.4	37	CCDS34599.1																																																																																				0.537	FAM220A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000242853.2	NM_001037163	
ITGB8	3696	broad.mit.edu	37	7	20418791	20418791	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:20418791T>G	ENST00000222573.4	+	4	1190	c.506T>G	c.(505-507)gTt>gGt	p.V169G	ITGB8_ENST00000537992.1_Missense_Mutation_p.V34G|SNORD56_ENST00000363883.1_RNA	NM_002214.2	NP_002205.1	P26012	ITB8_HUMAN	integrin, beta 8	169	VWFA.				cartilage development (GO:0051216)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|ganglioside metabolic process (GO:0001573)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of gene expression (GO:0010629)|placenta blood vessel development (GO:0060674)|positive regulation of gene expression (GO:0010628)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	extracellular matrix protein binding (GO:1990430)|receptor activity (GO:0004872)	p.V169G(2)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(17)|prostate(2)|skin(4)|stomach(2)|urinary_tract(1)	37						TTAAATTCCGTTGGAAACGAT	0.343																																					p.V169G												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T506G	7						.						87.0	91.0	90.0					7																	20418791		2203	4300	6503	20385316	SO:0001583	missense	3696	exon4				CCDS5370.1	7p15.3	2010-03-23			ENSG00000105855	ENSG00000105855		"""Integrins"""	6163	protein-coding gene	gene with protein product		604160					Standard	XM_005249751		Approved		uc003suu.3	P26012	OTTHUMG00000023594	ENST00000222573.4:c.506T>G	7.37:g.20418791T>G	ENSP00000222573:p.Val169Gly	Somatic		Capture	Illumina HiSeq	Phase_I	20385316	NM_002214	A4D133|B4DHD4	Missense_Mutation	SNP	ENST00000222573.4	37	CCDS5370.1	.	.	.	.	.	.	.	.	.	.	T	15.44	2.832967	0.50951	.	.	ENSG00000105855	ENST00000537992;ENST00000222573	D;D	0.92858	-3.12;-3.12	5.82	5.82	0.92795	Integrin beta subunit, N-terminal (2);von Willebrand factor, type A (1);	0.000000	0.64402	D	0.000003	D	0.94833	0.8331	L	0.56769	1.78	0.80722	D	1	P;D	0.57257	0.926;0.979	P;D	0.66497	0.889;0.944	D	0.95210	0.8324	10	0.72032	D	0.01	-19.1573	16.1775	0.81862	0.0:0.0:0.0:1.0	.	169;169	P26012;Q9BUG9	ITB8_HUMAN;.	G	34;169	ENSP00000441561:V34G;ENSP00000222573:V169G	ENSP00000222573:V169G	V	+	2	0	ITGB8	20385316	1.000000	0.71417	0.893000	0.35052	0.141000	0.21300	4.183000	0.58317	2.216000	0.71823	0.528000	0.53228	GTT		0.343	ITGB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059915.3	NM_002214	
FAM126A	84668	broad.mit.edu	37	7	23017931	23017931	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:23017931C>T	ENST00000432176.2	-	4	522	c.290G>A	c.(289-291)aGc>aAc	p.S97N	FAM126A_ENST00000409763.1_Missense_Mutation_p.S97N|FAM126A_ENST00000409923.1_Missense_Mutation_p.S97N	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	97					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)	p.S97N(1)		breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						GCATCCACTGCTATGCACATT	0.388																																					p.S97N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G290A	7						.						85.0	79.0	81.0					7																	23017931		2203	4300	6503	22984456	SO:0001583	missense	84668	exon4			BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.290G>A	7.37:g.23017931C>T	ENSP00000403396:p.Ser97Asn	Somatic		Capture	Illumina HiSeq	Phase_I	22984456	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Missense_Mutation	SNP	ENST00000432176.2	37	CCDS5377.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.9|21.9	4.211084|4.211084	0.79240|0.79240	.|.	.|.	ENSG00000122591|ENSG00000122591	ENST00000440481|ENST00000432176;ENST00000409923;ENST00000409763	.|T;T;T	.|0.81330	.|-1.48;-1.48;-1.48	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.129644	.|0.64402	.|D	.|0.000002	D|D	0.88855|0.88855	0.6550|0.6550	M|M	0.79123|0.79123	2.44|2.44	0.49051|0.49051	D|D	0.999743|0.999743	.|P;D	.|0.53312	.|0.908;0.959	.|P;P	.|0.57960	.|0.83;0.783	D|D	0.88359|0.88359	0.2986|0.2986	5|10	.|0.52906	.|T	.|0.07	-6.3689|-6.3689	20.1951|20.1951	0.98241|0.98241	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|97;97	.|B8ZZJ1;Q9BYI3	.|.;HYCCI_HUMAN	T|N	149|97	.|ENSP00000403396:S97N;ENSP00000386246:S97N;ENSP00000386624:S97N	.|ENSP00000386624:S97N	A|S	-|-	1|2	0|0	FAM126A|FAM126A	22984456|22984456	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.956000|0.956000	0.61745|0.61745	3.397000|3.397000	0.52572|0.52572	2.780000|2.780000	0.95670|0.95670	0.585000|0.585000	0.79938|0.79938	GCA|AGC		0.388	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
KLHL7	55975	broad.mit.edu	37	7	23163401	23163401	+	Silent	SNP	G	G	A	rs150640353		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:23163401G>A	ENST00000339077.5	+	2	369	c.126G>A	c.(124-126)acG>acA	p.T42T	KLHL7_ENST00000539124.1_Intron|KLHL7_ENST00000322275.5_Silent_p.T42T|KLHL7_ENST00000545771.1_Silent_p.T20T|KLHL7_ENST00000545443.1_Silent_p.T20T|KLHL7_ENST00000409689.1_De_novo_Start_InFrame|KLHL7_ENST00000322231.7_Silent_p.T20T|KLHL7_ENST00000410047.1_Silent_p.T20T|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000479288.1_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	42					protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)	p.T20T(1)		breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATTAGAAAACGTTGTGTGACG	0.373																																					p.T42T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G126A	7						.	G	,,	0,4406		0,0,2203	117.0	106.0	109.0		126,126,	-10.9	0.0	7	dbSNP_134	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,utr-5	KLHL7	NM_001031710.2,NM_001172428.1,NM_018846.4	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	42/587,42/167,	23163401	1,13005	2203	4300	6503	23129926	SO:0001819	synonymous_variant	55975	exon2				CCDS5378.1, CCDS34609.1, CCDS5378.2, CCDS55095.1	7p15.3	2013-01-30	2013-01-30		ENSG00000122550	ENSG00000122550		"""Kelch-like"", ""BTB/POZ domain containing"""	15646	protein-coding gene	gene with protein product	"""retinitis pigmentosa 42"""	611119	"""kelch-like 7 (Drosophila)"""			19520207	Standard	NM_001031710		Approved	KLHL6, SBBI26, RP42	uc003svs.4	Q8IXQ5	OTTHUMG00000094813	ENST00000339077.5:c.126G>A	7.37:g.23163401G>A		Somatic		Capture	Illumina HiSeq	Phase_I	23129926	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Silent	SNP	ENST00000339077.5	37	CCDS34609.1																																																																																				0.373	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846	
MPP6	51678	broad.mit.edu	37	7	24681355	24681355	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:24681355T>C	ENST00000222644.5	+	3	388	c.138T>C	c.(136-138)gaT>gaC	p.D46D	MPP6_ENST00000396475.2_Silent_p.D46D|MPP6_ENST00000409761.1_5'UTR			Q99547	MPH6_HUMAN	membrane protein, palmitoylated 6 (MAGUK p55 subfamily member 6)	0					maturation of 5.8S rRNA (GO:0000460)	cytoplasm (GO:0005737)|exosome (RNase complex) (GO:0000178)|nucleolus (GO:0005730)|nucleus (GO:0005634)	RNA binding (GO:0003723)	p.D46D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|skin(2)	20						GGCTAGAAGATTCCAAACTAG	0.323																																					p.D46D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T138C	7						.						71.0	73.0	73.0					7																	24681355		2203	4300	6503	24647880	SO:0001819	synonymous_variant	51678	exon4			AF162130	CCDS5388.1	7p15	2007-08-01			ENSG00000105926	ENSG00000105926			18167	protein-coding gene	gene with protein product		606959				10753959, 11311936	Standard	NM_016447		Approved	PALS2, VAM-1, p55T	uc003swx.3	Q9NZW5	OTTHUMG00000023507	ENST00000222644.5:c.138T>C	7.37:g.24681355T>C		Somatic		Capture	Illumina HiSeq	Phase_I	24647880	NM_016447	B2RAF0	Silent	SNP	ENST00000222644.5	37	CCDS5388.1																																																																																				0.323	MPP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250272.4		
NFE2L3	9603	broad.mit.edu	37	7	26217573	26217573	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:26217573T>C	ENST00000056233.3	+	2	840	c.581T>C	c.(580-582)gTa>gCa	p.V194A		NM_004289.6	NP_004280.5	Q9Y4A8	NF2L3_HUMAN	nuclear factor, erythroid 2-like 3	194					transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)	p.V194A(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|skin(5)|urinary_tract(7)	29						GAGAATGGGGTACTAAGAGAA	0.408																																					p.V194A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T581C	7						.						88.0	90.0	89.0					7																	26217573		2203	4300	6503	26184098	SO:0001583	missense	9603	exon2			AB010812	CCDS5396.1	7p15.2	2013-08-23	2013-08-23		ENSG00000050344	ENSG00000050344		"""basic leucine zipper proteins"""	7783	protein-coding gene	gene with protein product		604135	"""nuclear factor (erythroid-derived 2)-like 3"""			10037736	Standard	NM_004289		Approved	Nrf3	uc003sxq.3	Q9Y4A8	OTTHUMG00000023882	ENST00000056233.3:c.581T>C	7.37:g.26217573T>C	ENSP00000056233:p.Val194Ala	Somatic		Capture	Illumina HiSeq	Phase_I	26184098	NM_004289	Q6NUS0|Q7Z498|Q86UJ4|Q86VR5|Q9UQA4	Missense_Mutation	SNP	ENST00000056233.3	37	CCDS5396.1	.	.	.	.	.	.	.	.	.	.	T	8.183	0.794230	0.16327	.	.	ENSG00000050344	ENST00000056233	T	0.25414	1.8	4.52	3.34	0.38264	.	1.224910	0.05728	N	0.599137	T	0.22666	0.0547	L	0.48642	1.525	0.09310	N	1	B	0.26002	0.139	B	0.22601	0.04	T	0.31110	-0.9955	10	0.15499	T	0.54	-1.0971	7.4357	0.27154	0.1925:0.0:0.0:0.8075	.	194	Q9Y4A8	NF2L3_HUMAN	A	194	ENSP00000056233:V194A	ENSP00000056233:V194A	V	+	2	0	NFE2L3	26184098	0.000000	0.05858	0.008000	0.14137	0.337000	0.28794	0.452000	0.21795	1.023000	0.39654	0.533000	0.62120	GTA		0.408	NFE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214088.1		
HOXA1	3198	broad.mit.edu	37	7	27134329	27134329	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:27134329C>T	ENST00000343060.4	-	2	799	c.738G>A	c.(736-738)aaG>aaA	p.K246K	HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000429611.3_RNA|HOXA1_ENST00000355633.5_3'UTR|HOTAIRM1_ENST00000495032.1_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	246					abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.K246K(1)		endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						AGTGGAACTCCTTCTCCAGTT	0.582																																					p.K246K												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G738A	7						.						124.0	111.0	115.0					7																	27134329		2203	4300	6503	27100854	SO:0001819	synonymous_variant	3198	exon2				CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"""Homeoboxes / ANTP class : HOXL subclass"""	5099	protein-coding gene	gene with protein product		142955	"""homeo box A1"""	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.738G>A	7.37:g.27134329C>T		Somatic		Capture	Illumina HiSeq	Phase_I	27100854	NM_005522	A4D184|B2R8U7|O43363	Silent	SNP	ENST00000343060.4	37	CCDS5401.1																																																																																				0.582	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1		
NOD1	10392	broad.mit.edu	37	7	30491974	30491974	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:30491974G>T	ENST00000222823.4	-	6	1584	c.1059C>A	c.(1057-1059)tcC>tcA	p.S353S	NOD1_ENST00000423334.2_3'UTR	NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	353	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|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)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)	p.S353S(1)		breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						GGTGGCTGGGGGAGAAGCCCC	0.682																																					p.S353S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1059A	7						.						26.0	32.0	30.0					7																	30491974		2201	4300	6501	30458499	SO:0001819	synonymous_variant	10392	exon6			AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.1059C>A	7.37:g.30491974G>T		Somatic		Capture	Illumina HiSeq	Phase_I	30458499	NM_006092	B4DTU3|Q549U4|Q8IWF5	Silent	SNP	ENST00000222823.4	37	CCDS5427.1																																																																																				0.682	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
PDE1C	5137	broad.mit.edu	37	7	32209568	32209568	+	Splice_Site	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:32209568C>T	ENST00000396193.1	-	3	730	c.137G>A	c.(136-138)cGg>cAg	p.R46Q		NM_001191058.1	NP_001177987.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	0					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TGACTTAGACCCTGAGGCATG	0.527																																					p.R46Q												.	.	0			c.G137A	7						.						218.0	185.0	195.0					7																	32209568		876	1991	2867	32176093	SO:0001630	splice_region_variant	5137	exon3			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396193.1:c.137-1G>A	7.37:g.32209568C>T		Somatic		Capture	Illumina HiSeq	Phase_I	32176093	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396193.1	37	CCDS55100.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.017436	0.93404	.	.	ENSG00000154678	ENST00000396193	T	0.75821	-0.97	5.61	5.61	0.85477	.	4.420600	0.00628	N	0.000476	T	0.81763	0.4891	N	0.19112	0.55	0.80722	D	1	D	0.54601	0.967	P	0.60789	0.879	T	0.68334	-0.5436	10	0.66056	D	0.02	.	19.2227	0.93805	0.0:1.0:0.0:0.0	.	46	E9PE92	.	Q	46	ENSP00000379496:R46Q	ENSP00000379496:R46Q	R	-	2	0	PDE1C	32176093	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	6.511000	0.73733	2.652000	0.90054	0.655000	0.94253	CGG		0.527	PDE1C-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215075.1		Missense_Mutation
AMPH	273	broad.mit.edu	37	7	38505102	38505102	+	Silent	SNP	G	G	A	rs146457438	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:38505102G>A	ENST00000356264.2	-	9	929	c.714C>T	c.(712-714)caC>caT	p.H238H	AMPH_ENST00000428293.2_Silent_p.H238H|AMPH_ENST00000325590.5_Silent_p.H238H	NM_001635.3	NP_001626.1	P49418	AMPH_HUMAN	amphiphysin	238	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				endocytosis (GO:0006897)|learning (GO:0007612)|synaptic transmission (GO:0007268)|synaptic vesicle endocytosis (GO:0048488)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|leading edge membrane (GO:0031256)|synaptic vesicle (GO:0008021)	phospholipid binding (GO:0005543)	p.H238H(1)|p.H238Q(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(12)|liver(3)|lung(27)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)	62						CCTTGTCGGCGTGCTGGTCAC	0.502													G|||	2	0.000399361	0.0	0.0	5008	,	,		15366	0.0		0.002	False		,,,				2504	0.0				p.H238H												.	.	2	Substitution - Missense(1)|Substitution - coding silent(1)	large_intestine(1)|lung(1)	c.C714T	7						.	G	,	2,4404		0,2,2201	75.0	59.0	64.0		714,714	-11.7	0.0	7	dbSNP_134	64	11,8585		0,11,4287	no	coding-synonymous,coding-synonymous	AMPH	NM_001635.3,NM_139316.2	,	0,13,6488	AA,AG,GG		0.128,0.0454,0.1	,	238/696,238/654	38505102	13,12989	2203	4298	6501	38471627	SO:0001819	synonymous_variant	273	exon9				CCDS5456.1, CCDS47574.1	7p14-p13	2007-06-19	2007-06-19		ENSG00000078053	ENSG00000078053			471	protein-coding gene	gene with protein product		600418	"""amphiphysin (Stiff-Mann syndrome with breast cancer 128kD autoantigen)"", ""amphiphysin (Stiff-Man syndrome with breast cancer 128kDa autoantigen)"""			8245793	Standard	NM_139316		Approved		uc003tgu.3	P49418	OTTHUMG00000023725	ENST00000356264.2:c.714C>T	7.37:g.38505102G>A		Somatic		Capture	Illumina HiSeq	Phase_I	38471627	NM_139316	A4D1X8|A4D1X9|O43538|Q75MJ8|Q75MK5|Q75MM3|Q8N4G0	Silent	SNP	ENST00000356264.2	37	CCDS5456.1																																																																																				0.502	AMPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000226953.2	NM_001635	
GLI3	2737	broad.mit.edu	37	7	42004063	42004063	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:42004063G>A	ENST00000395925.3	-	15	4692	c.4608C>T	c.(4606-4608)tcC>tcT	p.S1536S	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1536					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S1536S(1)		NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						TGGTGAGGCGGGAGGAGCTAT	0.582									Pallister-Hall syndrome;Greig Cephalopolysyndactyly																												p.S1536S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4608T	7						.						100.0	96.0	98.0					7																	42004063		2203	4300	6503	41970588	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.4608C>T	7.37:g.42004063G>A		Somatic		Capture	Illumina HiSeq	Phase_I	41970588	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																				0.582	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
STK17A	9263	broad.mit.edu	37	7	43663332	43663332	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:43663332C>T	ENST00000319357.5	+	6	944	c.765C>T	c.(763-765)gtC>gtT	p.V255V		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	255	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast apoptotic process (GO:2000271)|protein phosphorylation (GO:0006468)|regulation of reactive oxygen species metabolic process (GO:2000377)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.V255V(1)		autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	11						TAACATATGTCATGCTTACAG	0.289																																					p.V255V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C765T	7						.						95.0	94.0	94.0					7																	43663332		2201	4297	6498	43629857	SO:0001819	synonymous_variant	9263	exon6			AB011420	CCDS5470.1	7p13	2008-05-15	2007-02-12		ENSG00000164543	ENSG00000164543			11395	protein-coding gene	gene with protein product	"""death-associated protein kinase-related 1"""	604726	"""serine/threonine kinase 17a (apoptosis-inducing)"""			9786912	Standard	NM_004760		Approved	DRAK1	uc003tih.3	Q9UEE5	OTTHUMG00000022825	ENST00000319357.5:c.765C>T	7.37:g.43663332C>T		Somatic		Capture	Illumina HiSeq	Phase_I	43629857	NM_004760	A4D1V6|Q8IVC8	Silent	SNP	ENST00000319357.5	37	CCDS5470.1																																																																																				0.289	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760	
PGAM2	5224	broad.mit.edu	37	7	44104599	44104599	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:44104599C>T	ENST00000297283.3	-	2	484	c.427G>A	c.(427-429)Gca>Aca	p.A143T	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	143					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)	p.A143T(1)		large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						TTCAGGCCTGCGTACCGACGC	0.657																																					p.A143T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G427A	7						.						31.0	32.0	32.0					7																	44104599		2202	4300	6502	44071124	SO:0001583	missense	5224	exon2				CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.427G>A	7.37:g.44104599C>T	ENSP00000297283:p.Ala143Thr	Somatic		Capture	Illumina HiSeq	Phase_I	44071124	NM_000290		Missense_Mutation	SNP	ENST00000297283.3	37	CCDS34624.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352322	0.61293	.	.	ENSG00000164708	ENST00000297283	T	0.80393	-1.37	5.85	5.85	0.93711	Histidine phosphatase superfamily, clade-1 (2);	0.103768	0.64402	D	0.000004	T	0.77968	0.4210	M	0.76433	2.335	0.37632	D	0.921716	B	0.30824	0.296	B	0.22601	0.04	T	0.80165	-0.1496	10	0.66056	D	0.02	-9.1473	11.0551	0.47913	0.0:0.916:0.0:0.084	.	143	P15259	PGAM2_HUMAN	T	143	ENSP00000297283:A143T	ENSP00000297283:A143T	A	-	1	0	PGAM2	44071124	0.024000	0.19004	0.995000	0.50966	0.979000	0.70002	1.638000	0.37165	2.791000	0.96007	0.650000	0.86243	GCA		0.657	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
CAMK2B	816	broad.mit.edu	37	7	44282198	44282198	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:44282198C>T	ENST00000395749.2	-	9	733	c.657G>A	c.(655-657)caG>caA	p.Q219Q	CAMK2B_ENST00000502837.2_Silent_p.Q90Q|CAMK2B_ENST00000346990.4_Silent_p.Q219Q|CAMK2B_ENST00000440254.2_Silent_p.Q219Q|CAMK2B_ENST00000350811.3_Silent_p.Q219Q|CAMK2B_ENST00000353625.4_Silent_p.Q219Q|CAMK2B_ENST00000347193.4_Silent_p.Q219Q|CAMK2B_ENST00000258682.6_Silent_p.Q219Q|CAMK2B_ENST00000395747.2_Silent_p.Q219Q|CAMK2B_ENST00000358707.3_Silent_p.Q219Q|CAMK2B_ENST00000457475.1_Silent_p.Q219Q	NM_001220.4	NP_001211.3	Q13554	KCC2B_HUMAN	calcium/calmodulin-dependent protein kinase II beta	219	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of meiosis involved in egg activation (GO:0060466)|calcium ion transport (GO:0006816)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|inhibitory G-protein coupled receptor phosphorylation (GO:0002030)|interferon-gamma-mediated signaling pathway (GO:0060333)|neuromuscular process controlling balance (GO:0050885)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of neuron projection development (GO:0010976)|positive regulation of synapse maturation (GO:0090129)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of calcium ion transport (GO:0051924)|regulation of dendritic spine development (GO:0060998)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of skeletal muscle adaptation (GO:0014733)|regulation of synapse structural plasticity (GO:0051823)|regulation of synaptic transmission, cholinergic (GO:0032222)|response to cadmium ion (GO:0046686)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|protein homodimerization activity (GO:0042803)	p.Q219Q(1)		cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)	18						ACAGCTTGTGCTGGTCCTCGT	0.632																																					p.Q219Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G657A	7						.						62.0	48.0	53.0					7																	44282198		2203	4299	6502	44248723	SO:0001819	synonymous_variant	816	exon9			U50358	CCDS5483.1, CCDS5484.1, CCDS5485.1, CCDS5486.1, CCDS5487.1, CCDS5488.1, CCDS5489.1, CCDS43573.1	7p14.3-p14.1	2008-10-30	2008-10-30		ENSG00000058404	ENSG00000058404			1461	protein-coding gene	gene with protein product	"""CaM-kinase II beta chain"", ""calcium/calmodulin-dependent protein kinase type II beta chain"", ""CaM kinase II beta subunit"", ""proline rich calmodulin-dependent protein kinase"""	607707	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II beta"""	CAMKB			Standard	NM_172079		Approved	CAM2, CAMK2	uc003tkq.2	Q13554	OTTHUMG00000023491	ENST00000395749.2:c.657G>A	7.37:g.44282198C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44248723	NM_172078	A4D2K0|A4D2K1|A4D2K2|A4D2K3|A4D2K4|A4D2K5|A4D2K6|O95437|O95438|O95599|Q9UGH7|Q9UGH8|Q9UGH9|Q9UNX0|Q9UNX7|Q9UP00|Q9Y5N4|Q9Y6F4	Silent	SNP	ENST00000395749.2	37	CCDS5483.1																																																																																				0.632	CAMK2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251138.2	NM_172084	
NPC1L1	29881	broad.mit.edu	37	7	44578622	44578622	+	Silent	SNP	C	C	T	rs148541253	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:44578622C>T	ENST00000289547.4	-	2	1429	c.1374G>A	c.(1372-1374)tcG>tcA	p.S458S	NPC1L1_ENST00000423141.1_Silent_p.S458S|NPC1L1_ENST00000381160.3_Silent_p.S458S|NPC1L1_ENST00000546276.1_Silent_p.S458S	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	458					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)	p.S458S(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	GTGCTTCGGGCGACCATACCT	0.607																																					p.S458S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1374A	7						.	C	,	0,4406		0,0,2203	90.0	84.0	86.0		1374,1374	-4.4	0.3	7	dbSNP_134	86	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	NPC1L1	NM_001101648.1,NM_013389.2	,	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	,	458/1333,458/1360	44578622	4,13002	2203	4300	6503	44545147	SO:0001819	synonymous_variant	29881	exon2				CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1374G>A	7.37:g.44578622C>T		Somatic		Capture	Illumina HiSeq	Phase_I	44545147	NM_013389	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Silent	SNP	ENST00000289547.4	37	CCDS5491.1																																																																																				0.607	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
OGDH	4967	broad.mit.edu	37	7	44746932	44746932	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:44746932G>A	ENST00000222673.5	+	21	2783	c.2741G>A	c.(2740-2742)cGg>cAg	p.R914Q	OGDH_ENST00000447398.1_Missense_Mutation_p.R925Q|OGDH_ENST00000449767.1_Missense_Mutation_p.R910Q|OGDH_ENST00000439616.2_Missense_Mutation_p.R764Q|OGDH_ENST00000543843.1_Missense_Mutation_p.R865Q|OGDH_ENST00000444676.1_Missense_Mutation_p.R929Q	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	914					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)	p.R914Q(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	GACCTCACCCGGGAGCGCAAA	0.592																																					p.R914Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2741A	7						.						61.0	54.0	56.0					7																	44746932		2203	4300	6503	44713457	SO:0001583	missense	4967	exon21			D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.2741G>A	7.37:g.44746932G>A	ENSP00000222673:p.Arg914Gln	Somatic		Capture	Illumina HiSeq	Phase_I	44713457	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	G	16.16	3.043258	0.55003	.	.	ENSG00000105953	ENST00000439616;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	T;T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78;2.78	5.64	5.64	0.86602	.	0.113631	0.53938	D	0.000045	T	0.06917	0.0176	N	0.11341	0.13	0.42169	D	0.991632	B;B;B;B;B	0.15473	0.007;0.013;0.001;0.001;0.001	B;B;B;B;B	0.08055	0.001;0.003;0.001;0.002;0.001	T	0.28681	-1.0036	10	0.48119	T	0.1	-16.823	12.6508	0.56759	0.0766:0.0:0.9234:0.0	.	709;764;910;925;914	B4E3E9;E9PFG7;E9PBM1;E9PDF2;Q02218	.;.;.;.;ODO1_HUMAN	Q	764;910;925;929;914;865	ENSP00000398576:R764Q;ENSP00000392878:R910Q;ENSP00000388183:R925Q;ENSP00000414662:R929Q;ENSP00000222673:R914Q;ENSP00000443821:R865Q	ENSP00000222673:R914Q	R	+	2	0	OGDH	44713457	0.141000	0.22595	0.928000	0.36995	0.690000	0.40134	2.593000	0.46180	2.662000	0.90505	0.491000	0.48974	CGG		0.592	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
VWC2	375567	broad.mit.edu	37	7	49815053	49815053	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:49815053G>A	ENST00000340652.4	+	2	578	c.22G>A	c.(22-24)Gca>Aca	p.A8T		NM_198570.3	NP_940972.2	Q2TAL6	VWC2_HUMAN	von Willebrand factor C domain containing 2	8					negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of neuron differentiation (GO:0045666)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|basement membrane (GO:0005604)|cell junction (GO:0030054)|extracellular space (GO:0005615)|interstitial matrix (GO:0005614)|synapse (GO:0045202)		p.A8T(1)		cervix(1)|endometrium(2)|large_intestine(1)|lung(3)|prostate(1)	8						CACTGCGATGGCAGTTGGCGC	0.721																																					p.A8T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G22A	7						.						22.0	17.0	19.0					7																	49815053		2194	4293	6487	49785599	SO:0001583	missense	375567	exon2			AY358393	CCDS5508.1	7p12.3-p12.2	2007-07-19			ENSG00000188730	ENSG00000188730			30200	protein-coding gene	gene with protein product	"""brorin"", ""brain-specific chordin-like"""	611108				17400546	Standard	NM_198570		Approved	PSST739, UNQ739	uc003tot.1	Q2TAL6	OTTHUMG00000129265	ENST00000340652.4:c.22G>A	7.37:g.49815053G>A	ENSP00000341819:p.Ala8Thr	Somatic		Capture	Illumina HiSeq	Phase_I	49785599	NM_198570	Q6UXE2	Missense_Mutation	SNP	ENST00000340652.4	37	CCDS5508.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.105239	0.77096	.	.	ENSG00000188730	ENST00000340652	T	0.40476	1.03	4.68	3.78	0.43462	.	0.086753	0.47852	D	0.000201	T	0.25754	0.0627	N	0.08118	0	0.30338	N	0.786006	B	0.18863	0.031	B	0.14023	0.01	T	0.20874	-1.0262	10	0.87932	D	0	-13.4335	14.5858	0.68322	0.0:0.1476:0.8524:0.0	.	8	Q2TAL6	VWC2_HUMAN	T	8	ENSP00000341819:A8T	ENSP00000341819:A8T	A	+	1	0	VWC2	49785599	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.886000	0.63149	0.903000	0.36546	0.561000	0.74099	GCA		0.721	VWC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251375.2	NM_198570	
IKZF1	10320	broad.mit.edu	37	7	50444360	50444360	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:50444360G>T	ENST00000331340.3	+	4	445	c.290G>T	c.(289-291)aGg>aTg	p.R97M	IKZF1_ENST00000349824.4_Missense_Mutation_p.R97M|IKZF1_ENST00000439701.1_Missense_Mutation_p.R97M|IKZF1_ENST00000440768.2_Missense_Mutation_p.R97M|IKZF1_ENST00000438033.1_Intron|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000357364.4_Missense_Mutation_p.R97M|IKZF1_ENST00000343574.5_Intron|IKZF1_ENST00000359197.5_Missense_Mutation_p.R97M	NM_001220769.1|NM_001220772.1|NM_001220773.1|NM_001220775.1|NM_006060.4	NP_001207698.1|NP_001207701.1|NP_001207702.1|NP_001207704.1|NP_006051.1	Q13422	IKZF1_HUMAN	IKAROS family zinc finger 1 (Ikaros)	97					B cell differentiation (GO:0030183)|cell cycle (GO:0007049)|chromatin modification (GO:0016568)|forebrain development (GO:0030900)|lymph node development (GO:0048535)|mesoderm development (GO:0007498)|natural killer cell differentiation (GO:0001779)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Peyer's patch development (GO:0048541)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neutrophil differentiation (GO:0045660)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|T cell differentiation (GO:0030217)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(131)|p.R97M(1)		haematopoietic_and_lymphoid_tissue(275)|lung(1)	276	Glioma(55;0.08)|all_neural(89;0.245)	Acute lymphoblastic leukemia(4;7.29e-10)|all_hematologic(4;4.8e-07)				GGCTCCCACAGGGACCAAGGC	0.502			"""D,T"""	BCL6	"""ALL, DLBCL"""																																p.R97M			"""Rec,Dom"""	yes		7	7p12.2	10320	IKAROS family zinc finger 1		L	.	.	132	Unknown(131)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(131)|large_intestine(1)	c.G290T	7						.						94.0	100.0	98.0					7																	50444360		1939	4132	6071	50411854	SO:0001583	missense	10320	exon4			U40462	CCDS59055.1, CCDS69299.1, CCDS75596.1, CCDS75597.1	7p12.2	2014-06-12	2006-08-25	2006-08-25	ENSG00000185811	ENSG00000185811		"""Zinc fingers, C2H2-type"", ""IKAROS zinc fingers"""	13176	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 92"""	603023	"""zinc finger protein, subfamily 1A, 1 (Ikaros)"""	ZNFN1A1		1439790, 7935426	Standard	NM_006060		Approved	hIk-1, LyF-1, Hs.54452, IKAROS, PPP1R92	uc003tow.4	Q13422	OTTHUMG00000155907	ENST00000331340.3:c.290G>T	7.37:g.50444360G>T	ENSP00000331614:p.Arg97Met	Somatic		Capture	Illumina HiSeq	Phase_I	50411854	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Missense_Mutation	SNP	ENST00000331340.3	37		.	.	.	.	.	.	.	.	.	.	G	13.40	2.225437	0.39300	.	.	ENSG00000185811	ENST00000359197;ENST00000440768;ENST00000349824;ENST00000357364;ENST00000331340;ENST00000439701	T;T;T;T;T;T	0.07114	3.32;3.22;4.41;3.4;3.31;3.32	4.45	3.55	0.40652	.	0.621024	0.17431	N	0.174465	T	0.08268	0.0206	.	.	.	0.27199	N	0.960221	P;P	0.45348	0.771;0.856	B;B	0.42319	0.383;0.213	T	0.13737	-1.0498	9	0.51188	T	0.08	-5.1939	8.3225	0.32136	0.2428:0.0:0.7572:0.0	.	97;97	Q13422-7;Q13422	.;IKZF1_HUMAN	M	97	ENSP00000352123:R97M;ENSP00000401507:R97M;ENSP00000342485:R97M;ENSP00000349928:R97M;ENSP00000331614:R97M;ENSP00000413025:R97M	ENSP00000331614:R97M	R	+	2	0	IKZF1	50411854	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.898000	0.48672	2.204000	0.70986	0.313000	0.20887	AGG		0.502	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060	
ZNF680	340252	broad.mit.edu	37	7	63981569	63981569	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:63981569T>C	ENST00000309683.6	-	4	1714	c.1563A>G	c.(1561-1563)gaA>gaG	p.E521E	ZNF680_ENST00000476563.1_5'Flank	NM_178558.4	NP_848653.2	Q8NEM1	ZN680_HUMAN	zinc finger protein 680	521					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E521E(1)		breast(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	27		Lung NSC(55;0.118)|all_lung(88;0.243)				TGTCACATTTTTCAGGTTTGT	0.343																																					p.E521E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1563G	7						.						59.0	67.0	64.0					7																	63981569		2199	4299	6498	63619004	SO:0001819	synonymous_variant	340252	exon4			AK074911	CCDS34644.1, CCDS47594.1	7q11.21	2013-01-08			ENSG00000173041	ENSG00000173041		"""Zinc fingers, C2H2-type"", ""-"""	26897	protein-coding gene	gene with protein product	"""hypothetical protein FLJ90430"""					12477932	Standard	NM_178558		Approved	FLJ90430	uc003tta.2	Q8NEM1	OTTHUMG00000156542	ENST00000309683.6:c.1563A>G	7.37:g.63981569T>C		Somatic		Capture	Illumina HiSeq	Phase_I	63619004	NM_178558	B3KVJ4|Q6ZNF3|Q8NC79	Silent	SNP	ENST00000309683.6	37	CCDS34644.1																																																																																				0.343	ZNF680-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344568.1	NM_178558	
KCTD7	154881	broad.mit.edu	37	7	66104185	66104185	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:66104185G>A	ENST00000275532.3	+	4	1020	c.836G>A	c.(835-837)cGc>cAc	p.R279H	KCTD7_ENST00000443322.1_Missense_Mutation_p.R279H	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	279					cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.R279H(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						TACTGCAAGCGCCCCATCTAT	0.592																																					p.R279H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G836A	7						.						74.0	64.0	68.0					7																	66104185		2203	4300	6503	65741620	SO:0001583	missense	154881	exon4			AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.836G>A	7.37:g.66104185G>A	ENSP00000275532:p.Arg279His	Somatic		Capture	Illumina HiSeq	Phase_I	65741620	NM_001167961	A4D2M4|Q8IVR0	Missense_Mutation	SNP	ENST00000275532.3	37	CCDS5534.1	.	.	.	.	.	.	.	.	.	.	G	32	5.181838	0.94885	.	.	ENSG00000243335	ENST00000275532;ENST00000443322	T;T	0.68181	-0.24;-0.31	5.33	5.33	0.75918	.	.	.	.	.	T	0.76176	0.3951	L	0.40543	1.245	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.77405	-0.2600	9	0.56958	D	0.05	.	18.012	0.89226	0.0:0.0:1.0:0.0	.	279	Q96MP8	KCTD7_HUMAN	H	279	ENSP00000275532:R279H;ENSP00000411624:R279H	ENSP00000275532:R279H	R	+	2	0	KCTD7	65741620	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	9.152000	0.94680	2.485000	0.83878	0.655000	0.94253	CGC		0.592	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033	
AUTS2	26053	broad.mit.edu	37	7	70228209	70228209	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:70228209T>C	ENST00000342771.4	+	7	1417	c.1096T>C	c.(1096-1098)Tcc>Ccc	p.S366P	AUTS2_ENST00000406775.2_Missense_Mutation_p.S366P	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	366								p.S366P(1)		breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CAGGCCACAGTCCCCCACCCA	0.652																																					p.S366P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1096C	7						.						55.0	57.0	56.0					7																	70228209		2203	4299	6502	69866145	SO:0001583	missense	26053	exon7			AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1096T>C	7.37:g.70228209T>C	ENSP00000344087:p.Ser366Pro	Somatic		Capture	Illumina HiSeq	Phase_I	69866145	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Missense_Mutation	SNP	ENST00000342771.4	37	CCDS5539.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.82|16.82	3.228443|3.228443	0.58777|0.58777	.|.	.|.	ENSG00000158321|ENSG00000158321	ENST00000406775;ENST00000342771|ENST00000416482	T;T|.	0.32515|.	1.45;1.45|.	5.51|5.51	2.93|2.93	0.34026|0.34026	.|.	0.309437|.	0.36303|.	N|.	0.002666|.	T|T	0.40862|0.40862	0.1134|0.1134	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D;D|.	0.53151|.	0.958;0.958|.	P;P|.	0.47981|.	0.563;0.563|.	T|T	0.18650|0.18650	-1.0330|-1.0330	9|5	.|.	.|.	.|.	-22.4051|-22.4051	3.1737|3.1737	0.06561|0.06561	0.1409:0.074:0.1474:0.6378|0.1409:0.074:0.1474:0.6378	.|.	366;366|.	Q8WXX7-2;Q8WXX7|.	.;AUTS2_HUMAN|.	P|A	366|146	ENSP00000385263:S366P;ENSP00000344087:S366P|.	.|.	S|V	+|+	1|2	0|0	AUTS2|AUTS2	69866145|69866145	1.000000|1.000000	0.71417|0.71417	0.975000|0.975000	0.42487|0.42487	0.973000|0.973000	0.67179|0.67179	2.318000|2.318000	0.43779|0.43779	0.881000|0.881000	0.35993|0.35993	0.460000|0.460000	0.39030|0.39030	TCC|GTC		0.652	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
NSUN5	55695	broad.mit.edu	37	7	72718795	72718795	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:72718795G>A	ENST00000252594.6	-	6	719	c.704C>T	c.(703-705)gCc>gTc	p.A235V	NSUN5_ENST00000428206.1_Missense_Mutation_p.A197V|NSUN5_ENST00000310326.8_Missense_Mutation_p.A235V|NSUN5_ENST00000438747.2_Missense_Mutation_p.A235V			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	235	S-adenosyl-L-methionine binding.				rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GCCTGGGGCGGCACAGGCATC	0.602																																					p.A235V												.	.	0			c.C704T	7						.						36.0	38.0	37.0					7																	72718795		2203	4300	6503	72356731	SO:0001583	missense	55695	exon6			AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.704C>T	7.37:g.72718795G>A	ENSP00000252594:p.Ala235Val	None		Capture	Illumina HiSeq	Phase_I	72356731	NM_001168347	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.729241	0.89390	.	.	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	4.5	4.5	0.54988	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.000000	0.85682	D	0.000000	T	0.54983	0.1892	H	0.99435	4.565	0.80722	D	1	D;D;D;D	0.67145	0.992;0.979;0.994;0.996	P;P;P;P	0.60886	0.768;0.483;0.88;0.866	T	0.77913	-0.2410	10	0.87932	D	0	.	16.4401	0.83898	0.0:0.0:1.0:0.0	.	235;197;235;235	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	V	197;235;235;235	ENSP00000393081:A197V;ENSP00000252594:A235V;ENSP00000388464:A235V;ENSP00000309126:A235V	ENSP00000252594:A235V	A	-	2	0	NSUN5	72356731	1.000000	0.71417	0.999000	0.59377	0.600000	0.36913	7.290000	0.78711	2.347000	0.79759	0.485000	0.47835	GCC		0.602	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
BAZ1B	9031	broad.mit.edu	37	7	72880669	72880669	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:72880669C>T	ENST00000339594.4	-	10	3267	c.2929G>A	c.(2929-2931)Gtt>Att	p.V977I	BAZ1B_ENST00000404251.1_Missense_Mutation_p.V977I	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	977					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.V977I(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TCTACAGCAACTTCTGTTGCT	0.363																																					p.V977I	Esophageal Squamous(112;1167 1561 21085 43672 48228)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2929A	7						.						362.0	298.0	319.0					7																	72880669		2203	4300	6503	72518605	SO:0001583	missense	9031	exon10			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.2929G>A	7.37:g.72880669C>T	ENSP00000342434:p.Val977Ile	Somatic		Capture	Illumina HiSeq	Phase_I	72518605	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	C	9.147	1.015418	0.19355	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.58358	0.34;0.34	5.48	-4.95	0.03048	.	1.135050	0.06381	N	0.715260	T	0.26231	0.0640	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21280	-1.0250	10	0.33141	T	0.24	-1.2866	13.2828	0.60226	0.0:0.6669:0.1101:0.223	.	977	Q9UIG0	BAZ1B_HUMAN	I	977	ENSP00000342434:V977I;ENSP00000385442:V977I	ENSP00000342434:V977I	V	-	1	0	BAZ1B	72518605	0.062000	0.20869	0.010000	0.14722	0.936000	0.57629	-0.128000	0.10531	-0.768000	0.04626	-0.471000	0.05019	GTT		0.363	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
BAZ1B	9031	broad.mit.edu	37	7	72892669	72892669	+	Silent	SNP	C	C	T	rs368146268		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:72892669C>T	ENST00000339594.4	-	7	1460	c.1122G>A	c.(1120-1122)tcG>tcA	p.S374S	BAZ1B_ENST00000404251.1_Silent_p.S374S	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	374	Lys-rich.				cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)	p.S374S(1)		NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				GCTTATTGGGCGACATCATCT	0.438																																					p.S374S	Esophageal Squamous(112;1167 1561 21085 43672 48228)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1122A	7						.	C		2,4404	4.2+/-10.8	0,2,2201	114.0	100.0	105.0		1122	-5.6	1.0	7		105	0,8600		0,0,4300	no	coding-synonymous	BAZ1B	NM_032408.3		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		374/1484	72892669	2,13004	2203	4300	6503	72530605	SO:0001819	synonymous_variant	9031	exon7			AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.1122G>A	7.37:g.72892669C>T		Somatic		Capture	Illumina HiSeq	Phase_I	72530605	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																				0.438	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
LAT2	7462	broad.mit.edu	37	7	73634320	73634320	+	Missense_Mutation	SNP	C	C	T	rs369645558		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:73634320C>T	ENST00000460943.1	+	6	1098	c.209C>T	c.(208-210)gCg>gTg	p.A70V	LAT2_ENST00000398475.1_Missense_Mutation_p.A70V|LAT2_ENST00000344995.5_Missense_Mutation_p.A70V|LAT2_ENST00000275635.7_Missense_Mutation_p.A70V	NM_032464.2	NP_115853.2	Q9UHI5	LAT2_HUMAN	linker for activation of T cells family, member 2	0					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)	p.A70V(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6					L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	GGACCCCTGGCGGACATGGCA	0.632																																					p.A70V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C209T	7						.						35.0	39.0	38.0					7																	73634320		1934	4126	6060	73272256	SO:0001583	missense	7462	exon6			AF257135	CCDS5566.2	7q11.23	2011-11-01	2005-04-26	2005-04-26	ENSG00000086730	ENSG00000086730			12749	protein-coding gene	gene with protein product	"""linker for activation of B cells"", ""non-T cell activation linker"", ""linker for activation of T cells, transmembrane adaptor 2"""	605719	"""Williams-Beuren syndrome chromosome region 5"""	WBSCR15, WBSCR5		8812460, 12514734	Standard	NM_032464		Approved	WSCR5, HSPC046, LAB, NTAL	uc003uai.3	Q9GZY6	OTTHUMG00000130151	ENST00000460943.1:c.209C>T	7.37:g.73634320C>T	ENSP00000420494:p.Ala70Val	Somatic		Capture	Illumina HiSeq	Phase_I	73272256	NM_032463	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Missense_Mutation	SNP	ENST00000460943.1	37	CCDS5566.2	.	.	.	.	.	.	.	.	.	.	c	2.026	-0.423537	0.04734	.	.	ENSG00000086730	ENST00000344995;ENST00000460943;ENST00000475494;ENST00000398475;ENST00000275635;ENST00000470709	T;T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69;3.69	3.17	-6.34	0.01982	.	2.801720	0.01464	N	0.016007	T	0.02267	0.0070	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39210	-0.9625	10	0.36615	T	0.2	-0.8287	3.4085	0.07350	0.2339:0.4702:0.1326:0.1633	.	70	Q9GZY6	NTAL_HUMAN	V	70;70;70;70;70;60	ENSP00000344881:A70V;ENSP00000420494:A70V;ENSP00000417533:A70V;ENSP00000381492:A70V;ENSP00000275635:A70V;ENSP00000419150:A60V	ENSP00000275635:A70V	A	+	2	0	LAT2	73272256	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.487000	0.00977	-2.814000	0.00346	-2.367000	0.00236	GCG		0.632	LAT2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277062.1		
NCF1	653361	broad.mit.edu	37	7	74193734	74193734	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:74193734C>T	ENST00000289473.4	+	4	431	c.361C>T	c.(361-363)Cgc>Tgc	p.R121C	NCF1_ENST00000443956.3_3'UTR	NM_000265.4	NP_000256.4	P14598	NCF1_HUMAN	neutrophil cytosolic factor 1	121	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular defense response (GO:0006968)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|leukotriene metabolic process (GO:0006691)|negative regulation of smooth muscle contraction (GO:0045986)|neutrophil mediated killing of fungus (GO:0070947)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|protein targeting to membrane (GO:0006612)|respiratory burst (GO:0045730)|respiratory burst involved in defense response (GO:0002679)|response to yeast (GO:0001878)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cytosol (GO:0005829)|dendrite (GO:0030425)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagolysosome (GO:0032010)|rough endoplasmic reticulum (GO:0005791)	electron carrier activity (GO:0009055)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)	p.R121C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|skin(3)	10					Dextromethorphan(DB00514)	CTTCAAGGTGCGCCCTGATGA	0.597																																					p.R121C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C361T	7						.						46.0	36.0	40.0					7																	74193734		2196	4283	6479	73831670	SO:0001583	missense	653361	exon4			M25665	CCDS34657.1	7q11.23	2014-09-17	2008-07-31		ENSG00000158517	ENSG00000158517			7660	protein-coding gene	gene with protein product	"""NADPH oxidase organizer 2"", ""chronic granulomatous disease, autosomal 1"""	608512	"""neutrophil cytosolic factor 1 (47kD, chronic granulomatous disease, autosomal 1)"""				Standard	NM_000265		Approved	p47phox, NOXO2, NCF1A, SH3PXD1A	uc022aft.1	P14598	OTTHUMG00000149965	ENST00000289473.4:c.361C>T	7.37:g.74193734C>T	ENSP00000289473:p.Arg121Cys	Somatic		Capture	Illumina HiSeq	Phase_I	73831670	NM_000265	A6NEH2|A8K7S9|O43842|Q2PP07|Q53FR5|Q9BU90|Q9BXI7|Q9BXI8|Q9UDV9|Q9UMU2	Missense_Mutation	SNP	ENST00000289473.4	37	CCDS34657.1	.	.	.	.	.	.	.	.	.	.	c	16.42	3.118318	0.56505	.	.	ENSG00000158517	ENST00000289473;ENST00000433458;ENST00000471594;ENST00000442021	T;T;T	0.70282	-0.47;-0.47;-0.47	3.48	2.5	0.30297	Phox homologous domain (4);	0.114786	0.56097	D	0.000040	D	0.83778	0.5328	M	0.88704	2.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.993;0.994	D	0.85789	0.1366	10	0.87932	D	0	-24.0235	10.0367	0.42133	0.3357:0.6643:0.0:0.0	.	121;121	P14598-2;P14598	.;NCF1_HUMAN	C	121;121;95;128	ENSP00000289473:R121C;ENSP00000392870:R121C;ENSP00000401935:R128C	ENSP00000289473:R121C	R	+	1	0	NCF1	73831670	0.963000	0.33076	0.992000	0.48379	0.940000	0.58332	1.549000	0.36212	1.690000	0.51089	0.442000	0.29010	CGC		0.597	NCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314560.1	NM_000265	
CCDC146	57639	broad.mit.edu	37	7	76916213	76916213	+	Silent	SNP	C	C	T	rs139431413	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:76916213C>T	ENST00000285871.4	+	16	2374	c.2247C>T	c.(2245-2247)acC>acT	p.T749T	CCDC146_ENST00000415740.2_3'UTR|CCDC146_ENST00000431197.1_Silent_p.T463T	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	749								p.T749T(1)		breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				AAGATCTGACCGAAAAAGAAA	0.388													C|||	2	0.000399361	0.0	0.0014	5008	,	,		20057	0.001		0.0	False		,,,				2504	0.0				p.T749T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2247T	7						.	C		1,4405	2.1+/-5.4	0,1,2202	94.0	100.0	98.0		2247	-7.8	0.3	7	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous	CCDC146	NM_020879.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		749/956	76916213	1,13005	2203	4300	6503	76754149	SO:0001819	synonymous_variant	57639	exon16			BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.2247C>T	7.37:g.76916213C>T		Somatic		Capture	Illumina HiSeq	Phase_I	76754149	NM_020879	A8K8X6|Q9P223	Silent	SNP	ENST00000285871.4	37	CCDS34671.1																																																																																				0.388	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
CFAP69	79846	broad.mit.edu	37	7	89874766	89874766	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:89874766G>A	ENST00000389297.4	+	1	279	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	C7orf63_ENST00000316089.8_Missense_Mutation_p.A10T|C7orf63_ENST00000463311.1_3'UTR|C7orf63_ENST00000497910.1_Missense_Mutation_p.A10T	NM_001039706.2|NM_001160138.1	NP_001034795.2|NP_001153610.1	A5D8W1	CG063_HUMAN		10								p.A10T(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(14)|ovary(1)|prostate(3)	37						CGGGGCGACCGCCGAGGCCCA	0.657																																					p.A10T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G28A	7						.						65.0	73.0	70.0					7																	89874766		1917	4124	6041	89712702	SO:0001583	missense	79846	exon1																														ENST00000389297.4:c.28G>A	7.37:g.89874766G>A	ENSP00000373948:p.Ala10Thr	Somatic		Capture	Illumina HiSeq	Phase_I	89712702	NM_001160138	A3KMP9|B4DYW6|B4DZP7|B9EIM7|Q6V705|Q8IY89|Q9H7C2	Missense_Mutation	SNP	ENST00000389297.4	37	CCDS43613.2	.	.	.	.	.	.	.	.	.	.	G	19.39	3.819241	0.71028	.	.	ENSG00000105792	ENST00000389297;ENST00000316089;ENST00000497910	T;T;T	0.16743	2.32;2.32;2.32	4.44	3.56	0.40772	.	.	.	.	.	T	0.11750	0.0286	L	0.31294	0.92	0.18873	N	0.999985	B;B;B	0.26041	0.01;0.01;0.14	B;B;B	0.15484	0.005;0.005;0.013	T	0.20009	-1.0288	9	0.33141	T	0.24	-0.0018	8.5044	0.33179	0.107:0.0:0.893:0.0	.	10;10;10	A5D8W1-5;A5D8W1;A5D8W1-4	.;CG063_HUMAN;.	T	10	ENSP00000373948:A10T;ENSP00000321753:A10T;ENSP00000419549:A10T	ENSP00000321753:A10T	A	+	1	0	C7orf63	89712702	0.022000	0.18835	0.078000	0.20375	0.016000	0.09150	0.411000	0.21115	1.211000	0.43351	0.655000	0.94253	GCC		0.657	C7orf63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139891.4		
AKAP9	10142	broad.mit.edu	37	7	91630771	91630771	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:91630771G>A	ENST00000359028.2	+	9	1801	c.1576G>A	c.(1576-1578)Gaa>Aaa	p.E526K	AKAP9_ENST00000358100.2_Missense_Mutation_p.E526K|AKAP9_ENST00000356239.3_Missense_Mutation_p.E514K			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	526	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.E514K(1)|p.E526K(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AAAACTCAAGGAAGAACTAGG	0.333			T	BRAF	papillary thyroid																																p.E514K			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1540A	7						.						61.0	68.0	66.0					7																	91630771		2200	4298	6498	91468707	SO:0001583	missense	10142	exon8			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.1576G>A	7.37:g.91630771G>A	ENSP00000351922:p.Glu526Lys	Somatic		Capture	Illumina HiSeq	Phase_I	91468707	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	G	9.541	1.113305	0.20795	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.41065	1.01;1.01;1.01	5.62	3.71	0.42584	.	0.533483	0.15801	N	0.243949	T	0.41213	0.1149	L	0.43152	1.355	0.23577	N	0.997379	B;P;B;P	0.38129	0.361;0.493;0.006;0.619	B;B;B;P	0.44359	0.046;0.099;0.003;0.447	T	0.21245	-1.0251	10	0.32370	T	0.25	.	11.4923	0.50387	0.0724:0.1946:0.733:0.0	.	526;514;514;526	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	K	514;526;526;526;526	ENSP00000348573:E514K;ENSP00000351922:E526K;ENSP00000350813:E526K	ENSP00000348573:E514K	E	+	1	0	AKAP9	91468707	1.000000	0.71417	0.996000	0.52242	0.826000	0.46750	2.852000	0.48310	1.521000	0.48983	0.655000	0.94253	GAA		0.333	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
ARPC1A	10552	broad.mit.edu	37	7	98957171	98957171	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:98957171C>A	ENST00000262942.5	+	8	917	c.793C>A	c.(793-795)Cat>Aat	p.H265N	ARPC1A_ENST00000432884.2_Missense_Mutation_p.H218N|ARPC1A_ENST00000471960.1_3'UTR	NM_001190996.1|NM_006409.3	NP_001177925.1|NP_006400.2	Q92747	ARC1A_HUMAN	actin related protein 2/3 complex, subunit 1A, 41kDa	265					actin cytoskeleton organization (GO:0030036)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of actin filament polymerization (GO:0030833)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	actin binding (GO:0003779)	p.H265N(1)		endometrium(3)|large_intestine(5)|liver(2)|lung(7)|ovary(1)|prostate(1)	19	all_cancers(62;4.46e-09)|all_epithelial(64;3.44e-10)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0258)		STAD - Stomach adenocarcinoma(171;0.215)			GTTTCAGGGCCATGACTGCTG	0.527																																					p.H251N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C751A	7						.						100.0	65.0	77.0					7																	98957171		2203	4300	6503	98795107	SO:0001583	missense	10552	exon8			Y08999	CCDS5660.1	7q22.1	2013-03-14	2002-08-29		ENSG00000241685	ENSG00000241685		"""Actin related protein 2/3 complex subunits"", ""WD repeat domain containing"""	703	protein-coding gene	gene with protein product	"""actin binding protein (Schizosaccharomyces pombe sop2-like)"", ""SOP2-like protein"""	604220	"""actin related protein 2/3 complex, subunit 1A (41 kD)"""			8978670, 9230079	Standard	NM_006409		Approved	SOP2Hs, SOP2L, Arc40	uc003upx.2	Q92747	OTTHUMG00000154553	ENST00000262942.5:c.793C>A	7.37:g.98957171C>A	ENSP00000262942:p.His265Asn	Somatic		Capture	Illumina HiSeq	Phase_I	98795107	NM_001190996	A4D276|B4DLQ7|D6W5S1|Q7Z5U8|Q86WU5|Q8IXQ0	Missense_Mutation	SNP	ENST00000262942.5	37	CCDS5660.1	.	.	.	.	.	.	.	.	.	.	C	31	5.088841	0.94100	.	.	ENSG00000241685	ENST00000432884;ENST00000262942	T;T	0.64618	-0.11;-0.11	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.83133	0.5188	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;0.991	D;P	0.76071	0.987;0.804	D	0.84807	0.0788	10	0.54805	T	0.06	.	19.7468	0.96255	0.0:1.0:0.0:0.0	.	260;265	Q53GB6;Q92747	.;ARC1A_HUMAN	N	218;265	ENSP00000408578:H218N;ENSP00000262942:H265N	ENSP00000262942:H265N	H	+	1	0	ARPC1A	98795107	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.797000	0.85911	2.731000	0.93534	0.650000	0.86243	CAT		0.527	ARPC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335908.1	NM_006409	
ZNF655	79027	broad.mit.edu	37	7	99170244	99170244	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:99170244C>A	ENST00000394163.2	+	3	696	c.513C>A	c.(511-513)gcC>gcA	p.A171A	ZNF655_ENST00000424881.1_Silent_p.A206A|ZNF655_ENST00000493277.1_Silent_p.A206A|ZNF655_ENST00000252713.4_Silent_p.A171A|ZNF655_ENST00000419215.2_3'UTR|GS1-259H13.10_ENST00000486324.1_Intron|ZNF655_ENST00000425063.1_3'UTR|GS1-259H13.10_ENST00000455905.1_Intron	NM_001009960.1|NM_138494.2	NP_001009960.1|NP_612503.1	Q8N720	ZN655_HUMAN	zinc finger protein 655	171					negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A171A(1)		NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	16	all_epithelial(64;3.19e-09)|Lung NSC(181;0.0066)|all_lung(186;0.011)|Esophageal squamous(72;0.0166)					AGAATTCAGCCTCTGGTAAAC	0.383																																					p.A206A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C618A	7						.						57.0	57.0	57.0					7																	99170244		2203	4300	6503	99008180	SO:0001819	synonymous_variant	79027	exon4			AY099353	CCDS5669.1, CCDS5670.1, CCDS34695.1, CCDS47655.1	7q22.1	2013-01-08			ENSG00000197343	ENSG00000197343		"""Zinc fingers, C2H2-type"", ""-"""	30899	protein-coding gene	gene with protein product						11179890, 15558030	Standard	NM_001083956		Approved	VIK-1, VIK	uc010lgc.3	Q8N720	OTTHUMG00000156637	ENST00000394163.2:c.513C>A	7.37:g.99170244C>A		Somatic		Capture	Illumina HiSeq	Phase_I	99008180	NM_001083956	A4D291|A6NGD3|B4E3M4|B7Z9Q9|D6W5T4|Q8IV00|Q8TA89|Q96EZ3|Q9BQ85	Silent	SNP	ENST00000394163.2	37	CCDS5669.1																																																																																				0.383	ZNF655-009	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000344929.1	NM_138494	
COPS6	10980	broad.mit.edu	37	7	99686655	99686655	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:99686655C>T	ENST00000303904.3	+	1	79	c.42C>T	c.(40-42)acC>acT	p.T14T	COPS6_ENST00000418625.1_Silent_p.T14T	NM_006833.4	NP_006824.2	Q7L5N1	CSN6_HUMAN	COP9 signalosome subunit 6	14					cullin deneddylation (GO:0010388)|viral process (GO:0016032)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)		p.T14T(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(2)|prostate(1)|stomach(1)	12	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)		STAD - Stomach adenocarcinoma(171;0.129)			CGAACGGGACCGGAGGAAGCA	0.716																																					p.T14T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C42T	7						.						24.0	23.0	23.0					7																	99686655		1849	3557	5406	99524591	SO:0001819	synonymous_variant	10980	exon1			BC002520	CCDS5682.1	7q22.1	2013-03-14	2013-03-14		ENSG00000168090	ENSG00000168090			21749	protein-coding gene	gene with protein product	"""COP9 subunit 6 (MOV34 homolog, 34 kD)"""	614729	"""COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)"""			12477932	Standard	NM_006833		Approved	MOV34-34KD, CSN6	uc003usu.3	Q7L5N1	OTTHUMG00000154632	ENST00000303904.3:c.42C>T	7.37:g.99686655C>T		Somatic		Capture	Illumina HiSeq	Phase_I	99524591	NM_006833	A4D2A3|O15387	Silent	SNP	ENST00000303904.3	37	CCDS5682.1																																																																																				0.716	COPS6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000336412.3	NM_006833	
AGFG2	3268	broad.mit.edu	37	7	100160278	100160278	+	Missense_Mutation	SNP	G	G	A	rs566927357	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100160278G>A	ENST00000300176.4	+	8	1182	c.1060G>A	c.(1060-1062)Ggc>Agc	p.G354S	AGFG2_ENST00000262935.4_3'UTR|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	354					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)	p.G354S(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CGGCGGCGGCGGCAGCAGCAC	0.657													G|||	3	0.000599042	0.0	0.0	5008	,	,		14259	0.003		0.0	False		,,,				2504	0.0				p.G354S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1060A	7						.						23.0	26.0	25.0					7																	100160278		2203	4300	6503	99998214	SO:0001583	missense	3268	exon8			AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.1060G>A	7.37:g.100160278G>A	ENSP00000300176:p.Gly354Ser	Somatic		Capture	Illumina HiSeq	Phase_I	99998214	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	.	.	.	.	.	.	.	.	.	.	G	2.126	-0.400376	0.04865	.	.	ENSG00000106351	ENST00000300176	T	0.21932	1.98	0.377	0.377	0.16198	.	1.017170	0.07951	U	0.980826	T	0.11922	0.0290	L	0.31207	0.915	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.35773	-0.9775	9	0.02654	T	1	-17.8087	.	.	.	.	354	O95081	AGFG2_HUMAN	S	354	ENSP00000300176:G354S	ENSP00000300176:G354S	G	+	1	0	AGFG2	99998214	0.029000	0.19370	0.006000	0.13384	0.379000	0.30106	0.000000	0.12993	0.488000	0.27723	0.271000	0.19318	GGC		0.657	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
PCOLCE	5118	broad.mit.edu	37	7	100202722	100202722	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:100202722delT	ENST00000223061.5	+	4	752	c.472delT	c.(472-474)tttfs	p.F158fs	PCOLCE-AS1_ENST00000442166.2_RNA|PCOLCE-AS1_ENST00000544873.1_RNA|PCOLCE-AS1_ENST00000446022.1_RNA	NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	158					multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)	p.C159fs*12(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					AGAGCACCAATTTTGCGGGGG	0.677																																					p.F158fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.472delT	7						.						12.0	15.0	14.0					7																	100202722		2193	4290	6483	100040658	SO:0001589	frameshift_variant	5118	exon4			L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.472delT	7.37:g.100202722delT	ENSP00000223061:p.Phe158fs	Somatic		Capture	Illumina HiSeq	Phase_I	100040658	NM_002593	B2R9E1|O14550	Frame_Shift_Del	DEL	ENST00000223061.5	37	CCDS5700.1																																																																																				0.677	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593	
SLC26A5	375611	broad.mit.edu	37	7	103061308	103061308	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:103061308delT	ENST00000306312.3	-	4	430	c.169delA	c.(169-171)atafs	p.I57fs	SLC26A5_ENST00000393730.1_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000393723.1_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000393727.1_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000393729.1_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000356767.4_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000393735.2_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000354356.4_5'UTR|SLC26A5_ENST00000339444.6_Frame_Shift_Del_p.I57fs|SLC26A5_ENST00000432958.2_Frame_Shift_Del_p.I57fs	NM_198999.2	NP_945350.1	P58743	S26A5_HUMAN	solute carrier family 26 (anion exchanger), member 5	57					regulation of cell shape (GO:0008360)|regulation of membrane potential (GO:0042391)|sensory perception of sound (GO:0007605)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)	secondary active sulfate transmembrane transporter activity (GO:0008271)	p.I57fs*1(1)		endometrium(5)|kidney(2)|large_intestine(9)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)	43						ATATTTCTTATTTTTTTAGGA	0.353																																					p.I57X												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.169delA	7						.						71.0	74.0	73.0					7																	103061308		2203	4300	6503	102848544	SO:0001589	frameshift_variant	375611	exon4			AC005064	CCDS5733.1, CCDS43630.1, CCDS55150.1, CCDS5732.1, CCDS43629.1	7q22	2013-07-18	2013-07-18	2005-09-13	ENSG00000170615	ENSG00000170615		"""Solute carriers"""	9359	protein-coding gene	gene with protein product	"""deafness, neurosensory, autosomal recessive, 61"""	604943	"""prestin (motor protein)"""	PRES		10821263	Standard	NM_206883		Approved	DFNB61	uc003vbz.3	P58743	OTTHUMG00000149911	ENST00000306312.3:c.169delA	7.37:g.103061308delT	ENSP00000304783:p.Ile57fs	Somatic		Capture	Illumina HiSeq	Phase_I	102848544	NM_206884	Q496J2|Q7Z7F3|Q86UF8|Q86UF9|Q86UG0	Frame_Shift_Del	DEL	ENST00000306312.3	37	CCDS5733.1																																																																																				0.353	SLC26A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313860.1	NM_198999	
AASS	10157	broad.mit.edu	37	7	121726174	121726174	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:121726174delA	ENST00000393376.1	-	18	2171	c.2076delT	c.(2074-2076)tttfs	p.F692fs	AASS_ENST00000473553.1_5'UTR|AASS_ENST00000417368.2_Frame_Shift_Del_p.F692fs			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	692	Saccharopine dehydrogenase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.P693fs*3(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTAATCCTGGAAAAAAATCCA	0.443																																					p.F692fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2076delT	7						.						81.0	79.0	80.0					7																	121726174		2203	4300	6503	121513410	SO:0001589	frameshift_variant	10157	exon19			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.2076delT	7.37:g.121726174delA	ENSP00000377040:p.Phe692fs	Somatic		Capture	Illumina HiSeq	Phase_I	121513410	NM_005763	O95462	Frame_Shift_Del	DEL	ENST00000393376.1	37	CCDS5783.1																																																																																				0.443	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763	
NOBOX	135935	broad.mit.edu	37	7	144096190	144096190	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:144096190delG	ENST00000467773.1	-	8	1321	c.1322delC	c.(1321-1323)ccafs	p.P441fs	NOBOX_ENST00000223140.5_Frame_Shift_Del_p.P324fs|NOBOX_ENST00000483238.1_Frame_Shift_Del_p.P409fs	NM_001080413.3	NP_001073882.3	O60393	NOBOX_HUMAN	NOBOX oogenesis homeobox	441	Pro-rich.				oogenesis (GO:0048477)|ovarian follicle development (GO:0001541)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.P409fs*25(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)	26	Melanoma(164;0.14)					GCTGAAGAGTGGGGGGGTCAC	0.622																																					p.P324fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.971delC	7						.						12.0	13.0	13.0					7																	144096190		1790	3873	5663	143727123	SO:0001589	frameshift_variant	135935	exon6					7q35	2011-06-20			ENSG00000106410	ENSG00000106410		"""Homeoboxes / PRD class"""	22448	protein-coding gene	gene with protein product	"""newborn ovary homeobox-encoding gene"""	610934				11804785, 16597639	Standard	NM_001080413		Approved	OG2, Og2x	uc022aoj.1	O60393	OTTHUMG00000158051	ENST00000467773.1:c.1322delC	7.37:g.144096190delG	ENSP00000419457:p.Pro441fs	Somatic		Capture	Illumina HiSeq	Phase_I	143727123	NM_001080413	A6NCD3|A8MZN5	Frame_Shift_Del	DEL	ENST00000467773.1	37																																																																																					0.622	NOBOX-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000350095.1	XM_001134420	
CHPF2	54480	broad.mit.edu	37	7	150932152	150932153	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:150932152_150932153delAG	ENST00000035307.2	+	2	1795_1796	c.282_283delAG	c.(280-285)acagagfs	p.E95fs	CHPF2_ENST00000495645.1_Frame_Shift_Del_p.E87fs	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	95					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)	p.E95fs*5(1)		breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						ACATCCAGACAGAGCTGGGCTC	0.564																																					p.94_95del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.282_283del	7						.																																			150563086	SO:0001589	frameshift_variant	54480	exon2			AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.282_283delAG	7.37:g.150932154_150932155delAG	ENSP00000035307:p.Glu95fs	Somatic		Capture	Illumina HiSeq	Phase_I	150563085	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Frame_Shift_Del	DEL	ENST00000035307.2	37	CCDS34779.1																																																																																				0.564	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
NUB1	51667	broad.mit.edu	37	7	151046311	151046311	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:151046311A>G	ENST00000355851.4	+	3	347	c.270A>G	c.(268-270)ccA>ccG	p.P90P	NUB1_ENST00000568733.1_Silent_p.P114P|NUB1_ENST00000413040.2_Silent_p.P114P|NUB1_ENST00000566856.1_Silent_p.P90P	NM_001243351.1	NP_001230280.1	Q9Y5A7	NUB1_HUMAN	negative regulator of ubiquitin-like proteins 1	90					positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein ubiquitination (GO:0016567)|response to interferon-gamma (GO:0034341)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)		p.P90P(1)		endometrium(1)|large_intestine(7)|lung(3)	11			OV - Ovarian serous cystadenocarcinoma(82;0.00569)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		TGTTTTTACCACCAAGACTAA	0.353																																					p.P90P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A270G	7						.						106.0	104.0	104.0					7																	151046311		1837	4090	5927	150677244	SO:0001819	synonymous_variant	51667	exon3			AF300717	CCDS47751.1, CCDS47751.2, CCDS59089.1	7q36	2006-07-27			ENSG00000013374	ENSG00000013374			17623	protein-coding gene	gene with protein product	"""NEDD8 ultimate buster-1"""	607981				10508479, 11259415	Standard	NM_001243351		Approved	BS4, NYREN18	uc003wjx.3	Q9Y5A7	OTTHUMG00000157365	ENST00000355851.4:c.270A>G	7.37:g.151046311A>G		Somatic		Capture	Illumina HiSeq	Phase_I	150677244	NM_016118	O95422|Q75MR9|Q8IX22|Q9BXR2	Silent	SNP	ENST00000355851.4	37																																																																																					0.353	NUB1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_016118	
GALNTL5	168391	broad.mit.edu	37	7	151684323	151684324	+	Frame_Shift_Del	DEL	GG	GG	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GG	GG	GG	-	GG	GG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:151684323_151684324delGG	ENST00000392800.2	+	5	869_870	c.615_616delGG	c.(613-618)gaggggfs	p.G206fs	GALNTL5_ENST00000431418.2_Frame_Shift_Del_p.G206fs	NM_145292.3	NP_660335.2	Q7Z4T8	GLTL5_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 5	206	Catalytic subdomain A.				spermatid development (GO:0007286)	endosome (GO:0005768)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)	p.G206fs*25(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(11)|ovary(2)|prostate(2)|skin(3)	32	all_neural(206;0.187)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00427)	UCEC - Uterine corpus endometrioid carcinoma (81;0.18)|BRCA - Breast invasive adenocarcinoma(188;0.166)		AAAAGAGAGAGGGGCTGATTCG	0.426																																					p.205_206del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.615_616del	7						.																																			151315257	SO:0001589	frameshift_variant	168391	exon5			AF440400	CCDS5929.1	7q36.2	2014-03-13	2014-03-13	2004-07-28	ENSG00000106648	ENSG00000106648		"""Glycosyltransferase family 2 domain containing"""	21725	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 5"""	615133	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 15"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 5"""	GALNT15			Standard	NM_145292		Approved	GalNAc-T5L	uc003wkp.3	Q7Z4T8	OTTHUMG00000157306	ENST00000392800.2:c.615_616delGG	7.37:g.151684325_151684326delGG	ENSP00000376548:p.Gly206fs	Somatic		Capture	Illumina HiSeq	Phase_I	151315256	NM_145292	Q75KN2|Q75MD3|Q8NCV4|Q8WW05|Q9UDR9	Frame_Shift_Del	DEL	ENST00000392800.2	37	CCDS5929.1																																																																																				0.426	GALNTL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348395.1	NM_145292	
GPR141	353345	broad.mit.edu	37	7	37780680	37780680	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:37780680delT	ENST00000447769.1	+	4	974	c.685delT	c.(685-687)tttfs	p.F230fs	GPR141_ENST00000334425.1_Frame_Shift_Del_p.F230fs|EPDR1_ENST00000476620.1_Intron|GPR141_ENST00000461610.1_Intron			Q7Z602	GP141_HUMAN	G protein-coupled receptor 141	230						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)	p.F230fs*2(1)		NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(13)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GAAAAACCTATTTTTTATAGG	0.433																																					p.F229fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.685delT	7						.						149.0	152.0	151.0					7																	37780680		2203	4300	6503	37747205	SO:0001589	frameshift_variant	353345	exon1			AY288420	CCDS5451.1	7p14.1	2012-08-21			ENSG00000187037	ENSG00000187037		"""GPCR / Class A : Orphans"""	19997	protein-coding gene	gene with protein product		609045				12679517, 14623098	Standard	NM_181791		Approved	PGR13	uc003tfm.1	Q7Z602	OTTHUMG00000102105	ENST00000447769.1:c.685delT	7.37:g.37780680delT	ENSP00000390410:p.Phe230fs	Somatic		Capture	Illumina HiSeq	Phase_I	37747205	NM_181791	A4D1X7|Q0VAR5|Q86SP3	Frame_Shift_Del	DEL	ENST00000447769.1	37	CCDS5451.1																																																																																				0.433	GPR141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219943.2	NM_181791	
PKD1L1	168507	broad.mit.edu	37	7	47944773	47944773	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:47944773delT	ENST00000289672.2	-	11	1722	c.1672delA	c.(1672-1674)agafs	p.R558fs		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	558	PKD 1. {ECO:0000255|PROSITE- ProRule:PRU00151}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)	p.R558fs*10(1)	BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						ATGCTGAGTCTTTTTTTAATG	0.443																																					p.R558fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1672delA	7						.						124.0	116.0	119.0					7																	47944773		2203	4300	6503	47911298	SO:0001589	frameshift_variant	168507	exon11			AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1672delA	7.37:g.47944773delT	ENSP00000289672:p.Arg558fs	Somatic		Capture	Illumina HiSeq	Phase_I	47911298	NM_138295	Q6UWK1	Frame_Shift_Del	DEL	ENST00000289672.2	37	CCDS34633.1																																																																																				0.443	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
MAGI2	9863	broad.mit.edu	37	7	77756653	77756653	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:77756653delG	ENST00000354212.4	-	19	3537	c.3284delC	c.(3283-3285)ccgfs	p.P1095fs	MAGI2_ENST00000522391.1_Frame_Shift_Del_p.P1095fs|MAGI2_ENST00000419488.1_Frame_Shift_Del_p.P1081fs	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	1095	Pro-rich.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.P1095fs*80(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				GTAATCCAGCGGGGGCTGCCT	0.572																																					p.P1095fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.3284delC	7						.						104.0	97.0	100.0					7																	77756653		2203	4300	6503	77594589	SO:0001589	frameshift_variant	9863	exon19			AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.3284delC	7.37:g.77756653delG	ENSP00000346151:p.Pro1095fs	Somatic		Capture	Illumina HiSeq	Phase_I	77594589	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Frame_Shift_Del	DEL	ENST00000354212.4	37	CCDS5594.1																																																																																				0.572	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
AKAP9	10142	broad.mit.edu	37	7	91603085	91603085	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr7:91603085delA	ENST00000359028.2	+	3	370	c.145delA	c.(145-147)aaafs	p.K51fs	AKAP9_ENST00000358100.2_Frame_Shift_Del_p.K51fs|AKAP9_ENST00000394564.1_Frame_Shift_Del_p.K39fs|AKAP9_ENST00000356239.3_Frame_Shift_Del_p.K39fs			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	51					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.K39fs*17(1)|p.K51fs*17(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CAAGAAGCAGAAAAAAAAGAG	0.353			T	BRAF	papillary thyroid																																p.K37fs			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.109delA	7						.																																			91441021	SO:0001589	frameshift_variant	10142	exon2			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.145delA	7.37:g.91603085delA	ENSP00000351922:p.Lys51fs	Somatic		Capture	Illumina HiSeq	Phase_I	91441021	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Frame_Shift_Del	DEL	ENST00000359028.2	37																																																																																					0.353	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
TMEM55A	55529	broad.mit.edu	37	8	92020971	92020972	+	Splice_Site	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:92020971_92020972insT	ENST00000285419.3	-	5	852_853	c.538_539insA	c.(538-540)atc>aAtc	p.I180fs		NM_018710.2	NP_061180.1	Q8N4L2	TM55A_HUMAN	transmembrane protein 55A	180						endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	hydrolase activity (GO:0016787)	p.I180fs*6(1)		breast(1)|endometrium(2)|large_intestine(5)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	13			BRCA - Breast invasive adenocarcinoma(11;0.033)			GGGAACTTACATTTTTTTGCAG	0.317																																					p.I180fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.539_540insA	8						.																																			92090148	SO:0001630	splice_region_variant	55529	exon5			BC033892	CCDS6252.1	8q21.3	2005-08-09			ENSG00000155099	ENSG00000155099			25452	protein-coding gene	gene with protein product		609864				12477932	Standard	NM_018710		Approved	DKFZp762O076	uc003yes.3	Q8N4L2	OTTHUMG00000164019	ENST00000285419.3:c.539+1->A	8.37:g.92020978_92020978dupT		Somatic		Capture	Illumina HiSeq	Phase_I	92090147	NM_018710	B2R9H4|Q68CU2	Frame_Shift_Ins	INS	ENST00000285419.3	37	CCDS6252.1																																																																																				0.317	TMEM55A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376778.1	NM_018710	Frame_Shift_Ins
CPSF1	29894	broad.mit.edu	37	8	145621958	145621959	+	Splice_Site	INS	-	-	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:145621958_145621959insG	ENST00000349769.3	-	25	2777		c.e25-2		MIR939_ENST00000401314.1_RNA|CPSF1_ENST00000531727.1_5'Flank	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)	p.?(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			GTGAGGGACCTGGGGGGGAACC	0.644																																					.	NSCLC(133;1088 1848 27708 34777 35269)											.	.	1	Unknown(1)	large_intestine(1)	.	8						.																																			145592767	SO:0001630	splice_region_variant	29894	.			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.2683-2->C	8.37:g.145621965_145621965dupG		Somatic		Capture	Illumina HiSeq	Phase_I	145592766	.	Q96AF0	Splice_Site	INS	ENST00000349769.3	37	CCDS34966.1																																																																																				0.644	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	Intron
PINX1	54984	broad.mit.edu	37	8	10689194	10689194	+	Silent	SNP	G	G	A	rs547975007		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:10689194G>A	ENST00000314787.3	-	4	401	c.282C>T	c.(280-282)tgC>tgT	p.C94C	SOX7_ENST00000553390.1_Silent_p.C94C|PINX1_ENST00000519088.1_Silent_p.C94C|PINX1_ENST00000520018.2_5'Flank|SOX7_ENST00000554914.1_Silent_p.C94C|PINX1_ENST00000426190.2_Silent_p.C92C	NM_017884.4	NP_060354.4	Q96BK5	PINX1_HUMAN	PIN2/TERF1 interacting, telomerase inhibitor 1	94					mitotic metaphase plate congression (GO:0007080)|negative regulation of cell proliferation (GO:0008285)|negative regulation of telomerase activity (GO:0051974)|regulation of telomerase activity (GO:0051972)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)|nucleolus (GO:0005730)|spindle (GO:0005819)	telomerase inhibitor activity (GO:0010521)|telomeric RNA binding (GO:0070034)	p.C94C(1)		kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(2)	17				Kidney(29;0.0595)|COAD - Colon adenocarcinoma(149;0.105)|KIRC - Kidney renal clear cell carcinoma(542;0.201)		CCTGCCCATGGCAAGTGTTCA	0.378																																					p.C94C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C282T	8						.						81.0	84.0	83.0					8																	10689194		1864	4098	5962	10726604	SO:0001819	synonymous_variant	54984	exon4			AF418553	CCDS47801.1, CCDS64825.1	8p23	2013-01-28				ENSG00000254093		"""G patch domain containing"""	30046	protein-coding gene	gene with protein product	"""PIN2 interacting protein 1"", ""liver-related putative tumor suppressor"""	606505				11003615, 11701125	Standard	NM_001284356		Approved	PinX1, LPTL, LPTS, FLJ20565, MGC8850		Q96BK5		ENST00000314787.3:c.282C>T	8.37:g.10689194G>A		Somatic		Capture	Illumina HiSeq	Phase_I	10726604	NM_017884	B2R9B1|Q548A5|Q6QWG9|Q7Z7J8|Q96QD7|Q9HBU7|Q9NWW2	Silent	SNP	ENST00000314787.3	37	CCDS47801.1																																																																																				0.378	PINX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375683.1	NM_017884	
GRHL2	79977	broad.mit.edu	37	8	102631913	102631913	+	Silent	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:102631913C>G	ENST00000251808.3	+	9	1583	c.1245C>G	c.(1243-1245)gtC>gtG	p.V415V	GRHL2_ENST00000395927.1_Silent_p.V399V	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	415			V -> I (in dbSNP:rs3779617).		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.V415V(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)			AGATCAAGGTCTTCTGTGACA	0.338																																					p.V415V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1245G	8						.						97.0	95.0	96.0					8																	102631913		2203	4300	6503	102701089	SO:0001819	synonymous_variant	79977	exon9			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.1245C>G	8.37:g.102631913C>G		Somatic		Capture	Illumina HiSeq	Phase_I	102701089	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																				0.338	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
MTMR9	66036	broad.mit.edu	37	8	11163823	11163823	+	Missense_Mutation	SNP	T	T	C	rs374898338		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:11163823T>C	ENST00000221086.3	+	5	1189	c.716T>C	c.(715-717)cTg>cCg	p.L239P	MTMR9_ENST00000526292.1_Missense_Mutation_p.L154P	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	239	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)	p.L239P(1)		cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		ACCCGATCCCTGAACGTGGCT	0.502																																					p.L239P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T716C	8						.	T	PRO/LEU	0,4406		0,0,2203	126.0	104.0	111.0		716	5.7	0.0	8		111	1,8599	1.2+/-3.3	0,1,4299	no	missense	MTMR9	NM_015458.3	98	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	239/550	11163823	1,13005	2203	4300	6503	11201233	SO:0001583	missense	66036	exon5			AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.716T>C	8.37:g.11163823T>C	ENSP00000221086:p.Leu239Pro	Somatic		Capture	Illumina HiSeq	Phase_I	11201233	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Missense_Mutation	SNP	ENST00000221086.3	37	CCDS5979.1	.	.	.	.	.	.	.	.	.	.	T	11.29	1.595414	0.28445	0.0	1.16E-4	ENSG00000104643	ENST00000221086;ENST00000526292	D;D	0.92805	-3.11;-3.11	5.68	5.68	0.88126	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.313001	0.33496	N	0.004841	D	0.83594	0.5288	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.78833	-0.2048	10	0.32370	T	0.25	.	15.1183	0.72423	0.0:0.0:0.0:1.0	.	239	Q96QG7	MTMR9_HUMAN	P	239;154	ENSP00000221086:L239P;ENSP00000433239:L154P	ENSP00000221086:L239P	L	+	2	0	MTMR9	11201233	0.986000	0.35501	0.011000	0.14972	0.881000	0.50899	6.150000	0.71801	2.170000	0.68504	0.460000	0.39030	CTG		0.502	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
RSPO2	340419	broad.mit.edu	37	8	109094785	109094785	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:109094785G>A	ENST00000276659.5	-	2	702	c.82C>T	c.(82-84)Cgc>Tgc	p.R28C	RSPO2_ENST00000378439.2_Missense_Mutation_p.R28C|RSPO2_ENST00000517781.1_Missense_Mutation_p.R28C|RSPO2_ENST00000517939.1_5'Flank	NM_178565.4	NP_848660.3	Q6UXX9	RSPO2_HUMAN	R-spondin 2	28					bone mineralization (GO:0030282)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|lung growth (GO:0060437)|osteoblast differentiation (GO:0001649)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|receptor binding (GO:0005102)	p.R28C(3)	EIF3E/RSPO2(6)	haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	28			OV - Ovarian serous cystadenocarcinoma(57;1.55e-09)			CGCTTACTGCGTCTCCATCGG	0.627																																					p.R28C												.	.	3	Substitution - Missense(3)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(1)	c.C82T	8						.						111.0	95.0	100.0					8																	109094785		2203	4300	6503	109163961	SO:0001583	missense	340419	exon2			AK123023	CCDS6307.1, CCDS64953.1	8q23.1	2014-01-30	2011-06-29		ENSG00000147655	ENSG00000147655		"""Endogenous ligands"""	28583	protein-coding gene	gene with protein product		610575	"""R-spondin 2 homolog (Xenopus laevis)"""			15469841	Standard	NM_178565		Approved	MGC35555	uc003yms.3	Q6UXX9	OTTHUMG00000164893	ENST00000276659.5:c.82C>T	8.37:g.109094785G>A	ENSP00000276659:p.Arg28Cys	Somatic		Capture	Illumina HiSeq	Phase_I	109163961	NM_178565	B3KVP0|Q4G0U4|Q8N6X6	Missense_Mutation	SNP	ENST00000276659.5	37	CCDS6307.1	.	.	.	.	.	.	.	.	.	.	G	17.76	3.468646	0.63625	.	.	ENSG00000147655	ENST00000517781;ENST00000378439;ENST00000276659;ENST00000521956;ENST00000522333	T;T;T;T;T	0.79247	1.55;1.55;-1.25;-1.25;-1.25	5.57	5.57	0.84162	Growth factor, receptor (1);	0.333064	0.26586	N	0.023556	D	0.86752	0.6008	L	0.60455	1.87	0.53005	D	0.999962	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.87128	0.2195	10	0.66056	D	0.02	-9.5123	19.1489	0.93479	0.0:0.0:1.0:0.0	.	28;28	Q6UXX9;Q6UXX9-3	RSPO2_HUMAN;.	C	28	ENSP00000427937:R28C;ENSP00000367698:R28C;ENSP00000276659:R28C;ENSP00000430010:R28C;ENSP00000430973:R28C	ENSP00000276659:R28C	R	-	1	0	RSPO2	109163961	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.099000	0.71466	2.622000	0.88805	0.591000	0.81541	CGC		0.627	RSPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380830.1	NM_178565	
BLK	640	broad.mit.edu	37	8	11406564	11406564	+	Missense_Mutation	SNP	G	G	A	rs371256341		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:11406564G>A	ENST00000259089.4	+	5	893	c.301G>A	c.(301-303)Gtc>Atc	p.V101I	BLK_ENST00000529894.1_Missense_Mutation_p.V30I	NM_001715.2	NP_001706.2	P51451	BLK_HUMAN	BLK proto-oncogene, Src family tyrosine kinase	101	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				B cell receptor signaling pathway (GO:0050853)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of insulin secretion (GO:0032024)	plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)	p.V101I(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(4)|stomach(1)	27			STAD - Stomach adenocarcinoma(15;0.00391)	COAD - Colon adenocarcinoma(149;0.207)		CAGGTCACTCGTCACAGGAAG	0.592																																					p.V101I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G301A	8						.	G	ILE/VAL	0,4406		0,0,2203	97.0	76.0	83.0		301	-5.6	0.0	8		83	1,8599		0,1,4299	no	missense	BLK	NM_001715.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	101/506	11406564	1,13005	2203	4300	6503	11443973	SO:0001583	missense	640	exon5			BC004473	CCDS5982.1	8p23-p22	2014-06-25	2014-06-25		ENSG00000136573	ENSG00000136573		"""SH2 domain containing"""	1057	protein-coding gene	gene with protein product		191305	"""B lymphoid tyrosine kinase"""			7845672	Standard	NM_001715		Approved	MGC10442	uc003wty.3	P51451	OTTHUMG00000090729	ENST00000259089.4:c.301G>A	8.37:g.11406564G>A	ENSP00000259089:p.Val101Ile	Somatic		Capture	Illumina HiSeq	Phase_I	11443973	NM_001715	Q16291|Q96IN1	Missense_Mutation	SNP	ENST00000259089.4	37	CCDS5982.1	.	.	.	.	.	.	.	.	.	.	G	6.790	0.514753	0.12944	0.0	1.16E-4	ENSG00000136573	ENST00000259089;ENST00000427279;ENST00000529894	T;T	0.49432	0.98;0.78	5.1	-5.55	0.02536	Src homology-3 domain (3);	0.955879	0.08518	N	0.933908	T	0.32556	0.0833	L	0.31526	0.94	0.09310	N	0.999999	B	0.09022	0.002	B	0.10450	0.005	T	0.24154	-1.0168	10	0.40728	T	0.16	.	11.6223	0.51126	0.6951:0.0919:0.213:0.0	.	101	P51451	BLK_HUMAN	I	101;101;30	ENSP00000259089:V101I;ENSP00000433663:V30I	ENSP00000259089:V101I	V	+	1	0	BLK	11443973	0.000000	0.05858	0.046000	0.18839	0.281000	0.26958	-0.611000	0.05622	-1.350000	0.02199	0.462000	0.41574	GTC		0.592	BLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207460.1		
CSMD3	114788	broad.mit.edu	37	8	113702221	113702221	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:113702221G>A	ENST00000297405.5	-	14	2275	c.2031C>T	c.(2029-2031)ggC>ggT	p.G677G	CSMD3_ENST00000455883.2_Silent_p.G573G|CSMD3_ENST00000343508.3_Silent_p.G637G|CSMD3_ENST00000352409.3_Silent_p.G677G	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	677	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.G677G(1)		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAAATCCATCGCCTTCTCTAA	0.368										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G677G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2031T	8						.						162.0	170.0	167.0					8																	113702221		2203	4300	6503	113771397	SO:0001819	synonymous_variant	114788	exon14			AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2031C>T	8.37:g.113702221G>A		Somatic		Capture	Illumina HiSeq	Phase_I	113771397	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																				0.368	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
CTSB	1508	broad.mit.edu	37	8	11708389	11708389	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:11708389A>G	ENST00000353047.6	-	4	566	c.313T>C	c.(313-315)Tgt>Cgt	p.C105R	CTSB_ENST00000434271.1_Missense_Mutation_p.C105R|CTSB_ENST00000525076.1_5'UTR|CTSB_ENST00000531089.1_Missense_Mutation_p.C105R|CTSB_ENST00000534510.1_Missense_Mutation_p.C105R|CTSB_ENST00000530640.2_Missense_Mutation_p.C105R|CTSB_ENST00000533455.1_Missense_Mutation_p.C105R|CTSB_ENST00000453527.2_Missense_Mutation_p.C105R|CTSB_ENST00000345125.3_Missense_Mutation_p.C105R|CTSB_ENST00000415599.2_Missense_Mutation_p.C105R	NM_001908.3	NP_001899.1	P07858	CATB_HUMAN	cathepsin B	105					cellular response to thyroid hormone stimulus (GO:0097067)|collagen catabolic process (GO:0030574)|decidualization (GO:0046697)|epithelial cell differentiation (GO:0030855)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of apoptotic process (GO:0042981)|regulation of catalytic activity (GO:0050790)|toll-like receptor signaling pathway (GO:0002224)	endolysosome lumen (GO:0036021)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)	collagen binding (GO:0005518)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|proteoglycan binding (GO:0043394)	p.C105R(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(1)	16	all_epithelial(15;0.205)		STAD - Stomach adenocarcinoma(15;0.00546)	COAD - Colon adenocarcinoma(149;0.184)		CAGGAGCCACAGGAGCCCTGG	0.587																																					p.C105R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T313C	8						.						63.0	58.0	59.0					8																	11708389		2203	4300	6503	11745798	SO:0001583	missense	1508	exon5			M14221	CCDS5986.1	8p23.1	2012-10-02			ENSG00000164733	ENSG00000164733	3.4.22.1	"""Cathepsins"""	2527	protein-coding gene	gene with protein product		116810				8112600, 3463996	Standard	XM_006716244		Approved		uc003wuq.3	P07858	OTTHUMG00000090799	ENST00000353047.6:c.313T>C	8.37:g.11708389A>G	ENSP00000345672:p.Cys105Arg	Somatic		Capture	Illumina HiSeq	Phase_I	11745798	NM_147781	B3KQR5|B3KRR5|Q503A6|Q96D87	Missense_Mutation	SNP	ENST00000353047.6	37	CCDS5986.1	.	.	.	.	.	.	.	.	.	.	A	18.56	3.650844	0.67472	.	.	ENSG00000164733	ENST00000434271;ENST00000353047;ENST00000530640;ENST00000531089;ENST00000453527;ENST00000415599;ENST00000345125;ENST00000533455;ENST00000534510;ENST00000534636;ENST00000533572;ENST00000530296;ENST00000526195;ENST00000527243;ENST00000534149;ENST00000526645;ENST00000530573	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.98164	-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76;-4.76	5.3	5.3	0.74995	Peptidase C1A, papain C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99321	0.9762	H	0.99992	5.355	0.80722	D	1	B	0.27765	0.188	B	0.38803	0.282	D	0.97919	1.0313	10	0.87932	D	0	.	14.4403	0.67311	1.0:0.0:0.0:0.0	.	105	P07858	CATB_HUMAN	R	105	ENSP00000415889:C105R;ENSP00000345672:C105R;ENSP00000435105:C105R;ENSP00000433215:C105R;ENSP00000409917:C105R;ENSP00000411254:C105R;ENSP00000342070:C105R;ENSP00000432244:C105R;ENSP00000434217:C105R;ENSP00000436159:C105R;ENSP00000433995:C105R;ENSP00000435074:C105R;ENSP00000436627:C105R;ENSP00000434725:C105R;ENSP00000436122:C105R;ENSP00000431518:C105R	ENSP00000342070:C105R	C	-	1	0	CTSB	11745798	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.048000	0.93830	2.010000	0.58986	0.379000	0.24179	TGT		0.587	CTSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207586.3	NM_147780	
TRPS1	7227	broad.mit.edu	37	8	116426763	116426763	+	Missense_Mutation	SNP	G	G	A	rs374896129		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:116426763G>A	ENST00000220888.5	-	6	3493	c.3334C>T	c.(3334-3336)Cgg>Tgg	p.R1112W	TRPS1_ENST00000520276.1_Missense_Mutation_p.R1116W|TRPS1_ENST00000519076.1_Missense_Mutation_p.R866W|TRPS1_ENST00000395715.3_Missense_Mutation_p.R1125W			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	1112	Mediates interaction with RNF4. {ECO:0000250}.				chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.R1112W(2)		autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTCCAGAACCGCAGCCAATCA	0.463									Langer-Giedion syndrome				G|||	1	0.000199681	0.0	0.0	5008	,	,		17996	0.001		0.0	False		,,,				2504	0.0				p.R1125W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C3373T	8						.	G	TRP/ARG	0,3818		0,0,1909	97.0	94.0	95.0		3373	5.7	1.0	8		95	1,8261		0,1,4130	no	missense	TRPS1	NM_014112.2	101	0,1,6039	AA,AG,GG		0.0121,0.0,0.0083	probably-damaging	1125/1295	116426763	1,12079	1909	4131	6040	116495939	SO:0001583	missense	7227	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.3334C>T	8.37:g.116426763G>A	ENSP00000220888:p.Arg1112Trp	Somatic		Capture	Illumina HiSeq	Phase_I	116495939	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Missense_Mutation	SNP	ENST00000220888.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.91|15.91	2.971894|2.971894	0.53614|0.53614	0.0|0.0	1.21E-4|1.21E-4	ENSG00000104447|ENSG00000104447	ENST00000518018|ENST00000395715;ENST00000220888;ENST00000519076;ENST00000520276	.|D;D;D;D	.|0.99376	.|-5.79;-5.76;-5.65;-5.76	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.98579|0.98579	0.9525|0.9525	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.998;0.999	D|D	0.98530|0.98530	1.0627|1.0627	5|10	.|0.87932	.|D	.|0	.|.	12.8772|12.8772	0.57998|0.57998	0.0:0.0:0.7295:0.2705|0.0:0.0:0.7295:0.2705	.|.	.|1116;1112;1125	.|Q9UHF7-3;Q9UHF7;Q9UHF7-2	.|.;TRPS1_HUMAN;.	V|W	236|1125;1112;866;1116	.|ENSP00000379065:R1125W;ENSP00000220888:R1112W;ENSP00000428910:R866W;ENSP00000428680:R1116W	.|ENSP00000220888:R1112W	A|R	-|-	2|1	0|2	TRPS1|TRPS1	116495939|116495939	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	1.000000|1.000000	0.99986|0.99986	2.932000|2.932000	0.48940|0.48940	2.685000|2.685000	0.91497|0.91497	0.655000|0.655000	0.94253|0.94253	GCG|CGG		0.463	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
TNFRSF11B	4982	broad.mit.edu	37	8	119936822	119936822	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:119936822G>A	ENST00000297350.4	-	5	1375	c.997C>T	c.(997-999)Cga>Tga	p.R333*		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	333	Death 2.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)	p.R333*(1)		breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			TTTTTTATTCGCCACAAACTG	0.453																																					p.R333X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C997T	8						.						234.0	204.0	214.0					8																	119936822		2203	4300	6503	120006003	SO:0001587	stop_gained	4982	exon5			U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.997C>T	8.37:g.119936822G>A	ENSP00000297350:p.Arg333*	Somatic		Capture	Illumina HiSeq	Phase_I	120006003	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Nonsense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	G	34	5.332512	0.95733	.	.	ENSG00000164761	ENST00000297350	.	.	.	5.43	1.61	0.23674	.	0.233838	0.43110	D	0.000607	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-20.8536	13.5122	0.61519	0.0:0.0:0.372:0.628	.	.	.	.	X	333	.	.	R	-	1	2	TNFRSF11B	120006003	1.000000	0.71417	0.931000	0.37212	0.393000	0.30537	0.931000	0.28871	0.093000	0.17368	-0.375000	0.07067	CGA		0.453	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
COL14A1	7373	broad.mit.edu	37	8	121322277	121322277	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:121322277C>T	ENST00000297848.3	+	37	4701	c.4431C>T	c.(4429-4431)ggC>ggT	p.G1477G	COL14A1_ENST00000309791.4_Silent_p.G1477G|COL14A1_ENST00000247781.3_Silent_p.G1382G	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.?(1)|p.G1477G(1)		NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			GACCAAAGGGCCAGCAAGGTG	0.433																																					p.G1477G												.	.	2	Unknown(1)|Substitution - coding silent(1)	large_intestine(1)|kidney(1)	c.C4431T	8						.						154.0	137.0	143.0					8																	121322277		2203	4300	6503	121391458	SO:0001819	synonymous_variant	7373	exon37				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4431C>T	8.37:g.121322277C>T		Somatic		Capture	Illumina HiSeq	Phase_I	121391458	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.433	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
EFR3A	23167	broad.mit.edu	37	8	132966148	132966148	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:132966148C>T	ENST00000254624.5	+	6	797	c.572C>T	c.(571-573)cCt>cTt	p.P191L	EFR3A_ENST00000334503.4_Missense_Mutation_p.P191L|EFR3A_ENST00000519656.1_Missense_Mutation_p.P155L	NM_015137.4	NP_055952.2	Q14156	EFR3A_HUMAN	EFR3 homolog A (S. cerevisiae)	191						extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|plasma membrane (GO:0005886)		p.P191L(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|skin(1)|stomach(2)	35	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)|LUAD - Lung adenocarcinoma(14;0.102)			ATTTGGGAACCTCAGCATATG	0.363																																					p.P191L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C572T	8						.						69.0	57.0	61.0					8																	132966148		2201	4298	6499	133035330	SO:0001583	missense	23167	exon6			D63477	CCDS34942.2	8q24.22	2008-10-23			ENSG00000132294	ENSG00000132294			28970	protein-coding gene	gene with protein product		611798				15363888	Standard	NM_015137		Approved	KIAA0143	uc003yte.3	Q14156	OTTHUMG00000150552	ENST00000254624.5:c.572C>T	8.37:g.132966148C>T	ENSP00000254624:p.Pro191Leu	Somatic		Capture	Illumina HiSeq	Phase_I	133035330	NM_015137	A7MD19|Q2VPK2|Q63HL7|Q68DX1|Q6IQ18	Missense_Mutation	SNP	ENST00000254624.5	37	CCDS34942.2	.	.	.	.	.	.	.	.	.	.	C	28.5	4.923554	0.92319	.	.	ENSG00000132294	ENST00000254624;ENST00000377917;ENST00000334503;ENST00000519656	T;T;T	0.19938	3.7;3.7;2.11	5.73	4.85	0.62838	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.34948	0.0915	M	0.69823	2.125	0.80722	D	1	P	0.50528	0.936	P	0.48873	0.593	T	0.28618	-1.0038	10	0.72032	D	0.01	-14.5454	15.908	0.79445	0.0:0.8646:0.1354:0.0	.	191	Q14156	EFR3A_HUMAN	L	191;191;191;155	ENSP00000254624:P191L;ENSP00000334769:P191L;ENSP00000428086:P155L	ENSP00000254624:P191L	P	+	2	0	EFR3A	133035330	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	7.818000	0.86416	1.402000	0.46780	0.585000	0.79938	CCT		0.363	EFR3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318886.1	NM_015137	
KCNQ3	3786	broad.mit.edu	37	8	133141916	133141916	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:133141916C>T	ENST00000388996.4	-	15	2632	c.2212G>A	c.(2212-2214)Gca>Aca	p.A738T	KCNQ3_ENST00000521134.1_Missense_Mutation_p.A618T|KCNQ3_ENST00000519445.1_Missense_Mutation_p.A726T	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	738					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.A738T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TACGTTGTTGCTGAGGAAGGA	0.582																																					p.A738T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2212A	8						.						40.0	41.0	40.0					8																	133141916		2203	4300	6503	133211098	SO:0001583	missense	3786	exon15			AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.2212G>A	8.37:g.133141916C>T	ENSP00000373648:p.Ala738Thr	Somatic		Capture	Illumina HiSeq	Phase_I	133211098	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	0.028	-1.355151	0.01256	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.98978	-5.25;-5.23;-5.29	5.27	3.35	0.38373	.	3.142800	0.00674	N	0.000647	D	0.95567	0.8559	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	D	0.92027	0.5630	10	0.12430	T	0.62	-0.0265	7.2364	0.26072	0.0:0.778:0.0:0.222	.	726;738	E7ET42;O43525	.;KCNQ3_HUMAN	T	738;618;726;715;617	ENSP00000373648:A738T;ENSP00000429799:A618T;ENSP00000428790:A726T	ENSP00000373648:A738T	A	-	1	0	KCNQ3	133211098	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.393000	0.20817	0.527000	0.28560	0.650000	0.86243	GCA		0.582	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
FAM135B	51059	broad.mit.edu	37	8	139164285	139164285	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:139164285A>C	ENST00000395297.1	-	13	2603	c.2433T>G	c.(2431-2433)tcT>tcG	p.S811S		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	811								p.S811S(2)		NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			GTTGAGAGCAAGATCCTGGGG	0.537										HNSCC(54;0.14)																											p.S811S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T2433G	8						.						69.0	65.0	66.0					8																	139164285		2203	4300	6503	139233467	SO:0001819	synonymous_variant	51059	exon13			AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2433T>G	8.37:g.139164285A>C		Somatic		Capture	Illumina HiSeq	Phase_I	139233467	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																				0.537	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
COL22A1	169044	broad.mit.edu	37	8	139609159	139609159	+	Missense_Mutation	SNP	T	T	C	rs267601787		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:139609159T>C	ENST00000303045.6	-	62	4866	c.4420A>G	c.(4420-4422)Aag>Gag	p.K1474E	COL22A1_ENST00000341807.4_5'UTR|COL22A1_ENST00000435777.1_Missense_Mutation_p.K1454E	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1474	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.K1474E(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			TCAAGCTGCTTCCCCAGCTCT	0.512										HNSCC(7;0.00092)																											p.K1474E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A4420G	8						.						181.0	181.0	181.0					8																	139609159		2203	4300	6503	139678341	SO:0001583	missense	169044	exon62			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4420A>G	8.37:g.139609159T>C	ENSP00000303153:p.Lys1474Glu	Somatic		Capture	Illumina HiSeq	Phase_I	139678341	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	T	18.35	3.604723	0.66445	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.88741	-2.42;-2.34	5.06	5.06	0.68205	.	0.000000	0.49305	U	0.000149	D	0.91942	0.7448	M	0.72118	2.19	0.51233	D	0.999912	P;D	0.69078	0.846;0.997	P;D	0.73380	0.806;0.98	D	0.89710	0.3911	10	0.02654	T	1	.	13.983	0.64317	0.0:0.0:0.0:1.0	.	1454;1474	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	1474;1454;1167	ENSP00000303153:K1474E;ENSP00000387655:K1454E	ENSP00000303153:K1474E	K	-	1	0	COL22A1	139678341	1.000000	0.71417	0.969000	0.41365	0.933000	0.57130	6.775000	0.75018	1.903000	0.55091	0.460000	0.39030	AAG		0.512	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
MROH5	389690	broad.mit.edu	37	8	142451779	142451779	+	RNA	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:142451779T>C	ENST00000430863.1	-	0	3000					NM_207414.2	NP_997297.2	Q6ZUA9	MROH5_HUMAN	maestro heat-like repeat family member 5																		TGGATGGTGGTGAAGAGCTCC	0.662																																					p.T974A												.	.	0			c.A2920G	8						.						58.0	72.0	67.0					8																	142451779		2112	4220	6332	142520961			389690	exon22					8q24.3	2012-12-20			ENSG00000226807	ENSG00000226807		"""maestro heat-like repeat containing"""	42976	protein-coding gene	gene with protein product							Standard	NM_207414		Approved	FLJ43860	uc003ywi.2	Q6ZUA9	OTTHUMG00000155944		8.37:g.142451779T>C		Somatic		Capture	Illumina HiSeq	Phase_I	142520961	NM_207414		Missense_Mutation	SNP	ENST00000430863.1	37																																																																																					0.662	MROH5-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000342412.4	NM_207414	
ARC	23237	broad.mit.edu	37	8	143694645	143694645	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:143694645G>A	ENST00000356613.2	-	1	2188	c.988C>T	c.(988-990)Cag>Tag	p.Q330*	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)	p.Q330*(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				AGCTTGGGCTGCAGGGTGCCC	0.657																																					p.Q330X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C988T	8						.						66.0	65.0	65.0					8																	143694645		2203	4300	6503	143691647	SO:0001587	stop_gained	23237	exon1			AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.988C>T	8.37:g.143694645G>A	ENSP00000349022:p.Gln330*	Somatic		Capture	Illumina HiSeq	Phase_I	143691647	NM_015193	B4DFL0|O60937	Nonsense_Mutation	SNP	ENST00000356613.2	37	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	G	48	14.098771	0.99779	.	.	ENSG00000198576	ENST00000356613	.	.	.	4.71	4.71	0.59529	.	0.112617	0.38897	U	0.001539	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.36615	T	0.2	.	16.7251	0.85419	0.0:0.0:1.0:0.0	.	.	.	.	X	330	.	ENSP00000349022:Q330X	Q	-	1	0	ARC	143691647	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.479000	0.53165	2.185000	0.69588	0.558000	0.71614	CAG		0.657	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
FAM83H	286077	broad.mit.edu	37	8	144812718	144812718	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:144812718T>C	ENST00000388913.3	-	2	160	c.35A>G	c.(34-36)gAc>gGc	p.D12G	MIR4664_ENST00000583819.1_RNA	NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	12					biomineral tissue development (GO:0031214)			p.D12G(1)		central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGTGGGTTGTCCCCCTGCGA	0.682																																					p.D12G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A35G	8						.						14.0	16.0	15.0					8																	144812718		1965	4101	6066	144884706	SO:0001583	missense	286077	exon2			AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.35A>G	8.37:g.144812718T>C	ENSP00000373565:p.Asp12Gly	Somatic		Capture	Illumina HiSeq	Phase_I	144884706	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	.	.	.	.	.	.	.	.	.	.	t	21.4	4.137500	0.77775	.	.	ENSG00000180921	ENST00000388913	T	0.12039	2.72	4.62	4.62	0.57501	.	0.515163	0.16312	N	0.219946	T	0.30008	0.0751	L	0.45285	1.41	0.44555	D	0.997511	D	0.89917	1.0	D	0.83275	0.996	T	0.01966	-1.1238	10	0.87932	D	0	.	13.4887	0.61382	0.0:0.0:0.0:1.0	.	12	Q6ZRV2	FA83H_HUMAN	G	12	ENSP00000373565:D12G	ENSP00000373565:D12G	D	-	2	0	FAM83H	144884706	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.319000	0.51983	1.851000	0.53745	0.391000	0.25812	GAC		0.682	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
MYOM2	9172	broad.mit.edu	37	8	2026940	2026940	+	Missense_Mutation	SNP	C	C	T	rs144104874		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:2026940C>T	ENST00000262113.4	+	12	1529	c.1388C>T	c.(1387-1389)gCg>gTg	p.A463V	MYOM2_ENST00000523438.1_Intron	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	463	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.A463V(1)		autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GTGAACAGTGCGGGCATCAGC	0.537																																					p.A463V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1388T	8						.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	154.0	165.0	162.0		1388	4.7	0.1	8	dbSNP_134	162	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYOM2	NM_003970.2	64	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	463/1466	2026940	2,13004	2203	4300	6503	2014347	SO:0001583	missense	9172	exon12				CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.1388C>T	8.37:g.2026940C>T	ENSP00000262113:p.Ala463Val	Somatic		Capture	Illumina HiSeq	Phase_I	2014347	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.907117	0.52333	2.27E-4	1.16E-4	ENSG00000036448	ENST00000262113	T	0.57273	0.41	4.71	4.71	0.59529	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.149518	0.43579	D	0.000553	T	0.66470	0.2792	L	0.53729	1.69	0.80722	D	1	D	0.67145	0.996	P	0.62813	0.907	T	0.66964	-0.5790	10	0.44086	T	0.13	.	18.0367	0.89305	0.0:1.0:0.0:0.0	.	463	P54296	MYOM2_HUMAN	V	463	ENSP00000262113:A463V	ENSP00000262113:A463V	A	+	2	0	MYOM2	2014347	0.921000	0.31238	0.064000	0.19789	0.292000	0.27327	3.745000	0.55119	2.308000	0.77769	0.561000	0.74099	GCG		0.537	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
SGK223	157285	broad.mit.edu	37	8	8175926	8175926	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:8175926A>G	ENST00000520004.1	-	6	4223	c.3959T>C	c.(3958-3960)gTg>gCg	p.V1320A	SGK223_ENST00000330777.4_Missense_Mutation_p.V1320A			Q86YV5	SG223_HUMAN		1324	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)	p.V1322A(1)|p.V1320A(1)									GCACTGCAGCACGCGCTTGGC	0.692																																					p.V1320A	GBM(34;731 755 10259 33573 33867)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T3959C	8						.						35.0	38.0	37.0					8																	8175926		2035	4177	6212	8213336	SO:0001583	missense	157285	exon5																														ENST00000520004.1:c.3959T>C	8.37:g.8175926A>G	ENSP00000428054:p.Val1320Ala	Somatic		Capture	Illumina HiSeq	Phase_I	8213336	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	A	16.46	3.129488	0.56721	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.13089	2.62;2.62	4.86	2.54	0.30619	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.199357	0.42294	D	0.000721	T	0.12902	0.0313	L	0.39397	1.21	0.35566	D	0.805099	B	0.33171	0.4	B	0.38880	0.284	T	0.18618	-1.0331	10	0.39692	T	0.17	.	9.044	0.36336	0.842:0.0:0.158:0.0	.	1320	Q86YV5	SG223_HUMAN	A	1320	ENSP00000330930:V1320A;ENSP00000428054:V1320A	ENSP00000330930:V1320A	V	-	2	0	AC068353.1	8213336	0.990000	0.36364	0.986000	0.45419	0.811000	0.45836	3.477000	0.53151	1.004000	0.39156	0.379000	0.24179	GTG		0.692	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
SOX7	83595	broad.mit.edu	37	8	10583646	10583646	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:10583646delG	ENST00000304501.1	-	2	847	c.769delC	c.(769-771)ctgfs	p.L257fs	SOX7_ENST00000553390.1_Frame_Shift_Del_p.L309fs|SOX7_ENST00000554914.1_Frame_Shift_Del_p.L309fs	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	257					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.L257fs*14(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		AGGGAGCCCAGGGGGTGGCTA	0.687																																					p.L257fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.769delC	8						.						21.0	29.0	27.0					8																	10583646		2196	4278	6474	10621056	SO:0001589	frameshift_variant	83595	exon2			AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.769delC	8.37:g.10583646delG	ENSP00000301921:p.Leu257fs	Somatic		Capture	Illumina HiSeq	Phase_I	10621056	NM_031439	B4DKV0|Q53YD0	Frame_Shift_Del	DEL	ENST00000304501.1	37	CCDS5977.1																																																																																				0.687	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
MSR1	4481	broad.mit.edu	37	8	16026093	16026093	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:16026093T>A	ENST00000262101.5	-	4	625	c.504A>T	c.(502-504)ggA>ggT	p.G168G	MSR1_ENST00000381998.4_Silent_p.G168G|MSR1_ENST00000445506.2_Silent_p.G186G|MSR1_ENST00000350896.3_Silent_p.G168G|MSR1_ENST00000355282.2_Silent_p.G168G|MSR1_ENST00000536385.1_Intron			P21757	MSRE_HUMAN	macrophage scavenger receptor 1	168					cholesterol transport (GO:0030301)|lipoprotein transport (GO:0042953)|plasma lipoprotein particle clearance (GO:0034381)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|receptor-mediated endocytosis (GO:0006898)	collagen trimer (GO:0005581)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)	p.G168G(1)		haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(7)|lung(14)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	37				Colorectal(111;0.00475)|COAD - Colon adenocarcinoma(73;0.0164)		CATTCCCATGTCCCTGGACTG	0.378																																					p.G168G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A504T	8						.						180.0	167.0	171.0					8																	16026093		2203	4300	6503	16070464	SO:0001819	synonymous_variant	4481	exon4			D13263	CCDS5995.1, CCDS5996.1, CCDS5997.1	8p22	2006-02-22			ENSG00000038945	ENSG00000038945		"""CD molecules"""	7376	protein-coding gene	gene with protein product		153622				2251254	Standard	NM_138715		Approved	SCARA1, CD204	uc003wwz.3	P21757	OTTHUMG00000094809	ENST00000262101.5:c.504A>T	8.37:g.16026093T>A		Somatic		Capture	Illumina HiSeq	Phase_I	16070464	NM_138716	D3DSP3|O60505|P21759|Q45F10	Silent	SNP	ENST00000262101.5	37	CCDS5995.1																																																																																				0.378	MSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211627.2		
PCM1	5108	broad.mit.edu	37	8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	rs565676613		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:17824674C>T	ENST00000519253.1	+	21	3658	c.3407C>T	c.(3406-3408)gCa>gTa	p.A1136V	PCM1_ENST00000325083.8_Missense_Mutation_p.A1136V|PCM1_ENST00000524226.1_Missense_Mutation_p.A1137V			Q15154	PCM1_HUMAN	pericentriolar material 1	1136					centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)	p.A1136V(1)	PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		TCATCATTTGCACCAGGTAGG	0.353			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""																																p.A1136V			Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3407T	8						.						43.0	42.0	42.0					8																	17824674		1826	4087	5913	17868954	SO:0001583	missense	5108	exon21				CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3407C>T	8.37:g.17824674C>T	ENSP00000431099:p.Ala1136Val	Somatic		Capture	Illumina HiSeq	Phase_I	17868954	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	C	15.01	2.707472	0.48412	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.56776	0.44;0.44;0.44	5.7	4.83	0.62350	.	0.317735	0.40302	N	0.001125	T	0.32882	0.0844	N	0.14661	0.345	0.80722	D	1	P;B;P	0.35575	0.51;0.001;0.51	B;B;B	0.31442	0.13;0.004;0.13	T	0.19976	-1.0289	10	0.40728	T	0.16	-3.1369	11.1977	0.48722	0.0:0.8595:0.0:0.1405	.	1136;1137;1136	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	V	1136;1136;1137	ENSP00000327077:A1136V;ENSP00000431099:A1136V;ENSP00000430521:A1137V	ENSP00000327077:A1136V	A	+	2	0	PCM1	17868954	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.612000	0.46343	1.584000	0.49913	-0.151000	0.13558	GCA		0.353	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
PIWIL2	55124	broad.mit.edu	37	8	22140573	22140573	+	Missense_Mutation	SNP	C	C	T	rs181413985		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:22140573C>T	ENST00000454009.2	+	5	961	c.452C>T	c.(451-453)gCg>gTg	p.A151V	PIWIL2_ENST00000521356.1_Missense_Mutation_p.A151V|PIWIL2_ENST00000356766.6_Missense_Mutation_p.A151V	NM_001135721.1	NP_001129193.1	Q8TC59	PIWL2_HUMAN	piwi-like RNA-mediated gene silencing 2	151					DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|germ-line stem cell maintenance (GO:0030718)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|piRNA metabolic process (GO:0034587)|positive regulation of meiosis I (GO:0060903)|positive regulation of translation (GO:0045727)|RNA 5'-end processing (GO:0000966)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|P granule (GO:0043186)|pi-body (GO:0071546)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)	p.A151V(1)		NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(14)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	46				Colorectal(74;0.018)|COAD - Colon adenocarcinoma(73;0.0707)		AGTTCAGATGCGTCTTTATTA	0.522													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18736	0.0		0.0	False		,,,				2504	0.0				p.A151V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C452T	8						.						88.0	79.0	82.0					8																	22140573		2203	4300	6503	22196518	SO:0001583	missense	55124	exon5			AK001213	CCDS6029.1	8p24	2013-02-15	2013-02-15		ENSG00000197181	ENSG00000197181		"""Argonaute/PIWI family"""	17644	protein-coding gene	gene with protein product	"""Hiwi-like"", ""cancer/testis antigen 80"""	610312	"""piwi-like 2 (Drosophila)"""			11279525, 12906857	Standard	NM_018068		Approved	HILI, FLJ10351, Mili, CT80	uc003xbn.2	Q8TC59	OTTHUMG00000097767	ENST00000454009.2:c.452C>T	8.37:g.22140573C>T	ENSP00000406956:p.Ala151Val	Somatic		Capture	Illumina HiSeq	Phase_I	22196518	NM_018068	A8K4S3|A8K8S5|B0AZN9|B0AZP2|B4DR22|E7ECA4|Q96SW6|Q9NW28	Missense_Mutation	SNP	ENST00000454009.2	37	CCDS6029.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	2.959	-0.215048	0.06101	.	.	ENSG00000197181	ENST00000356766;ENST00000521356;ENST00000454009	T;T;T	0.04406	3.64;3.63;3.64	5.42	-3.64	0.04515	.	2.108310	0.01570	N	0.020538	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.43015	-0.9417	10	0.11794	T	0.64	-14.2209	8.2732	0.31857	0.0:0.1632:0.134:0.7028	.	151;151	E7ECA4;Q8TC59	.;PIWL2_HUMAN	V	151	ENSP00000349208:A151V;ENSP00000428267:A151V;ENSP00000406956:A151V	ENSP00000349208:A151V	A	+	2	0	PIWIL2	22196518	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-1.762000	0.01803	-0.848000	0.04163	-0.145000	0.13849	GCG		0.522	PIWIL2-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000375438.1		
PPP3CC	5533	broad.mit.edu	37	8	22298929	22298929	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:22298929G>A	ENST00000240139.5	+	1	334	c.7G>A	c.(7-9)Ggg>Agg	p.G3R	PPP3CC_ENST00000397775.3_Missense_Mutation_p.G3R|PPP3CC_ENST00000518852.1_Missense_Mutation_p.G3R|PPP3CC_ENST00000289963.8_Missense_Mutation_p.G3R	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	3					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.G3R(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		GACCATGTCCGGGAGGCGCTT	0.741																																					p.G3R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G7A	8						.						10.0	12.0	11.0					8																	22298929		2093	4118	6211	22354874	SO:0001583	missense	5533	exon1				CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9316	protein-coding gene	gene with protein product	"""calcineurin A gamma"", ""protein phosphatase 2B, catalytic subunit, gamma isoform"""	114107	"""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"""			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.7G>A	8.37:g.22298929G>A	ENSP00000240139:p.Gly3Arg	Somatic		Capture	Illumina HiSeq	Phase_I	22354874	NM_005605	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	.	.	.	.	.	.	.	.	.	.	G	7.985	0.752012	0.15778	.	.	ENSG00000120910	ENST00000518852;ENST00000240139;ENST00000289963;ENST00000397775;ENST00000522000	T;T;T;T;T	0.44083	2.25;2.52;2.52;2.52;0.93	3.57	2.59	0.31030	.	1.292080	0.05906	U	0.630760	T	0.28863	0.0716	L	0.38175	1.15	0.09310	N	1	B;P;P;B	0.42123	0.0;0.771;0.661;0.004	B;B;B;B	0.28385	0.0;0.089;0.041;0.002	T	0.18304	-1.0341	10	0.36615	T	0.2	0.217	9.2425	0.37504	0.0:0.223:0.777:0.0	.	3;3;3;3	B4DRT5;P48454-2;P48454;G3V111	.;.;PP2BC_HUMAN;.	R	3;3;3;3;18	ENSP00000429379:G3R;ENSP00000240139:G3R;ENSP00000289963:G3R;ENSP00000380878:G3R;ENSP00000428358:G18R	ENSP00000240139:G3R	G	+	1	0	PPP3CC	22354874	0.558000	0.26554	0.854000	0.33618	0.311000	0.27955	0.664000	0.25068	1.667000	0.50832	0.313000	0.20887	GGG		0.741	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605	
SORBS3	10174	broad.mit.edu	37	8	22429908	22429908	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:22429908G>C	ENST00000240123.7	+	20	2286	c.1903G>C	c.(1903-1905)Gag>Cag	p.E635Q	SORBS3_ENST00000428103.1_Missense_Mutation_p.E293Q	NM_005775.4	NP_005766.3	O60504	VINEX_HUMAN	sorbin and SH3 domain containing 3	635	Binds to SOS.|SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|muscle contraction (GO:0006936)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of stress fiber assembly (GO:0051496)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)	p.E635Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(9)	18		Prostate(55;0.0421)|Breast(100;0.102)		BRCA - Breast invasive adenocarcinoma(99;0.00566)|Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		GGAGCTGCGCGAGGGGGACAG	0.632																																					p.E293Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G877C	8						.						151.0	126.0	134.0					8																	22429908		2203	4300	6503	22485853	SO:0001583	missense	10174	exon9				CCDS6031.1	8p21.3	2008-02-05			ENSG00000120896	ENSG00000120896			30907	protein-coding gene	gene with protein product		610795				9885244, 12510380	Standard	NM_001018003		Approved	SCAM-1, SH3D4, vinexin	uc003xbv.3	O60504	OTTHUMG00000131728	ENST00000240123.7:c.1903G>C	8.37:g.22429908G>C	ENSP00000240123:p.Glu635Gln	Somatic		Capture	Illumina HiSeq	Phase_I	22485853	NM_001018003	Q5BJE4|Q6NX54|Q96FY4|Q9UQE4	Missense_Mutation	SNP	ENST00000240123.7	37	CCDS6031.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.540062	0.85917	.	.	ENSG00000120896	ENST00000240123;ENST00000428103	T;T	0.33865	1.39;1.39	5.49	4.58	0.56647	Src homology-3 domain (5);	0.000000	0.48286	D	0.000185	T	0.42337	0.1198	L	0.57536	1.79	0.49687	D	0.99981	B	0.30889	0.299	B	0.40864	0.342	T	0.41556	-0.9502	10	0.72032	D	0.01	-13.5749	11.2237	0.48871	0.096:0.0:0.904:0.0	.	635	O60504	VINEX_HUMAN	Q	635;293	ENSP00000240123:E635Q;ENSP00000408476:E293Q	ENSP00000240123:E635Q	E	+	1	0	SORBS3	22485853	1.000000	0.71417	0.799000	0.32177	0.796000	0.44982	7.728000	0.84847	1.218000	0.43458	0.563000	0.77884	GAG		0.632	SORBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254647.3	NM_005775	
TNFRSF10A	8797	broad.mit.edu	37	8	23058258	23058258	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:23058258C>A	ENST00000221132.3	-	5	709	c.645G>T	c.(643-645)atG>atT	p.M215I		NM_003844.3	NP_003835.3	O00220	TR10A_HUMAN	tumor necrosis factor receptor superfamily, member 10a	215					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|signal transduction (GO:0007165)|TRAIL-activated apoptotic signaling pathway (GO:0036462)	integral component of membrane (GO:0016021)	death receptor activity (GO:0005035)|protease binding (GO:0002020)|receptor activity (GO:0004872)|TRAIL binding (GO:0045569)|transcription factor binding (GO:0008134)	p.M215I(1)		NS(2)|central_nervous_system(3)|endometrium(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(1)|skin(1)	16		Prostate(55;0.0421)|Breast(100;0.14)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)		TGACCTTGACCATCCCTCTGG	0.592																																					p.M215I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G645T	8						.						97.0	95.0	96.0					8																	23058258		2203	4300	6503	23114203	SO:0001583	missense	8797	exon5			U90875	CCDS6039.1	8p21	2006-02-22			ENSG00000104689	ENSG00000104689		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11904	protein-coding gene	gene with protein product		603611				9311998, 9082980	Standard	NM_003844		Approved	DR4, Apo2, TRAILR-1, CD261	uc003xda.3	O00220	OTTHUMG00000097843	ENST00000221132.3:c.645G>T	8.37:g.23058258C>A	ENSP00000221132:p.Met215Ile	Somatic		Capture	Illumina HiSeq	Phase_I	23114203	NM_003844	A8K5I4|Q53Y72|Q96E62	Missense_Mutation	SNP	ENST00000221132.3	37	CCDS6039.1	.	.	.	.	.	.	.	.	.	.	C	9.967	1.224308	0.22457	.	.	ENSG00000104689	ENST00000221132;ENST00000524158	D;T	0.90844	-2.74;1.53	3.18	1.26	0.21427	TNFR/CD27/30/40/95 cysteine-rich region (4);	0.539994	0.17194	U	0.183372	D	0.89178	0.6641	M	0.79805	2.47	0.09310	N	1	P	0.38504	0.634	B	0.41135	0.348	T	0.80209	-0.1477	10	0.40728	T	0.16	.	5.5479	0.17073	0.0:0.7189:0.0:0.2811	.	215	O00220	TR10A_HUMAN	I	215;13	ENSP00000221132:M215I;ENSP00000428884:M13I	ENSP00000221132:M215I	M	-	3	0	TNFRSF10A	23114203	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.036000	0.12185	0.158000	0.19367	0.655000	0.94253	ATG		0.592	TNFRSF10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215133.2	NM_003844	
ADAMDEC1	27299	broad.mit.edu	37	8	24256522	24256522	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:24256522A>G	ENST00000256412.4	+	9	1118	c.898A>G	c.(898-900)Aaa>Gaa	p.K300E	RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.K221E|RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.K221E	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	300	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.K300E(1)		NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TAACCTGGGGAAAAAGATCCA	0.512																																					p.K221E	Ovarian(147;687 1849 3699 25981 31337)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A661G	8						.						95.0	84.0	88.0					8																	24256522		2203	4300	6503	24312467	SO:0001583	missense	27299	exon8			Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.898A>G	8.37:g.24256522A>G	ENSP00000256412:p.Lys300Glu	Somatic		Capture	Illumina HiSeq	Phase_I	24312467	NM_001145272	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.579833	0.28180	.	.	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.63744	-0.06;-0.06;-0.06	5.51	-0.272	0.12919	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.454266	0.22584	N	0.058169	T	0.59715	0.2214	L	0.37561	1.115	0.09310	N	1	P	0.47962	0.903	P	0.60415	0.874	T	0.51490	-0.8699	10	0.62326	D	0.03	-8.2361	3.4713	0.07569	0.5578:0.2466:0.0758:0.1199	.	300	O15204	ADEC1_HUMAN	E	300;221;221	ENSP00000256412:K300E;ENSP00000442592:K221E;ENSP00000428993:K221E	ENSP00000256412:K300E	K	+	1	0	ADAMDEC1	24312467	0.084000	0.21492	0.000000	0.03702	0.008000	0.06430	1.517000	0.35867	-0.222000	0.09958	-1.139000	0.01908	AAA		0.512	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
ADRA1A	148	broad.mit.edu	37	8	26722444	26722444	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:26722444T>C	ENST00000519229.1	-	1	49	c.43A>G	c.(43-45)Acc>Gcc	p.T15A	ADRA1A_ENST00000380587.1_Missense_Mutation_p.T15A|ADRA1A_ENST00000380586.1_Missense_Mutation_p.T15A|ADRA1A_ENST00000380572.3_Missense_Mutation_p.T15A|ADRA1A_ENST00000358857.5_Missense_Mutation_p.T15A|ADRA1A_ENST00000380582.3_Missense_Mutation_p.T15A|ADRA1A_ENST00000354550.4_Missense_Mutation_p.T15A|ADRA1A_ENST00000380573.3_Missense_Mutation_p.T15A|ADRA1A_ENST00000276393.4_Missense_Mutation_p.T15A|ADRA1A_ENST00000380581.2_Missense_Mutation_p.T15A			P25100	ADA1D_HUMAN	adrenoceptor alpha 1A	0				MTFRDLLSVSFEGPRPDSSAGGSSAGGGGGSAGGAAPSEGP AVGGVPGGAGGGGGVVGAGSGEDNRSSAGEPGSAGAGGDVN G -> MAAALRSVMMAGYLSEWRTPTYRSTEMVQRLRMEAV QHSTS (in Ref. 1). {ECO:0000305}.	adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)	p.T15A(2)		breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|skin(1)	36		all_cancers(63;0.122)|Ovarian(32;2.61e-05)|all_epithelial(46;0.118)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0228)|Epithelial(17;4.92e-10)|Colorectal(74;0.0132)|READ - Rectum adenocarcinoma(644;0.115)	Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	GGCGGTTGGGTGCAGTTGGAG	0.637																																					p.T15A												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A43G	8						.						101.0	121.0	114.0					8																	26722444		2203	4300	6503	26778361	SO:0001583	missense	148	exon1			L31774	CCDS6052.1, CCDS6053.1, CCDS6054.1, CCDS34869.1	8p21.2	2012-08-08	2012-05-09		ENSG00000120907	ENSG00000120907		"""GPCR / Class A : Adrenoceptors : alpha"""	277	protein-coding gene	gene with protein product		104221	"""adrenergic, alpha-1A-, receptor"""	ADRA1C			Standard	NM_033303		Approved	ADRA1L1	uc003xfh.1	P35348	OTTHUMG00000099459	ENST00000519229.1:c.43A>G	8.37:g.26722444T>C	ENSP00000430793:p.Thr15Ala	Somatic		Capture	Illumina HiSeq	Phase_I	26778361	NM_033302	Q9NPY0	Missense_Mutation	SNP	ENST00000519229.1	37		.	.	.	.	.	.	.	.	.	.	T	15.75	2.926914	0.52759	.	.	ENSG00000120907	ENST00000380586;ENST00000380587;ENST00000380582;ENST00000380581;ENST00000519229;ENST00000354550;ENST00000276393;ENST00000380573;ENST00000380572;ENST00000358857	T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.37	5.37	0.77165	.	0.529823	0.21007	N	0.081759	T	0.44685	0.1305	N	0.24115	0.695	0.45403	D	0.998388	B;P;B;P;P;P	0.43287	0.366;0.507;0.155;0.749;0.802;0.656	B;B;B;B;B;B	0.44108	0.241;0.241;0.084;0.441;0.389;0.391	T	0.36504	-0.9745	10	0.33940	T	0.23	.	15.0418	0.71796	0.0:0.0:0.0:1.0	.	15;15;15;15;15;15	P35348-9;P35348-8;P35348;P35348-4;P35348-3;B0ZBD3	.;.;ADA1A_HUMAN;.;.;.	A	15	ENSP00000369960:T15A;ENSP00000369961:T15A;ENSP00000369956:T15A;ENSP00000369955:T15A;ENSP00000430793:T15A;ENSP00000346557:T15A;ENSP00000276393:T15A;ENSP00000369947:T15A;ENSP00000369946:T15A;ENSP00000351725:T15A	ENSP00000276393:T15A	T	-	1	0	ADRA1A	26778361	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.928000	0.70088	2.016000	0.59253	0.533000	0.62120	ACC		0.637	ADRA1A-009	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000376207.1	NM_033303	
NUGGC	389643	broad.mit.edu	37	8	27915781	27915781	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:27915781T>C	ENST00000413272.2	-	9	1252	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	NUGGC_ENST00000341513.6_Intron	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	370					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.A370A(1)									TTACATTTCCTGCCTTTCTTT	0.299																																					p.A370A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1110G	8						.						35.0	33.0	33.0					8																	27915781		1332	3009	4341	27971700	SO:0001819	synonymous_variant	389643	exon9			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.1110A>G	8.37:g.27915781T>C		Somatic		Capture	Illumina HiSeq	Phase_I	27971700	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																				0.299	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
NUGGC	389643	broad.mit.edu	37	8	27925207	27925207	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:27925207G>T	ENST00000413272.2	-	6	677	c.535C>A	c.(535-537)Ctg>Atg	p.L179M	NUGGC_ENST00000341513.6_Missense_Mutation_p.L179M	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	179					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.L179M(1)									TCTCTGCTCAGCTCCTCCGTC	0.542																																					p.L179M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C535A	8						.						78.0	81.0	80.0					8																	27925207		2058	4221	6279	27981126	SO:0001583	missense	389643	exon6			AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.535C>A	8.37:g.27925207G>T	ENSP00000408697:p.Leu179Met	Somatic		Capture	Illumina HiSeq	Phase_I	27981126	NM_001010906	Q6ZP73	Missense_Mutation	SNP	ENST00000413272.2	37	CCDS47833.1	.	.	.	.	.	.	.	.	.	.	G	10.87	1.473583	0.26423	.	.	ENSG00000189233	ENST00000413272;ENST00000341513	D;D	0.97138	-4.26;-4.26	6.1	0.829	0.18847	Dynamin, GTPase domain (1);	1.456400	0.04469	N	0.375657	D	0.93115	0.7808	N	0.22421	0.69	0.09310	N	1	P	0.46142	0.873	B	0.41440	0.357	D	0.87717	0.2570	10	0.38643	T	0.18	2.6797	6.3828	0.21544	0.2283:0.54:0.2317:0.0	.	179	Q68CJ6	SLIP_HUMAN	M	179	ENSP00000408697:L179M;ENSP00000345031:L179M	ENSP00000345031:L179M	L	-	1	2	C8orf80	27981126	0.043000	0.20138	0.000000	0.03702	0.314000	0.28054	0.374000	0.20501	0.128000	0.18479	0.603000	0.83216	CTG		0.542	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
SARAF	51669	broad.mit.edu	37	8	29931478	29931478	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:29931478C>A	ENST00000256255.6	-	2	454	c.197G>T	c.(196-198)tGt>tTt	p.C66F	TMEM66_ENST00000521083.1_5'UTR|TMEM66_ENST00000536273.1_Intron|TMEM66_ENST00000545648.1_Intron	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		66					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)		p.C66F(1)		endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		GCCTCCAACACATTTCAACTG	0.478																																					p.C66F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G197T	8						.						183.0	165.0	171.0					8																	29931478		2203	4300	6503	30051020	SO:0001583	missense	51669	exon2																														ENST00000256255.6:c.197G>T	8.37:g.29931478C>A	ENSP00000256255:p.Cys66Phe	Somatic		Capture	Illumina HiSeq	Phase_I	30051020	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	37	CCDS6074.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.5|23.5	4.428412|4.428412	0.83667|0.83667	.|.	.|.	ENSG00000133872|ENSG00000133872	ENST00000256255;ENST00000541035;ENST00000522794;ENST00000523761|ENST00000521265	T;T;T|.	0.74632|.	-0.86;-0.86;-0.86|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.84497|0.84497	0.5485|0.5485	M|M	0.90922|0.90922	3.16|3.16	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.999|.	D|D	0.87696|0.87696	0.2557|0.2557	10|5	0.87932|.	D|.	0|.	-18.6828|-18.6828	15.9519|15.9519	0.79846|0.79846	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	66;66|.	B3KQQ4;Q96BY9|.	.;TMM66_HUMAN|.	F|L	66;30;30;57|66	ENSP00000256255:C66F;ENSP00000429630:C30F;ENSP00000428832:C57F|.	ENSP00000256255:C66F|.	C|V	-|-	2|1	0|0	TMEM66|TMEM66	30051020|30051020	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	7.215000|7.215000	0.77966|0.77966	2.623000|2.623000	0.88846|0.88846	0.563000|0.563000	0.77884|0.77884	TGT|GTG		0.478	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4		
KCNU1	157855	broad.mit.edu	37	8	36698090	36698090	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:36698090C>T	ENST00000399881.3	+	15	1665	c.1628C>T	c.(1627-1629)gCc>gTc	p.A543V		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	543	Segment S8.				multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.A543V(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		CCTGAAGTTGCCCGGTAAGTG	0.428																																					p.A543V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1628T	8						.						84.0	77.0	79.0					8																	36698090		1895	4106	6001	36817248	SO:0001583	missense	157855	exon15			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1628C>T	8.37:g.36698090C>T	ENSP00000382770:p.Ala543Val	Somatic		Capture	Illumina HiSeq	Phase_I	36817248	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.680804	0.29872	.	.	ENSG00000215262	ENST00000399881	T	0.42131	0.98	5.7	1.55	0.23275	Potassium channel, calcium-activated, BK, alpha subunit (2);	0.436377	0.15569	U	0.255576	T	0.32675	0.0837	L	0.42245	1.32	0.80722	D	1	B	0.21071	0.051	B	0.20577	0.03	T	0.08659	-1.0711	10	0.41790	T	0.15	-4.5914	8.6853	0.34234	0.0:0.4328:0.4822:0.085	.	543	A8MYU2	KCNU1_HUMAN	V	543	ENSP00000382770:A543V	ENSP00000382770:A543V	A	+	2	0	KCNU1	36817248	0.993000	0.37304	0.238000	0.24106	0.389000	0.30415	0.428000	0.21395	0.291000	0.22468	-0.136000	0.14681	GCC		0.428	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
KCNU1	157855	broad.mit.edu	37	8	36766937	36766937	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:36766937A>G	ENST00000399881.3	+	21	2252	c.2215A>G	c.(2215-2217)Aga>Gga	p.R739G		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	739					multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)	p.R739G(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		AATGCCCTTGAGAGCCAGCAA	0.468																																					p.R739G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2215G	8						.						201.0	197.0	198.0					8																	36766937		1884	4109	5993	36886095	SO:0001583	missense	157855	exon21			BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.2215A>G	8.37:g.36766937A>G	ENSP00000382770:p.Arg739Gly	Somatic		Capture	Illumina HiSeq	Phase_I	36886095	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623719	0.66901	.	.	ENSG00000215262	ENST00000399881	T	0.52526	0.66	5.8	1.74	0.24563	.	0.000000	0.36268	U	0.002694	T	0.70509	0.3232	M	0.86502	2.82	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.76375	-0.2982	10	0.87932	D	0	-17.3931	13.9865	0.64339	0.5073:0.4926:0.0:0.0	.	739	A8MYU2	KCNU1_HUMAN	G	739	ENSP00000382770:R739G	ENSP00000382770:R739G	R	+	1	2	KCNU1	36886095	0.995000	0.38212	0.995000	0.50966	0.949000	0.60115	0.453000	0.21811	0.409000	0.25649	0.533000	0.62120	AGA		0.468	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	
DDHD2	23259	broad.mit.edu	37	8	38117622	38117622	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:38117622G>A	ENST00000397166.2	+	17	2644	c.2119G>A	c.(2119-2121)Gat>Aat	p.D707N	DDHD2_ENST00000529845.1_Missense_Mutation_p.D158N|DDHD2_ENST00000520272.2_Missense_Mutation_p.D707N|DDHD2_ENST00000517385.1_Missense_Mutation_p.D326N	NM_015214.2	NP_056029.2	O94830	DDHD2_HUMAN	DDHD domain containing 2	707					cell death (GO:0008219)|lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.D707N(1)		endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)|urinary_tract(2)	28	Colorectal(12;0.000442)	all_lung(54;0.0657)|Lung NSC(58;0.175)	BRCA - Breast invasive adenocarcinoma(5;3.76e-25)|COAD - Colon adenocarcinoma(9;0.0977)			TATCTTCCTTGATCAGCCTTT	0.323																																					p.D707N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2119A	8						.						135.0	131.0	133.0					8																	38117622		2203	4300	6503	38236779	SO:0001583	missense	23259	exon17			AK056525	CCDS34883.1	8p11.23	2014-03-03	2004-04-05	2004-04-07				"""Sterile alpha motif (SAM) domain containing"""	29106	protein-coding gene	gene with protein product		615003	"""SAM, WWE and DDHD domain containing 1"""	SAMWD1		9872452, 11788596, 19632984, 20932832	Standard	NM_015214		Approved	KIAA0725, SPG54	uc003xlc.3	O94830		ENST00000397166.2:c.2119G>A	8.37:g.38117622G>A	ENSP00000380352:p.Asp707Asn	Somatic		Capture	Illumina HiSeq	Phase_I	38236779	NM_001164232	B3KWV2|B3KXB5|Q9H8X7	Missense_Mutation	SNP	ENST00000397166.2	37	CCDS34883.1	.	.	.	.	.	.	.	.	.	.	G	35	5.469358	0.96274	.	.	ENSG00000085788	ENST00000397166;ENST00000520272;ENST00000517385;ENST00000529845;ENST00000528613	T;T	0.35236	1.32;1.32	5.62	5.62	0.85841	.	0.178958	0.49305	D	0.000160	T	0.58906	0.2155	M	0.73217	2.22	0.80722	D	1	D	0.62365	0.991	P	0.61477	0.889	T	0.61505	-0.7049	10	0.87932	D	0	-24.2941	18.6525	0.91435	0.0:0.0:1.0:0.0	.	707	O94830	DDHD2_HUMAN	N	707;707;326;158;75	ENSP00000380352:D707N;ENSP00000429932:D707N	ENSP00000380352:D707N	D	+	1	0	DDHD2	38236779	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.680000	0.98651	2.650000	0.89964	0.655000	0.94253	GAT		0.323	DDHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377251.2	XM_291291	
ADAM32	203102	broad.mit.edu	37	8	39091527	39091527	+	Missense_Mutation	SNP	G	G	A	rs569444981		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:39091527G>A	ENST00000379907.4	+	16	1871	c.1744G>A	c.(1744-1746)Gta>Ata	p.V582I	ADAM32_ENST00000519315.1_Missense_Mutation_p.V476I|ADAM32_ENST00000437682.2_Missense_Mutation_p.V483I	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	582						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			ATGCATAACTGTAGACTACAA	0.373																																					p.V582I												.	.	0			c.G1744A	8						.						69.0	61.0	63.0					8																	39091527		1856	4088	5944	39210684	SO:0001583	missense	203102	exon16			BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1744G>A	8.37:g.39091527G>A	ENSP00000369238:p.Val582Ile	None		Capture	Illumina HiSeq	Phase_I	39210684	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	G	1.148	-0.647625	0.03506	.	.	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.22134	1.97;1.97;1.97	4.88	-9.76	0.00503	ADAM, cysteine-rich (2);	0.964919	0.08390	N	0.953007	T	0.06050	0.0157	N	0.05280	-0.08	0.09310	N	1	B;B;B	0.18461	0.008;0.028;0.022	B;B;B	0.19946	0.01;0.009;0.027	T	0.27020	-1.0086	10	0.27082	T	0.32	.	1.6983	0.02866	0.1355:0.3152:0.2962:0.2531	.	483;476;582	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	I	483;476;582	ENSP00000405978:V483I;ENSP00000429422:V476I;ENSP00000369238:V582I	ENSP00000369238:V582I	V	+	1	0	ADAM32	39210684	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.887000	0.01617	-1.714000	0.01390	-1.283000	0.01379	GTA		0.373	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
AGPAT6	137964	broad.mit.edu	37	8	41467214	41467214	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:41467214C>T	ENST00000396987.3	+	4	1203	c.276C>T	c.(274-276)atC>atT	p.I92I	RP11-360L9.8_ENST00000581909.1_RNA	NM_178819.3	NP_848934.1	Q86UL3	GPAT4_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 6	92					acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|fatty acid metabolic process (GO:0006631)|glandular epithelial cell maturation (GO:0002071)|glycerophospholipid biosynthetic process (GO:0046474)|lactation (GO:0007595)|lipid biosynthetic process (GO:0008610)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			endometrium(3)|kidney(2)|large_intestine(3)|lung(6)	14	Ovarian(28;0.00769)|Colorectal(14;0.0202)|Lung SC(25;0.211)	all_lung(54;0.0131)|Lung NSC(58;0.0363)|Hepatocellular(245;0.0462)|Esophageal squamous(32;0.0844)	OV - Ovarian serous cystadenocarcinoma(14;0.00126)|Colorectal(10;0.0014)|Lung(22;0.00177)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0147)			AAGAAGAGATCAAAGAGATTC	0.478																																					p.I92I												.	.	0			c.C276T	8						.						104.0	102.0	103.0					8																	41467214		2203	4300	6503	41586371	SO:0001819	synonymous_variant	137964	exon4			AF406612	CCDS6117.1	8p11.21	2013-02-05	2013-02-05			ENSG00000158669	2.3.1.15	"""1-acylglycerol-3-phosphate O-acyltransferases"""	20880	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, zeta"""	608143	"""1-acylglycerol-3-phosphate O-acyltransferase 6 (lysophosphatidic acid acyltransferase, zeta)"""			12938015	Standard	NM_178819		Approved	DKFZp586M1819, LPAAT-zeta	uc003xnz.2	Q86UL3		ENST00000396987.3:c.276C>T	8.37:g.41467214C>T		None		Capture	Illumina HiSeq	Phase_I	41586371	NM_178819	Q86V89	Silent	SNP	ENST00000396987.3	37	CCDS6117.1																																																																																				0.478	AGPAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377158.1	NM_178819	
SDR16C5	195814	broad.mit.edu	37	8	57219303	57219303	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:57219303C>A	ENST00000303749.3	-	5	1279	c.642G>T	c.(640-642)aaG>aaT	p.K214N	SDR16C5_ENST00000522671.1_Missense_Mutation_p.K214N|SDR16C5_ENST00000396721.2_Missense_Mutation_p.K170N	NM_138969.2	NP_620419.2	Q8N3Y7	RDHE2_HUMAN	short chain dehydrogenase/reductase family 16C, member 5	214					detection of light stimulus involved in visual perception (GO:0050908)|keratinocyte proliferation (GO:0043616)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	retinol dehydrogenase activity (GO:0004745)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)	16						TTTTGATCCCCTTTTGTTTTT	0.348																																					p.K214N												.	.	0			c.G642T	8						.						80.0	77.0	78.0					8																	57219303		2203	4300	6503	57381857	SO:0001583	missense	195814	exon5				CCDS6167.1	8q12.1	2011-09-20			ENSG00000170786	ENSG00000170786	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	30311	protein-coding gene	gene with protein product		608989				12372410	Standard	NM_138969		Approved	RDHE2, RDH-E2	uc003xsy.1	Q8N3Y7	OTTHUMG00000164311	ENST00000303749.3:c.642G>T	8.37:g.57219303C>A	ENSP00000307607:p.Lys214Asn	None		Capture	Illumina HiSeq	Phase_I	57381857	NM_138969	B4DGK2|Q330K3|Q8TDV9|Q96LX1	Missense_Mutation	SNP	ENST00000303749.3	37	CCDS6167.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.334303	0.24253	.	.	ENSG00000170786	ENST00000396721;ENST00000303749;ENST00000522671;ENST00000538514	D;D;T	0.89875	-2.58;-2.58;0.71	5.55	-9.82	0.00484	NAD(P)-binding domain (1);	0.932070	0.09190	N	0.836129	T	0.62282	0.2415	N	0.02765	-0.5	0.21740	N	0.99956	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.12156	0.005;0.007;0.002	T	0.57248	-0.7844	10	0.16896	T	0.51	.	1.9853	0.03435	0.4811:0.1153:0.2157:0.1879	.	170;214;214	Q8N3Y7-2;G3V145;Q8N3Y7	.;.;RDHE2_HUMAN	N	170;214;214;214	ENSP00000379947:K170N;ENSP00000307607:K214N;ENSP00000431010:K214N	ENSP00000307607:K214N	K	-	3	2	SDR16C5	57381857	0.001000	0.12720	0.000000	0.03702	0.675000	0.39556	-0.829000	0.04415	-1.294000	0.02360	0.655000	0.94253	AAG		0.348	SDR16C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378235.1	NM_138969	
FAM110B	90362	broad.mit.edu	37	8	59059301	59059301	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:59059301G>A	ENST00000361488.3	+	5	1392	c.512G>A	c.(511-513)cGc>cAc	p.R171H	FAM110B_ENST00000520369.1_Intron	NM_147189.2	NP_671722.1	Q8TC76	F110B_HUMAN	family with sequence similarity 110, member B	171						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.R171H(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(10)|lung(9)|skin(2)	26		all_epithelial(80;0.025)|all_lung(136;0.0274)|Lung NSC(129;0.0355)				ACGCAGGGCCGCAGGAGCCCG	0.682																																					p.R171H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G512A	8						.						21.0	22.0	22.0					8																	59059301		2202	4300	6502	59221855	SO:0001583	missense	90362	exon5			U79298	CCDS6170.1	8q12.1	2007-06-21	2007-03-21	2007-03-21		ENSG00000169122			28587	protein-coding gene	gene with protein product		611394	"""chromosome 8 open reading frame 72"""	C8orf72		8619474, 9110174, 17499476	Standard	XM_005251324		Approved	MGC39325	uc003xtj.1	Q8TC76		ENST00000361488.3:c.512G>A	8.37:g.59059301G>A	ENSP00000355204:p.Arg171His	Somatic		Capture	Illumina HiSeq	Phase_I	59221855	NM_147189	Q5BM08|Q9Y4K2	Missense_Mutation	SNP	ENST00000361488.3	37	CCDS6170.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.025572	0.35701	.	.	ENSG00000169122	ENST00000361488	T	0.32988	1.43	5.49	1.89	0.25635	.	0.342627	0.31268	N	0.007945	T	0.16769	0.0403	N	0.19112	0.55	0.34563	D	0.712592	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	9	.	.	.	-10.0304	9.4771	0.38878	0.3204:0.0:0.6796:0.0	.	171	Q8TC76	F110B_HUMAN	H	171	ENSP00000355204:R171H	.	R	+	2	0	FAM110B	59221855	0.279000	0.24239	0.998000	0.56505	0.902000	0.53008	1.929000	0.40114	0.553000	0.29044	0.561000	0.74099	CGC		0.682	FAM110B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378095.2	NM_147189	
PREX2	80243	broad.mit.edu	37	8	68864669	68864669	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:68864669G>A	ENST00000288368.4	+	1	317	c.40G>A	c.(40-42)Gcc>Acc	p.A14T	PREX2_ENST00000529398.1_3'UTR	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	14					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.A14T(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CGCCGAGAGCGCCAAGGACCT	0.721																																					p.A14T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G40A	8						.						21.0	21.0	21.0					8																	68864669		2190	4290	6480	69027223	SO:0001583	missense	80243	exon1			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.40G>A	8.37:g.68864669G>A	ENSP00000288368:p.Ala14Thr	Somatic		Capture	Illumina HiSeq	Phase_I	69027223	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	19.21	3.783422	0.70222	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.67865	-0.29	5.38	4.49	0.54785	Dbl homology (DH) domain (1);	0.291823	0.30649	N	0.009170	T	0.69424	0.3109	N	0.19112	0.55	0.37199	D	0.904301	P;B;B;D	0.89917	0.89;0.007;0.068;1.0	B;B;B;D	0.69307	0.221;0.004;0.021;0.963	T	0.74447	-0.3662	10	0.39692	T	0.17	.	15.9666	0.79979	0.0:0.1354:0.8646:0.0	.	14;14;14;14	Q70Z35-2;Q70Z35;Q70Z35-3;F8WD63	.;PREX2_HUMAN;.;.	T	14	ENSP00000288368:A14T	ENSP00000288368:A14T	A	+	1	0	PREX2	69027223	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.685000	0.61693	1.231000	0.43661	0.484000	0.47621	GCC		0.721	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
PREX2	80243	broad.mit.edu	37	8	69002879	69002879	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:69002879G>A	ENST00000288368.4	+	20	2456	c.2179G>A	c.(2179-2181)Gtc>Atc	p.V727I	PREX2_ENST00000529398.1_3'UTR|RP11-403D15.2_ENST00000526901.1_RNA	NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	727	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)	p.V727I(2)		NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						TGGAATCAATGTCAGCAAAGA	0.453																																					p.V727I												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G2179A	8						.						125.0	109.0	115.0					8																	69002879		2203	4300	6503	69165433	SO:0001583	missense	80243	exon20			AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.2179G>A	8.37:g.69002879G>A	ENSP00000288368:p.Val727Ile	Somatic		Capture	Illumina HiSeq	Phase_I	69165433	NM_025170	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Missense_Mutation	SNP	ENST00000288368.4	37	CCDS6201.1	.	.	.	.	.	.	.	.	.	.	G	36	5.870873	0.97049	.	.	ENSG00000046889	ENST00000288368;ENST00000396539;ENST00000354677	T	0.26810	1.71	5.89	5.89	0.94794	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.44286	0.1286	L	0.41710	1.295	0.80722	D	1	D;D;P	0.58620	0.983;0.981;0.937	P;D;P	0.63957	0.835;0.92;0.73	T	0.21075	-1.0256	10	0.87932	D	0	.	20.2508	0.98407	0.0:0.0:1.0:0.0	.	727;727;727	Q70Z35-2;Q70Z35;Q70Z35-3	.;PREX2_HUMAN;.	I	727	ENSP00000288368:V727I	ENSP00000288368:V727I	V	+	1	0	PREX2	69165433	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.525000	0.98039	2.788000	0.95919	0.585000	0.79938	GTC		0.453	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
JPH1	56704	broad.mit.edu	37	8	75227412	75227412	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:75227412C>T	ENST00000342232.4	-	2	863	c.823G>A	c.(823-825)Gcc>Acc	p.A275T		NM_020647.2	NP_065698.1	Q9HDC5	JPH1_HUMAN	junctophilin 1	275					calcium ion transport into cytosol (GO:0060402)|muscle organ development (GO:0007517)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.A275T(2)		endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	24	Breast(64;0.00576)		BRCA - Breast invasive adenocarcinoma(89;0.0499)|Epithelial(68;0.0728)|all cancers(69;0.176)			GTGGTGGTGGCGTCCACGTGG	0.562																																					p.A275T												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.G823A	8						.						116.0	111.0	113.0					8																	75227412		2203	4300	6503	75389967	SO:0001583	missense	56704	exon2			AB042634	CCDS6217.1	8q21	2008-07-03			ENSG00000104369	ENSG00000104369			14201	protein-coding gene	gene with protein product		605266				10891348, 10949023	Standard	XM_005251273		Approved	JP-1	uc003yae.3	Q9HDC5	OTTHUMG00000164524	ENST00000342232.4:c.823G>A	8.37:g.75227412C>T	ENSP00000344488:p.Ala275Thr	Somatic		Capture	Illumina HiSeq	Phase_I	75389967	NM_020647	B2RTZ0	Missense_Mutation	SNP	ENST00000342232.4	37	CCDS6217.1	.	.	.	.	.	.	.	.	.	.	C	33	5.280215	0.95489	.	.	ENSG00000104369	ENST00000342232	T	0.46063	0.88	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.66036	0.2749	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.63497	-0.6624	10	0.23302	T	0.38	.	18.2573	0.90023	0.0:1.0:0.0:0.0	.	275	Q9HDC5	JPH1_HUMAN	T	275	ENSP00000344488:A275T	ENSP00000344488:A275T	A	-	1	0	JPH1	75389967	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.597000	0.82733	2.519000	0.84933	0.655000	0.94253	GCC		0.562	JPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379102.1		
HNF4G	3174	broad.mit.edu	37	8	76471256	76471256	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:76471256G>T	ENST00000354370.1	+	9	1236	c.966G>T	c.(964-966)caG>caT	p.Q322H	HNF4G_ENST00000396423.2_Missense_Mutation_p.Q359H			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	322					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ATCTACTTCAGGAAATGCTAT	0.338																																					p.Q359H												.	.	0			c.G1077T	8						.						67.0	70.0	69.0					8																	76471256		2203	4300	6503	76633811	SO:0001583	missense	3174	exon8				CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.966G>T	8.37:g.76471256G>T	ENSP00000346339:p.Gln322His	None		Capture	Illumina HiSeq	Phase_I	76633811	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	G	12.07	1.828067	0.32329	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94687	-3.49;-3.49	5.52	3.62	0.41486	Nuclear hormone receptor, ligand-binding (2);	0.156567	0.64402	N	0.000013	D	0.91102	0.7199	L	0.47190	1.495	0.54753	D	0.999988	B;B	0.22541	0.071;0.054	B;B	0.23275	0.017;0.045	D	0.88710	0.3222	10	0.59425	D	0.04	.	10.8244	0.46622	0.0711:0.1309:0.798:0.0	.	359;322	F1D8Q4;Q14541	.;HNF4G_HUMAN	H	322;359	ENSP00000346339:Q322H;ENSP00000379701:Q359H	ENSP00000346339:Q322H	Q	+	3	2	HNF4G	76633811	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	2.624000	0.46444	1.325000	0.45301	0.655000	0.94253	CAG		0.338	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
ZFHX4	79776	broad.mit.edu	37	8	77765696	77765696	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:77765696C>T	ENST00000521891.2	+	10	6987	c.6539C>T	c.(6538-6540)aCg>aTg	p.T2180M	ZFHX4_ENST00000518282.1_Missense_Mutation_p.T2154M|ZFHX4_ENST00000050961.6_Missense_Mutation_p.T2135M|ZFHX4_ENST00000455469.2_Missense_Mutation_p.T2135M	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2135					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.T2164M(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			TTTAGAAATACGCTTTTTAAG	0.373										HNSCC(33;0.089)																											p.T2180M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C6539T	8						.						112.0	109.0	110.0					8																	77765696		1835	4088	5923	77928251	SO:0001583	missense	79776	exon10				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.6539C>T	8.37:g.77765696C>T	ENSP00000430497:p.Thr2180Met	Somatic		Capture	Illumina HiSeq	Phase_I	77928251	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.528804	0.44969	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93	3.92	3.92	0.45320	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.45867	U	0.000339	D	0.97291	0.9114	M	0.73598	2.24	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	D	0.97314	0.9939	10	0.48119	T	0.1	.	16.4682	0.84092	0.0:1.0:0.0:0.0	.	2135;2135;2180	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	M	2180;2164;2135;2135;2154	ENSP00000430497:T2180M;ENSP00000399605:T2135M;ENSP00000050961:T2135M;ENSP00000430848:T2154M	ENSP00000050961:T2135M	T	+	2	0	ZFHX4	77928251	1.000000	0.71417	0.774000	0.31636	0.697000	0.40408	7.548000	0.82154	2.200000	0.70718	0.455000	0.32223	ACG		0.373	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
RALYL	138046	broad.mit.edu	37	8	85686889	85686889	+	Splice_Site	SNP	G	G	T	rs202116573	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:85686889G>T	ENST00000521268.1	+	3	1437	c.332G>T	c.(331-333)aGa>aTa	p.R111I	RALYL_ENST00000521376.1_Splice_Site_p.R38I|RALYL_ENST00000522455.1_Splice_Site_p.R111I|RALYL_ENST00000523850.1_Splice_Site_p.R38I|RALYL_ENST00000517638.1_Splice_Site_p.R124I|RALYL_ENST00000521695.1_Splice_Site_p.R111I|RALYL_ENST00000518566.1_Splice_Site_p.S111I	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	111							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						GCACTTTACAGGTAAGTAGAT	0.348																																					p.R111I												.	.	0			c.G332T	8						.						57.0	56.0	56.0					8																	85686889		1813	4087	5900	85849444	SO:0001630	splice_region_variant	138046	exon4				CCDS55252.1, CCDS55253.1, CCDS75760.1, CCDS75761.1	8q21.2	2013-07-16			ENSG00000184672	ENSG00000184672		"""RNA binding motif (RRM) containing"""	27036	protein-coding gene	gene with protein product		614648				12688537	Standard	NM_001100391		Approved	HNRPCL3	uc003yct.4	Q86SE5	OTTHUMG00000164628	ENST00000521268.1:c.332+1G>T	8.37:g.85686889G>T		None		Capture	Illumina HiSeq	Phase_I	85849444	NM_001100392	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	37	CCDS55253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	28.3|28.3	4.904187|4.904187	0.92035|0.92035	.|.	.|.	ENSG00000184672|ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000517638;ENST00000523850;ENST00000521376|ENST00000518566	T;T;T;T;T;T|T	0.18960|0.12879	2.78;2.78;2.78;2.78;2.46;2.18|2.64	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.199659|.	0.53938|.	D|.	0.000053|.	T|T	0.12646|0.12646	0.0307|0.0307	L|L	0.34521|0.34521	1.04|1.04	0.48135|0.48135	D|D	0.999594|0.999594	P;P;D;P|B	0.57257|0.19331	0.944;0.911;0.979;0.944|0.035	B;P;P;B|B	0.54889|0.17098	0.395;0.461;0.763;0.395|0.017	T|T	0.11891|0.11891	-1.0569|-1.0569	10|8	0.72032|.	D|.	0.01|.	-8.0326|-8.0326	16.9159|16.9159	0.86152|0.86152	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	111;38;124;111|111	B3KSX3;Q86SE5-2;G3V129;Q86SE5|B3KT61	.;.;.;RALYL_HUMAN|.	I|I	111;111;111;124;38;38|111	ENSP00000430394:R111I;ENSP00000428667:R111I;ENSP00000430367:R111I;ENSP00000430128:R124I;ENSP00000428807:R38I;ENSP00000428310:R38I|ENSP00000430065:S111I	ENSP00000430128:R124I|.	R|S	+|+	2|2	0|0	RALYL|RALYL	85849444|85849444	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	5.747000|5.747000	0.68689|0.68689	2.724000|2.724000	0.93272|0.93272	0.655000|0.655000	0.94253|0.94253	AGA|AGC		0.348	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1		Missense_Mutation
E2F5	1875	broad.mit.edu	37	8	86121614	86121614	+	Nonsense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:86121614C>T	ENST00000416274.2	+	6	887	c.853C>T	c.(853-855)Cag>Tag	p.Q285*	E2F5_ENST00000521429.1_Nonsense_Mutation_p.Q112*|E2F5_ENST00000418930.2_Nonsense_Mutation_p.Q285*|E2F5_ENST00000519128.1_3'UTR|E2F5_ENST00000517476.1_Nonsense_Mutation_p.Q124*|E2F5_ENST00000256117.5_Nonsense_Mutation_p.Q286*	NM_001083588.1|NM_001951.3	NP_001077057.1|NP_001942.2	Q15329	E2F5_HUMAN	E2F transcription factor 5, p130-binding	285					gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Q285*(1)		NS(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	8						CCAGGCTCTGCAGCAGACATC	0.458																																					p.Q285X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C853T	8						.						35.0	34.0	35.0					8																	86121614		1894	4137	6031	86308866	SO:0001587	stop_gained	1875	exon6			X86097	CCDS47885.1, CCDS47886.1, CCDS55254.1	8q21.2	2004-01-29			ENSG00000133740	ENSG00000133740			3119	protein-coding gene	gene with protein product		600967				7892279	Standard	NM_001083588		Approved		uc003ycz.4	Q15329	OTTHUMG00000164785	ENST00000416274.2:c.853C>T	8.37:g.86121614C>T	ENSP00000398124:p.Gln285*	Somatic		Capture	Illumina HiSeq	Phase_I	86308866	NM_001083588	E9PBN9|Q16601|Q92756	Nonsense_Mutation	SNP	ENST00000416274.2	37	CCDS47885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.643942|7.643942	0.98409|0.98409	.|.	.|.	ENSG00000133740|ENSG00000133740	ENST00000520225|ENST00000418930;ENST00000256117;ENST00000416274;ENST00000517476;ENST00000521429;ENST00000518234	.|.	.|.	.|.	6.17|6.17	5.29|5.29	0.74685|0.74685	.|.	.|1.266670	.|0.04849	.|N	.|0.442044	T|.	0.31420|.	0.0796|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.23619|.	-1.0183|.	3|.	.|0.12766	.|T	.|0.61	-4.6481|-4.6481	10.1556|10.1556	0.42820|0.42820	0.0:0.7919:0.1375:0.0705|0.0:0.7919:0.1375:0.0705	.|.	.|.	.|.	.|.	V|X	56|285;286;285;124;112;121	.|.	.|ENSP00000256117:Q286X	A|Q	+|+	2|1	0|0	E2F5|E2F5	86308866|86308866	0.956000|0.956000	0.32656|0.32656	0.906000|0.906000	0.35671|0.35671	0.820000|0.820000	0.46376|0.46376	2.624000|2.624000	0.46444|0.46444	1.593000|1.593000	0.50029|0.50029	0.655000|0.655000	0.94253|0.94253	GCA|CAG		0.458	E2F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380274.1	NM_001951	
CNGB3	54714	broad.mit.edu	37	8	87590976	87590976	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:87590976C>T	ENST00000320005.5	-	17	2091	c.2044G>A	c.(2044-2046)Ggc>Agc	p.G682S		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	682					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.G682S(1)		NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						TTTCCTGTGCCTCCTAGGAGA	0.493																																					p.G682S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2044A	8						.						168.0	157.0	161.0					8																	87590976		2203	4300	6503	87660092	SO:0001583	missense	54714	exon17			AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.2044G>A	8.37:g.87590976C>T	ENSP00000316605:p.Gly682Ser	Somatic		Capture	Illumina HiSeq	Phase_I	87660092	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	C	7.925	0.739361	0.15642	.	.	ENSG00000170289	ENST00000517327;ENST00000320005	T;T	0.76709	-1.04;0.23	5.34	-0.76	0.11041	.	0.637827	0.14922	N	0.290583	T	0.58075	0.2097	N	0.19112	0.55	0.09310	N	1	B;B	0.16166	0.016;0.009	B;B	0.23852	0.049;0.022	T	0.41233	-0.9520	10	0.08837	T	0.75	.	9.7421	0.40424	0.0:0.5746:0.0:0.4254	.	677;682	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	S	73;682	ENSP00000428329:G73S;ENSP00000316605:G682S	ENSP00000316605:G682S	G	-	1	0	CNGB3	87660092	0.004000	0.15560	0.000000	0.03702	0.255000	0.26057	0.333000	0.19768	-0.509000	0.06532	0.467000	0.42956	GGC		0.493	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
OTUD6B	51633	broad.mit.edu	37	8	92090840	92090840	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:92090840T>C	ENST00000285420.4	+	4	761	c.662T>C	c.(661-663)gTg>gCg	p.V221A	OTUD6B_ENST00000404789.3_Missense_Mutation_p.V90A	NM_016023.3	NP_057107.3	Q8N6M0	OTU6B_HUMAN	OTU domain containing 6B	191	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|Variable-loop. {ECO:0000250}.						cysteine-type peptidase activity (GO:0008234)	p.V191A(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11			BRCA - Breast invasive adenocarcinoma(11;0.0187)			CAAAGCCATGTGGAAGACTTT	0.358																																					p.V221A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T662C	8						.						55.0	51.0	52.0					8																	92090840		2202	4300	6502	92160016	SO:0001583	missense	51633	exon4				CCDS6253.2, CCDS69513.1	8q21.3	2013-01-21			ENSG00000155100	ENSG00000155100		"""OTU domain containing"""	24281	protein-coding gene	gene with protein product		612021					Standard	NM_016023		Approved	CGI-77, DUBA5	uc003yeu.4	Q8N6M0	OTTHUMG00000150758	ENST00000285420.4:c.662T>C	8.37:g.92090840T>C	ENSP00000285420:p.Val221Ala	Somatic		Capture	Illumina HiSeq	Phase_I	92160016	NM_016023	A8K6I1|B4DEY0|Q9NTA4|Q9Y387	Missense_Mutation	SNP	ENST00000285420.4	37	CCDS6253.2	.	.	.	.	.	.	.	.	.	.	T	2.102	-0.405863	0.04832	.	.	ENSG00000155100	ENST00000285420;ENST00000404789	T;T	0.27256	1.68;1.68	5.56	1.85	0.25348	Ovarian tumour, otubain (2);	0.525259	0.20894	N	0.083767	T	0.09024	0.0223	N	0.05280	-0.08	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.14023	0.01;0.002	T	0.37174	-0.9717	10	0.07813	T	0.8	-0.6467	5.2388	0.15460	0.0:0.2888:0.2681:0.4431	.	90;191	B4DEY0;Q8N6M0	.;OTU6B_HUMAN	A	221;90	ENSP00000285420:V221A;ENSP00000384190:V90A	ENSP00000285420:V221A	V	+	2	0	OTUD6B	92160016	0.015000	0.18098	0.354000	0.25760	0.904000	0.53231	1.022000	0.30052	0.080000	0.16959	-0.263000	0.10527	GTG		0.358	OTUD6B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319968.1	NM_016023	
INTS8	55656	broad.mit.edu	37	8	95885679	95885679	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:95885679G>A	ENST00000523731.1	+	22	2744	c.2611G>A	c.(2611-2613)Gtg>Atg	p.V871M	INTS8_ENST00000447247.1_Missense_Mutation_p.V871M	NM_017864.2	NP_060334.2	Q75QN2	INT8_HUMAN	integrator complex subunit 8	871					snRNA processing (GO:0016180)	integrator complex (GO:0032039)		p.V871M(1)		breast(3)|endometrium(3)|kidney(1)|large_intestine(9)|liver(1)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	28	Breast(36;1.05e-06)					TAACAAGGCTGTGCCCCCTGA	0.458																																					p.V871M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2611A	8						.						238.0	225.0	229.0					8																	95885679		2203	4300	6503	95954855	SO:0001583	missense	55656	exon22			AK091278	CCDS34925.1	8q22.1	2007-05-03	2006-03-15	2006-03-15	ENSG00000164941	ENSG00000164941			26048	protein-coding gene	gene with protein product		611351	"""chromosome 8 open reading frame 52"""	C8orf52		16239144	Standard	NM_017864		Approved	FLJ20530, INT8, MGC131633	uc003yhb.4	Q75QN2	OTTHUMG00000164695	ENST00000523731.1:c.2611G>A	8.37:g.95885679G>A	ENSP00000430338:p.Val871Met	Somatic		Capture	Illumina HiSeq	Phase_I	95954855	NM_017864	B2RN92|Q5RKZ3|Q6P1R5|Q7Z314|Q9NVS6|Q9NWY7	Missense_Mutation	SNP	ENST00000523731.1	37	CCDS34925.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720889	0.89205	.	.	ENSG00000164941	ENST00000523731;ENST00000447247	T;T	0.39056	1.1;1.1	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.61009	0.2313	L	0.55834	1.745	0.80722	D	1	D	0.71674	0.998	D	0.73380	0.98	T	0.65319	-0.6197	10	0.87932	D	0	-20.5555	17.9015	0.88905	0.0:0.0:1.0:0.0	.	871	Q75QN2	INT8_HUMAN	M	871	ENSP00000430338:V871M;ENSP00000398203:V871M	ENSP00000398203:V871M	V	+	1	0	INTS8	95954855	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.210000	0.71456	0.655000	0.94253	GTG		0.458	INTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379794.1	NM_017864	
PTDSS1	9791	broad.mit.edu	37	8	97274282	97274282	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:97274282T>C	ENST00000517309.1	+	1	340	c.14T>C	c.(13-15)gTg>gCg	p.V5A	MTERFD1_ENST00000287025.3_5'Flank|PTDSS1_ENST00000455950.2_5'UTR|MTERFD1_ENST00000523821.1_5'Flank	NM_014754.1	NP_055569.1	P48651	PTSS1_HUMAN	phosphatidylserine synthase 1	5					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)	p.V5A(1)		endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|stomach(1)	29	Breast(36;6.18e-05)				Phosphatidylserine(DB00144)	GCGTCCTGCGTGGGGAGCCGG	0.617																																					p.V5A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T14C	8						.						103.0	83.0	89.0					8																	97274282		2203	4300	6503	97343458	SO:0001583	missense	9791	exon1			D14694	CCDS6271.1	8q22	2008-05-02			ENSG00000156471	ENSG00000156471			9587	protein-coding gene	gene with protein product		612792					Standard	NM_014754		Approved	KIAA0024, PSSA, PSS1	uc003yht.1	P48651	OTTHUMG00000164687	ENST00000517309.1:c.14T>C	8.37:g.97274282T>C	ENSP00000430548:p.Val5Ala	Somatic		Capture	Illumina HiSeq	Phase_I	97343458	NM_014754	E5RFC5|Q9BUQ5	Missense_Mutation	SNP	ENST00000517309.1	37	CCDS6271.1	.	.	.	.	.	.	.	.	.	.	T	11.43	1.635331	0.29068	.	.	ENSG00000156471	ENST00000517309	T	0.42513	0.97	4.04	4.04	0.47022	.	0.373742	0.25666	N	0.029105	T	0.15565	0.0375	N	0.02011	-0.69	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08806	-1.0704	10	0.14656	T	0.56	-1.8187	8.8582	0.35240	0.0:0.0:0.1888:0.8111	.	5	P48651	PTSS1_HUMAN	A	5	ENSP00000430548:V5A	ENSP00000337331:V5A	V	+	2	0	PTDSS1	97343458	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.288000	0.33296	1.690000	0.51089	0.455000	0.32223	GTG		0.617	PTDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379743.2		
PLEC	5339	broad.mit.edu	37	8	145000974	145000975	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	AG	AG	AG	-	AG	AG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:145000974_145000975delAG	ENST00000322810.4	-	30	4601_4602	c.4432_4433delCT	c.(4432-4434)ctgfs	p.L1478fs	PLEC_ENST00000345136.3_Frame_Shift_Del_p.L1341fs|PLEC_ENST00000354589.3_Frame_Shift_Del_p.L1341fs|PLEC_ENST00000436759.2_Frame_Shift_Del_p.L1368fs|PLEC_ENST00000357649.2_Frame_Shift_Del_p.L1345fs|PLEC_ENST00000527096.1_Frame_Shift_Del_p.L1364fs|PLEC_ENST00000398774.2_Frame_Shift_Del_p.L1309fs|PLEC_ENST00000354958.2_Frame_Shift_Del_p.L1319fs|PLEC_ENST00000356346.3_Frame_Shift_Del_p.L1327fs	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1478	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)	p.L1478fs*11(1)|p.L1368fs*11(1)		NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CATGCGCCGCAGAGTCTCGCTG	0.604																																					p.1345_1345del												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.4033_4034del	8						.																																			145072963	SO:0001589	frameshift_variant	5339	exon30			U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.4432_4433delCT	8.37:g.145000976_145000977delAG	ENSP00000323856:p.Leu1478fs	Somatic		Capture	Illumina HiSeq	Phase_I	145072962	NM_201383	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Frame_Shift_Del	DEL	ENST00000322810.4	37	CCDS43772.1																																																																																				0.604	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
DGAT1	8694	broad.mit.edu	37	8	145541223	145541223	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:145541223C>T	ENST00000332324.4	-	12	1238	c.965G>A	c.(964-966)cGc>cAc	p.R322H	GS1-393G12.12_ENST00000525023.1_RNA|DGAT1_ENST00000527438.1_5'Flank	NM_012079.4	NP_036211.2	O75907	DGAT1_HUMAN	diacylglycerol O-acyltransferase 1	322					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|diacylglycerol metabolic process (GO:0046339)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|triglyceride metabolic process (GO:0006641)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	diacylglycerol O-acyltransferase activity (GO:0004144)|retinol O-fatty-acyltransferase activity (GO:0050252)|transferase activity, transferring acyl groups (GO:0016746)	p.R322H(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	9	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.94e-40)|Epithelial(56;7.67e-40)|all cancers(56;7.88e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0441)|Colorectal(110;0.055)			CTTCAGGAGGCGCTCGATGAT	0.617																																					p.R322H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G965A	8						.						174.0	163.0	167.0					8																	145541223		2203	4296	6499	145512031	SO:0001583	missense	8694	exon12			AF059202	CCDS6420.1	8q24.3	2014-05-06	2010-06-24	2001-11-09	ENSG00000185000	ENSG00000185000	2.3.1.20		2843	protein-coding gene	gene with protein product		604900	"""diacylglycerol O-acyltransferase homolog 1 (mouse)"""			9756920	Standard	NM_012079		Approved	ARGP1, DGAT	uc003zbv.3	O75907	OTTHUMG00000174606	ENST00000332324.4:c.965G>A	8.37:g.145541223C>T	ENSP00000332258:p.Arg322His	Somatic		Capture	Illumina HiSeq	Phase_I	145512031	NM_012079	B2RWQ2|D3DWL6|Q96BB8	Missense_Mutation	SNP	ENST00000332324.4	37	CCDS6420.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.852345	0.71719	.	.	ENSG00000185000	ENST00000332324	T	0.73047	-0.71	5.27	4.33	0.51752	.	0.000000	0.85682	D	0.000000	D	0.85128	0.5626	M	0.88450	2.955	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.87469	0.2413	10	0.87932	D	0	-1.788	12.352	0.55153	0.1695:0.8305:0.0:0.0	.	322	O75907	DGAT1_HUMAN	H	322	ENSP00000332258:R322H	ENSP00000332258:R322H	R	-	2	0	DGAT1	145512031	0.998000	0.40836	0.998000	0.56505	0.567000	0.35839	3.781000	0.55394	2.475000	0.83589	0.555000	0.69702	CGC		0.617	DGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382059.3	NM_012079	
COMMD5	28991	broad.mit.edu	37	8	146076499	146076501	+	In_Frame_Del	DEL	GGC	GGC	-	rs369531136		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	GGC	GGC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:146076499_146076501delGGC	ENST00000305103.3	-	2	475_477	c.223_225delGCC	c.(223-225)gccdel	p.A75del	COMMD5_ENST00000450361.2_In_Frame_Del_p.A75del|AF235103.1_ENST00000578937.1_RNA|COMMD5_ENST00000402718.3_In_Frame_Del_p.A75del	NM_014066.3	NP_054785.2	Q9GZQ3	COMD5_HUMAN	COMM domain containing 5	75						nucleus (GO:0005634)		p.A75delA(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|ovary(1)|pancreas(1)	11	all_cancers(97;1.14e-11)|all_epithelial(106;7.74e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;8.75e-39)|OV - Ovarian serous cystadenocarcinoma(54;1.13e-38)|all cancers(56;8.48e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CCGGCAGGTTGGCGCTGACCCCA	0.645																																					p.75_75del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.223_225del	8						.																																			146047305	SO:0001651	inframe_deletion	28991	exon2			AK023070	CCDS6436.1	8q24.3	2006-11-06				ENSG00000170619			17902	protein-coding gene	gene with protein product		608216				15799966, 10918053	Standard	NM_014066		Approved	HT002, FLJ13008, HCaRG	uc003zem.3	Q9GZQ3		ENST00000305103.3:c.223_225delGCC	8.37:g.146076499_146076501delGGC	ENSP00000304544:p.Ala75del	Somatic		Capture	Illumina HiSeq	Phase_I	146047303	NM_001081004	D3DWN7|Q9NVN6|Q9UHX5	In_Frame_Del	DEL	ENST00000305103.3	37	CCDS6436.1																																																																																				0.645	COMMD5-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382962.1	NM_014066	
ZNF395	55893	broad.mit.edu	37	8	28210809	28210809	+	Frame_Shift_Del	DEL	G	G	-	rs145352684	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:28210809delG	ENST00000344423.5	-	5	831	c.700delC	c.(700-702)cacfs	p.H234fs	ZNF395_ENST00000523202.1_Frame_Shift_Del_p.H234fs|ZNF395_ENST00000523095.1_Frame_Shift_Del_p.H234fs	NM_018660.2	NP_061130.1	Q9H8N7	ZN395_HUMAN	zinc finger protein 395	234					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.H234fs*43(1)|p.H234fs*19(1)		cervix(1)|endometrium(1)|kidney(5)|large_intestine(6)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.102)|Kidney(114;0.123)|Colorectal(74;0.142)		GCCTGGGGGTGGGGGGGCGAG	0.612																																					p.H234fs												.	.	2	Deletion - Frameshift(1)|Insertion - Frameshift(1)	large_intestine(2)	c.700delC	8						.						16.0	20.0	19.0					8																	28210809		2200	4294	6494	28266728	SO:0001589	frameshift_variant	55893	exon5			AB044750	CCDS6067.1	8p21	2008-05-02			ENSG00000186918	ENSG00000186918		"""Zinc fingers, C2H2-type"""	18737	protein-coding gene	gene with protein product		609494				14625278	Standard	NM_018660		Approved	PRF-1, HDBP2, PBF, DKFZp434K1210	uc003xgr.3	Q9H8N7	OTTHUMG00000102137	ENST00000344423.5:c.700delC	8.37:g.28210809delG	ENSP00000340494:p.His234fs	Somatic		Capture	Illumina HiSeq	Phase_I	28266728	NM_018660	B3KUY7|D3DST4|Q6F6H2|Q9BY72|Q9NPB2|Q9NS57|Q9NS58|Q9NS59	Frame_Shift_Del	DEL	ENST00000344423.5	37	CCDS6067.1																																																																																				0.612	ZNF395-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219976.1		
ASPH	444	broad.mit.edu	37	8	62596743	62596744	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	TG	TG	TG	-	TG	TG	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:62596743_62596744delTG	ENST00000379454.4	-	2	294_295	c.107_108delCA	c.(106-108)acafs	p.T36fs	ASPH_ENST00000522603.1_Frame_Shift_Del_p.T7fs|ASPH_ENST00000518068.1_Frame_Shift_Del_p.T36fs|ASPH_ENST00000379449.6_Frame_Shift_Del_p.T36fs|ASPH_ENST00000541428.1_Frame_Shift_Del_p.T7fs|ASPH_ENST00000517661.1_Frame_Shift_Del_p.T7fs|ASPH_ENST00000517847.2_Frame_Shift_Del_p.T7fs|ASPH_ENST00000356457.5_Frame_Shift_Del_p.T36fs|ASPH_ENST00000389204.4_Frame_Shift_Del_p.T7fs|ASPH_ENST00000517856.1_Frame_Shift_Del_p.T36fs|ASPH_ENST00000445642.3_Frame_Shift_Del_p.T7fs|ASPH_ENST00000517903.1_Frame_Shift_Del_p.T7fs|ASPH_ENST00000522835.1_Frame_Shift_Del_p.T7fs	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	36					activation of cysteine-type endopeptidase activity (GO:0097202)|activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular response to calcium ion (GO:0071277)|detection of calcium ion (GO:0005513)|face morphogenesis (GO:0060325)|limb morphogenesis (GO:0035108)|muscle contraction (GO:0006936)|negative regulation of cell proliferation (GO:0008285)|palate development (GO:0060021)|pattern specification process (GO:0007389)|peptidyl-aspartic acid hydroxylation (GO:0042264)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of proteolysis (GO:0045862)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|regulation of protein depolymerization (GO:1901879)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|response to ATP (GO:0033198)	calcium channel complex (GO:0034704)|cortical endoplasmic reticulum (GO:0032541)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|electron carrier activity (GO:0009055)|ion channel binding (GO:0044325)|peptide-aspartate beta-dioxygenase activity (GO:0004597)|structural constituent of muscle (GO:0008307)|structural molecule activity (GO:0005198)	p.T36fs*40(1)		breast(1)|cervix(1)|endometrium(5)|large_intestine(5)|lung(16)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	Lung SC(2;0.153)	Lung NSC(129;0.0358)|all_lung(136;0.0654)|all_epithelial(80;0.101)			L-Aspartic Acid(DB00128)|Succinic acid(DB00139)	CTCCATGCTTTGTCTCTGTTTA	0.376																																					p.7_7del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.20_21del	8						.																																			62759298	SO:0001589	frameshift_variant	444	exon2			AF224468	CCDS34898.1, CCDS34899.1, CCDS34900.1, CCDS43742.1, CCDS47866.1, CCDS55234.1, CCDS55235.1, CCDS55236.1, CCDS55237.1, CCDS55238.1, CCDS75746.1	8q12.1	2008-02-05			ENSG00000198363	ENSG00000198363	1.14.11.16		757	protein-coding gene	gene with protein product	"""junctin"", ""humbug"", ""junctate"""	600582				7821814, 10974562	Standard	NM_004318		Approved	CASQ2BP1, BAH, JCTN, HAAH	uc003xuj.3	Q12797	OTTHUMG00000164375	ENST00000379454.4:c.107_108delCA	8.37:g.62596743_62596744delTG	ENSP00000368767:p.Thr36fs	Somatic		Capture	Illumina HiSeq	Phase_I	62759297	NM_001164753	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Frame_Shift_Del	DEL	ENST00000379454.4	37	CCDS34898.1																																																																																				0.376	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318	
LRRCC1	85444	broad.mit.edu	37	8	86041489	86041489	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:86041489delA	ENST00000360375.3	+	10	1650	c.1501delA	c.(1501-1503)aaafs	p.K502fs	LRRCC1_ENST00000414626.2_Frame_Shift_Del_p.K482fs	NM_033402.4	NP_208325.3	Q9C099	LRCC1_HUMAN	leucine rich repeat and coiled-coil centrosomal protein 1	502					mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K482fs*2(1)|p.K502fs*2(1)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(9)|large_intestine(7)|lung(16)|skin(1)|upper_aerodigestive_tract(2)	43						AAATGAAATTAAAAAACTGAC	0.318																																					p.K501fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.1501delA	8						.						100.0	102.0	102.0					8																	86041489		1810	4073	5883	86228741	SO:0001589	frameshift_variant	85444	exon10			BC030701	CCDS43750.1	8q21.2	2012-04-10	2012-04-10		ENSG00000133739	ENSG00000133739			29373	protein-coding gene	gene with protein product	"""centrosomal leucine-rich repeat and coiled-coil containing protein"", ""variable number of flagella 1 homolog (Chlamydomonas)"""		"""leucine rich repeat and coiled-coil domain containing 1"""			11214970, 18728398	Standard	NM_033402		Approved	KIAA1764, CLERC, VFL1	uc003ycw.3	Q9C099	OTTHUMG00000164784	ENST00000360375.3:c.1501delA	8.37:g.86041489delA	ENSP00000353538:p.Lys502fs	Somatic		Capture	Illumina HiSeq	Phase_I	86228741	NM_033402	B4DYX6|B5RI11|Q8N768|Q96DK7|Q96N01	Frame_Shift_Del	DEL	ENST00000360375.3	37	CCDS43750.1																																																																																				0.318	LRRCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380267.1	NM_033402	
LRRC69	100130742	broad.mit.edu	37	8	92212945	92212945	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:92212945delA	ENST00000448384.2	+	7	858	c.858delA	c.(856-858)ggafs	p.G286fs	LRRC69_ENST00000343709.3_Frame_Shift_Del_p.G130fs	NM_001129890.1	NP_001123362.1	Q6ZNQ3	LRC69_HUMAN	leucine rich repeat containing 69	286								p.T132fs*10(1)		endometrium(1)	1						TCTCTCAGGGAAAAACATGTG	0.388																																					p.G286fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.858delA	8						.						264.0	219.0	232.0					8																	92212945		692	1591	2283	92282121	SO:0001589	frameshift_variant	100130742	exon7			AK130865		8q21.3	2010-07-14			ENSG00000214954	ENSG00000214954			34303	protein-coding gene	gene with protein product							Standard	NM_001129890		Approved		uc010mal.1	Q6ZNQ3	OTTHUMG00000164023	ENST00000448384.2:c.858delA	8.37:g.92212945delA	ENSP00000400803:p.Gly286fs	Somatic		Capture	Illumina HiSeq	Phase_I	92282121	NM_001129890		Frame_Shift_Del	DEL	ENST00000448384.2	37																																																																																					0.388	LRRC69-007	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000415207.1	NM_001129890	
HRSP12	10247	broad.mit.edu	37	8	99118544	99118544	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr8:99118544delT	ENST00000254878.3	-	3	326	c.182delA	c.(181-183)aacfs	p.N61fs		NM_005836.2	NP_005827.1	P52758	UK114_HUMAN	heat-responsive protein 12	61					regulation of translational termination (GO:0006449)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deaminase activity (GO:0019239)|endonuclease activity (GO:0004519)|poly(A) RNA binding (GO:0044822)	p.N61fs*6(1)		large_intestine(3)|lung(1)|ovary(1)|urinary_tract(1)	6	Breast(36;1.78e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.214)			TTCACCCATGTTTTTAAGAGC	0.333																																					p.N61fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.182delA	8						.						105.0	108.0	107.0					8																	99118544		2203	4300	6503	99187720	SO:0001589	frameshift_variant	10247	exon3			BC008418	CCDS6276.1	8q22	2014-05-09			ENSG00000132541	ENSG00000132541			16897	protein-coding gene	gene with protein product	"""translational inhibitor p14.5"""	602487				8973653, 9405234, 20817725	Standard	NM_005836		Approved	UK114, P14.5, PSP	uc003yii.1	P52758	OTTHUMG00000164670	ENST00000254878.3:c.182delA	8.37:g.99118544delT	ENSP00000254878:p.Asn61fs	Somatic		Capture	Illumina HiSeq	Phase_I	99187720	NM_005836	Q6FHU9|Q6IBG0	Frame_Shift_Del	DEL	ENST00000254878.3	37	CCDS6276.1																																																																																				0.333	HRSP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379687.1	NM_005836	
INVS	27130	broad.mit.edu	37	9	103062934	103062935	+	Frame_Shift_Ins	INS	-	-	A	rs372899699		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	A	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:103062934_103062935insA	ENST00000262457.2	+	17	3361_3362	c.3176_3177insA	c.(3175-3180)ccaaaafs	p.PK1059fs	TEX10_ENST00000477648.1_5'Flank|INVS_ENST00000262456.2_Frame_Shift_Ins_p.PK889fs	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	1059					embryonic heart tube left/right pattern formation (GO:0060971)|kidney development (GO:0001822)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|pancreas development (GO:0031016)|post-embryonic development (GO:0009791)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)		p.N1061fs*>6(1)		breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31		Acute lymphoblastic leukemia(62;0.056)				GCTACTCAGCCAAAAAACAAAA	0.396																																					p.P1059fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.3176_3177insA	9						.		,	5,4259		0,5,2127					,	4.4	0.8			55	1,8253		0,1,4126	no	frameshift,frameshift	INVS	NM_183245.1,NM_014425.2	,	0,6,6253	A1A1,A1R,RR		0.0121,0.1173,0.0479	,	,		6,12512				102102756	SO:0001589	frameshift_variant	27130	exon17			AF039217	CCDS6746.1, CCDS6747.1	9q31	2013-01-10	2003-08-11		ENSG00000119509	ENSG00000119509		"""Ankyrin repeat domain containing"""	17870	protein-coding gene	gene with protein product	"""nephrocystin 2"""	243305	"""nephronophthisis 2 (infantile)"""	NPHP2		12872123	Standard	NM_014425		Approved		uc004bap.2	Q9Y283	OTTHUMG00000020364	ENST00000262457.2:c.3182dupA	9.37:g.103062940_103062940dupA	ENSP00000262457:p.Pro1059fs	Somatic		Capture	Illumina HiSeq	Phase_I	102102755	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Frame_Shift_Ins	INS	ENST00000262457.2	37	CCDS6746.1																																																																																				0.396	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425	
SLC25A51	92014	broad.mit.edu	37	9	37887696	37887697	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	C	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:37887696_37887697insC	ENST00000377716.2	-	3	1594_1595	c.851_852insG	c.(850-852)ggcfs	p.G284fs	SLC25A51_ENST00000242275.6_Frame_Shift_Ins_p.G284fs|SLC25A51_ENST00000380590.3_Frame_Shift_Ins_p.G284fs|RP11-613M10.9_ENST00000540557.1_Intron|SLC25A51_ENST00000496760.1_Intron			Q9H1U9	S2551_HUMAN	solute carrier family 25, member 51	284					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.I285fs*7(1)									CATTGATTATGCCCCAAGAGAT	0.391																																					p.G284fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.852_853insG	9						.																																			37877697	SO:0001589	frameshift_variant	92014	exon3			BC008500	CCDS6614.1	9p13.3-p12	2013-05-22	2012-03-29	2012-03-29	ENSG00000122696	ENSG00000122696		"""Solute carriers"""	23323	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 1"""	MCART1		12477932	Standard	NM_033412		Approved	MGC14836, CG7943	uc004aav.2	Q9H1U9	OTTHUMG00000019935	ENST00000377716.2:c.852dupG	9.37:g.37887700_37887700dupC	ENSP00000366945:p.Gly284fs	Somatic		Capture	Illumina HiSeq	Phase_I	37877696	NM_033412		Frame_Shift_Ins	INS	ENST00000377716.2	37	CCDS6614.1																																																																																				0.391	SLC25A51-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313746.1	NM_033412	
GABBR2	9568	broad.mit.edu	37	9	101056174	101056174	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:101056174C>A	ENST00000259455.2	-	18	3012	c.2553G>T	c.(2551-2553)aaG>aaT	p.K851N		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	851					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.K851N(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TTAAAATGGCCTTTCCTCCAT	0.383																																					p.K851N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2553T	9						.						199.0	192.0	195.0					9																	101056174		2203	4300	6503	100095995	SO:0001583	missense	9568	exon18			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2553G>T	9.37:g.101056174C>A	ENSP00000259455:p.Lys851Asn	Somatic		Capture	Illumina HiSeq	Phase_I	100095995	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.099759	0.76983	.	.	ENSG00000136928	ENST00000259455	T	0.80738	-1.41	5.11	4.19	0.49359	.	0.000000	0.85682	D	0.000000	T	0.79329	0.4427	N	0.14661	0.345	0.58432	D	0.999996	D	0.57899	0.981	D	0.69824	0.966	T	0.79463	-0.1793	10	0.46703	T	0.11	.	11.8456	0.52383	0.0:0.9121:0.0:0.0879	.	851	O75899	GABR2_HUMAN	N	851	ENSP00000259455:K851N	ENSP00000259455:K851N	K	-	3	2	GABBR2	100095995	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.366000	0.34193	2.645000	0.89757	0.655000	0.94253	AAG		0.383	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
GABBR2	9568	broad.mit.edu	37	9	101065617	101065617	+	Missense_Mutation	SNP	G	G	A	rs138346207	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:101065617G>A	ENST00000259455.2	-	16	2777	c.2318C>T	c.(2317-2319)aCg>aTg	p.T773M		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	773					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)	p.T773M(1)	NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	CGAGGTGGACGTTTTAGAATC	0.507													G|||	3	0.000599042	0.0	0.0	5008	,	,		18953	0.003		0.0	False		,,,				2504	0.0				p.T773M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2318T	9						.	G	MET/THR	0,4406		0,0,2203	161.0	145.0	150.0		2318	5.7	0.9	9	dbSNP_134	150	1,8599	1.2+/-3.3	0,1,4299	no	missense	GABBR2	NM_005458.7	81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	773/942	101065617	1,13005	2203	4300	6503	100105438	SO:0001583	missense	9568	exon16			AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.2318C>T	9.37:g.101065617G>A	ENSP00000259455:p.Thr773Met	Somatic		Capture	Illumina HiSeq	Phase_I	100105438	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	19.21	3.783542	0.70222	0.0	1.16E-4	ENSG00000136928	ENST00000259455	T	0.79454	-1.27	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.77651	0.4162	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.80589	-0.1315	10	0.44086	T	0.13	.	17.4184	0.87507	0.0:0.0:1.0:0.0	.	773	O75899	GABR2_HUMAN	M	773	ENSP00000259455:T773M	ENSP00000259455:T773M	T	-	2	0	GABBR2	100105438	1.000000	0.71417	0.870000	0.34147	0.929000	0.56500	9.852000	0.99516	2.717000	0.92951	0.505000	0.49811	ACG		0.507	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
COL15A1	1306	broad.mit.edu	37	9	101810282	101810282	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:101810282G>A	ENST00000375001.3	+	28	3216	c.2793G>A	c.(2791-2793)caG>caA	p.Q931Q		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	931	Triple-helical region 5 (COL5).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)	p.Q931Q(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TCATTATGCAGGTGAGTCACC	0.592																																					p.Q931Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2793A	9						.						53.0	45.0	48.0					9																	101810282		2195	4281	6476	100850103	SO:0001630	splice_region_variant	1306	exon28			L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2793+1G>A	9.37:g.101810282G>A		Somatic		Capture	Illumina HiSeq	Phase_I	100850103	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																				0.592	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	Silent
TEX10	54881	broad.mit.edu	37	9	103088644	103088644	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:103088644C>G	ENST00000374902.4	-	9	2095	c.1919G>C	c.(1918-1920)tGt>tCt	p.C640S	TEX10_ENST00000535814.1_Missense_Mutation_p.C643S	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	640						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|MLL1 complex (GO:0071339)				NS(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	38		Acute lymphoblastic leukemia(62;0.0527)		OV - Ovarian serous cystadenocarcinoma(323;0.157)		TCCCATAATACAGCAACGACT	0.463																																					p.C640S												.	.	0			c.G1919C	9						.						113.0	92.0	99.0					9																	103088644		2203	4300	6503	102128465	SO:0001583	missense	54881	exon9			AB060968	CCDS6748.1, CCDS55330.1	9q31.1	2012-05-02	2007-03-13		ENSG00000136891	ENSG00000136891			25988	protein-coding gene	gene with protein product			"""testis expressed gene 10"", ""testis expressed sequence 10"""			12477932	Standard	NM_017746		Approved	FLJ20287, bA208F1.2, Ipi1	uc004bas.3	Q9NXF1	OTTHUMG00000020366	ENST00000374902.4:c.1919G>C	9.37:g.103088644C>G	ENSP00000364037:p.Cys640Ser	None		Capture	Illumina HiSeq	Phase_I	102128465	NM_017746	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	37	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.873053	0.91664	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730	.	.	.	5.67	5.67	0.87782	.	0.044896	0.85682	N	0.000000	T	0.72993	0.3530	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.85130	0.994;0.996;0.997	T	0.75169	-0.3412	9	0.87932	D	0	-4.2833	19.7607	0.96316	0.0:1.0:0.0:0.0	.	643;508;640	B4DYV2;E7ERG2;Q9NXF1	.;.;TEX10_HUMAN	S	643;640;508	.	ENSP00000364037:C640S	C	-	2	0	TEX10	102128465	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.113000	0.77095	2.662000	0.90505	0.591000	0.81541	TGT		0.463	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746	
MSANTD3	91283	broad.mit.edu	37	9	103204414	103204414	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:103204414G>A	ENST00000395067.2	+	2	465	c.194G>A	c.(193-195)cGg>cAg	p.R65Q	MSANTD3_ENST00000374885.1_Missense_Mutation_p.R65Q|MSANTD3-TMEFF1_ENST00000502978.1_5'Flank|TMEFF1_ENST00000334943.6_5'Flank	NM_001198805.1|NM_001198806.1|NM_080655.2	NP_001185734.1|NP_001185735.1|NP_542386.1	Q96H12	MSD3_HUMAN	Myb/SANT-like DNA-binding domain containing 3	65	Myb-like.							p.R65Q(1)		endometrium(2)|lung(2)	4						GTGTCCCTGCGGGATTTCAAA	0.517																																					p.R65Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G194A	9						.						43.0	43.0	43.0					9																	103204414		2203	4300	6503	102244235	SO:0001583	missense	8577	exon2			BC008993	CCDS6749.1, CCDS56579.1	9q31.1	2012-03-13	2012-03-13	2012-03-13	ENSG00000066697	ENSG00000066697			23370	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 30"""	C9orf30			Standard	NM_080655		Approved	MGC17337		Q96H12	OTTHUMG00000020365	ENST00000395067.2:c.194G>A	9.37:g.103204414G>A	ENSP00000378506:p.Arg65Gln	Somatic		Capture	Illumina HiSeq	Phase_I	102244235	NM_080655	B2RC35|Q5T726|Q5T727|Q5T728	Missense_Mutation	SNP	ENST00000395067.2	37	CCDS6749.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.035498	0.93630	.	.	ENSG00000066697	ENST00000395067;ENST00000398977;ENST00000374885;ENST00000374886	.	.	.	5.88	5.88	0.94601	.	.	.	.	.	T	0.71929	0.3398	M	0.82823	2.61	0.43942	D	0.996605	P	0.52577	0.954	P	0.45428	0.48	T	0.77648	-0.2509	8	0.87932	D	0	-0.5064	19.2934	0.94112	0.0:0.0:1.0:0.0	.	65	Q96H12	CI030_HUMAN	Q	65	.	ENSP00000364020:R65Q	R	+	2	0	C9orf30	102244235	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.715000	0.74697	2.814000	0.96858	0.650000	0.86243	CGG		0.517	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655	
RNF20	56254	broad.mit.edu	37	9	104312951	104312951	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:104312951T>C	ENST00000389120.3	+	10	1246	c.1156T>C	c.(1156-1158)Tca>Cca	p.S386P	AL591377.1_ENST00000584534.1_RNA	NM_019592.5	NP_062538.5	Q5VTR2	BRE1A_HUMAN	ring finger protein 20, E3 ubiquitin protein ligase	386					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|negative regulation of cell migration (GO:0030336)|positive regulation of histone methylation (GO:0031062)|positive regulation of transcription, DNA-templated (GO:0045893)|protein polyubiquitination (GO:0000209)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|ligase activity (GO:0016874)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.S386P(1)		breast(3)|endometrium(3)|kidney(6)|large_intestine(7)|lung(23)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_hematologic(171;8.99e-06)|Acute lymphoblastic leukemia(62;0.000365)|Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.88e-19)|STAD - Stomach adenocarcinoma(157;0.00311)		CTGCATGCAGTCACAGTTCTC	0.512																																					p.S386P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1156C	9						.						221.0	215.0	217.0					9																	104312951		2203	4300	6503	103352772	SO:0001583	missense	56254	exon10			AF265230	CCDS35084.1	9q22	2012-02-23	2012-02-23	2008-12-12	ENSG00000155827	ENSG00000155827		"""RING-type (C3HC4) zinc fingers"""	10062	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog (S. cerevisiae)"""	607699	"""ring finger protein 20"""			16337599, 12876294, 18832071, 19037095	Standard	NM_019592		Approved	FLJ20382, FLJ11189, KAIA2779, BRE1A, hBRE1, BRE1	uc004bbn.3	Q5VTR2	OTTHUMG00000020385	ENST00000389120.3:c.1156T>C	9.37:g.104312951T>C	ENSP00000373772:p.Ser386Pro	Somatic		Capture	Illumina HiSeq	Phase_I	103352772	NM_019592	A7MCT5|Q2TB34|Q69YL5|Q6P527|Q8N3J4|Q96JD3|Q9H9Y7|Q9HA51|Q9NUR4|Q9NWQ3|Q9NX83	Missense_Mutation	SNP	ENST00000389120.3	37	CCDS35084.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.244940	0.79912	.	.	ENSG00000155827	ENST00000389120	T	0.33438	1.41	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.57242	0.2040	M	0.77486	2.375	0.80722	D	1	D	0.65815	0.995	D	0.70487	0.969	T	0.59836	-0.7379	10	0.54805	T	0.06	-6.9558	16.0251	0.80538	0.0:0.0:0.0:1.0	.	386	Q5VTR2	BRE1A_HUMAN	P	386	ENSP00000373772:S386P	ENSP00000373772:S386P	S	+	1	0	RNF20	103352772	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.484000	0.81180	2.267000	0.75376	0.528000	0.53228	TCA		0.512	RNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356402.1	NM_019592	
FOXD4	2298	broad.mit.edu	37	9	117800	117800	+	Missense_Mutation	SNP	G	G	T	rs2492217	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:117800G>T	ENST00000382500.2	-	1	617	c.320C>A	c.(319-321)tCc>tAc	p.S107Y		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	107					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding, bending (GO:0008301)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GATGTACGAGGAGGGGGGCTT	0.662													T|||	85	0.0169728	0.0083	0.0274	5008	,	,		13564	0.0347		0.005	False		,,,				2504	0.0153				p.S107Y												.	.	0			c.C320A	9						.						69.0	98.0	88.0					9																	117800		2199	4299	6498	107800	SO:0001583	missense	2298	exon1			U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"""Forkhead boxes"""	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.320C>A	9.37:g.117800G>T	ENSP00000371940:p.Ser107Tyr	Germline		Capture	Illumina HiSeq	Phase_I	107800	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	0.278	-0.988522	0.02162	.	.	ENSG00000170122	ENST00000382500	D	0.94723	-3.5	2.24	2.24	0.28232	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.000000	0.34507	N	0.003917	T	0.58004	0.2092	N	0.00001	-3.725	0.26151	N	0.980136	B	0.02656	0.0	B	0.01281	0.0	T	0.71066	-0.4700	10	0.02654	T	1	.	7.4985	0.27503	0.0:0.0:0.22:0.78	rs2492217;rs2777287	107	Q12950	FOXD4_HUMAN	Y	107	ENSP00000371940:S107Y	ENSP00000371940:S107Y	S	-	2	0	FOXD4	107800	1.000000	0.71417	0.996000	0.52242	0.527000	0.34593	3.537000	0.53590	0.124000	0.18369	-1.316000	0.01300	TCC		0.662	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
OR13C9	286362	broad.mit.edu	37	9	107380191	107380191	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:107380191C>T	ENST00000259362.1	-	1	294	c.295G>A	c.(295-297)Gtg>Atg	p.V99M		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	99						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V99M(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(9)|prostate(1)|skin(4)	22						AACATCTGCACTGCACAGCCA	0.507																																					p.V99M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G295A	9						.						122.0	136.0	131.0					9																	107380191		2203	4300	6503	106420012	SO:0001583	missense	286362	exon1				CCDS35093.1	9q31.1	2013-09-24			ENSG00000136839	ENSG00000136839		"""GPCR / Class A : Olfactory receptors"""	15104	protein-coding gene	gene with protein product							Standard	NM_001001956		Approved		uc011lvr.2	Q8NGT0	OTTHUMG00000020416	ENST00000259362.1:c.295G>A	9.37:g.107380191C>T	ENSP00000259362:p.Val99Met	Somatic		Capture	Illumina HiSeq	Phase_I	106420012	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	.	.	.	.	.	.	.	.	.	.	C	10.27	1.303614	0.23736	.	.	ENSG00000136839	ENST00000259362	T	0.02032	4.49	4.64	2.75	0.32379	GPCR, rhodopsin-like superfamily (1);	0.382664	0.19051	N	0.124032	T	0.02230	0.0069	L	0.28458	0.855	0.09310	N	1	B	0.14805	0.011	B	0.19391	0.025	T	0.42430	-0.9452	10	0.56958	D	0.05	.	7.909	0.29778	0.0:0.746:0.1626:0.0915	.	99	Q8NGT0	O13C9_HUMAN	M	99	ENSP00000259362:V99M	ENSP00000259362:V99M	V	-	1	0	OR13C9	106420012	0.000000	0.05858	0.959000	0.39883	0.946000	0.59487	-2.160000	0.01279	0.532000	0.28657	0.637000	0.83480	GTG		0.507	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1		
UGCG	7357	broad.mit.edu	37	9	114677012	114677012	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:114677012T>A	ENST00000374279.3	+	2	676	c.226T>A	c.(226-228)Ttg>Atg	p.L76M	UGCG_ENST00000495085.1_3'UTR	NM_003358.1	NP_003349.1	Q16739	CEGT_HUMAN	UDP-glucose ceramide glucosyltransferase	76					epidermis development (GO:0008544)|glucosylceramide biosynthetic process (GO:0006679)|glycosphingolipid biosynthetic process (GO:0006688)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ceramide glucosyltransferase activity (GO:0008120)	p.L76M(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(1)|ovary(1)|urinary_tract(1)	12				OV - Ovarian serous cystadenocarcinoma(323;0.0433)	Miglustat(DB00419)	ATTCTTTGAATTGGATTATCC	0.363																																					p.L76M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T226A	9						.						99.0	99.0	99.0					9																	114677012		2203	4300	6503	113716833	SO:0001583	missense	7357	exon2			D50840	CCDS6782.1	9q31	2014-03-13			ENSG00000148154	ENSG00000148154	2.4.1.80	"""Glycosyltransferase family 2 domain containing"""	12524	protein-coding gene	gene with protein product	"""glucosylceramide synthase"", ""ceramide glucosyltransferase"""	602874				8643456, 9605861	Standard	NM_003358		Approved	GCS	uc004bft.3	Q16739	OTTHUMG00000020498	ENST00000374279.3:c.226T>A	9.37:g.114677012T>A	ENSP00000363397:p.Leu76Met	Somatic		Capture	Illumina HiSeq	Phase_I	113716833	NM_003358	Q5T258	Missense_Mutation	SNP	ENST00000374279.3	37	CCDS6782.1	.	.	.	.	.	.	.	.	.	.	T	11.03	1.519663	0.27211	.	.	ENSG00000148154	ENST00000374279	T	0.61274	0.12	5.88	3.22	0.36961	Glycosyl transferase, family 2 (1);	0.000000	0.85682	D	0.000000	T	0.47893	0.1470	L	0.41492	1.28	0.54753	D	0.999982	B	0.29988	0.264	B	0.35727	0.209	T	0.39375	-0.9617	10	0.38643	T	0.18	.	8.2538	0.31743	0.0:0.2842:0.0:0.7158	.	76	Q16739	CEGT_HUMAN	M	76	ENSP00000363397:L76M	ENSP00000363397:L76M	L	+	1	2	UGCG	113716833	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.351000	0.44071	0.844000	0.35094	0.533000	0.62120	TTG		0.363	UGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053661.1	NM_003358	
KIAA1958	158405	broad.mit.edu	37	9	115421591	115421591	+	Missense_Mutation	SNP	G	G	A	rs141479985		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:115421591G>A	ENST00000337530.6	+	4	1689	c.1393G>A	c.(1393-1395)Gtc>Atc	p.V465I	KIAA1958_ENST00000536272.1_Missense_Mutation_p.V493I	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	465								p.V465I(1)		endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						TTATGTCACCGTCAAGAAGAG	0.537																																					p.V465I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1393A	9						.	G	ILE/VAL	0,4406		0,0,2203	78.0	68.0	71.0		1393	5.1	1.0	9	dbSNP_134	71	2,8598	1.2+/-3.3	0,2,4298	no	missense	KIAA1958	NM_133465.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	465/717	115421591	2,13004	2203	4300	6503	114461412	SO:0001583	missense	158405	exon4			AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1393G>A	9.37:g.115421591G>A	ENSP00000336940:p.Val465Ile	Somatic		Capture	Illumina HiSeq	Phase_I	114461412	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	37	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.798139	0.50208	0.0	2.33E-4	ENSG00000165185	ENST00000337530;ENST00000536272	T	0.44083	0.93	5.1	5.1	0.69264	.	.	.	.	.	T	0.24928	0.0605	N	0.14661	0.345	0.23624	N	0.997262	P;P	0.44946	0.846;0.846	B;B	0.34242	0.178;0.125	T	0.11446	-1.0587	9	0.13853	T	0.58	.	18.1317	0.89604	0.0:0.0:1.0:0.0	.	493;465	B7ZKW6;Q8N8K9	.;K1958_HUMAN	I	465;493	ENSP00000336940:V465I	ENSP00000336940:V465I	V	+	1	0	KIAA1958	114461412	0.999000	0.42202	0.999000	0.59377	0.997000	0.91878	2.987000	0.49378	2.361000	0.80049	0.655000	0.94253	GTC		0.537	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465	
SNX30	401548	broad.mit.edu	37	9	115580071	115580071	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:115580071A>T	ENST00000374232.3	+	3	599	c.435A>T	c.(433-435)gaA>gaT	p.E145D		NM_001012994.1	NP_001013012.1	Q5VWJ9	SNX30_HUMAN	sorting nexin family member 30	145	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	endosome (GO:0005768)	phosphatidylinositol binding (GO:0035091)	p.E145D(1)		large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8						AACTGGAAGAATCCCAGCCCA	0.468																																					p.E145D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A435T	9						.						135.0	129.0	131.0					9																	115580071		1903	4127	6030	114619892	SO:0001583	missense	401548	exon3			AK126644	CCDS43865.1	9q33.1	2014-02-12			ENSG00000148158	ENSG00000148158		"""Sorting nexins"""	23685	protein-coding gene	gene with protein product							Standard	NM_001012994		Approved	ATG24A	uc004bgj.4	Q5VWJ9	OTTHUMG00000020512	ENST00000374232.3:c.435A>T	9.37:g.115580071A>T	ENSP00000363349:p.Glu145Asp	Somatic		Capture	Illumina HiSeq	Phase_I	114619892	NM_001012994		Missense_Mutation	SNP	ENST00000374232.3	37	CCDS43865.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.218006	0.39201	.	.	ENSG00000148158	ENST00000374232	T	0.41758	0.99	5.55	-3.58	0.04597	Phox homologous domain (5);	0.217551	0.47455	N	0.000228	T	0.27278	0.0669	L	0.48877	1.53	0.41532	D	0.988462	B	0.02656	0.0	B	0.01281	0.0	T	0.02512	-1.1148	10	0.30078	T	0.28	.	6.9638	0.24611	0.3972:0.226:0.3768:0.0	.	145	Q5VWJ9	SNX30_HUMAN	D	145	ENSP00000363349:E145D	ENSP00000363349:E145D	E	+	3	2	SNX30	114619892	0.994000	0.37717	0.950000	0.38849	0.992000	0.81027	0.433000	0.21477	-0.823000	0.04301	-0.371000	0.07208	GAA		0.468	SNX30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053700.1		
RGS3	5998	broad.mit.edu	37	9	116299157	116299157	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:116299157G>A	ENST00000374140.2	+	20	2205	c.1996G>A	c.(1996-1998)Gcc>Acc	p.A666T	RGS3_ENST00000462143.1_5'UTR|RGS3_ENST00000350696.5_Missense_Mutation_p.A666T|RGS3_ENST00000343817.5_Missense_Mutation_p.A385T|RGS3_ENST00000394646.3_Missense_Mutation_p.A385T|RGS3_ENST00000374136.1_Missense_Mutation_p.A292T|RGS3_ENST00000317613.6_Missense_Mutation_p.A554T	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	666					inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.A666T(1)|p.A562T(1)		cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GGAGAACATCGCCAAGCAGCA	0.577																																					p.A666T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1996A	9						.						104.0	93.0	97.0					9																	116299157		2203	4300	6503	115338978	SO:0001583	missense	5998	exon20			AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.1996G>A	9.37:g.116299157G>A	ENSP00000363255:p.Ala666Thr	Somatic		Capture	Illumina HiSeq	Phase_I	115338978	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.87|11.87	1.766290|1.766290	0.31228|0.31228	.|.	.|.	ENSG00000138835|ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613;ENST00000343817;ENST00000394646;ENST00000374136|ENST00000496113	T;T;T;T;T|.	0.58060|.	0.86;0.86;1.21;0.36;2.56|.	5.68|5.68	1.71|1.71	0.24356|0.24356	.|.	0.286229|.	0.33534|.	N|.	0.004816|.	T|T	0.46405|0.46405	0.1391|0.1391	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	D|D	1|1	B;B;B;B;B;B|.	0.27380|.	0.0;0.006;0.009;0.068;0.019;0.177|.	B;B;B;B;B;B|.	0.17433|.	0.0;0.003;0.009;0.011;0.008;0.018|.	T|T	0.26052|0.26052	-1.0114|-1.0114	10|5	0.33141|.	T|.	0.24|.	.|.	4.3995|4.3995	0.11379|0.11379	0.3157:0.0:0.5381:0.1462|0.3157:0.0:0.5381:0.1462	.|.	385;292;385;556;554;666|.	B3KUB2;Q5VXC0;P49796-4;B3KWG8;P49796-5;P49796|.	.;.;.;.;.;RGS3_HUMAN|.	T|H	666;666;554;385;385;292|120	ENSP00000363255:A666T;ENSP00000259406:A666T;ENSP00000312844:A554T;ENSP00000340284:A385T;ENSP00000378141:A385T|.	ENSP00000312844:A554T|.	A|R	+|+	1|2	0|0	RGS3|RGS3	115338978|115338978	0.964000|0.964000	0.33143|0.33143	0.995000|0.995000	0.50966|0.50966	0.992000|0.992000	0.81027|0.81027	0.968000|0.968000	0.29357|0.29357	0.356000|0.356000	0.24157|0.24157	-0.244000|-0.244000	0.11960|0.11960	GCC|CGC		0.577	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
AMBP	259	broad.mit.edu	37	9	116831994	116831994	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:116831994C>T	ENST00000265132.3	-	6	850	c.588G>A	c.(586-588)gaG>gaA	p.E196E		NM_001633.3	NP_001624.1	P02760	AMBP_HUMAN	alpha-1-microglobulin/bikunin precursor	196					cell adhesion (GO:0007155)|female pregnancy (GO:0007565)|heme catabolic process (GO:0042167)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of JNK cascade (GO:0046329)|protein catabolic process (GO:0030163)|protein-chromophore linkage (GO:0018298)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calcium channel inhibitor activity (GO:0019855)|calcium oxalate binding (GO:0046904)|heme binding (GO:0020037)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)|serine-type endopeptidase inhibitor activity (GO:0004867)|small molecule binding (GO:0036094)	p.E196E(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	11					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	TTAAGATGGGCTCTGGTTCCT	0.622																																					p.E196E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G588A	9						.						98.0	78.0	84.0					9																	116831994		2203	4300	6503	115871815	SO:0001819	synonymous_variant	259	exon6			X04494	CCDS6800.1	9q32-q33	2014-01-22			ENSG00000106927	ENSG00000106927		"""Lipocalins"""	453	protein-coding gene	gene with protein product	"""growth-inhibiting protein 19"", ""uristatin"", ""complex-forming glycoprotein heterogeneous in charge"", ""bikunin"", ""inter-alpha-trypsin inhibitor light chain"", ""protein HC"", ""uronic-acid-rich protein"", ""trypstatin"""	176870		ITI, ITIL		1708673, 1385302	Standard	NM_001633		Approved	UTI, HCP, EDC1, HI30, IATIL, ITILC	uc004bie.4	P02760	OTTHUMG00000020534	ENST00000265132.3:c.588G>A	9.37:g.116831994C>T		Somatic		Capture	Illumina HiSeq	Phase_I	115871815	NM_001633	P00977|P02759|P78491|Q2TU33|Q5TBD7|Q9UC58|Q9UDI8	Silent	SNP	ENST00000265132.3	37	CCDS6800.1																																																																																				0.622	AMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053758.2	NM_001633	
TNC	3371	broad.mit.edu	37	9	117788813	117788813	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:117788813C>A	ENST00000350763.4	-	26	6742	c.6331G>T	c.(6331-6333)Ggt>Tgt	p.G2111C	TNC_ENST00000341037.4_Splice_Site_p.G1929C|TNC_ENST00000423613.2_Splice_Site_p.G1838C|TNC_ENST00000542877.1_Splice_Site_p.G1748C|TNC_ENST00000340094.3_Splice_Site_p.G1747C|TNC_ENST00000535648.1_Splice_Site_p.G1656C|TNC_ENST00000345230.3_Splice_Site_p.G1474C|TNC_ENST00000537320.1_Splice_Site_p.G1474C|TNC_ENST00000346706.3_Splice_Site_p.G1565C	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	2111	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)	p.G2111C(1)		NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ACTACTGTACCTGCTGTCCCA	0.493																																					p.G2111C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6331T	9						.						133.0	98.0	110.0					9																	117788813		2203	4300	6503	116828634	SO:0001630	splice_region_variant	3371	exon26				CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.6331+1G>T	9.37:g.117788813C>A		Somatic		Capture	Illumina HiSeq	Phase_I	116828634	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.899211	0.91962	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66;1.66;1.66;1.66;1.66	5.61	5.61	0.85477	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.76772	0.4034	H	0.99619	4.66	0.58432	D	0.999996	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87764	0.2600	9	.	.	.	.	19.6248	0.95674	0.0:1.0:0.0:0.0	.	1838;2111	E9PC84;P24821	.;TENA_HUMAN	C	1747;1656;1565;1474;2111;1929;1838;1474;1748	ENSP00000344400:G1747C;ENSP00000438152:G1656C;ENSP00000344555:G1565C;ENSP00000345861:G1474C;ENSP00000265131:G2111C;ENSP00000339553:G1929C;ENSP00000411406:G1838C;ENSP00000443478:G1474C;ENSP00000442242:G1748C	.	G	-	1	0	TNC	116828634	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	7.487000	0.81328	2.631000	0.89168	0.655000	0.94253	GGT		0.493	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	Missense_Mutation
LHX6	26468	broad.mit.edu	37	9	124989255	124989255	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:124989255C>T	ENST00000373755.2	-	2	232	c.124G>A	c.(124-126)Gcc>Acc	p.A42T	LHX6_ENST00000541397.2_Missense_Mutation_p.A60T|LHX6_ENST00000340587.3_Missense_Mutation_p.A71T|LHX6_ENST00000373754.2_Missense_Mutation_p.A42T|LHX6_ENST00000394319.4_Missense_Mutation_p.A71T|LHX6_ENST00000559529.1_5'Flank	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	42					cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.A71T(1)		endometrium(2)|kidney(1)|large_intestine(5)	8						CATGGGGAGGCCTGACCCTCG	0.682																																					p.A71T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G211A	9						.						68.0	52.0	57.0					9																	124989255		2172	4242	6414	124029076	SO:0001583	missense	26468	exon3			AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"""Homeoboxes / LIM class"""	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.124G>A	9.37:g.124989255C>T	ENSP00000362860:p.Ala42Thr	Somatic		Capture	Illumina HiSeq	Phase_I	124029076	NM_199160	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	37	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	C	15.13	2.741798	0.49151	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.87809	-2.3;-2.27;-2.2;-2.15;-2.19	5.44	4.46	0.54185	.	0.114260	0.64402	D	0.000009	T	0.72244	0.3436	N	0.08118	0	0.80722	D	1	B;B;B	0.27823	0.19;0.073;0.008	B;B;B	0.24701	0.046;0.055;0.034	T	0.69183	-0.5212	10	0.27082	T	0.32	.	10.5871	0.45288	0.3783:0.6217:0.0:0.0	.	42;71;71	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	T	42;42;71;71;60	ENSP00000362860:A42T;ENSP00000362859:A42T;ENSP00000377854:A71T;ENSP00000340137:A71T;ENSP00000441464:A60T	ENSP00000340137:A71T	A	-	1	0	LHX6	124029076	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.124000	0.50461	2.541000	0.85698	0.462000	0.41574	GCC		0.682	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368	
OR1B1	347169	broad.mit.edu	37	9	125391333	125391333	+	Missense_Mutation	SNP	C	C	T	rs377379891		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:125391333C>T	ENST00000304833.3	-	1	519	c.482G>A	c.(481-483)cGt>cAt	p.R161H	RP11-64P14.7_ENST00000431442.1_RNA|RP11-64P14.7_ENST00000419604.1_RNA	NM_001004450.1	NP_001004450.1	Q8NGR6	OR1B1_HUMAN	olfactory receptor, family 1, subfamily B, member 1	161						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R161H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|prostate(1)	16						GAGTCCCACACGCAACATGGT	0.552																																					p.R161H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G482A	9						.	T	HIS/ARG	0,4406		0,0,2203	86.0	66.0	73.0		482	3.1	0.9	9		73	2,8598	819.0+/-406.8	0,2,4298	no	missense	OR1B1	NM_001004450.1	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	161/319	125391333	2,13004	2203	4300	6503	124431154	SO:0001583	missense	347169	exon1			AC006313	CCDS35126.1	9q33.2	2012-08-09			ENSG00000171484	ENSG00000171484		"""GPCR / Class A : Olfactory receptors"""	8181	protein-coding gene	gene with protein product							Standard	NM_001004450		Approved	OR9-B	uc011lyz.2	Q8NGR6	OTTHUMG00000020616	ENST00000304833.3:c.482G>A	9.37:g.125391333C>T	ENSP00000303151:p.Arg161His	Somatic		Capture	Illumina HiSeq	Phase_I	124431154	NM_001004450	Q6IFN3	Missense_Mutation	SNP	ENST00000304833.3	37	CCDS35126.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.964445	0.00461	0.0	2.33E-4	ENSG00000171484	ENST00000304833	T	0.00017	9.1	4.26	3.12	0.35913	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	N	0.000310	T	0.00039	0.0001	N	0.00042	-2.48	0.21355	N	0.999717	B	0.02656	0.0	B	0.01281	0.0	T	0.41538	-0.9503	10	0.02654	T	1	-6.8699	7.0181	0.24899	0.0:0.2734:0.0:0.7266	.	161	Q8NGR6	OR1B1_HUMAN	H	161	ENSP00000303151:R161H	ENSP00000303151:R161H	R	-	2	0	OR1B1	124431154	0.004000	0.15560	0.877000	0.34402	0.036000	0.12997	0.429000	0.21412	0.287000	0.22375	-0.275000	0.10095	CGT		0.552	OR1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053947.2	NM_001004450	
STRBP	55342	broad.mit.edu	37	9	125887900	125887900	+	Silent	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:125887900A>C	ENST00000348403.5	-	19	2424	c.1995T>G	c.(1993-1995)ccT>ccG	p.P665P	STRBP_ENST00000447404.2_Silent_p.P665P|STRBP_ENST00000360998.3_Silent_p.P651P	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	665					cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)	p.P665P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						AGTGGGGAACAGGATATGTTG	0.363																																					p.P651P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1953G	9						.						167.0	168.0	167.0					9																	125887900		2203	4300	6503	124927721	SO:0001819	synonymous_variant	55342	exon19			AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"""spermatid perinuclear RNA-binding protein"", ""interleukin enhancer binding factor 3-like"""	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1995T>G	9.37:g.125887900A>C		Somatic		Capture	Illumina HiSeq	Phase_I	124927721	NM_001171137	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	ENST00000348403.5	37	CCDS6851.1																																																																																				0.363	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1		
DENND1A	57706	broad.mit.edu	37	9	126214594	126214594	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:126214594C>A	ENST00000373624.2	-	17	1461	c.1260G>T	c.(1258-1260)aaG>aaT	p.K420N	DENND1A_ENST00000373618.1_Missense_Mutation_p.K388N|DENND1A_ENST00000542603.1_Missense_Mutation_p.K162N|DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000394215.2_Missense_Mutation_p.K390N|DENND1A_ENST00000394219.3_Missense_Mutation_p.K388N|DENND1A_ENST00000373620.3_Missense_Mutation_p.K420N	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	420					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.K420N(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						TTGCTTTGGTCTTTACAGTAT	0.418																																					p.K420N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1260T	9						.						188.0	161.0	170.0					9																	126214594		2203	4300	6503	125254415	SO:0001583	missense	57706	exon17			AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.1260G>T	9.37:g.126214594C>A	ENSP00000362727:p.Lys420Asn	Somatic		Capture	Illumina HiSeq	Phase_I	125254415	NM_024820	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	C	19.34	3.809520	0.70797	.	.	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219;ENST00000373620;ENST00000394215;ENST00000373618	T;T;T;T;T;T	0.32023	2.93;1.47;2.92;2.99;2.88;2.94	5.62	4.5	0.54988	.	0.047415	0.85682	D	0.000000	T	0.50990	0.1648	M	0.77616	2.38	0.58432	D	0.999999	D;D;D;P;D;D;D	0.89917	0.998;0.999;0.997;0.941;0.997;0.999;1.0	D;D;D;P;D;D;D	0.80764	0.991;0.994;0.94;0.796;0.975;0.986;0.984	T	0.51474	-0.8701	10	0.59425	D	0.04	-16.6749	6.0464	0.19762	0.0:0.3186:0.0:0.6814	.	388;378;388;390;420;420;240	Q8TEH3-6;Q8TEH3-7;Q8TEH3-4;Q8TEH3-5;Q8TEH3-2;Q8TEH3;Q9HCG4	.;.;.;.;.;DEN1A_HUMAN;.	N	420;162;388;420;390;388	ENSP00000362727:K420N;ENSP00000437457:K162N;ENSP00000377766:K388N;ENSP00000362722:K420N;ENSP00000377763:K390N;ENSP00000362720:K388N	ENSP00000362720:K388N	K	-	3	2	DENND1A	125254415	1.000000	0.71417	0.999000	0.59377	0.901000	0.52897	1.795000	0.38784	0.978000	0.38470	-0.367000	0.07326	AAG		0.418	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
OLFML2A	169611	broad.mit.edu	37	9	127549424	127549424	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:127549424C>T	ENST00000373580.3	+	2	261	c.261C>T	c.(259-261)cgC>cgT	p.R87R		NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	87					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.R87R(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CTGACTGCCGCTGCTCCTGTA	0.622																																					p.R87R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C261T	9						.						49.0	57.0	54.0					9																	127549424		2162	4260	6422	126589245	SO:0001819	synonymous_variant	169611	exon2			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.261C>T	9.37:g.127549424C>T		Somatic		Capture	Illumina HiSeq	Phase_I	126589245	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	37	CCDS6857.2																																																																																				0.622	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
OLFML2A	169611	broad.mit.edu	37	9	127549505	127549505	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:127549505C>T	ENST00000373580.3	+	2	342	c.342C>T	c.(340-342)ccC>ccT	p.P114P		NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	114					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)	p.P114P(1)		endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						AGCAGGCGCCCGAGCTCCTCA	0.577																																					p.P114P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C342T	9						.						52.0	60.0	57.0					9																	127549505		2004	4167	6171	126589326	SO:0001819	synonymous_variant	169611	exon2			AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.342C>T	9.37:g.127549505C>T		Somatic		Capture	Illumina HiSeq	Phase_I	126589326	NM_182487	Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	37	CCDS6857.2																																																																																				0.577	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
MAPKAP1	79109	broad.mit.edu	37	9	128434744	128434744	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:128434744T>C	ENST00000373498.1	-	1	178	c.110A>G	c.(109-111)gAc>gGc	p.D37G	MAPKAP1_ENST00000394063.1_Intron|MAPKAP1_ENST00000394060.3_Missense_Mutation_p.D37G|MAPKAP1_ENST00000373503.3_Intron|MAPKAP1_ENST00000373511.2_Missense_Mutation_p.D37G|MAPKAP1_ENST00000350766.3_Missense_Mutation_p.D37G|MAPKAP1_ENST00000265960.3_Missense_Mutation_p.D37G			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	37	Interaction with MAP3K2.|Interaction with NBN.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)	p.D37G(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						CTTCTCTAGGTCAACATCATG	0.453																																					p.D37G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A110G	9						.						155.0	113.0	127.0					9																	128434744		2203	4300	6503	127474565	SO:0001583	missense	79109	exon2			M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.110A>G	9.37:g.128434744T>C	ENSP00000362597:p.Asp37Gly	Somatic		Capture	Illumina HiSeq	Phase_I	127474565	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	37	CCDS35140.1	.	.	.	.	.	.	.	.	.	.	T	27.5	4.837264	0.91117	.	.	ENSG00000119487	ENST00000373511;ENST00000350766;ENST00000373498;ENST00000265960;ENST00000394060;ENST00000373496;ENST00000433483	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.76912	0.4054	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.76494	0.997;0.999;0.998;0.998	D;D;D;D	0.71656	0.942;0.974;0.937;0.955	T	0.77376	-0.2611	9	0.46703	T	0.11	-3.6983	15.9736	0.80040	0.0:0.0:0.0:1.0	.	37;37;37;37	Q9BPZ7-5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.;.;.;SIN1_HUMAN	G	37	.	ENSP00000265960:D37G	D	-	2	0	MAPKAP1	127474565	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.165000	0.68154	0.533000	0.62120	GAC		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
GARNL3	84253	broad.mit.edu	37	9	130155492	130155492	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:130155492C>A	ENST00000373387.4	+	28	3353	c.3001C>A	c.(3001-3003)Ctc>Atc	p.L1001I	GARNL3_ENST00000314904.5_3'UTR|GARNL3_ENST00000496711.1_3'UTR|GARNL3_ENST00000435213.2_Missense_Mutation_p.L979I	NM_032293.4	NP_115669.3	Q5VVW2	GARL3_HUMAN	GTPase activating Rap/RanGAP domain-like 3	1001					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)|small GTPase regulator activity (GO:0005083)	p.L983I(1)		NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(24)|ovary(1)|skin(1)|urinary_tract(2)	41						CCCCTTCCAGCTCACGGCTTT	0.507																																					p.L1001I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3001A	9						.						64.0	73.0	70.0					9																	130155492		2203	4300	6503	129195313	SO:0001583	missense	84253	exon28			BC034983	CCDS6869.2, CCDS69663.1	9q34.13	2009-09-14	2004-08-09		ENSG00000136895	ENSG00000136895			25425	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 3"""			11230166	Standard	NM_032293		Approved	DKFZp761J1523, bA356B19.1	uc011mae.2	Q5VVW2	OTTHUMG00000020700	ENST00000373387.4:c.3001C>A	9.37:g.130155492C>A	ENSP00000362485:p.Leu1001Ile	Somatic		Capture	Illumina HiSeq	Phase_I	129195313	NM_032293	B4DEP7|B7Z3Q6|Q8IYU1|Q8N951|Q8ND89|Q9BQH6	Missense_Mutation	SNP	ENST00000373387.4	37	CCDS6869.2	.	.	.	.	.	.	.	.	.	.	C	12.49	1.954934	0.34471	.	.	ENSG00000136895	ENST00000435213;ENST00000373387	D;D	0.89939	-2.57;-2.59	5.73	5.73	0.89815	.	0.354654	0.31415	N	0.007687	T	0.79528	0.4461	N	0.14661	0.345	0.80722	D	1	B;B	0.32302	0.363;0.363	B;B	0.31946	0.138;0.138	T	0.76305	-0.3008	9	.	.	.	.	13.7631	0.62979	0.1536:0.8464:0.0:0.0	.	1001;979	Q5VVW2;B7Z3Q6	GARL3_HUMAN;.	I	979;1001	ENSP00000396205:L979I;ENSP00000362485:L1001I	.	L	+	1	0	GARNL3	129195313	1.000000	0.71417	1.000000	0.80357	0.507000	0.33981	3.285000	0.51716	2.854000	0.98071	0.655000	0.94253	CTC		0.507	GARNL3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054151.3	NM_032293	
FAM102A	399665	broad.mit.edu	37	9	130710482	130710482	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:130710482T>C	ENST00000373095.1	-	6	859	c.484A>G	c.(484-486)Atc>Gtc	p.I162V	FAM102A_ENST00000373084.4_Missense_Mutation_p.I20V|FAM102A_ENST00000300434.3_Intron	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	162	Ser-rich.							p.I162V(1)		breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						GGGATGGAGATGGACTTGGCA	0.612																																					p.I162V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A484G	9						.						93.0	83.0	86.0					9																	130710482		2203	4300	6503	129750303	SO:0001583	missense	399665	exon6				CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.484A>G	9.37:g.130710482T>C	ENSP00000362187:p.Ile162Val	Somatic		Capture	Illumina HiSeq	Phase_I	129750303	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	T	12.92	2.083121	0.36758	.	.	ENSG00000167106	ENST00000373095;ENST00000373084	.	.	.	4.99	4.99	0.66335	.	0.123714	0.56097	D	0.000025	T	0.54711	0.1875	L	0.46741	1.465	0.45791	D	0.998678	B	0.12013	0.005	B	0.08055	0.003	T	0.54153	-0.8336	9	0.51188	T	0.08	-34.7427	12.0728	0.53626	0.0:0.0:0.0:1.0	.	162	Q5T9C2	F102A_HUMAN	V	162;20	.	ENSP00000362176:I20V	I	-	1	0	FAM102A	129750303	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	3.632000	0.54287	1.870000	0.54199	0.460000	0.39030	ATC		0.612	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
DNM1	1759	broad.mit.edu	37	9	131012470	131012470	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:131012470C>A	ENST00000372923.3	+	20	2245	c.2153C>A	c.(2152-2154)tCg>tAg	p.S718*	DNM1_ENST00000475805.1_Nonsense_Mutation_p.S718*|DNM1_ENST00000486160.1_Nonsense_Mutation_p.S718*|DNM1_ENST00000393594.3_Nonsense_Mutation_p.S718*|DNM1_ENST00000341179.7_Nonsense_Mutation_p.S718*	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	718	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				endocytosis (GO:0006897)|endosome organization (GO:0007032)|GTP catabolic process (GO:0006184)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)	extracellular vesicular exosome (GO:0070062)|membrane coat (GO:0030117)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.S718*(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						ATGGAGGAGTCGGCGGAGCAG	0.612																																					p.R718R	GBM(113;146 1575 2722 28670 29921)											.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C2152A	9						.						42.0	33.0	36.0					9																	131012470		2203	4300	6503	130052291	SO:0001587	stop_gained	1759	exon19			L07807	CCDS6895.1, CCDS43882.1, CCDS75911.1, CCDS75912.1	9q34	2013-01-10			ENSG00000106976	ENSG00000106976		"""Pleckstrin homology (PH) domain containing"""	2972	protein-coding gene	gene with protein product		602377		DNM		2144893, 9143509	Standard	XM_005251763		Approved		uc022bob.1	Q05193	OTTHUMG00000020733	ENST00000372923.3:c.2153C>A	9.37:g.131012470C>A	ENSP00000362014:p.Ser718*	Somatic		Capture	Illumina HiSeq	Phase_I	130052291	NM_001005336	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Nonsense_Mutation	SNP	ENST00000372923.3	37	CCDS6895.1	.	.	.	.	.	.	.	.	.	.	.	39	7.736275	0.98462	.	.	ENSG00000106976	ENST00000475805;ENST00000341179;ENST00000372923;ENST00000393594;ENST00000486160;ENST00000543158	.	.	.	4.52	4.52	0.55395	.	0.067472	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.2431	17.4162	0.87500	0.0:1.0:0.0:0.0	.	.	.	.	X	718;718;718;718;718;263	.	ENSP00000345680:S718X	S	+	2	0	DNM1	130052291	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	7.587000	0.82613	2.340000	0.79590	0.542000	0.68232	TCG		0.612	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408	
GLE1	2733	broad.mit.edu	37	9	131286114	131286114	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:131286114G>T	ENST00000309971.4	+	6	992	c.886G>T	c.(886-888)Gcc>Tcc	p.A296S	GLE1_ENST00000372770.4_Missense_Mutation_p.A296S|GLE1_ENST00000494417.1_3'UTR|GLE1_ENST00000539582.1_Missense_Mutation_p.A42S	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	296					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.A296S(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						GATCATCCGGGCCTCTTCAGA	0.512																																					p.A296S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G886T	9						.						24.0	26.0	25.0					9																	131286114		2203	4300	6503	130325935	SO:0001583	missense	2733	exon6			AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"""GLE1 (yeast homolog)-like, RNA export mediator"", ""GLE1 RNA export mediator-like (yeast)"", ""GLE1 RNA export mediator (yeast)"", ""lethal congenital contracture syndrome 1"", ""GLE1 RNA export mediator homolog (yeast)"""	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.886G>T	9.37:g.131286114G>T	ENSP00000308622:p.Ala296Ser	Somatic		Capture	Illumina HiSeq	Phase_I	130325935	NM_001003722	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	37	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	G	9.410	1.080387	0.20309	.	.	ENSG00000119392	ENST00000309971;ENST00000372770;ENST00000539582	T;T;T	0.77098	-0.07;0.34;-1.07	5.66	-0.00822	0.14005	.	0.399850	0.30085	N	0.010450	T	0.48003	0.1476	N	0.08118	0	0.24848	N	0.992422	B;B	0.13145	0.003;0.007	B;B	0.09377	0.004;0.003	T	0.25257	-1.0137	10	0.11485	T	0.65	-6.505	3.935	0.09302	0.3721:0.0:0.3655:0.2625	.	296;296	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	S	296;296;42	ENSP00000308622:A296S;ENSP00000361856:A296S;ENSP00000438670:A42S	ENSP00000308622:A296S	A	+	1	0	GLE1	130325935	0.001000	0.12720	0.612000	0.29024	0.915000	0.54546	0.013000	0.13310	0.061000	0.16311	-0.152000	0.13540	GCC		0.512	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722	
ABL1	25	broad.mit.edu	37	9	133755462	133755462	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:133755462G>A	ENST00000318560.5	+	9	1812	c.1431G>A	c.(1429-1431)caG>caA	p.Q477Q		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	477	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)	p.Q477Q(1)		breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CAGGTTGGCAGTGGAATCCCT	0.488			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""																																p.Q477Q			Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1431A	9						.						115.0	103.0	107.0					9																	133755462		2203	4300	6503	132745283	SO:0001819	synonymous_variant	25	exon9			M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1431G>A	9.37:g.133755462G>A		Somatic		Capture	Illumina HiSeq	Phase_I	132745283	NM_005157	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																				0.488	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
FAM78A	286336	broad.mit.edu	37	9	134136311	134136311	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:134136311C>T	ENST00000372271.3	-	2	1117	c.750G>A	c.(748-750)ccG>ccA	p.P250P	FAM78A_ENST00000372269.3_Silent_p.P247P|FAM78A_ENST00000247295.4_5'UTR	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	250										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		GGGCGCTGGGCGGGATGGGCT	0.687																																					p.P250P												.	.	0			c.G750A	9						.						87.0	93.0	91.0					9																	134136311		2203	4300	6503	133126132	SO:0001819	synonymous_variant	286336	exon2			AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 59"""	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.750G>A	9.37:g.134136311C>T		None		Capture	Illumina HiSeq	Phase_I	133126132	NM_033387	Q86VQ9|Q9H7P4	Silent	SNP	ENST00000372271.3	37	CCDS6941.2																																																																																				0.687	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387	
ADAMTS13	11093	broad.mit.edu	37	9	136304526	136304526	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:136304526G>T	ENST00000371929.3	+	15	2189	c.1745G>T	c.(1744-1746)aGt>aTt	p.S582I	ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Missense_Mutation_p.S551I|ADAMTS13_ENST00000355699.2_Missense_Mutation_p.S582I|ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000536611.1_Missense_Mutation_p.S254I	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	582	Spacer.				cell-matrix adhesion (GO:0007160)|glycoprotein metabolic process (GO:0009100)|integrin-mediated signaling pathway (GO:0007229)|peptide catabolic process (GO:0043171)|platelet activation (GO:0030168)|protein processing (GO:0016485)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to interleukin-4 (GO:0070670)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(4)	36				OV - Ovarian serous cystadenocarcinoma(145;1.06e-07)|Epithelial(140;1.28e-06)|all cancers(34;1.46e-05)		AACCTGACCAGTGTCTACATT	0.502																																					p.S582I												.	.	0			c.G1745T	9						.						161.0	139.0	147.0					9																	136304526		2203	4300	6503	135294347	SO:0001583	missense	11093	exon15			AJ011374	CCDS6970.1, CCDS6971.1, CCDS6972.1	9q34	2008-07-21	2005-08-19	2001-09-21	ENSG00000160323	ENSG00000160323		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	1366	protein-coding gene	gene with protein product		604134	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 13"""	C9orf8		11557746, 11535495	Standard	NM_139025		Approved	VWFCP, TTP, vWF-CP, FLJ42993, MGC118899, MGC118900, DKFZp434C2322	uc004cdv.4	Q76LX8	OTTHUMG00000020876	ENST00000371929.3:c.1745G>T	9.37:g.136304526G>T	ENSP00000360997:p.Ser582Ile	None		Capture	Illumina HiSeq	Phase_I	135294347	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	G	11.94	1.787362	0.31593	.	.	ENSG00000160323	ENST00000371929;ENST00000355699;ENST00000356589;ENST00000536611	T;T;T;T	0.70045	-0.43;-0.45;-0.43;0.01	5.13	0.952	0.19584	.	.	.	.	.	T	0.69540	0.3122	M	0.84948	2.725	0.09310	N	1	D;D;D;P	0.56968	0.963;0.978;0.962;0.808	B;P;P;B	0.48454	0.374;0.578;0.578;0.193	T	0.58713	-0.7588	9	0.33141	T	0.24	.	5.5126	0.16888	0.3011:0.2934:0.4054:0.0	.	582;551;582;254	Q76LX8;Q76LX8-3;Q76LX8-2;Q9UGQ1	ATS13_HUMAN;.;.;.	I	582;582;551;254	ENSP00000360997:S582I;ENSP00000347927:S582I;ENSP00000348997:S551I;ENSP00000444504:S254I	ENSP00000347927:S582I	S	+	2	0	ADAMTS13	135294347	0.000000	0.05858	0.025000	0.17156	0.434000	0.31775	-0.066000	0.11598	0.178000	0.19917	0.462000	0.41574	AGT		0.502	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025	
TMEM8C	389827	broad.mit.edu	37	9	136389833	136389833	+	Splice_Site	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:136389833G>A	ENST00000339996.3	-	1	235	c.134C>T	c.(133-135)gCg>gTg	p.A45V	TMEM8C_ENST00000413714.1_Intron	NM_001080483.2	NP_001073952.1	A6NI61	TMM8C_HUMAN	transmembrane protein 8C	45					muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|plasma membrane fusion (GO:0045026)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|large_intestine(2)|lung(4)	8						CAGACTCACCGCCACGAAGAA	0.612																																					p.A45V												.	.	0			c.C134T	9						.						84.0	66.0	72.0					9																	136389833		2203	4300	6503	135379654	SO:0001630	splice_region_variant	389827	exon1			BX324209	CCDS35170.1	9q34.2	2009-06-19		2009-06-19	ENSG00000187616	ENSG00000187616			33778	protein-coding gene	gene with protein product	"""transmembrane protein 226"""	615345					Standard	NM_001080483		Approved	TMEM226	uc011mdk.2	A6NI61	OTTHUMG00000131685	ENST00000339996.3:c.135+1C>T	9.37:g.136389833G>A		None		Capture	Illumina HiSeq	Phase_I	135379654	NM_001080483		Missense_Mutation	SNP	ENST00000339996.3	37	CCDS35170.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689131	0.88735	.	.	ENSG00000187616	ENST00000339996	T	0.46819	0.86	4.38	3.47	0.39725	.	0.068770	0.56097	N	0.000025	T	0.43166	0.1235	M	0.67953	2.075	0.51767	D	0.999939	B	0.33612	0.419	B	0.25140	0.058	T	0.45454	-0.9260	10	0.62326	D	0.03	-28.8254	12.1745	0.54178	0.0846:0.0:0.9154:0.0	.	45	A6NI61	TMM8C_HUMAN	V	45	ENSP00000419712:A45V	ENSP00000419712:A45V	A	-	2	0	TMEM8C	135379654	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	6.529000	0.73812	0.842000	0.35045	0.484000	0.47621	GCG		0.612	TMEM8C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356200.2	NM_001080483	Missense_Mutation
SARDH	1757	broad.mit.edu	37	9	136531966	136531966	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:136531966G>T	ENST00000371872.4	-	20	2779	c.2522C>A	c.(2521-2523)gCc>gAc	p.A841D	SARDH_ENST00000422262.2_Missense_Mutation_p.A673D|SARDH_ENST00000371868.1_Missense_Mutation_p.A291D|SARDH_ENST00000439388.1_Missense_Mutation_p.A841D|SARDH_ENST00000469828.1_5'UTR	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	841					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)	p.A841D(1)		central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CCTCCAGATGGCCTCCAGGCC	0.612																																					p.A841D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2522A	9						.						53.0	46.0	48.0					9																	136531966		2201	4296	6497	135521787	SO:0001583	missense	1757	exon20				CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2522C>A	9.37:g.136531966G>T	ENSP00000360938:p.Ala841Asp	Somatic		Capture	Illumina HiSeq	Phase_I	135521787	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.603719	0.87157	.	.	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;D;T;T	0.81499	-0.97;-1.5;-0.97;-0.97	4.69	4.69	0.59074	Glycine cleavage T-protein, C-terminal barrel (1);	0.000000	0.85682	D	0.000000	D	0.88757	0.6523	M	0.74389	2.26	0.80722	D	1	D;D	0.60160	0.972;0.987	P;D	0.64410	0.9;0.925	D	0.90285	0.4318	10	0.66056	D	0.02	-28.8984	17.6256	0.88093	0.0:0.0:1.0:0.0	.	841;291	Q9UL12;Q5SYV2	SARDH_HUMAN;.	D	841;291;841;673	ENSP00000360938:A841D;ENSP00000360934:A291D;ENSP00000403084:A841D;ENSP00000415537:A673D	ENSP00000360934:A291D	A	-	2	0	SARDH	135521787	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.385000	0.97223	2.161000	0.67846	0.455000	0.32223	GCC		0.612	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
COL5A1	1289	broad.mit.edu	37	9	137687112	137687112	+	Missense_Mutation	SNP	C	C	T	rs375600865		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:137687112C>T	ENST00000371817.3	+	34	3164	c.2750C>T	c.(2749-2751)cCg>cTg	p.P917L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	917	Triple-helical region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)	p.P917L(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		GTCCAGGGTCCGAGGGGTGAA	0.632																																					p.P917L												.	.	2	Substitution - Missense(2)	large_intestine(1)|endometrium(1)	c.C2750T	9						.	C	LEU/PRO	0,4406		0,0,2203	82.0	88.0	86.0		2750	4.2	0.9	9		86	1,8599	1.2+/-3.3	0,1,4299	no	missense	COL5A1	NM_000093.3	98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	917/1839	137687112	1,13005	2203	4300	6503	136826933	SO:0001583	missense	1289	exon34			D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.2750C>T	9.37:g.137687112C>T	ENSP00000360882:p.Pro917Leu	Somatic		Capture	Illumina HiSeq	Phase_I	136826933	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000058	0.74818	0.0	1.16E-4	ENSG00000130635	ENST00000371817	D	0.96885	-4.16	4.22	4.22	0.49857	.	0.000000	0.64402	U	0.000001	D	0.95847	0.8648	N	0.21448	0.665	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94278	0.7517	10	0.19147	T	0.46	.	16.5867	0.84729	0.0:1.0:0.0:0.0	.	917	P20908	CO5A1_HUMAN	L	917	ENSP00000360882:P917L	ENSP00000360882:P917L	P	+	2	0	COL5A1	136826933	1.000000	0.71417	0.871000	0.34182	0.700000	0.40528	7.279000	0.78599	1.904000	0.55121	0.297000	0.19635	CCG		0.632	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	
PPP1R26	9858	broad.mit.edu	37	9	138378381	138378381	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:138378381C>T	ENST00000356818.2	+	4	2574	c.2025C>T	c.(2023-2025)gaC>gaT	p.D675D	PPP1R26_ENST00000604351.1_Silent_p.D675D|PPP1R26_ENST00000401470.3_Silent_p.D675D|PPP1R26_ENST00000605660.1_Silent_p.D675D|PPP1R26_ENST00000605286.1_Silent_p.D675D|PPP1R26_ENST00000602993.1_Intron	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	675					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.D675D(1)									GGCGCCTAGACGAGAAAGAGA	0.597																																					p.D675D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2025T	9						.						63.0	62.0	62.0					9																	138378381		2203	4300	6503	137518202	SO:0001819	synonymous_variant	9858	exon4			AB014549	CCDS6988.1	9q34.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000196422	ENSG00000196422		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29089	protein-coding gene	gene with protein product	"""DRIM/UTP20 interacting protein"", ""1A6/DRIM (down-regulated in metastasis) interacting protein"""	614056	"""KIAA0649"""	KIAA0649		9734811, 16053918	Standard	NM_014811		Approved		uc004cfr.1	Q5T8A7	OTTHUMG00000020904	ENST00000356818.2:c.2025C>T	9.37:g.138378381C>T		Somatic		Capture	Illumina HiSeq	Phase_I	137518202	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																				0.597	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
SMARCA2	6595	broad.mit.edu	37	9	2182151	2182151	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:2182151G>A	ENST00000382203.1	+	31	4579	c.4370G>A	c.(4369-4371)cGt>cAt	p.R1457H	SMARCA2_ENST00000349721.2_Missense_Mutation_p.R1457H|SMARCA2_ENST00000302401.3_Missense_Mutation_p.R145H|SMARCA2_ENST00000382194.1_Missense_Mutation_p.R1439H|SMARCA2_ENST00000382186.1_Missense_Mutation_p.R121H|SMARCA2_ENST00000382185.1_Missense_Mutation_p.R103H|SMARCA2_ENST00000357248.2_Missense_Mutation_p.R1439H|SMARCA2_ENST00000324954.5_Missense_Mutation_p.R103H			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	1457	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|chromatin remodeling (GO:0006338)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	ATP binding (GO:0005524)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		all_lung(10;2.06e-09)|Lung NSC(10;2.43e-09)		GBM - Glioblastoma multiforme(50;0.0475)		GAAAGGATTCGTAATCATAAG	0.443																																					p.R1439H												.	.	0			c.G4316A	9						.						134.0	132.0	133.0					9																	2182151		2203	4300	6503	2172151	SO:0001583	missense	6595	exon30			D26155	CCDS34977.1, CCDS34978.1, CCDS75807.1, CCDS75808.1	9p24.3	2008-11-11	2006-11-09		ENSG00000080503	ENSG00000080503			11098	protein-coding gene	gene with protein product		600014		SNF2L2		8012116	Standard	NM_003070		Approved	BAF190, hSNF2a, hBRM, Sth1p, SNF2LA, BRM, SNF2, SWI2	uc003zhc.3	P51531	OTTHUMG00000019445	ENST00000382203.1:c.4370G>A	9.37:g.2182151G>A	ENSP00000371638:p.Arg1457His	None		Capture	Illumina HiSeq	Phase_I	2172151	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.237097	0.58886	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194;ENST00000452193;ENST00000302401;ENST00000324954;ENST00000423555;ENST00000382186;ENST00000417599;ENST00000382185;ENST00000382183;ENST00000416751	T;T;T;T;T;T;T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51;1.51	5.84	5.84	0.93424	Bromodomain (6);Bromodomain, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.54287	0.1849	L	0.55103	1.725	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.996;0.997	D;D;D;D	0.80764	0.982;0.982;0.989;0.994	T	0.51741	-0.8667	10	0.72032	D	0.01	-11.9829	20.1579	0.98126	0.0:0.0:1.0:0.0	.	143;145;1439;1457	B4DNT1;B1ALF6;P51531-2;P51531	.;.;.;SMCA2_HUMAN	H	1457;1439;1457;1439;121;145;103;143;121;143;103;103;103	ENSP00000265773:R1457H;ENSP00000349788:R1439H;ENSP00000371638:R1457H;ENSP00000371629:R1439H;ENSP00000401096:R121H;ENSP00000305411:R145H;ENSP00000324770:R103H;ENSP00000413057:R143H;ENSP00000371621:R121H;ENSP00000387486:R143H;ENSP00000371620:R103H;ENSP00000371618:R103H;ENSP00000412242:R103H	ENSP00000305411:R145H	R	+	2	0	SMARCA2	2172151	1.000000	0.71417	0.983000	0.44433	0.120000	0.20174	9.845000	0.99498	2.767000	0.95098	0.555000	0.69702	CGT		0.443	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
VLDLR	7436	broad.mit.edu	37	9	2639950	2639950	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:2639950A>G	ENST00000382100.3	+	3	650	c.294A>G	c.(292-294)gaA>gaG	p.E98E	RP11-125B21.2_ENST00000599229.1_RNA|VLDLR_ENST00000382099.2_Silent_p.E98E	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	98	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.E98E(1)		breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		CTGACTGCGAAGATGGTTCAG	0.468																																					p.E98E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A294G	9						.						278.0	245.0	256.0					9																	2639950		2203	4300	6503	2629950	SO:0001819	synonymous_variant	7436	exon3				CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.294A>G	9.37:g.2639950A>G		Somatic		Capture	Illumina HiSeq	Phase_I	2629950	NM_001018056	B2RMZ7|D3DRH6|Q5VVF6	Silent	SNP	ENST00000382100.3	37	CCDS6446.1																																																																																				0.468	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
PTPRD	5789	broad.mit.edu	37	9	8389326	8389326	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:8389326G>T	ENST00000381196.4	-	34	4835	c.4292C>A	c.(4291-4293)tCt>tAt	p.S1431Y	PTPRD_ENST00000358503.5_Missense_Mutation_p.S1409Y|PTPRD_ENST00000540109.1_Missense_Mutation_p.S1431Y|PTPRD_ENST00000355233.5_Missense_Mutation_p.S1025Y|PTPRD_ENST00000397617.3_Missense_Mutation_p.S1024Y|PTPRD_ENST00000356435.5_Missense_Mutation_p.S1431Y|PTPRD_ENST00000397606.3_Missense_Mutation_p.S1024Y|PTPRD_ENST00000486161.1_Missense_Mutation_p.S1024Y|PTPRD_ENST00000397611.3_Missense_Mutation_p.S1021Y|PTPRD_ENST00000537002.1_Missense_Mutation_p.S1021Y|PTPRD_ENST00000360074.4_Missense_Mutation_p.S1418Y	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1431	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.S1431Y(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		TTCGGGGAGAGATCCCTGTGT	0.433										TSP Lung(15;0.13)																											p.S1021Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3062A	9						.						190.0	179.0	183.0					9																	8389326		2203	4300	6503	8379326	SO:0001583	missense	5789	exon21			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.4292C>A	9.37:g.8389326G>T	ENSP00000370593:p.Ser1431Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	8379326	NM_001040712	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.007076	0.93287	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56;1.56	5.65	5.65	0.86999	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.279632	0.37261	N	0.002162	T	0.39332	0.1074	N	0.14661	0.345	0.48288	D	0.999622	D;D;D;D;D;P;D;D;D	0.76494	0.999;0.963;0.963;0.963;0.999;0.954;0.999;0.997;0.998	P;P;P;P;D;B;D;D;D	0.68353	0.756;0.551;0.551;0.551;0.919;0.416;0.939;0.957;0.93	T	0.21965	-1.0230	9	.	.	.	.	19.7173	0.96127	0.0:0.0:1.0:0.0	.	1024;1015;1024;1025;1021;1021;1418;1431;1431	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	Y	1431;1431;1418;1409;1025;1024;1021;1021;902;1431;1024;1024	ENSP00000370593:S1431Y;ENSP00000348812:S1431Y;ENSP00000353187:S1418Y;ENSP00000351293:S1409Y;ENSP00000347373:S1025Y;ENSP00000380741:S1024Y;ENSP00000380735:S1021Y;ENSP00000440515:S1021Y;ENSP00000438164:S1431Y;ENSP00000417093:S1024Y;ENSP00000380731:S1024Y	.	S	-	2	0	PTPRD	8379326	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.661000	0.90470	0.555000	0.69702	TCT		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
PTPRD	5789	broad.mit.edu	37	9	8501056	8501056	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:8501056G>A	ENST00000381196.4	-	21	2369	c.1826C>T	c.(1825-1827)cCg>cTg	p.P609L	PTPRD_ENST00000358503.5_Missense_Mutation_p.P596L|PTPRD_ENST00000355233.5_Intron|PTPRD_ENST00000397617.3_Intron|PTPRD_ENST00000540109.1_Missense_Mutation_p.P609L|PTPRD_ENST00000356435.5_Missense_Mutation_p.P609L|PTPRD_ENST00000397606.3_Intron|PTPRD_ENST00000486161.1_Intron|PTPRD_ENST00000397611.3_Intron|PTPRD_ENST00000537002.1_Intron|PTPRD_ENST00000360074.4_Missense_Mutation_p.P596L|PTPRD_ENST00000471274.1_5'UTR	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	609					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.P609L(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		AGGAGCTGACGGCTCTTATTT	0.378										TSP Lung(15;0.13)																											p.P609L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1826T	9						.						67.0	63.0	64.0					9																	8501056		2203	4300	6503	8491056	SO:0001583	missense	5789	exon24			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1826C>T	9.37:g.8501056G>A	ENSP00000370593:p.Pro609Leu	Somatic		Capture	Illumina HiSeq	Phase_I	8491056	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.884847	0.72410	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000540109	T;T;T;T;T	0.62364	0.03;0.03;0.03;0.03;0.03	5.76	5.76	0.90799	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.84977	0.5592	H	0.96691	3.865	0.80722	D	1	D;D;B	0.67145	0.957;0.996;0.337	P;P;B	0.58210	0.63;0.835;0.117	D	0.89750	0.3939	9	.	.	.	.	19.9574	0.97228	0.0:0.0:1.0:0.0	.	596;609;609	G3XAE2;Q2HXI4;P23468	.;.;PTPRD_HUMAN	L	609;609;596;596;609	ENSP00000370593:P609L;ENSP00000348812:P609L;ENSP00000353187:P596L;ENSP00000351293:P596L;ENSP00000438164:P609L	.	P	-	2	0	PTPRD	8491056	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.715000	0.92844	0.561000	0.74099	CCG		0.378	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
PTPRD	5789	broad.mit.edu	37	9	8504274	8504274	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:8504274T>G	ENST00000381196.4	-	20	2352	c.1809A>C	c.(1807-1809)agA>agC	p.R603S	PTPRD_ENST00000358503.5_Missense_Mutation_p.R590S|PTPRD_ENST00000355233.5_Missense_Mutation_p.R603S|PTPRD_ENST00000397617.3_Missense_Mutation_p.R593S|PTPRD_ENST00000540109.1_Missense_Mutation_p.R603S|PTPRD_ENST00000356435.5_Missense_Mutation_p.R603S|PTPRD_ENST00000397606.3_Missense_Mutation_p.R593S|PTPRD_ENST00000486161.1_Missense_Mutation_p.R603S|PTPRD_ENST00000397611.3_Missense_Mutation_p.R600S|PTPRD_ENST00000537002.1_Missense_Mutation_p.R600S|PTPRD_ENST00000360074.4_Missense_Mutation_p.R590S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	603	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.R603S(1)		NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ACTGCATGGTTCTAGCTGATA	0.468										TSP Lung(15;0.13)																											p.R600S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1800C	9						.						188.0	170.0	176.0					9																	8504274		2203	4300	6503	8494274	SO:0001583	missense	5789	exon11			X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.1809A>C	9.37:g.8504274T>G	ENSP00000370593:p.Arg603Ser	Somatic		Capture	Illumina HiSeq	Phase_I	8494274	NM_001040712	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	14.17	2.455690	0.43634	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.55760	0.5;0.5;0.5;0.5;0.55;0.55;0.55;0.55;0.5;0.55;0.55	5.53	4.4	0.53042	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.098941	0.64402	D	0.000001	T	0.57784	0.2077	M	0.76938	2.355	0.53005	D	0.99996	B;B;P;B;B;B;P;B;B	0.40834	0.004;0.008;0.57;0.017;0.182;0.014;0.73;0.228;0.423	B;B;B;B;B;B;B;B;B	0.44044	0.016;0.016;0.146;0.016;0.439;0.036;0.284;0.103;0.206	T	0.58047	-0.7705	9	.	.	.	.	11.1624	0.48522	0.0:0.0719:0.0:0.9281	.	593;597;603;603;600;600;590;603;603	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	603;603;590;590;603;593;600;600;603;603;603;593	ENSP00000370593:R603S;ENSP00000348812:R603S;ENSP00000353187:R590S;ENSP00000351293:R590S;ENSP00000347373:R603S;ENSP00000380741:R593S;ENSP00000380735:R600S;ENSP00000440515:R600S;ENSP00000438164:R603S;ENSP00000417093:R603S;ENSP00000380731:R593S	.	R	-	3	2	PTPRD	8494274	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.003000	0.40844	0.946000	0.37632	0.383000	0.25322	AGA		0.468	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
FREM1	158326	broad.mit.edu	37	9	14851520	14851520	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:14851520A>C	ENST00000380880.3	-	6	1697	c.914T>G	c.(913-915)cTg>cGg	p.L305R	FREM1_ENST00000422223.2_Missense_Mutation_p.L305R|RNU6-1260P_ENST00000362944.1_RNA|FREM1_ENST00000380881.4_Missense_Mutation_p.L306R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	305					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)	p.L306R(1)		breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		ATCCACTTCCAGAATAAACAC	0.453																																					p.L305R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T914G	9						.						119.0	118.0	118.0					9																	14851520		1948	4147	6095	14841520	SO:0001583	missense	158326	exon7			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.914T>G	9.37:g.14851520A>C	ENSP00000370262:p.Leu305Arg	Somatic		Capture	Illumina HiSeq	Phase_I	14841520	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.916092	0.92178	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.15952	2.4;2.38;2.38	6.11	6.11	0.99139	.	0.000000	0.85682	D	0.000000	T	0.48589	0.1508	M	0.85197	2.74	0.54753	D	0.999987	D	0.89917	1.0	D	0.83275	0.996	T	0.54180	-0.8332	10	0.87932	D	0	-9.6822	16.7021	0.85357	1.0:0.0:0.0:0.0	.	305	Q5H8C1	FREM1_HUMAN	R	306;305;305	ENSP00000370263:L306R;ENSP00000412940:L305R;ENSP00000370262:L305R	ENSP00000370257:L308R	L	-	2	0	FREM1	14841520	1.000000	0.71417	0.998000	0.56505	0.924000	0.55760	8.962000	0.93254	2.343000	0.79666	0.533000	0.62120	CTG		0.453	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
ADAMTSL1	92949	broad.mit.edu	37	9	18675874	18675874	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:18675874A>G	ENST00000380548.4	+	10	1444	c.1105A>G	c.(1105-1107)Atg>Gtg	p.M369V	ADAMTSL1_ENST00000276935.6_Missense_Mutation_p.M369V|ADAMTSL1_ENST00000380566.4_Intron|ADAMTSL1_ENST00000327883.7_Missense_Mutation_p.M369V	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	369						proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.M369V(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(2)|lung(17)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(50;1.29e-17)		CAAGCAGATCATGCCTTATGA	0.358																																					p.M369V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1105G	9						.						243.0	184.0	204.0					9																	18675874		2203	4300	6503	18665874	SO:0001583	missense	92949	exon10			AF176313	CCDS6485.1, CCDS47954.1	9p21.3	2013-01-11			ENSG00000178031	ENSG00000178031		"""Immunoglobulin superfamily / I-set domain containing"""	14632	protein-coding gene	gene with protein product	"""punctin"""	609198	"""chromosome 9 open reading frame 94"""	C9orf94		9628581, 11805097	Standard	NM_001040272		Approved	ADAMTSR1, FLJ35283	uc003zne.4	Q8N6G6	OTTHUMG00000019604	ENST00000380548.4:c.1105A>G	9.37:g.18675874A>G	ENSP00000369921:p.Met369Val	Somatic		Capture	Illumina HiSeq	Phase_I	18665874	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Missense_Mutation	SNP	ENST00000380548.4	37	CCDS47954.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.068536	0.76301	.	.	ENSG00000178031	ENST00000380548;ENST00000327883;ENST00000276935	T;T;T	0.62498	0.02;0.12;0.05	5.59	5.59	0.84812	.	.	.	.	.	T	0.64724	0.2624	L	0.39633	1.23	0.80722	D	1	P	0.50369	0.934	P	0.53146	0.719	T	0.60840	-0.7183	9	0.25106	T	0.35	.	15.7538	0.78009	1.0:0.0:0.0:0.0	.	369	Q8N6G6	ATL1_HUMAN	V	369	ENSP00000369921:M369V;ENSP00000327887:M369V;ENSP00000276935:M369V	ENSP00000276935:M369V	M	+	1	0	ADAMTSL1	18665874	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.731000	0.91529	2.137000	0.66172	0.533000	0.62120	ATG		0.358	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		
SLC24A2	25769	broad.mit.edu	37	9	19786464	19786464	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:19786464G>A	ENST00000341998.2	-	1	462	c.401C>T	c.(400-402)gCg>gTg	p.A134V	SLC24A2_ENST00000286344.3_Missense_Mutation_p.A134V	NM_001193288.2|NM_020344.3	NP_001180217.1|NP_065077.1	Q9UI40	NCKX2_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 2	134					cellular calcium ion homeostasis (GO:0006874)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|learning (GO:0007612)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	cadmium ion binding (GO:0046870)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium, potassium:sodium antiporter activity (GO:0008273)|manganese ion binding (GO:0030145)|nickel cation binding (GO:0016151)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|symporter activity (GO:0015293)	p.A134V(3)		endometrium(3)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33				GBM - Glioblastoma multiforme(1;1.67e-55)|Lung(42;0.0443)		CAGAATGATCGCACCTTTTCT	0.433																																					p.A134V												.	.	3	Substitution - Missense(3)	large_intestine(2)|lung(1)	c.C401T	9						.						104.0	99.0	101.0					9																	19786464		2203	4300	6503	19776464	SO:0001583	missense	25769	exon2			AF097366	CCDS6493.1, CCDS55297.1	9p22.1	2013-05-22			ENSG00000155886	ENSG00000155886		"""Solute carriers"""	10976	protein-coding gene	gene with protein product		609838				10662833	Standard	NM_020344		Approved	NCKX2	uc003zoa.2	Q9UI40	OTTHUMG00000019646	ENST00000341998.2:c.401C>T	9.37:g.19786464G>A	ENSP00000344801:p.Ala134Val	Somatic		Capture	Illumina HiSeq	Phase_I	19776464	NM_020344	B7ZLL8|Q9NTN5|Q9NZQ4	Missense_Mutation	SNP	ENST00000341998.2	37	CCDS6493.1	.	.	.	.	.	.	.	.	.	.	G	18.50	3.638031	0.67130	.	.	ENSG00000155886	ENST00000341998;ENST00000286344	T;T	0.77489	-1.09;-1.1	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.85031	0.5604	M	0.74881	2.28	0.80722	D	1	P;D	0.69078	0.952;0.997	P;P	0.53760	0.526;0.734	D	0.84699	0.0727	9	.	.	.	.	19.967	0.97274	0.0:0.0:1.0:0.0	.	134;134	Q9UI40-2;Q9UI40	.;NCKX2_HUMAN	V	134	ENSP00000344801:A134V;ENSP00000286344:A134V	.	A	-	2	0	SLC24A2	19776464	1.000000	0.71417	0.998000	0.56505	0.788000	0.44548	6.562000	0.73960	2.714000	0.92807	0.655000	0.94253	GCG		0.433	SLC24A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051866.2	NM_020344	
CAAP1	79886	broad.mit.edu	37	9	26887366	26887366	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:26887366C>T	ENST00000333916.5	-	2	537	c.449G>A	c.(448-450)tGc>tAc	p.C150Y	CAAP1_ENST00000495958.1_5'UTR|CAAP1_ENST00000535437.1_Missense_Mutation_p.C5Y|CAAP1_ENST00000520187.1_Intron	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	150					apoptotic process (GO:0006915)			p.C150Y(1)									AATACAGAAGCACTGCTGAAG	0.383																																					p.C150Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G449A	9						.						34.0	34.0	34.0					9																	26887366		2203	4300	6503	26877366	SO:0001583	missense	79886	exon2			BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.449G>A	9.37:g.26887366C>T	ENSP00000369431:p.Cys150Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	26877366	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Missense_Mutation	SNP	ENST00000333916.5	37	CCDS6516.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.473718	0.84640	.	.	ENSG00000120159	ENST00000333916;ENST00000535437	T;T	0.51071	0.72;0.75	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.65512	0.2698	L	0.46157	1.445	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65545	-0.6142	10	0.72032	D	0.01	-10.9233	20.0114	0.97452	0.0:1.0:0.0:0.0	.	150	Q9H8G2	CI082_HUMAN	Y	150;5	ENSP00000369431:C150Y;ENSP00000444885:C5Y	ENSP00000369431:C150Y	C	-	2	0	C9orf82	26877366	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.194000	0.77789	2.732000	0.93576	0.591000	0.81541	TGC		0.383	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
TEK	7010	broad.mit.edu	37	9	27212815	27212815	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:27212815G>A	ENST00000380036.4	+	17	3239	c.2797G>A	c.(2797-2799)Gcg>Acg	p.A933T	TEK_ENST00000406359.4_Missense_Mutation_p.A890T|TEK_ENST00000519097.1_Missense_Mutation_p.A785T	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	933	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|definitive hemopoiesis (GO:0060216)|endochondral ossification (GO:0001958)|endothelial cell proliferation (GO:0001935)|glomerulus vasculature development (GO:0072012)|heart development (GO:0007507)|heart trabecula formation (GO:0060347)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of inflammatory response (GO:0050728)|organ regeneration (GO:0031100)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|regulation of endothelial cell apoptotic process (GO:2000351)|regulation of establishment or maintenance of cell polarity (GO:0032878)|regulation of vascular permeability (GO:0043114)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to peptide hormone (GO:0043434)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|sprouting angiogenesis (GO:0002040)|substrate adhesion-dependent cell spreading (GO:0034446)|Tie signaling pathway (GO:0048014)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.A933T(1)		breast(3)|central_nervous_system(3)|kidney(1)|lung(2)|ovary(3)|skin(3)	15		all_neural(11;7.57e-10)|Myeloproliferative disorder(762;0.0255)		Lung(218;4.08e-05)|LUSC - Lung squamous cell carcinoma(38;0.00027)	Ponatinib(DB08901)|Regorafenib(DB08896)|Vandetanib(DB05294)	CAATAGCACCGCGTCCACACT	0.597																																					p.A933T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2797A	9						.						93.0	74.0	80.0					9																	27212815		2203	4300	6503	27202815	SO:0001583	missense	7010	exon17			L06139	CCDS6519.1, CCDS75825.1	9p21	2013-02-11	2008-07-31		ENSG00000120156	ENSG00000120156		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	11724	protein-coding gene	gene with protein product		600221	"""venous malformations, multiple cutaneous and mucosal"""	VMCM		1312667, 7833915	Standard	XM_005251561		Approved	TIE2, TIE-2, VMCM1, CD202b	uc003zqi.4	Q02763	OTTHUMG00000019712	ENST00000380036.4:c.2797G>A	9.37:g.27212815G>A	ENSP00000369375:p.Ala933Thr	Somatic		Capture	Illumina HiSeq	Phase_I	27202815	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537000	0.85812	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	D;D;D	0.82619	-1.63;-1.63;-1.63	5.37	4.45	0.53987	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.50627	D	0.000101	D	0.87128	0.6100	L	0.38733	1.17	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	P;D;D	0.91635	0.842;0.993;0.999	D	0.88515	0.3092	10	0.66056	D	0.02	.	16.159	0.81683	0.0:0.1338:0.8662:0.0	.	785;966;933	E7EWI2;Q59HG2;Q02763	.;.;TIE2_HUMAN	T	785;933;890	ENSP00000430686:A785T;ENSP00000369375:A933T;ENSP00000383977:A890T	ENSP00000369375:A933T	A	+	1	0	TEK	27202815	1.000000	0.71417	0.482000	0.27366	0.605000	0.37080	9.738000	0.98835	1.359000	0.45940	0.591000	0.81541	GCG		0.597	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3		
TAF1L	138474	broad.mit.edu	37	9	32635317	32635317	+	Silent	SNP	A	A	G	rs16918395	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:32635317A>G	ENST00000242310.4	-	1	350	c.261T>C	c.(259-261)acT>acC	p.T87T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	87					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)	p.T87T(1)		breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		CGCCAGTCCCAGTCAATTCTT	0.493													G|||	47	0.00938498	0.0318	0.0072	5008	,	,		16137	0.0		0.0	False		,,,				2504	0.0				p.T87T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T261C	9						.	G		132,4274	814.2+/-416.2	5,122,2076	182.0	178.0	179.0		261	-1.0	0.1	9	dbSNP_123	179	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	TAF1L	NM_153809.2		5,124,6374	GG,GA,AA		0.0233,2.9959,1.0303		87/1827	32635317	134,12872	2203	4300	6503	32625317	SO:0001819	synonymous_variant	138474	exon1			AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.261T>C	9.37:g.32635317A>G		Somatic		Capture	Illumina HiSeq	Phase_I	32625317	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																				0.493	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
RPP25L	138716	broad.mit.edu	37	9	34611094	34611094	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:34611094G>A	ENST00000297613.4	-	2	480	c.200C>T	c.(199-201)gCt>gTt	p.A67V	DCTN3_ENST00000479399.1_5'Flank|RPP25L_ENST00000378959.4_Missense_Mutation_p.A67V	NM_148179.2	NP_680545.1	Q8N5L8	RP25L_HUMAN	ribonuclease P/MRP 25kDa subunit-like	67						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A67V(1)									GCAGCTGACAGCCTTTCCTGC	0.607																																					p.A67V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C200T	9						.						63.0	62.0	63.0					9																	34611094		2203	4300	6503	34601094	SO:0001583	missense	138716	exon2			BC032136	CCDS6559.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164967	ENSG00000164967			19909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 23"""	C9orf23		16998185	Standard	NM_148178		Approved	bA296L22.5, MGC29635	uc003zuv.3	Q8N5L8	OTTHUMG00000000443	ENST00000297613.4:c.200C>T	9.37:g.34611094G>A	ENSP00000297613:p.Ala67Val	Somatic		Capture	Illumina HiSeq	Phase_I	34601094	NM_148178	D3DRM5	Missense_Mutation	SNP	ENST00000297613.4	37	CCDS6559.1	.	.	.	.	.	.	.	.	.	.	G	34	5.382141	0.95967	.	.	ENSG00000164967	ENST00000378959;ENST00000297613	.	.	.	4.72	4.72	0.59763	.	0.120851	0.64402	D	0.000011	T	0.71837	0.3387	L	0.54323	1.7	0.47862	D	0.999533	D	0.60160	0.987	P	0.58660	0.843	T	0.74377	-0.3685	9	0.56958	D	0.05	-2.1241	16.8747	0.86048	0.0:0.0:1.0:0.0	.	67	Q8N5L8	CI023_HUMAN	V	67	.	ENSP00000297613:A67V	A	-	2	0	C9orf23	34601094	1.000000	0.71417	0.945000	0.38365	0.992000	0.81027	7.100000	0.76989	2.448000	0.82819	0.643000	0.83706	GCT		0.607	RPP25L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001130.1	NM_148179	
TLN1	7094	broad.mit.edu	37	9	35717759	35717759	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:35717759C>A	ENST00000314888.9	-	18	2373	c.2020G>T	c.(2020-2022)Gct>Tct	p.A674S	TLN1_ENST00000540444.1_Missense_Mutation_p.A674S	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	674					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.A674S(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)			CTTGCCACAGCTTTGGCGAGC	0.557																																					p.A674S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2020T	9						.						119.0	100.0	107.0					9																	35717759		2203	4300	6503	35707759	SO:0001583	missense	7094	exon18			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.2020G>T	9.37:g.35717759C>A	ENSP00000316029:p.Ala674Ser	Somatic		Capture	Illumina HiSeq	Phase_I	35707759	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.760244	0.89932	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.70631	-0.48;-0.5	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.78368	0.4272	M	0.74389	2.26	0.80722	D	1	P	0.37441	0.595	P	0.45998	0.5	T	0.77509	-0.2561	10	0.40728	T	0.16	-10.8825	18.2231	0.89907	0.0:1.0:0.0:0.0	.	674	Q9Y490	TLN1_HUMAN	S	674	ENSP00000316029:A674S;ENSP00000442981:A674S	ENSP00000316029:A674S	A	-	1	0	TLN1	35707759	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	6.092000	0.71414	2.571000	0.86741	0.561000	0.74099	GCT		0.557	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
NPR2	4882	broad.mit.edu	37	9	35805897	35805897	+	Silent	SNP	C	C	T	rs559838429		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:35805897C>T	ENST00000342694.2	+	14	2373	c.2118C>T	c.(2116-2118)gaC>gaT	p.D706D		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	706	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)	p.D706D(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	AGAAGGCTGACGTCTATAGCT	0.557																																					p.D706D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2118T	9						.						84.0	86.0	86.0					9																	35805897		2203	4300	6503	35795897	SO:0001819	synonymous_variant	4882	exon14			AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.2118C>T	9.37:g.35805897C>T		Somatic		Capture	Illumina HiSeq	Phase_I	35795897	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	3.856	-0.030846	0.07543	.	.	ENSG00000159899	ENST00000421267	.	.	.	5.82	-0.448	0.12230	.	.	.	.	.	T	0.55561	0.1928	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49542	-0.8929	4	.	.	.	.	9.666	0.39986	0.0:0.3947:0.0:0.6053	.	.	.	.	M	53	.	.	T	+	2	0	NPR2	35795897	0.047000	0.20315	0.996000	0.52242	0.967000	0.64934	-0.689000	0.05144	-0.081000	0.12662	-1.264000	0.01445	ACG		0.557	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
FBXO10	26267	broad.mit.edu	37	9	37516059	37516059	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:37516059C>T	ENST00000432825.2	-	10	2586	c.2538G>A	c.(2536-2538)tcG>tcA	p.S846S	FBXO10_ENST00000541829.1_Silent_p.S371S|RP11-613M10.8_ENST00000544475.1_5'UTR	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	846					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)	p.S852S(1)		breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		AGGCCCGGAACGAGTGGATCC	0.552																																					p.S846S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G2538A	9						.						98.0	85.0	89.0					9																	37516059		1897	4111	6008	37506059	SO:0001819	synonymous_variant	26267	exon10			AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.2538G>A	9.37:g.37516059C>T		Somatic		Capture	Illumina HiSeq	Phase_I	37506059	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Silent	SNP	ENST00000432825.2	37	CCDS47966.1																																																																																				0.552	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
TRMT10B	158234	broad.mit.edu	37	9	37763636	37763636	+	Silent	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:37763636C>A	ENST00000297994.3	+	4	371	c.306C>A	c.(304-306)ccC>ccA	p.P102P	TRMT10B_ENST00000537911.1_Silent_p.P102P|TRMT10B_ENST00000377754.2_Silent_p.P7P|TRMT10B_ENST00000377753.2_Intron|RP11-613M10.9_ENST00000540557.1_Intron	NM_144964.2	NP_659401.2	Q6PF06	TM10B_HUMAN	tRNA methyltransferase 10 homolog B (S. cerevisiae)	102							methyltransferase activity (GO:0008168)	p.P102P(1)									GCATTTGCCCCCAGCACAGCA	0.393																																					p.P102P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C306A	9						.						94.0	85.0	88.0					9																	37763636		1843	4092	5935	37753636	SO:0001819	synonymous_variant	158234	exon4			BC057774	CCDS43804.1, CCDS69598.1, CCDS69600.1, CCDS69601.1	9p13.1	2012-06-28	2012-06-28	2012-06-28	ENSG00000165275	ENSG00000165275			26454	protein-coding gene	gene with protein product			"""RNA (guanine-9-) methyltransferase domain containing 3"""	RG9MTD3		14702039	Standard	XM_005251373		Approved	FLJ31455, bA3J10.9	uc004aai.3	Q6PF06	OTTHUMG00000019933	ENST00000297994.3:c.306C>A	9.37:g.37763636C>A		Somatic		Capture	Illumina HiSeq	Phase_I	37753636	NM_144964	B7Z216|B7Z3D3|Q05DJ4|Q5QP83|Q8NAG2|Q96N36	Silent	SNP	ENST00000297994.3	37	CCDS43804.1																																																																																				0.393	TRMT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052482.1	NM_144964	
PRKACG	5568	broad.mit.edu	37	9	71628409	71628409	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:71628409G>A	ENST00000377276.2	-	1	630	c.600C>T	c.(598-600)tgC>tgT	p.C200C		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.C200C(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CTGGGGTCCCGCACAAGGTCC	0.617																																					p.C200C	Esophageal Squamous(110;2236 2623 32146)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C600T	9						.						51.0	52.0	51.0					9																	71628409		2203	4300	6503	70818229	SO:0001819	synonymous_variant	5568	exon1			M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.600C>T	9.37:g.71628409G>A		Somatic		Capture	Illumina HiSeq	Phase_I	70818229	NM_002732	O60850|Q5VZ02|Q86YI1	Silent	SNP	ENST00000377276.2	37	CCDS6625.1																																																																																				0.617	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
PCSK5	5125	broad.mit.edu	37	9	78749068	78749068	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:78749068A>G	ENST00000545128.1	+	10	1790	c.1252A>G	c.(1252-1254)Act>Gct	p.T418A	PCSK5_ENST00000376767.3_Missense_Mutation_p.T418A|PCSK5_ENST00000376752.4_Missense_Mutation_p.T418A	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	418	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)	p.T418A(3)		NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TATTGTCAGGACTTCCCGTGC	0.423																																					p.T418A												.	.	3	Substitution - Missense(3)	large_intestine(3)	c.A1252G	9						.						136.0	126.0	129.0					9																	78749068		2203	4300	6503	77938888	SO:0001583	missense	5125	exon10				CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1252A>G	9.37:g.78749068A>G	ENSP00000446280:p.Thr418Ala	Somatic		Capture	Illumina HiSeq	Phase_I	77938888	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.404550	0.83230	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.93035	0.7783	L	0.58925	1.835	0.58432	D	0.999997	D;P	0.63046	0.992;0.49	D;P	0.74348	0.983;0.6	D	0.93119	0.6523	10	0.52906	T	0.07	-13.3352	16.1611	0.81712	1.0:0.0:0.0:0.0	.	418;418	Q92824-2;B1AMG5	.;.	A	418;121;418;418;418;91	ENSP00000446280:T418A;ENSP00000365958:T418A;ENSP00000365943:T418A;ENSP00000411654:T91A	ENSP00000365943:T418A	T	+	1	0	PCSK5	77938888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.910000	0.92685	2.272000	0.75746	0.460000	0.39030	ACT		0.423	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PRUNE2	158471	broad.mit.edu	37	9	79318313	79318313	+	Missense_Mutation	SNP	G	G	A	rs114619409	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:79318313G>A	ENST00000376718.3	-	9	8339	c.8216C>T	c.(8215-8217)aCg>aTg	p.T2739M	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T2380M	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2739					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)	p.T2739M(1)		endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTCCATTTCCGTGTCAGGGAT	0.463													G|||	66	0.0131789	0.0477	0.0014	5008	,	,		19101	0.0		0.002	False		,,,				2504	0.0				p.T2739M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C8216T	9						.	G	MET/THR	130,3006		1,128,1439	95.0	82.0	86.0		8216	-4.6	0.0	9	dbSNP_132	86	3,7161		0,3,3579	yes	missense	PRUNE2	NM_015225.2	81	1,131,5018	AA,AG,GG		0.0419,4.1454,1.2913	benign	2739/3089	79318313	133,10167	1568	3582	5150	78508133	SO:0001583	missense	158471	exon9			BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.8216C>T	9.37:g.79318313G>A	ENSP00000365908:p.Thr2739Met	Somatic		Capture	Illumina HiSeq	Phase_I	78508133	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	11.11	1.541979	0.27563	0.041454	4.19E-4	ENSG00000106772	ENST00000376718;ENST00000428286;ENST00000422033	T;T	0.46063	0.88;0.88	5.6	-4.6	0.03390	.	0.967446	0.08503	N	0.936113	T	0.04227	0.0117	L	0.27053	0.805	0.18873	N	0.999987	B;B	0.33694	0.421;0.297	B;B	0.21360	0.034;0.015	T	0.09552	-1.0669	10	0.42905	T	0.14	2.2141	0.8297	0.01128	0.3279:0.108:0.1726:0.3914	.	2739;2739	Q8WUY3-3;Q8WUY3	.;PRUN2_HUMAN	M	2739;2380;2738	ENSP00000365908:T2739M;ENSP00000397425:T2380M	ENSP00000365908:T2739M	T	-	2	0	PRUNE2	78508133	0.000000	0.05858	0.003000	0.11579	0.912000	0.54170	-0.037000	0.12164	-0.663000	0.05331	0.591000	0.81541	ACG		0.463	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
DAPK1	1612	broad.mit.edu	37	9	90321475	90321475	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:90321475C>T	ENST00000408954.3	+	26	3824	c.3489C>T	c.(3487-3489)ggC>ggT	p.G1163G	DAPK1_ENST00000358077.5_Silent_p.G1163G|DAPK1_ENST00000472284.1_Silent_p.G1163G|DAPK1_ENST00000491893.1_Silent_p.G1097G|DAPK1_ENST00000469640.2_Silent_p.G1188G	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1163					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.G1164G(1)|p.G1163G(1)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						GCACAGAGGGCGACGCGGACA	0.637									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.G1163G												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C3489T	9						.						55.0	60.0	58.0					9																	90321475		2159	4265	6424	89511295	SO:0001819	synonymous_variant	1612	exon26	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3489C>T	9.37:g.90321475C>T		Somatic		Capture	Illumina HiSeq	Phase_I	89511295	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																				0.637	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
DAPK1	1612	broad.mit.edu	37	9	90321664	90321664	+	Silent	SNP	G	G	A	rs202069940		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:90321664G>A	ENST00000408954.3	+	26	4013	c.3678G>A	c.(3676-3678)acG>acA	p.T1226T	DAPK1_ENST00000358077.5_Silent_p.T1226T|DAPK1_ENST00000472284.1_Silent_p.T1226T|DAPK1_ENST00000491893.1_Silent_p.T1160T|DAPK1_ENST00000469640.2_Silent_p.T1251T	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1226					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.T1226T(2)|p.T1227T(2)		breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TGGCCACCACGCTGCCAGGGC	0.627									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	1	0.000199681	0.0008	0.0	5008	,	,		18160	0.0		0.0	False		,,,				2504	0.0				p.T1226T												.	.	4	Substitution - coding silent(4)	large_intestine(2)|lung(2)	c.G3678A	9						.						32.0	37.0	35.0					9																	90321664		2173	4278	6451	89511484	SO:0001819	synonymous_variant	1612	exon26	Familial Cancer Database	Familial CLL	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3678G>A	9.37:g.90321664G>A		Somatic		Capture	Illumina HiSeq	Phase_I	89511484	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																				0.627	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
CTSL3P	392360	broad.mit.edu	37	9	90387871	90387871	+	RNA	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:90387871G>T	ENST00000354530.2	+	0	42					NR_027917.1		Q5NE16	CATL3_HUMAN	cathepsin L family member 3, pseudogene								cysteine-type peptidase activity (GO:0008234)	p.G14G(1)									ACAGGGAAGGGAAACACAGCT	0.463																																					.												.	.	1	Substitution - coding silent(1)	large_intestine(1)	.	9						.						134.0	124.0	127.0					9																	90387871		2203	4300	6503	89577691			392360	.			AJ851862		9q21.33	2013-01-07	2013-01-07	2013-01-07	ENSG00000188029	ENSG00000188029		"""Cathepsins"""	33132	pseudogene	pseudogene			"""cathepsin L family member 3"""	CTSL3		19663681	Standard	NR_027917		Approved	HCTSL-s	uc004apm.1	Q5NE16	OTTHUMG00000020152		9.37:g.90387871G>T		Somatic		Capture	Illumina HiSeq	Phase_I	89577691	.		Silent	SNP	ENST00000354530.2	37																																																																																					0.463	CTSL3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000356542.1	NR_027917	
WNK2	65268	broad.mit.edu	37	9	96051831	96051831	+	Frame_Shift_Del	DEL	G	G	-	rs372738488		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:96051831delG	ENST00000297954.4	+	20	4906	c.4906delG	c.(4906-4908)gggfs	p.G1637fs	WNK2_ENST00000427277.2_Frame_Shift_Del_p.G1212fs|WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000395477.2_Frame_Shift_Del_p.G1600fs|WNK2_ENST00000349097.3_Frame_Shift_Del_p.G1249fs|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1637					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.D1587fs*35(1)|p.D1638fs*35(1)		breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						AGAGGTCTGCGGGGGGGACCT	0.687																																					p.G1599fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.4795delG	9						.						9.0	12.0	11.0					9																	96051831		2188	4278	6466	95091652	SO:0001589	frameshift_variant	65268	exon19			AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.4906delG	9.37:g.96051831delG	ENSP00000297954:p.Gly1637fs	Somatic		Capture	Illumina HiSeq	Phase_I	95091652	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Frame_Shift_Del	DEL	ENST00000297954.4	37																																																																																					0.687	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
FAM120A	23196	broad.mit.edu	37	9	96324491	96324491	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:96324491C>A	ENST00000277165.6	+	17	3144	c.2950C>A	c.(2950-2952)Cgt>Agt	p.R984S	FAM120A_ENST00000340893.4_Splice_Site_p.R938S|FAM120A_ENST00000333936.5_Splice_Site_p.R1012S	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	984	RNA binding.					cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)	p.R984S(1)		endometrium(5)|kidney(3)|large_intestine(8)|lung(12)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTCATTTAGGCGTCCAAGAGG	0.368																																					p.R984S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2950A	9						.						144.0	124.0	131.0					9																	96324491		2203	4300	6503	95364312	SO:0001630	splice_region_variant	23196	exon17			AF214737	CCDS6706.1, CCDS75859.1	9q22.31	2013-03-08	2006-07-04	2006-07-04	ENSG00000048828	ENSG00000048828			13247	protein-coding gene	gene with protein product	"""DNA polymerase-transactivated protein 1"", ""oxidative stess-associated Src activator"""	612265	"""chromosome 9 open reading frame 10"""	C9orf10		14585507	Standard	NM_001286722		Approved	KIAA0183, DNAPTP1, OSSA	uc004atw.3	Q9NZB2	OTTHUMG00000020252	ENST00000277165.6:c.2949-1C>A	9.37:g.96324491C>A		Somatic		Capture	Illumina HiSeq	Phase_I	95364312	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595700	0.86953	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.47177	1.4;1.38;1.42;0.85	5.64	5.64	0.86602	.	0.068391	0.64402	D	0.000008	T	0.62307	0.2417	L	0.42245	1.32	0.58432	D	0.999999	D;D;D	0.69078	0.996;0.997;0.992	D;D;D	0.79108	0.992;0.986;0.979	T	0.54214	-0.8327	10	0.26408	T	0.33	-8.5952	19.7003	0.96050	0.0:1.0:0.0:0.0	.	938;1012;984	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	S	984;1012;938;360	ENSP00000277165:R984S;ENSP00000334918:R1012S;ENSP00000344698:R938S;ENSP00000412440:R360S	ENSP00000277165:R984S	R	+	1	0	FAM120A	95364312	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.970000	0.63742	2.657000	0.90304	0.655000	0.94253	CGT		0.368	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612	Missense_Mutation
NUTM2F	54754	broad.mit.edu	37	9	97082793	97082793	+	Missense_Mutation	SNP	C	C	G	rs577940402		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:97082793C>G	ENST00000253262.4	-	5	1085	c.1065G>C	c.(1063-1065)aaG>aaC	p.K355N	NUTM2F_ENST00000335456.7_Missense_Mutation_p.K355N|NUTM2F_ENST00000341207.4_Missense_Mutation_p.K355N	NM_017561.1	NP_060031.1	A1L443	NTM2F_HUMAN	NUT family member 2F	355	Pro-rich.							p.K236N(5)									GCAGGTGGGCCTTGGTCTCCG	0.706													.|||	1	0.000199681	0.0	0.0	5008	,	,		14002	0.0		0.0	False		,,,				2504	0.001				p.K355N												.	.	5	Substitution - Missense(5)	large_intestine(5)	c.G1065C	9						.						17.0	24.0	21.0					9																	97082793		1985	4123	6108	96122614	SO:0001583	missense	54754	exon5				CCDS47994.1	9q22.32	2013-05-02	2013-03-14	2013-05-02	ENSG00000130950	ENSG00000130950			23450	protein-coding gene	gene with protein product			"""family with sequence similarity 22, member F"""	FAM22F			Standard	NM_017561		Approved	DKFZp434I1117		A1L443	OTTHUMG00000020260	ENST00000253262.4:c.1065G>C	9.37:g.97082793C>G	ENSP00000253262:p.Lys355Asn	None		Capture	Illumina HiSeq	Phase_I	96122614	NM_017561	B6ZDF0|Q5SR58|Q5SR59|Q9UFB1	Missense_Mutation	SNP	ENST00000253262.4	37	CCDS47994.1	.	.	.	.	.	.	.	.	.	.	.	10.88	1.475748	0.26511	.	.	ENSG00000130950	ENST00000335456;ENST00000253262;ENST00000341207	T;T;T	0.24151	1.87;2.67;2.67	0.1	0.1	0.14510	.	.	.	.	.	T	0.30070	0.0753	N	0.24115	0.695	0.09310	N	1	D	0.57899	0.981	D	0.69824	0.966	T	0.14062	-1.0486	9	0.62326	D	0.03	.	5.97	0.19346	0.0:0.9994:0.0:6.0E-4	.	355	A1L443	FA22F_HUMAN	N	355	ENSP00000335067:K355N;ENSP00000253262:K355N;ENSP00000343865:K355N	ENSP00000253262:K355N	K	-	3	2	FAM22F	96122614	0.001000	0.12720	0.113000	0.21522	0.093000	0.18481	0.349000	0.20055	0.170000	0.19704	0.173000	0.16961	AAG		0.706	NUTM2F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053173.2	NM_017561	
ZNF782	158431	broad.mit.edu	37	9	99581115	99581115	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:99581115G>T	ENST00000481138.1	-	6	1851	c.1190C>A	c.(1189-1191)cCt>cAt	p.P397H	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.P265H	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	397					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P397H(1)		NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				CCCGCACTCAGGACATTCATA	0.433																																					p.P397H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1190A	9						.						114.0	113.0	113.0					9																	99581115		2203	4300	6503	98620936	SO:0001583	missense	158431	exon6			AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.1190C>A	9.37:g.99581115G>T	ENSP00000419397:p.Pro397His	Somatic		Capture	Illumina HiSeq	Phase_I	98620936	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	g	0.188	-1.056224	0.01965	.	.	ENSG00000196597	ENST00000481138;ENST00000535338	T;T	0.03801	3.8;3.8	3.33	-0.398	0.12418	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.235611	0.21987	N	0.066204	T	0.03095	0.0091	L	0.31157	0.91	0.21627	N	0.99962	B	0.02656	0.0	B	0.01281	0.0	T	0.39231	-0.9624	10	0.35671	T	0.21	.	4.1264	0.10129	0.0:0.1998:0.3528:0.4474	.	397	Q6ZMW2	ZN782_HUMAN	H	397;265	ENSP00000419397:P397H;ENSP00000440624:P265H	ENSP00000419397:P397H	P	-	2	0	ZNF782	98620936	0.000000	0.05858	0.996000	0.52242	0.603000	0.37013	-2.388000	0.01059	-0.088000	0.12506	-3.143000	0.00059	CCT		0.433	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
ENG	2022	broad.mit.edu	37	9	130587213	130587213	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:130587213delT	ENST00000373203.4	-	7	1257	c.857delA	c.(856-858)aacfs	p.N286fs	ENG_ENST00000480266.1_5'UTR|RP11-228B15.4_ENST00000439298.1_RNA|ENG_ENST00000344849.3_Frame_Shift_Del_p.N286fs	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	286	Required for interaction with EGL.				artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in endocardial cushion formation (GO:0003273)|cell motility (GO:0048870)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|chronological cell aging (GO:0001300)|detection of hypoxia (GO:0070483)|extracellular matrix constituent secretion (GO:0070278)|extracellular matrix disassembly (GO:0022617)|heart looping (GO:0001947)|intracellular signal transduction (GO:0035556)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|patterning of blood vessels (GO:0001569)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of gene expression (GO:0010628)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of phosphorylation (GO:0042325)|regulation of transcription, DNA-templated (GO:0006355)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to corticosteroid (GO:0031960)|response to hypoxia (GO:0001666)|response to statin (GO:0036273)|response to transforming growth factor beta (GO:0071559)|smooth muscle tissue development (GO:0048745)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|wound healing (GO:0042060)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endothelial microparticle (GO:0072563)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|transforming growth factor beta receptor homodimeric complex (GO:0070022)	activin binding (GO:0048185)|galactose binding (GO:0005534)|glycosaminoglycan binding (GO:0005539)|protein homodimerization activity (GO:0042803)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor, cytoplasmic mediator activity (GO:0005072)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane signaling receptor activity (GO:0004888)|type I transforming growth factor beta receptor binding (GO:0034713)|type II transforming growth factor beta receptor binding (GO:0005114)	p.N286fs*73(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						GCCACGAATGTTTTTCTCTGG	0.567									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.N286fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.857delA	9						.						86.0	93.0	91.0					9																	130587213		2203	4300	6503	129627034	SO:0001589	frameshift_variant	2022	exon7	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	AF035753	CCDS6880.1, CCDS48029.1, CCDS75906.1	9q34.11	2014-09-17	2008-09-04		ENSG00000106991	ENSG00000106991		"""CD molecules"""	3349	protein-coding gene	gene with protein product		131195	"""Osler-Rendu-Weber syndrome 1"""	ORW1, ORW		8404038, 10548503	Standard	NM_001278138		Approved	END, HHT1, CD105	uc031tfe.1	P17813	OTTHUMG00000020723	ENST00000373203.4:c.857delA	9.37:g.130587213delT	ENSP00000362299:p.Asn286fs	Somatic		Capture	Illumina HiSeq	Phase_I	129627034	NM_001114753	Q14248|Q14926|Q5T9C0	Frame_Shift_Del	DEL	ENST00000373203.4	37	CCDS48029.1																																																																																				0.567	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1		
FCN2	2220	broad.mit.edu	37	9	137777694	137777694	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:137777694delG	ENST00000291744.6	+	6	520	c.510delG	c.(508-510)ctgfs	p.L170fs	FCN2_ENST00000350339.2_Frame_Shift_Del_p.L132fs	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	170	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)	p.E172fs*12(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		GCAGTCGGCTGGGGGAGTTCT	0.672																																					p.L170fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.510delG	9						.						57.0	56.0	57.0					9																	137777694		2203	4300	6503	136917515	SO:0001589	frameshift_variant	2220	exon6			D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.510delG	9.37:g.137777694delG	ENSP00000291744:p.Leu170fs	Somatic		Capture	Illumina HiSeq	Phase_I	136917515	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Frame_Shift_Del	DEL	ENST00000291744.6	37	CCDS6983.1																																																																																				0.672	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
SEC16A	9919	broad.mit.edu	37	9	139351946	139351946	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chr9:139351946G>T	ENST00000371706.3	-	16	4999	c.4966C>A	c.(4966-4968)Ctg>Atg	p.L1656M	SEC16A_ENST00000290037.6_Missense_Mutation_p.L1656M|SEC16A_ENST00000431893.2_Missense_Mutation_p.L1656M|SEC16A_ENST00000313050.7_Missense_Mutation_p.L1834M			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1656					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.L1834M(1)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GGCTGCGTCAGGATGCTCTTC	0.607																																					p.L1834M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5500A	9						.						38.0	52.0	48.0					9																	139351946		2070	4218	6288	138471767	SO:0001583	missense	9919	exon18			AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.4966C>A	9.37:g.139351946G>T	ENSP00000360771:p.Leu1656Met	Somatic		Capture	Illumina HiSeq	Phase_I	138471767	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.826529	0.50739	.	.	ENSG00000148396	ENST00000313050;ENST00000277537;ENST00000453963;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925	T;T;T;T;T;T	0.49720	1.75;0.77;1.36;1.76;1.75;1.75	4.6	4.6	0.57074	.	0.000000	0.64402	D	0.000001	T	0.70806	0.3266	M	0.83223	2.63	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.992;0.982;0.989	T	0.73717	-0.3895	10	0.42905	T	0.14	-18.497	16.7423	0.85462	0.0:0.0:1.0:0.0	.	1834;1656;1656;1224	F1T0I1;O15027-5;O15027-4;A4QN19	.;.;.;.	M	1834;228;556;1656;1656;1656;1224	ENSP00000325827:L1834M;ENSP00000277537:L228M;ENSP00000403525:L556M;ENSP00000360771:L1656M;ENSP00000290037:L1656M;ENSP00000387583:L1656M	ENSP00000277537:L228M	L	-	1	2	SEC16A	138471767	1.000000	0.71417	0.994000	0.49952	0.100000	0.18952	4.694000	0.61760	2.258000	0.74832	0.655000	0.94253	CTG		0.607	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
MID1	4281	broad.mit.edu	37	X	10437562	10437563	+	Intron	INS	-	-	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:10437562_10437563insT	ENST00000317552.4	-	7	1686				MID1_ENST00000453318.2_Intron|MID1_ENST00000380780.1_Intron|MID1_ENST00000380779.1_Intron|MID1_ENST00000380785.1_Intron|MID1_ENST00000380782.2_Intron|MID1_ENST00000380787.1_Intron	NM_000381.3|NM_033289.1	NP_000372.1|NP_150631.1	O15344	TRI18_HUMAN	midline 1						microtubule cytoskeleton organization (GO:0000226)|negative regulation of microtubule depolymerization (GO:0007026)|pattern specification process (GO:0007389)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein localization to microtubule (GO:0035372)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	26						TTAGCCAGCTGTTTTTACTAAT	0.322																																					p.T487fs												.	.	0			c.1460_1461insA	X						.																																			10397563	SO:0001627	intron_variant	4281	exon6			Y13667	CCDS14138.1, CCDS75952.1, CCDS75953.1	Xp22	2014-06-18	2014-06-18		ENSG00000101871	ENSG00000101871		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	7095	protein-coding gene	gene with protein product	"""Opitz/BBB syndrome"""	300552				9354791, 9425238	Standard	NM_001098624		Approved	OS, FXY, TRIM18, RNF59	uc004cti.4	O15344	OTTHUMG00000021127	ENST00000317552.4:c.1285+173->A	X.37:g.10437567_10437567dupT		Somatic		Capture	Illumina HiSeq	Phase_I	10397562	NM_001193279	B2RCG2|O75361|Q9BZX5	Frame_Shift_Ins	INS	ENST00000317552.4	37	CCDS14138.1																																																																																				0.322	MID1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055738.1		
PNPLA4	8228	broad.mit.edu	37	X	7889833	7889834	+	In_Frame_Ins	INS	-	-	GTC			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-	-	GTC	-	-	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:7889833_7889834insGTC	ENST00000381042.4	-	4	501_502	c.331_332insGAC	c.(331-333)ctg>cGACtg	p.110_111insR	PNPLA4_ENST00000444736.1_In_Frame_Ins_p.110_111insR|PNPLA4_ENST00000537427.1_In_Frame_Ins_p.23_24insR	NM_004650.2	NP_004641.1	P41247	PLPL4_HUMAN	patatin-like phospholipase domain containing 4	110	Patatin.				lipid catabolic process (GO:0016042)		triglyceride lipase activity (GO:0004806)	p.L111M(1)|p.R110_L111insR(1)		kidney(1)|large_intestine(3)|lung(2)|prostate(1)	7		Colorectal(8;0.0329)|Medulloblastoma(8;0.232)				GGATACGTGCAGTCGGTTCTGG	0.45																																					p.L24delinsRL												.	.	2	Insertion - In frame(1)|Substitution - Missense(1)	large_intestine(1)|kidney(1)	c.71_72insGAC	X						.																																			7849834	SO:0001652	inframe_insertion	8228	exon3			U03886	CCDS14129.1, CCDS55368.1	Xp22.3	2014-03-14			ENSG00000006757	ENSG00000006757	3.1.1.3	"""Patatin-like phospholipase domain containing"""	24887	protein-coding gene	gene with protein product		300102				7806223, 16799181, 19029121	Standard	NM_004650		Approved	DXS1283E, GS2, iPLA2eta	uc011mhr.1	P41247	OTTHUMG00000021103	ENST00000381042.4:c.329_331dupGAC	X.37:g.7889834_7889836dupGTC	ENSP00000370430:p.Arg110_Arg110dup	Somatic		Capture	Illumina HiSeq	Phase_I	7849833	NM_001172672	A8K1H3|B4E362|Q8WW83	In_Frame_Ins	INS	ENST00000381042.4	37	CCDS14129.1																																																																																				0.450	PNPLA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055687.1	NM_004650	
PORCN	64840	broad.mit.edu	37	X	48368118	48368119	+	Intron	INS	-	-	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48368118_48368119insA	ENST00000537758.1	+	2	116				PORCN_ENST00000367574.4_5'UTR|PORCN_ENST00000361988.3_Intron|PORCN_ENST00000359882.4_Intron|AF196972.9_ENST00000445586.1_RNA|PORCN_ENST00000355961.4_Intron|PORCN_ENST00000326194.6_5'Flank|PORCN_ENST00000486272.1_Intron|PORCN_ENST00000355092.3_5'Flank			Q9H237	PORCN_HUMAN	porcupine homolog (Drosophila)						glycoprotein metabolic process (GO:0009100)|Wnt signaling pathway (GO:0016055)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups (GO:0016746)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GTGCATCCTTTAAGCGAGGTCT	0.584																																					.												.	.	0			.	X						.																																			48253063	SO:0001627	intron_variant	64840	.			AF317058	CCDS14296.1, CCDS14297.1, CCDS14298.1, CCDS14299.1	Xp11.23	2014-02-05			ENSG00000102312	ENSG00000102312			17652	protein-coding gene	gene with protein product		300651	"""dermal hypoplasia, focal"""	DHOF		10866835, 12034504, 17546030	Standard	NM_203474		Approved	MG61, PORC, PPN, por	uc004djv.1	Q9H237	OTTHUMG00000024116	ENST00000537758.1:c.-37-53->A	X.37:g.48368120_48368120dupA		Somatic		Capture	Illumina HiSeq	Phase_I	48253062	.	B2RBN8|B7ZAR3|Q14829|Q9H234|Q9H235|Q9H236|Q9UJU7	Frame_Shift_Ins	INS	ENST00000537758.1	37	CCDS14299.1																																																																																				0.584	PORCN-203	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022825	
XKRX	402415	broad.mit.edu	37	X	100169968	100169968	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:100169968G>A	ENST00000372956.2	-	3	1313	c.709C>T	c.(709-711)Cca>Tca	p.P237S	XKRX_ENST00000468904.1_3'UTR|XKRX_ENST00000328526.5_Missense_Mutation_p.P250S			Q6PP77	XKR2_HUMAN	XK, Kell blood group complex subunit-related, X-linked	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P250S(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(3)	22						ACTTCTAGTGGCCCAAGGCGA	0.493																																					p.P237S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C709T	X						.						106.0	96.0	100.0					X																	100169968		2203	4300	6503	100056624	SO:0001583	missense	402415	exon3			AY589511	CCDS14476.1, CCDS14476.2	Xq22	2008-02-05	2006-01-12		ENSG00000182489	ENSG00000182489			29845	protein-coding gene	gene with protein product		300684	"""X Kell blood group precursor-related, X-linked"""				Standard	NM_212559		Approved	XPLAC, XKR2	uc004egn.2	Q6PP77	OTTHUMG00000022010	ENST00000372956.2:c.709C>T	X.37:g.100169968G>A	ENSP00000362047:p.Pro237Ser	Somatic		Capture	Illumina HiSeq	Phase_I	100056624	NM_212559	B2RNN6|B4DKU2|Q5H9J6	Missense_Mutation	SNP	ENST00000372956.2	37	CCDS14476.2	.	.	.	.	.	.	.	.	.	.	G	12.62	1.992831	0.35131	.	.	ENSG00000182489	ENST00000328526;ENST00000372956	T;T	0.65178	-0.14;-0.13	5.36	3.4	0.38934	.	0.342131	0.34725	N	0.003735	T	0.49932	0.1586	L	0.54323	1.7	0.09310	N	0.999997	P	0.39352	0.669	B	0.38106	0.265	T	0.35425	-0.9789	10	0.22109	T	0.4	-2.532	5.6394	0.17554	0.0842:0.1274:0.6377:0.1506	.	237	Q6PP77	XKR2_HUMAN	S	250;237	ENSP00000327570:P250S;ENSP00000362047:P237S	ENSP00000327570:P250S	P	-	1	0	XKRX	100056624	0.996000	0.38824	0.993000	0.49108	0.986000	0.74619	3.001000	0.49488	2.213000	0.71641	0.422000	0.28245	CCA		0.493	XKRX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057501.3	NM_212559	
CLCN4	1183	broad.mit.edu	37	X	10176182	10176182	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:10176182G>T	ENST00000380833.4	+	9	1332	c.941G>T	c.(940-942)aGc>aTc	p.S314I	CLCN4_ENST00000380829.1_Missense_Mutation_p.S314I|CLCN4_ENST00000421085.2_Missense_Mutation_p.S220I	NM_001256944.1|NM_001830.3	NP_001243873.1|NP_001821.2	P51793	CLCN4_HUMAN	chloride channel, voltage-sensitive 4	314					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)	p.S314I(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(11)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TTTGGGAATAGCCGTCTCGTT	0.537																																					p.S314I	Melanoma(74;1050 1296 1576 30544 38374)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G941T	X						.						154.0	146.0	149.0					X																	10176182		2203	4300	6503	10136182	SO:0001583	missense	1183	exon9			X77197	CCDS14137.1, CCDS59159.1	Xp22.3	2012-09-26	2012-02-23		ENSG00000073464	ENSG00000073464		"""Ion channels / Chloride channels : Voltage-sensitive"""	2022	protein-coding gene	gene with protein product		302910	"""chloride channel 4"""			8069296	Standard	NM_001830		Approved	CLC4, ClC-4	uc004csy.4	P51793	OTTHUMG00000021125	ENST00000380833.4:c.941G>T	X.37:g.10176182G>T	ENSP00000370213:p.Ser314Ile	Somatic		Capture	Illumina HiSeq	Phase_I	10136182	NM_001830	A1L3U1|B7Z5Z4|Q9UBU1	Missense_Mutation	SNP	ENST00000380833.4	37	CCDS14137.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.363811	0.82353	.	.	ENSG00000073464	ENST00000380833;ENST00000380829;ENST00000421085	D;D;D	0.94232	-3.38;-2.94;-3.38	5.69	5.69	0.88448	Chloride channel, core (2);	0.035375	0.85682	D	0.000000	D	0.95815	0.8638	M	0.81614	2.55	0.80722	D	1	P	0.40107	0.703	P	0.50162	0.633	D	0.95753	0.8793	10	0.59425	D	0.04	-51.0501	18.981	0.92755	0.0:0.0:1.0:0.0	.	314	P51793	CLCN4_HUMAN	I	314;314;220	ENSP00000370213:S314I;ENSP00000370209:S314I;ENSP00000405754:S220I	ENSP00000370209:S314I	S	+	2	0	CLCN4	10136182	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.485000	0.81204	2.431000	0.82371	0.586000	0.80456	AGC		0.537	CLCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055730.1		
ARMCX3	51566	broad.mit.edu	37	X	100879978	100879978	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:100879978C>T	ENST00000341189.4	+	5	875	c.9C>T	c.(7-9)taC>taT	p.Y3Y	RP4-545K15.5_ENST00000564612.1_RNA|ARMCX3-AS1_ENST00000454228.1_RNA|ARMCX3_ENST00000537169.1_Silent_p.Y3Y|ARMCX3_ENST00000471229.2_Silent_p.Y3Y	NM_016607.3	NP_057691.1	Q9UH62	ARMX3_HUMAN	armadillo repeat containing, X-linked 3	3					cellular protein localization (GO:0034613)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of mitochondrial outer membrane (GO:0031307)		p.Y3Y(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)	11						GCATGGGCTACGCCAGGAAAG	0.557																																					p.Y3Y												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C9T	X						.						71.0	68.0	69.0					X																	100879978		2203	4300	6503	100766634	SO:0001819	synonymous_variant	51566	exon5			AY359079	CCDS14489.1	Xq22.1	2014-03-21			ENSG00000102401	ENSG00000102401		"""Armadillo repeat containing"""	24065	protein-coding gene	gene with protein product		300364				11162520, 11042152, 19304657, 16221301, 22569362	Standard	NM_016607		Approved	ALEX3, GASP6	uc004eia.1	Q9UH62	OTTHUMG00000022035	ENST00000341189.4:c.9C>T	X.37:g.100879978C>T		Somatic		Capture	Illumina HiSeq	Phase_I	100766634	NM_177948	Q53HC6|Q7LCF5|Q9NPE4	Silent	SNP	ENST00000341189.4	37	CCDS14489.1																																																																																				0.557	ARMCX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057568.2	NM_016607	
ESX1	80712	broad.mit.edu	37	X	103499517	103499517	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:103499517C>T	ENST00000372588.4	-	1	97	c.14G>A	c.(13-15)cGc>cAc	p.R5H		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	5					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)	p.R5H(1)		endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						GGTGTACCCGCGAAGAGACTC	0.592																																					p.R5H	Pancreas(200;1705 2227 25194 28471 45274)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G14A	X						.						167.0	136.0	147.0					X																	103499517		2203	4300	6503	103386173	SO:0001583	missense	80712	exon1			AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.14G>A	X.37:g.103499517C>T	ENSP00000361669:p.Arg5His	Somatic		Capture	Illumina HiSeq	Phase_I	103386173	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	c	10.75	1.439389	0.25900	.	.	ENSG00000123576	ENST00000372588	D	0.91351	-2.83	3.45	-4.57	0.03421	POU (1);	.	.	.	.	T	0.72700	0.3493	N	0.08118	0	0.09310	N	1	D	0.63880	0.993	B	0.41088	0.347	T	0.69011	-0.5258	9	0.39692	T	0.17	15.4065	0.3515	0.00349	0.3043:0.1362:0.1844:0.3751	.	5	Q8N693	ESX1_HUMAN	H	5	ENSP00000361669:R5H	ENSP00000361669:R5H	R	-	2	0	ESX1	103386173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.435000	0.06931	-1.499000	0.01821	-1.250000	0.01514	CGC		0.592	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
IL1RAPL2	26280	broad.mit.edu	37	X	105011182	105011182	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:105011182T>G	ENST00000372582.1	+	11	2345	c.1589T>G	c.(1588-1590)cTt>cGt	p.L530R	IL1RAPL2_ENST00000344799.4_Missense_Mutation_p.L530R	NM_017416.1	NP_059112.1	Q9NP60	IRPL2_HUMAN	interleukin 1 receptor accessory protein-like 2	530	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				central nervous system development (GO:0007417)|cytokine-mediated signaling pathway (GO:0019221)	integral component of membrane (GO:0016021)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)	p.L530R(1)		breast(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(23)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						AGCATCAAACTTCTGTCCCTG	0.368																																					p.L530R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1589G	X						.						114.0	117.0	116.0					X																	105011182		2203	4300	6503	104897838	SO:0001583	missense	26280	exon11			AF181285	CCDS14517.1	Xq22	2013-01-11			ENSG00000189108	ENSG00000189108		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5997	protein-coding gene	gene with protein product		300277				10757639	Standard	NM_017416		Approved	IL-1R9, TIGIRR-1, IL1RAPL-2, IL1R9	uc004elz.1	Q9NP60	OTTHUMG00000022141	ENST00000372582.1:c.1589T>G	X.37:g.105011182T>G	ENSP00000361663:p.Leu530Arg	Somatic		Capture	Illumina HiSeq	Phase_I	104897838	NM_017416	Q2M3U3|Q9NZN0	Missense_Mutation	SNP	ENST00000372582.1	37	CCDS14517.1	.	.	.	.	.	.	.	.	.	.	T	11.79	1.744315	0.30865	.	.	ENSG00000189108	ENST00000372582;ENST00000344799;ENST00000538500	T;T;T	0.08634	3.07;3.07;3.07	5.87	4.71	0.59529	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.304968	0.28630	N	0.014668	T	0.09379	0.0231	M	0.61703	1.905	0.34623	D	0.71876	P	0.40197	0.706	B	0.39590	0.304	T	0.27468	-1.0073	10	0.24483	T	0.36	.	5.5179	0.16916	0.1541:0.0812:0.0:0.7648	.	530	Q9NP60	IRPL2_HUMAN	R	530;530;135	ENSP00000361663:L530R;ENSP00000344976:L530R;ENSP00000445576:L135R	ENSP00000344976:L530R	L	+	2	0	IL1RAPL2	104897838	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.956000	0.49129	0.837000	0.34925	0.486000	0.48141	CTT		0.368	IL1RAPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057785.1	NM_017416	
MUM1L1	139221	broad.mit.edu	37	X	105451039	105451039	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:105451039A>C	ENST00000357175.2	+	4	2263	c.1614A>C	c.(1612-1614)caA>caC	p.Q538H	MUM1L1_ENST00000337685.2_Missense_Mutation_p.Q538H|MUM1L1_ENST00000372552.1_Missense_Mutation_p.Q538H	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	538						extracellular vesicular exosome (GO:0070062)		p.Q538H(2)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						TGTCCTTCCAAAAAATTCTCC	0.468																																					p.Q538H												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A1614C	X						.						57.0	50.0	52.0					X																	105451039		1857	4075	5932	105337695	SO:0001583	missense	139221	exon5			AK090835	CCDS55469.1	Xq22.3	2008-02-05			ENSG00000157502	ENSG00000157502			26583	protein-coding gene	gene with protein product							Standard	NM_152423		Approved	FLJ33516	uc004emf.2	Q5H9M0	OTTHUMG00000022146	ENST00000357175.2:c.1614A>C	X.37:g.105451039A>C	ENSP00000349699:p.Gln538His	Somatic		Capture	Illumina HiSeq	Phase_I	105337695	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Missense_Mutation	SNP	ENST00000357175.2	37	CCDS55469.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.660147	0.47572	.	.	ENSG00000157502	ENST00000357175;ENST00000337685;ENST00000372552	T;T;T	0.45668	0.89;0.89;0.89	5.08	3.24	0.37175	.	0.424369	0.19662	N	0.108943	T	0.45397	0.1340	L	0.44542	1.39	0.28919	N	0.892248	D	0.64830	0.994	P	0.55999	0.789	T	0.39035	-0.9633	10	0.72032	D	0.01	-12.7575	7.0202	0.24910	0.2128:0.0:0.7872:0.0	.	538	Q5H9M0	MUML1_HUMAN	H	538	ENSP00000349699:Q538H;ENSP00000338641:Q538H;ENSP00000361632:Q538H	ENSP00000338641:Q538H	Q	+	3	2	MUM1L1	105337695	1.000000	0.71417	0.989000	0.46669	0.822000	0.46500	2.598000	0.46223	0.629000	0.30376	-0.233000	0.12211	CAA		0.468	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423	
CXorf57	55086	broad.mit.edu	37	X	105905498	105905498	+	Silent	SNP	C	C	T	rs140805762	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:105905498C>T	ENST00000372548.4	+	12	2341	c.2232C>T	c.(2230-2232)agC>agT	p.S744S	CXorf57_ENST00000372544.2_Silent_p.S647S|CXorf57_ENST00000497124.1_3'UTR	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	744							poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						ATTTTAAGAGCGCCCGAAGCC	0.358																																					p.S744S												.	.	0			c.C2232T	X						.	C	,	0,3833		0,0,0,1631,571	71.0	69.0	69.0		1941,2232	-3.3	0.1	X	dbSNP_134	69	3,6725		0,2,1,2426,1871	no	coding-synonymous,coding-synonymous	CXorf57	NM_001184782.1,NM_018015.5	,	0,2,1,4057,2442	TT,TC,T,CC,C		0.0446,0.0,0.0284	,	647/759,744/856	105905498	3,10558	2202	4300	6502	105792154	SO:0001819	synonymous_variant	55086	exon12			AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.2232C>T	X.37:g.105905498C>T		None		Capture	Illumina HiSeq	Phase_I	105792154	NM_018015	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Silent	SNP	ENST00000372548.4	37	CCDS14519.1																																																																																				0.358	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015	
MORC4	79710	broad.mit.edu	37	X	106201599	106201599	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:106201599C>A	ENST00000355610.4	-	11	1626	c.1352G>T	c.(1351-1353)tGg>tTg	p.W451L	MORC4_ENST00000535534.1_Missense_Mutation_p.W199L|MORC4_ENST00000255495.7_Missense_Mutation_p.W451L	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	451						nucleus (GO:0005634)	zinc ion binding (GO:0008270)	p.W274L(1)		endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						ATAACAAAACCATCTTGCAGG	0.398																																					p.W451L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1352T	X						.						137.0	116.0	123.0					X																	106201599		2203	4300	6503	106088255	SO:0001583	missense	79710	exon11			AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1352G>T	X.37:g.106201599C>A	ENSP00000347821:p.Trp451Leu	Somatic		Capture	Illumina HiSeq	Phase_I	106088255	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	C	19.02	3.745042	0.69418	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.68903	0.82;-0.36;0.83	5.93	4.14	0.48551	Zinc finger, CW-type (2);	0.307789	0.32533	N	0.005971	D	0.85835	0.5789	H	0.97265	3.97	0.33497	D	0.589432	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.83275	0.996;0.996;0.996	D	0.89457	0.3734	10	0.87932	D	0	-5.6222	7.1211	0.25446	0.1686:0.7409:0.0:0.0905	.	199;451;451	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	L	451;199;451	ENSP00000347821:W451L;ENSP00000440359:W199L;ENSP00000255495:W451L	ENSP00000255495:W451L	W	-	2	0	MORC4	106088255	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	2.896000	0.48656	1.243000	0.43853	0.544000	0.68410	TGG		0.398	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
TEX13B	56156	broad.mit.edu	37	X	107225316	107225316	+	Silent	SNP	G	G	A	rs376883010		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:107225316G>A	ENST00000302917.1	-	2	134	c.42C>T	c.(40-42)caC>caT	p.H14H		NM_031273.2	NP_112563.1	Q9BXU2	TX13B_HUMAN	testis expressed 13B	14								p.H14H(1)		breast(1)|endometrium(5)|large_intestine(4)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	28						CCACGTTTCCGTGCCGGAACC	0.547																																					p.H14H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C42T	X						.	G		1,3830		0,1,1631,567	72.0	64.0	67.0		42	-5.0	0.0	X		67	0,6728		0,0,2428,1872	no	coding-synonymous	TEX13B	NM_031273.2		0,1,4059,2439	AA,AG,GG,G		0.0,0.0261,0.0095		14/313	107225316	1,10558	2199	4300	6499	107111972	SO:0001819	synonymous_variant	56156	exon2			AF285598	CCDS14534.1	Xq23	2008-02-05	2007-03-13		ENSG00000170925	ENSG00000170925			11736	protein-coding gene	gene with protein product		300313	"""testis expressed sequence 13B"""			11279525	Standard	NM_031273		Approved	TSGA5, TGC3B	uc004enn.1	Q9BXU2	OTTHUMG00000022174	ENST00000302917.1:c.42C>T	X.37:g.107225316G>A		Somatic		Capture	Illumina HiSeq	Phase_I	107111972	NM_031273	Q5JYF6	Silent	SNP	ENST00000302917.1	37	CCDS14534.1																																																																																				0.547	TEX13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057857.1		
COL4A5	1287	broad.mit.edu	37	X	107826127	107826127	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:107826127A>G	ENST00000361603.2	+	17	1194	c.950A>G	c.(949-951)gAt>gGt	p.D317G	COL4A5_ENST00000328300.6_Missense_Mutation_p.D317G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	317	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.D317G(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						TTGCCTGGTGATCCTGGTTAC	0.398									Alport syndrome with Diffuse Leiomyomatosis																												p.D317G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A950G	X						.						222.0	190.0	201.0					X																	107826127		2203	4300	6503	107712783	SO:0001583	missense	1287	exon17	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.950A>G	X.37:g.107826127A>G	ENSP00000354505:p.Asp317Gly	Somatic		Capture	Illumina HiSeq	Phase_I	107712783	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	A	14.18	2.457186	0.43634	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.94417	-3.42;-3.42	5.74	5.74	0.90152	.	0.187051	0.46442	D	0.000290	D	0.90400	0.6995	L	0.42744	1.35	0.44409	D	0.997323	B;B	0.11235	0.004;0.004	B;B	0.17722	0.019;0.019	D	0.85359	0.1106	10	0.21540	T	0.41	.	9.6404	0.39835	0.9118:0.0:0.0882:0.0	.	317;317	E7EVY4;P29400	.;CO4A5_HUMAN	G	317	ENSP00000331902:D317G;ENSP00000354505:D317G	ENSP00000331902:D317G	D	+	2	0	COL4A5	107712783	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.206000	0.58473	1.915000	0.55452	0.486000	0.48141	GAT		0.398	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
COL4A5	1287	broad.mit.edu	37	X	107865096	107865096	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:107865096G>A	ENST00000361603.2	+	32	2985	c.2741G>A	c.(2740-2742)gGc>gAc	p.G914D	COL4A5_ENST00000328300.6_Missense_Mutation_p.G914D	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	914	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.G914D(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GGAATTCCTGGCAGGAGTGGT	0.413									Alport syndrome with Diffuse Leiomyomatosis																												p.G914D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2741A	X						.						74.0	67.0	69.0					X																	107865096		2203	4300	6503	107751752	SO:0001583	missense	1287	exon32	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2741G>A	X.37:g.107865096G>A	ENSP00000354505:p.Gly914Asp	Somatic		Capture	Illumina HiSeq	Phase_I	107751752	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.246462	0.80024	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.99353	-5.77;-5.77	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	D	0.99701	0.9886	H	0.98178	4.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97255	0.9900	10	0.87932	D	0	.	18.8057	0.92037	0.0:0.0:1.0:0.0	.	914;522;914	E7EVY4;Q49AM6;P29400	.;.;CO4A5_HUMAN	D	914	ENSP00000331902:G914D;ENSP00000354505:G914D	ENSP00000331902:G914D	G	+	2	0	COL4A5	107751752	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.823000	0.92018	2.387000	0.81309	0.594000	0.82650	GGC		0.413	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
IRS4	8471	broad.mit.edu	37	X	107978207	107978207	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:107978207C>T	ENST00000372129.2	-	1	1444	c.1368G>A	c.(1366-1368)ctG>ctA	p.L456L	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.3_ENST00000608811.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	456					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)	p.L456L(1)		NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						CTTCAGAAGACAGGCGAGCTC	0.592																																					p.L456L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1368A	X						.						86.0	83.0	84.0					X																	107978207		2203	4300	6503	107864863	SO:0001819	synonymous_variant	8471	exon1			AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1368G>A	X.37:g.107978207C>T		Somatic		Capture	Illumina HiSeq	Phase_I	107864863	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																				0.592	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
LONRF3	79836	broad.mit.edu	37	X	118109298	118109298	+	Silent	SNP	G	G	A	rs201682368		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:118109298G>A	ENST00000371628.3	+	1	586	c.555G>A	c.(553-555)ggG>ggA	p.G185G	LONRF3_ENST00000304778.7_Silent_p.G185G|LONRF3_ENST00000422289.2_5'Flank	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	185							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)	p.G185G(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						TGGAACGTGGGCGGGCCGCCG	0.657																																					p.G185G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G555A	X						.	G	,	0,3775		0,0,1616,543	23.0	17.0	19.0		555,555	1.5	1.0	X		19	1,6604		0,1,2411,1781	no	coding-synonymous,coding-synonymous	LONRF3	NM_001031855.1,NM_024778.4	,	0,1,4027,2324	AA,AG,GG,G		0.0151,0.0,0.0096	,	185/760,185/719	118109298	1,10379	2159	4193	6352	117993326	SO:0001819	synonymous_variant	79836	exon1			AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.555G>A	X.37:g.118109298G>A		Somatic		Capture	Illumina HiSeq	Phase_I	117993326	NM_024778	Q5JPN6|Q8NB00|Q9H647	Silent	SNP	ENST00000371628.3	37	CCDS35374.1																																																																																				0.657	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
ZBTB33	10009	broad.mit.edu	37	X	119389249	119389249	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:119389249G>A	ENST00000326624.2	+	2	2207	c.1979G>A	c.(1978-1980)gGc>gAc	p.G660D	ZBTB33_ENST00000557385.1_Missense_Mutation_p.G660D	NM_006777.3	NP_006768.1	Q86T24	KAISO_HUMAN	zinc finger and BTB domain containing 33	660	Interaction with CTNND1. {ECO:0000250}.				intracellular signal transduction (GO:0035556)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|sequence-specific DNA binding (GO:0043565)	p.G660D(1)		breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	26						GTAACAGATGGCAGTACTGAG	0.358																																					p.G660D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1979A	X						.						52.0	56.0	54.0					X																	119389249		2201	4296	6497	119273277	SO:0001583	missense	10009	exon2			BC042753	CCDS14596.1	Xq23	2013-01-09			ENSG00000177485	ENSG00000177485		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16682	protein-coding gene	gene with protein product		300329					Standard	NM_001184742		Approved	ZNF-kaiso, kaiso, WUGSC:H_DJ525N14.1, KAISO, ZNF348	uc004esn.1	Q86T24	OTTHUMG00000171159	ENST00000326624.2:c.1979G>A	X.37:g.119389249G>A	ENSP00000314153:p.Gly660Asp	Somatic		Capture	Illumina HiSeq	Phase_I	119273277	NM_006777	B2R5U6|O00319|Q7Z361|Q8IVP6|Q8N3P0	Missense_Mutation	SNP	ENST00000326624.2	37	CCDS14596.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887973	0.52014	.	.	ENSG00000177485;ENSG00000177485;ENSG00000258974	ENST00000326624;ENST00000540105;ENST00000557385	T;T	0.14022	2.54;2.54	5.88	5.88	0.94601	.	0.142257	0.45867	D	0.000333	T	0.12902	0.0313	N	0.24115	0.695	0.50171	D	0.999853	P	0.37015	0.578	B	0.36845	0.234	T	0.03354	-1.1045	10	0.87932	D	0	-7.6683	18.0058	0.89209	0.0:0.0:1.0:0.0	.	660	Q86T24	KAISO_HUMAN	D	660	ENSP00000314153:G660D;ENSP00000450969:G660D	ENSP00000314153:G660D	G	+	2	0	ZBTB33;AC002086.1	119273277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.168000	0.64978	2.474000	0.83562	0.600000	0.82982	GGC		0.358	ZBTB33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058085.2	NM_006777	
TENM1	10178	broad.mit.edu	37	X	123518404	123518404	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:123518404A>T	ENST00000371130.3	-	29	6419	c.6356T>A	c.(6355-6357)aTt>aAt	p.I2119N	TENM1_ENST00000422452.2_Missense_Mutation_p.I2126N|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2119					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.I2121N(1)									CCAGTAGGCAATTGCCTTTAG	0.378																																					p.I2119N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T6356A	X						.						209.0	172.0	184.0					X																	123518404		2203	4300	6503	123346085	SO:0001583	missense	10178	exon29			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.6356T>A	X.37:g.123518404A>T	ENSP00000360171:p.Ile2119Asn	Somatic		Capture	Illumina HiSeq	Phase_I	123346085	NM_014253	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	17.51	3.406728	0.62399	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85411	-1.98;-1.95	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.89487	0.6729	L	0.47716	1.5	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.83275	0.991;0.996;0.959	D	0.89118	0.3501	10	0.42905	T	0.14	.	14.6972	0.69132	1.0:0.0:0.0:0.0	.	2125;2126;2119	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	N	2119;2126	ENSP00000360171:I2119N;ENSP00000403954:I2126N	ENSP00000360171:I2119N	I	-	2	0	ODZ1	123346085	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	1.851000	0.53745	0.486000	0.48141	ATT		0.378	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
TENM1	10178	broad.mit.edu	37	X	123539054	123539054	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:123539054C>T	ENST00000371130.3	-	26	5260	c.5197G>A	c.(5197-5199)Ggg>Agg	p.G1733R	TENM1_ENST00000422452.2_Missense_Mutation_p.G1740R|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1733					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.G1735R(1)|p.G1735W(1)									ATCTCCATCCCGCTGGCAAAA	0.547																																					p.G1733R												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G5197A	X						.						89.0	74.0	79.0					X																	123539054		2203	4300	6503	123366735	SO:0001583	missense	10178	exon26			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5197G>A	X.37:g.123539054C>T	ENSP00000360171:p.Gly1733Arg	Somatic		Capture	Illumina HiSeq	Phase_I	123366735	NM_014253	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.838062	0.91117	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.86627	-2.15;-2.12	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.93041	0.7785	M	0.81802	2.56	0.80722	D	1	D;D;D	0.63046	0.979;0.979;0.992	P;P;P	0.60286	0.701;0.759;0.872	D	0.93862	0.7154	10	0.87932	D	0	.	18.5718	0.91138	0.0:1.0:0.0:0.0	.	1739;1740;1733	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	R	1733;1740	ENSP00000360171:G1733R;ENSP00000403954:G1740R	ENSP00000360171:G1733R	G	-	1	0	ODZ1	123366735	1.000000	0.71417	0.973000	0.42090	0.971000	0.66376	7.451000	0.80668	2.328000	0.79073	0.600000	0.82982	GGG		0.547	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
TENM1	10178	broad.mit.edu	37	X	124028164	124028164	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:124028164A>G	ENST00000371130.3	-	3	579	c.516T>C	c.(514-516)gcT>gcC	p.A172A	TENM1_ENST00000422452.2_Silent_p.A172A	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	172	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.A172A(1)									ACCCAGCTTGAGCCTCCATGT	0.418																																					p.A172A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T516C	X						.						126.0	115.0	119.0					X																	124028164		2203	4300	6503	123855845	SO:0001819	synonymous_variant	10178	exon3			AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.516T>C	X.37:g.124028164A>G		Somatic		Capture	Illumina HiSeq	Phase_I	123855845	NM_014253	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																				0.418	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
BCORL1	63035	broad.mit.edu	37	X	129146590	129146590	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:129146590C>T	ENST00000218147.7	+	3	320	c.123C>T	c.(121-123)ggC>ggT	p.G41G	BCORL1_ENST00000540052.1_Silent_p.G41G|BCORL1_ENST00000359304.2_Silent_p.G41G|BCORL1_ENST00000303743.5_Silent_p.G41G			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	41					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.G41G(1)		breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						CAACGACAGGCGACTGCCAGC	0.512																																					p.G41G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C123T	X						.						171.0	155.0	161.0					X																	129146590		2203	4300	6503	128974271	SO:0001819	synonymous_variant	63035	exon2			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.123C>T	X.37:g.129146590C>T		Somatic		Capture	Illumina HiSeq	Phase_I	128974271	NM_021946	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Silent	SNP	ENST00000218147.7	37	CCDS14616.1																																																																																				0.512	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1	NM_021946	
ENOX2	10495	broad.mit.edu	37	X	129799652	129799652	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:129799652G>A	ENST00000370927.1	-	7	1087	c.1066C>T	c.(1066-1068)Cgg>Tgg	p.R356W	ENOX2_ENST00000338144.3_Missense_Mutation_p.R356W|ENOX2_ENST00000394363.1_Missense_Mutation_p.R327W|ENOX2_ENST00000370935.1_Missense_Mutation_p.R327W			Q16206	ENOX2_HUMAN	ecto-NOX disulfide-thiol exchanger 2	356					cell growth (GO:0016049)|oxidation-reduction process (GO:0055114)|regulation of growth (GO:0040008)|ultradian rhythm (GO:0007624)	cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|protein disulfide oxidoreductase activity (GO:0015035)	p.R356W(2)		breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(3)	33						ATGTTCTTCCGCTGGGCTTTT	0.483																																					p.R356W	Ovarian(101;828 1506 2951 9500 35258)											.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1066T	X						.						106.0	69.0	81.0					X																	129799652		2203	4300	6503	129627333	SO:0001583	missense	10495	exon10			AF207881	CCDS14626.1, CCDS14627.1	Xq25	2013-02-12	2007-03-23	2007-03-23	ENSG00000165675	ENSG00000165675		"""RNA binding motif (RRM) containing"""	2259	protein-coding gene	gene with protein product		300282	"""cytosolic ovarian carcinoma antigen 1"""	COVA1		8150545, 11888291	Standard	NM_006375		Approved	APK1, tNOX	uc004evw.3	Q16206	OTTHUMG00000022401	ENST00000370927.1:c.1066C>T	X.37:g.129799652G>A	ENSP00000359965:p.Arg356Trp	Somatic		Capture	Illumina HiSeq	Phase_I	129627333	NM_182314	A8K197|A8K1C2|Q5VTJ1|Q5VTJ2|Q8WUX0|Q9NTP6|Q9UH82	Missense_Mutation	SNP	ENST00000370927.1	37	CCDS14626.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.022392	0.75275	.	.	ENSG00000165675	ENST00000538435;ENST00000370935;ENST00000338144;ENST00000394363;ENST00000350369;ENST00000370927;ENST00000432489	T;T	0.31247	1.5;1.5	5.44	4.57	0.56435	.	0.117298	0.64402	D	0.000015	T	0.54159	0.1841	M	0.78637	2.42	0.50632	D	0.999887	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.977	T	0.56619	-0.7949	9	.	.	.	-5.478	12.2059	0.54353	0.0:0.0:0.829:0.171	.	356;384	Q16206;A4QPE1	ENOX2_HUMAN;.	W	327;327;356;327;384;356;327	ENSP00000337146:R356W;ENSP00000359965:R356W	.	R	-	1	2	ENOX2	129627333	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.371000	0.79600	1.257000	0.44085	0.594000	0.82650	CGG		0.483	ENOX2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058277.1	NM_182314	
ATXN3L	92552	broad.mit.edu	37	X	13337285	13337285	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:13337285C>A	ENST00000380622.2	-	1	1233	c.769G>T	c.(769-771)Ggt>Tgt	p.G257C	GS1-600G8.3_ENST00000431486.1_RNA	NM_001135995.1	NP_001129467.1	Q9H3M9	ATX3L_HUMAN	ataxin 3-like	257					protein deubiquitination (GO:0016579)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	omega peptidase activity (GO:0008242)|ubiquitin-specific protease activity (GO:0004843)	p.G257C(1)		endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	28						CCGGAACTACCTTGCATGCTT	0.423																																					p.G257C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G769T	X						.						357.0	308.0	323.0					X																	13337285		1568	3582	5150	13247206	SO:0001583	missense	92552	exon1				CCDS48080.1	Xp22	2010-09-30			ENSG00000123594	ENSG00000123594			24173	protein-coding gene	gene with protein product		300920					Standard	NM_001135995		Approved	MJDL	uc010ned.3	Q9H3M9	OTTHUMG00000021146	ENST00000380622.2:c.769G>T	X.37:g.13337285C>A	ENSP00000369996:p.Gly257Cys	Somatic		Capture	Illumina HiSeq	Phase_I	13247206	NM_001135995	B2RNY8	Missense_Mutation	SNP	ENST00000380622.2	37	CCDS48080.1	.	.	.	.	.	.	.	.	.	.	c	13.16	2.153652	0.38021	.	.	ENSG00000123594	ENST00000380622	T	0.21361	2.01	0.793	0.793	0.18632	Ubiquitin interacting motif (2);	0.098941	0.64402	D	0.000002	T	0.33498	0.0865	L	0.49126	1.545	0.51233	D	0.999913	D	0.89917	1.0	D	0.91635	0.999	T	0.07083	-1.0791	10	0.87932	D	0	.	7.1894	0.25816	0.0:0.9999:0.0:1.0E-4	.	257	Q9H3M9	ATX3L_HUMAN	C	257	ENSP00000369996:G257C	ENSP00000369996:G257C	G	-	1	0	ATXN3L	13247206	1.000000	0.71417	0.021000	0.16686	0.010000	0.07245	1.862000	0.39448	0.661000	0.30985	0.417000	0.27973	GGT		0.423	ATXN3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055785.2	NM_001135995	
FRMD7	90167	broad.mit.edu	37	X	131212641	131212641	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:131212641A>G	ENST00000298542.4	-	12	1579	c.1404T>C	c.(1402-1404)cgT>cgC	p.R468R	FRMD7_ENST00000464296.1_Silent_p.R453R|FRMD7_ENST00000370879.1_Silent_p.R348R	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	468			R -> H (in dbSNP:rs6637934).		regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)		p.R468R(1)		breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					GCTTTGCTGGACGCACTTTGC	0.438																																					p.R468R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T1404C	X						.						174.0	158.0	163.0					X																	131212641		2203	4300	6503	131040322	SO:0001819	synonymous_variant	90167	exon12			AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1404T>C	X.37:g.131212641A>G		Somatic		Capture	Illumina HiSeq	Phase_I	131040322	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																				0.438	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
HPRT1	3251	broad.mit.edu	37	X	133632688	133632688	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:133632688T>A	ENST00000298556.7	+	8	742	c.583T>A	c.(583-585)Tat>Aat	p.Y195N		NM_000194.2	NP_000185.1	P00492	HPRT_HUMAN	hypoxanthine phosphoribosyltransferase 1	195			Y -> C (in GOUT-HPRT; Dirranbandi, Asia). {ECO:0000269|PubMed:15571223, ECO:0000269|PubMed:17027311}.		adenine salvage (GO:0006168)|central nervous system neuron development (GO:0021954)|cerebral cortex neuron differentiation (GO:0021895)|cytolysis (GO:0019835)|dendrite morphogenesis (GO:0048813)|dopamine metabolic process (GO:0042417)|GMP catabolic process (GO:0046038)|GMP salvage (GO:0032263)|grooming behavior (GO:0007625)|guanine salvage (GO:0006178)|hypoxanthine metabolic process (GO:0046100)|hypoxanthine salvage (GO:0043103)|IMP metabolic process (GO:0046040)|IMP salvage (GO:0032264)|locomotory behavior (GO:0007626)|lymphocyte proliferation (GO:0046651)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of dopamine metabolic process (GO:0045964)|protein homotetramerization (GO:0051289)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|purine ribonucleoside salvage (GO:0006166)|purine-containing compound salvage (GO:0043101)|response to amphetamine (GO:0001975)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	guanine phosphoribosyltransferase activity (GO:0052657)|hypoxanthine phosphoribosyltransferase activity (GO:0004422)|magnesium ion binding (GO:0000287)|nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)	p.Y195N(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)	9	Acute lymphoblastic leukemia(192;0.000127)				Azathioprine(DB00993)|Mercaptopurine(DB01033)|Tioguanine(DB00352)	TGCCCTTGACTATAATGAATA	0.284																																					p.Y195N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T583A	X						.						80.0	73.0	75.0					X																	133632688		2203	4299	6502	133460354	SO:0001583	missense	3251	exon8			M26434	CCDS14641.1	Xq26.2	2012-10-02	2008-08-01		ENSG00000165704	ENSG00000165704	2.4.2.8		5157	protein-coding gene	gene with protein product	"""Lesch-Nyhan syndrome"""	308000		HPRT		12175903	Standard	NM_000194		Approved	HGPRT	uc004exl.4	P00492	OTTHUMG00000022452	ENST00000298556.7:c.583T>A	X.37:g.133632688T>A	ENSP00000298556:p.Tyr195Asn	Somatic		Capture	Illumina HiSeq	Phase_I	133460354	NM_000194	A6NHF0|B2R8M9	Missense_Mutation	SNP	ENST00000298556.7	37	CCDS14641.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.402682	0.83230	.	.	ENSG00000165704	ENST00000298556;ENST00000370796	D	0.99732	-6.57	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	D	0.99843	0.9928	H	0.98507	4.25	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	D	0.96566	0.9419	10	0.87932	D	0	-15.9911	14.1526	0.65395	0.0:0.0:0.0:1.0	.	195	P00492	HPRT_HUMAN	N	195	ENSP00000298556:Y195N	ENSP00000298556:Y195N	Y	+	1	0	HPRT1	133460354	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.339000	0.79282	1.940000	0.56252	0.486000	0.48141	TAT		0.284	HPRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058361.1	NM_000194	
FAM127B	26071	broad.mit.edu	37	X	134185867	134185867	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:134185867A>G	ENST00000370775.2	-	1	338	c.272T>C	c.(271-273)cTc>cCc	p.L91P	FAM127B_ENST00000520964.1_Intron	NM_001078172.1	NP_001071640.1	Q9BWD3	F127B_HUMAN	family with sequence similarity 127, member B	91								p.L91P(1)		breast(3)|endometrium(2)|large_intestine(3)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;0.000127)					GTAATCATTGAGCAGGGGGCT	0.637																																					p.L91P												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T272C	X						.						49.0	53.0	52.0					X																	134185867		2186	4270	6456	134013533	SO:0001583	missense	26071	exon1			AL117556	CCDS43998.1	Xq26.3	2014-05-16			ENSG00000203950	ENSG00000203950			24514	protein-coding gene	gene with protein product						9403077, 15716091	Standard	NM_001078172		Approved	DKFZP564B147, MAR8A, CXX1b	uc004eyf.3	Q9BWD3	OTTHUMG00000022466	ENST00000370775.2:c.272T>C	X.37:g.134185867A>G	ENSP00000375267:p.Leu91Pro	Somatic		Capture	Illumina HiSeq	Phase_I	134013533	NM_001078172	A2A2V9|Q8TBU2	Missense_Mutation	SNP	ENST00000370775.2	37	CCDS43998.1	.	.	.	.	.	.	.	.	.	.	a	11.44	1.639109	0.29157	.	.	ENSG00000203950	ENST00000370775	T	0.39229	1.09	2.38	2.38	0.29361	.	0.238125	0.20392	U	0.093225	T	0.51092	0.1654	L	0.48986	1.54	0.46654	D	0.999143	D	0.89917	1.0	D	0.97110	1.0	T	0.46289	-0.9202	9	.	.	.	.	5.9447	0.19211	1.0:0.0:0.0:0.0	.	91	Q9BWD3	F127B_HUMAN	P	91	ENSP00000375267:L91P	.	L	-	2	0	FAM127B	134013533	0.976000	0.34144	0.734000	0.30879	0.015000	0.08874	2.390000	0.44416	1.190000	0.43042	0.242000	0.17961	CTC		0.637	FAM127B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058393.2	NM_001078172	
CT45A5	441521	broad.mit.edu	37	X	134947966	134947966	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:134947966T>C	ENST00000463085.2	-	3	448	c.359A>G	c.(358-360)cAa>cGa	p.Q120R	CT45A5_ENST00000370724.3_Missense_Mutation_p.Q120R|CT45A4_ENST00000420087.2_Intron|CT45A5_ENST00000491480.1_Missense_Mutation_p.Q120R			Q6NSH3	CT455_HUMAN	cancer/testis antigen family 45, member A5	120								p.Q120R(2)		endometrium(1)|large_intestine(2)|lung(6)	9						ATTAATTTCTTGTTGGCTTTT	0.408																																					p.Q120R												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.A359G	X						.						212.0	182.0	192.0					X																	134947966		2188	4272	6460	134775632	SO:0001583	missense	441521	exon3			AY743713	CCDS35406.1	Xq26.3	2009-03-12				ENSG00000269586			33270	protein-coding gene	gene with protein product	"""cancer/testis antigen CT45-5"""	300796				15905330	Standard	XM_006724759		Approved	CT45-5, CT45.5	uc022ces.1	Q6NSH3		ENST00000463085.2:c.359A>G	X.37:g.134947966T>C	ENSP00000424778:p.Gln120Arg	Somatic		Capture	Illumina HiSeq	Phase_I	134775632	NM_001172288	A8K842|B7ZMC5	Missense_Mutation	SNP	ENST00000463085.2	37	CCDS35406.1	.	.	.	.	.	.	.	.	.	.	T	7.345	0.621673	0.14193	.	.	ENSG00000242284	ENST00000370724;ENST00000491480	T;T	0.45668	0.89;0.89	2.4	1.11	0.20524	.	0.417425	0.24774	U	0.035720	T	0.21387	0.0515	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10823	-1.0613	10	0.41790	T	0.15	-0.7886	4.1442	0.10209	0.3134:0.0:0.0:0.6866	.	120	Q6NSH3	CT455_HUMAN	R	120	ENSP00000359759:Q120R;ENSP00000425997:Q120R	ENSP00000359759:Q120R	Q	-	2	0	CT45A5	134775632	0.051000	0.20477	0.000000	0.03702	0.204000	0.24138	1.290000	0.33319	0.066000	0.16515	0.299000	0.19835	CAA		0.408	CT45A5-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472589.1	NM_001007551	
EGFL6	25975	broad.mit.edu	37	X	13612989	13612989	+	Silent	SNP	C	C	T	rs138875572	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:13612989C>T	ENST00000361306.1	+	3	479	c.222C>T	c.(220-222)tgC>tgT	p.C74C	EGFL6_ENST00000380602.3_Silent_p.C74C|RN7SKP20_ENST00000362752.1_RNA	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	74	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)	p.C74C(1)		breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						TTGGTGAGTGCGTGGGACCAA	0.433													C|||	3	0.000794702	0.0015	0.0	3775	,	,		14391	0.001		0.0	False		,,,				2504	0.0				p.C74C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C222T	X						.	C	,	11,3824		0,8,3,1624,568	185.0	128.0	147.0		222,222	-0.7	1.0	X	dbSNP_134	147	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous	EGFL6	NM_001167890.1,NM_015507.3	,	0,8,3,4052,2440	TT,TC,T,CC,C		0.0,0.2868,0.1041	,	74/555,74/554	13612989	11,10552	2203	4300	6503	13522910	SO:0001819	synonymous_variant	25975	exon3			AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.222C>T	X.37:g.13612989C>T		Somatic		Capture	Illumina HiSeq	Phase_I	13522910	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Silent	SNP	ENST00000361306.1	37	CCDS14155.1																																																																																				0.433	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507	
FHL1	2273	broad.mit.edu	37	X	135291596	135291596	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:135291596G>T	ENST00000345434.3	+	6	964	c.883G>T	c.(883-885)Ggc>Tgc	p.G295C	FHL1_ENST00000394153.2_Intron|FHL1_ENST00000394155.2_Missense_Mutation_p.G295C|FHL1_ENST00000370690.3_Intron|FHL1_ENST00000535737.1_Intron|FHL1_ENST00000543669.1_Intron|FHL1_ENST00000370683.1_Intron|FHL1_ENST00000539015.1_Intron|FHL1_ENST00000370676.3_Intron			Q13642	FHL1_HUMAN	four and a half LIM domains 1	295					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					AGCTCCTCGAGGCCCGGTAAG	0.557											OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G295C												.	.	0			c.G883T	X						.						50.0	43.0	45.0					X																	135291596		1568	3581	5149	135119262	SO:0001583	missense	2273	exon7			U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"""Four-and-a-half LIM domains 1"", ""LIM protein SLIMMER"""	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.883G>T	X.37:g.135291596G>T	ENSP00000071281:p.Gly295Cys	None	1617	Capture	Illumina HiSeq	Phase_I	135119262	NM_001159702	B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Missense_Mutation	SNP	ENST00000345434.3	37	CCDS55507.1	.	.	.	.	.	.	.	.	.	.	g	15.21	2.765626	0.49574	.	.	ENSG00000022267	ENST00000394155;ENST00000345434	T;T	0.70399	-0.48;-0.48	4.59	4.59	0.56863	.	0.000000	0.64402	D	0.000010	T	0.53965	0.1829	N	0.08118	0	0.31779	N	0.631162	D	0.65815	0.995	P	0.45577	0.486	T	0.66208	-0.5981	10	0.87932	D	0	.	11.7655	0.51928	0.0:0.0:1.0:0.0	.	295	Q13642	FHL1_HUMAN	C	295	ENSP00000377710:G295C;ENSP00000071281:G295C	ENSP00000071281:G295C	G	+	1	0	FHL1	135119262	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.339000	0.59322	2.259000	0.74868	0.525000	0.51046	GGC		0.557	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449	
ARHGEF6	9459	broad.mit.edu	37	X	135764062	135764062	+	Silent	SNP	T	T	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:135764062T>A	ENST00000250617.6	-	14	2750	c.1545A>T	c.(1543-1545)acA>acT	p.T515T	ARHGEF6_ENST00000370622.1_Silent_p.T361T|ARHGEF6_ENST00000370620.1_Silent_p.T361T|ARHGEF6_ENST00000535227.1_Silent_p.T388T	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	515	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.T515T(1)		cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					TGATTTCAAATGTGCAGTCAT	0.328																																					p.T515T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1545T	X						.						178.0	152.0	161.0					X																	135764062		2202	4300	6502	135591728	SO:0001819	synonymous_variant	9459	exon14			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1545A>T	X.37:g.135764062T>A		Somatic		Capture	Illumina HiSeq	Phase_I	135591728	NM_004840	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Silent	SNP	ENST00000250617.6	37	CCDS14660.1																																																																																				0.328	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058511.2	NM_004840	
GPR101	83550	broad.mit.edu	37	X	136113350	136113350	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:136113350G>A	ENST00000298110.1	-	1	483	c.484C>T	c.(484-486)Cag>Tag	p.Q162*		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.Q162*(1)		autonomic_ganglia(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(18)|ovary(3)|skin(1)|urinary_tract(1)	42	Acute lymphoblastic leukemia(192;0.000127)					GGAGTGCTCTGCAGGATGGCC	0.597																																					p.Q162X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C484T	X						.						50.0	41.0	44.0					X																	136113350		2203	4300	6503	135941016	SO:0001587	stop_gained	83550	exon1			AF411115	CCDS14662.1	Xq26.3	2014-01-30			ENSG00000165370	ENSG00000165370		"""GPCR / Class A : Orphans"""	14963	protein-coding gene	gene with protein product		300393				11574155	Standard	NM_054021		Approved		uc011mwh.2	Q96P66	OTTHUMG00000022521	ENST00000298110.1:c.484C>T	X.37:g.136113350G>A	ENSP00000298110:p.Gln162*	Somatic		Capture	Illumina HiSeq	Phase_I	135941016	NM_054021	Q5JSM8|Q8NG93	Nonsense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000472	0.93227	.	.	ENSG00000165370	ENST00000298110	.	.	.	5.04	5.04	0.67666	.	0.000000	0.32093	N	0.006590	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-15.3908	14.8214	0.70077	0.0:0.0:1.0:0.0	.	.	.	.	X	162	.	ENSP00000298110:Q162X	Q	-	1	0	GPR101	135941016	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.502000	0.73695	2.081000	0.62600	0.600000	0.82982	CAG		0.597	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1		
ATP11C	286410	broad.mit.edu	37	X	138878545	138878545	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:138878545T>C	ENST00000327569.3	-	12	1200	c.1102A>G	c.(1102-1104)Atg>Gtg	p.M368V	ATP11C_ENST00000370557.1_Missense_Mutation_p.M365V|ATP11C_ENST00000460773.1_5'UTR|ATP11C_ENST00000370543.1_Missense_Mutation_p.M368V|ATP11C_ENST00000361648.2_Missense_Mutation_p.M368V|ATP11C_ENST00000359686.2_Missense_Mutation_p.M368V	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	368					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|positive regulation of B cell differentiation (GO:0045579)|pre-B cell differentiation (GO:0002329)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.M368V(1)		breast(2)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(31)|ovary(5)|prostate(1)|skin(3)	75	Acute lymphoblastic leukemia(192;0.000127)					AATTTCTGCATTTCTACTGTG	0.353																																					p.M368V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A1102G	X						.						69.0	64.0	66.0					X																	138878545		2203	4300	6503	138706211	SO:0001583	missense	286410	exon12			AJ580094	CCDS14668.1, CCDS35410.1	Xq27.1	2011-06-09	2007-09-19		ENSG00000101974	ENSG00000101974		"""ATPases / P-type"""	13554	protein-coding gene	gene with protein product		300516	"""ATPase, Class VI, type 11C"""			11015572	Standard	NM_173694		Approved	ATPIG, ATPIQ	uc004faz.3	Q8NB49	OTTHUMG00000022538	ENST00000327569.3:c.1102A>G	X.37:g.138878545T>C	ENSP00000332756:p.Met368Val	Somatic		Capture	Illumina HiSeq	Phase_I	138706211	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.021687	0.54576	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.89270	-2.49;-2.49;-2.49;-2.49;-2.49	5.88	5.88	0.94601	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.87402	0.6168	L	0.39147	1.195	0.54753	D	0.999989	P;P	0.47106	0.866;0.89	P;P	0.52957	0.591;0.714	D	0.84363	0.0539	10	0.02654	T	1	.	14.2923	0.66286	0.0:0.0:0.0:1.0	.	368;368	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	V	365;368;368;368;368	ENSP00000359588:M365V;ENSP00000355165:M368V;ENSP00000332756:M368V;ENSP00000359574:M368V;ENSP00000352715:M368V	ENSP00000332756:M368V	M	-	1	0	ATP11C	138706211	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.040000	0.89188	1.973000	0.57446	0.486000	0.48141	ATG		0.353	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
MAGEC3	139081	broad.mit.edu	37	X	140967176	140967176	+	Silent	SNP	C	C	T	rs373457144		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:140967176C>T	ENST00000298296.1	+	3	474	c.474C>T	c.(472-474)gcC>gcT	p.A158A	MAGEC3_ENST00000443323.2_5'Flank|MAGEC3_ENST00000536088.1_5'Flank|MAGEC3_ENST00000448920.1_5'Flank	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	158								p.A158A(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					CCCTTCCTGCCGTCAGCCCTG	0.567																																					p.A158A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C474T	X						.	T		0,3822		0,0,0,1630,562	31.0	27.0	28.0		474	-0.1	0.0	X		28	1,6721		0,0,1,2428,1865	no	coding-synonymous	MAGEC3	NM_138702.1		0,0,1,4058,2427	TT,TC,T,CC,C		0.0149,0.0,0.0095		158/644	140967176	1,10543	2192	4294	6486	140794842	SO:0001819	synonymous_variant	139081	exon3			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.474C>T	X.37:g.140967176C>T		Somatic		Capture	Illumina HiSeq	Phase_I	140794842	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Silent	SNP	ENST00000298296.1	37	CCDS14676.1																																																																																				0.567	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
MAGEC3	139081	broad.mit.edu	37	X	140985599	140985599	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:140985599C>T	ENST00000298296.1	+	8	1913	c.1913C>T	c.(1912-1914)aCc>aTc	p.T638I	MAGEC3_ENST00000443323.2_3'UTR|MAGEC3_ENST00000544766.1_3'UTR|MAGEC3_ENST00000409007.1_3'UTR|MAGEC3_ENST00000536088.1_3'UTR	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3	638	MAGE 2. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.T638I(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|liver(1)|lung(32)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(2)	69	Acute lymphoblastic leukemia(192;6.56e-05)					GTCATGTCCACCAACTTCTGT	0.527																																					p.T638I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1913T	X						.						65.0	55.0	58.0					X																	140985599		2203	4299	6502	140813265	SO:0001583	missense	139081	exon8			AF490508	CCDS14676.1, CCDS14677.1	Xq27.2	2009-03-25			ENSG00000165509	ENSG00000165509			23798	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 2"""	300469				10861452	Standard	NM_138702		Approved	HCA2, MAGE-C3, CT7.2	uc011mwp.2	Q8TD91	OTTHUMG00000022570	ENST00000298296.1:c.1913C>T	X.37:g.140985599C>T	ENSP00000298296:p.Thr638Ile	Somatic		Capture	Illumina HiSeq	Phase_I	140813265	NM_138702	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	c	8.523	0.869107	0.17322	.	.	ENSG00000165509	ENST00000298296	T	0.03301	3.98	1.18	-0.0818	0.13701	.	.	.	.	.	T	0.02610	0.0079	N	0.14661	0.345	0.09310	N	1	P	0.51537	0.946	B	0.43386	0.418	T	0.46512	-0.9186	9	0.66056	D	0.02	.	5.2682	0.15611	0.0:0.5085:0.4915:0.0	.	638	Q8TD91	MAGC3_HUMAN	I	638	ENSP00000298296:T638I	ENSP00000298296:T638I	T	+	2	0	MAGEC3	140813265	0.001000	0.12720	0.001000	0.08648	0.136000	0.21042	0.235000	0.17948	-0.119000	0.11830	0.179000	0.17066	ACC		0.527	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702	
UBE2NL	389898	broad.mit.edu	37	X	142967242	142967242	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:142967242C>A	ENST00000370494.1	+	1	70	c.40C>A	c.(40-42)Cgt>Agt	p.R14S		NM_001012989.1	NP_001013007.1	Q5JXB2	UE2NL_HUMAN	ubiquitin-conjugating enzyme E2N-like (gene/pseudogene)	14						extracellular vesicular exosome (GO:0070062)	acid-amino acid ligase activity (GO:0016881)	p.R14S(1)		breast(1)|endometrium(1)|large_intestine(8)|lung(12)|prostate(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(192;6.56e-05)					GGAAACCCAGCGTTTGCTGGC	0.483																																					p.R14S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C40A	X						.						64.0	64.0	64.0					X																	142967242		2203	4300	6503	142794908	SO:0001583	missense	389898	exon1					Xq27.3	2014-06-11	2014-06-11		ENSG00000102069			"""Ubiquitin-conjugating enzymes E2"""	31710	protein-coding gene	gene with protein product			"""ubiquitin-conjugating enzyme E2N-like"""			20736409	Standard	NM_001012989		Approved		uc004fca.3	Q5JXB2	OTTHUMG00000022586	ENST00000370494.1:c.40C>A	X.37:g.142967242C>A	ENSP00000359525:p.Arg14Ser	Somatic		Capture	Illumina HiSeq	Phase_I	142794908	NM_001012989	E9KL27	Missense_Mutation	SNP	ENST00000370494.1	37	CCDS35420.1	.	.	.	.	.	.	.	.	.	.	C	13.19	2.164054	0.38217	.	.	ENSG00000102069	ENST00000370494	T	0.36520	1.25	1.1	1.1	0.20463	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.45361	U	0.000372	T	0.42698	0.1214	M	0.68593	2.085	0.80722	D	1	P	0.48589	0.912	P	0.51999	0.687	T	0.33854	-0.9852	10	0.48119	T	0.1	15.4265	7.8005	0.29172	0.0:1.0:0.0:0.0	.	14	Q5JXB2	UE2NL_HUMAN	S	14	ENSP00000359525:R14S	ENSP00000359525:R14S	R	+	1	0	UBE2NL	142794908	1.000000	0.71417	0.997000	0.53966	0.167000	0.22549	5.342000	0.65970	0.849000	0.35215	0.190000	0.17370	CGT		0.483	UBE2NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058624.1	NM_001012989	
SLITRK2	84631	broad.mit.edu	37	X	144906363	144906363	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:144906363C>T	ENST00000370490.1	+	1	6675	c.2420C>T	c.(2419-2421)cCc>cTc	p.P807L	SLITRK2_ENST00000434188.2_Missense_Mutation_p.P807L|SLITRK2_ENST00000413937.2_Missense_Mutation_p.P807L|SLITRK2_ENST00000428560.2_Missense_Mutation_p.P807L|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000447897.2_Missense_Mutation_p.P807L			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	807					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.P807L(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					TATGGAACTCCCAGGAAATGC	0.433																																					p.P807L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2420T	X						.						97.0	95.0	96.0					X																	144906363		2203	4300	6503	144714055	SO:0001583	missense	84631	exon3			Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.2420C>T	X.37:g.144906363C>T	ENSP00000359521:p.Pro807Leu	Somatic		Capture	Illumina HiSeq	Phase_I	144714055	NM_001144006	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.969985	0.74246	.	.	ENSG00000185985	ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37	5.38	5.38	0.77491	.	0.060354	0.64402	D	0.000002	T	0.68091	0.2963	M	0.61703	1.905	0.80722	D	1	D	0.62365	0.991	D	0.63957	0.92	T	0.70828	-0.4766	10	0.62326	D	0.03	-7.4119	15.4932	0.75629	0.0:1.0:0.0:0.0	.	807	Q9H156	SLIK2_HUMAN	L	807	ENSP00000411681:P807L;ENSP00000359521:P807L;ENSP00000397015:P807L;ENSP00000407347:P807L;ENSP00000412010:P807L	ENSP00000359521:P807L	P	+	2	0	SLITRK2	144714055	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.487000	0.81328	2.251000	0.74343	0.600000	0.82982	CCC		0.433	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
FMR1NB	158521	broad.mit.edu	37	X	147090171	147090171	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:147090171G>A	ENST00000370467.3	+	4	646	c.572G>A	c.(571-573)gGt>gAt	p.G191D	5S_rRNA_ENST00000364415.1_RNA	NM_152578.2	NP_689791.1	Q8N0W7	FMR1N_HUMAN	fragile X mental retardation 1 neighbor	191						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)		p.G191D(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(7)|lung(10)|ovary(1)|skin(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					TTTGGGCTTGGTGCGATCAGC	0.393																																					p.G191D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G572A	X						.						233.0	171.0	192.0					X																	147090171		2203	4300	6503	146897863	SO:0001583	missense	158521	exon4				CCDS14683.1	Xq28	2009-03-25			ENSG00000176988	ENSG00000176988			26372	protein-coding gene	gene with protein product	"""cancer/testis antigen 37"""					12601173	Standard	NM_152578		Approved	FLJ25736, NY-SAR-35, CT37	uc004fcm.3	Q8N0W7	OTTHUMG00000022608	ENST00000370467.3:c.572G>A	X.37:g.147090171G>A	ENSP00000359498:p.Gly191Asp	Somatic		Capture	Illumina HiSeq	Phase_I	146897863	NM_152578	D3DWT3	Missense_Mutation	SNP	ENST00000370467.3	37	CCDS14683.1	.	.	.	.	.	.	.	.	.	.	G	10.46	1.357746	0.24598	.	.	ENSG00000176988	ENST00000370467	T	0.37584	1.19	5.64	2.86	0.33363	.	0.535989	0.15769	N	0.245534	T	0.40347	0.1113	N	0.19112	0.55	0.09310	N	1	D	0.76494	0.999	D	0.74674	0.984	T	0.18304	-1.0341	10	0.62326	D	0.03	-3.0419	7.8232	0.29300	0.0:0.1548:0.5182:0.327	.	191	Q8N0W7	FMR1N_HUMAN	D	191	ENSP00000359498:G191D	ENSP00000359498:G191D	G	+	2	0	FMR1NB	146897863	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.304000	0.19228	0.173000	0.19788	0.544000	0.68410	GGT		0.393	FMR1NB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058667.1	NM_152578	
Unknown	0	broad.mit.edu	37	Unknown	0	0	+	IGR	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrUnknown:0C>A								None (None upstream) : None (None downstream)																								0.0																																					p.K327N												.	.	0			c.G981T	X						.																																			148576191	SO:0001628	intergenic_variant	4110	exon5																															Unknown.37:g.0C>A		Somatic		Capture	Illumina HiSeq	Phase_I	148576191	NM_001011544		Missense_Mutation	SNP		37																																																																																				0	0								
Unknown	0	broad.mit.edu	37	Unknown	0	0	+	IGR	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Invalid:failed_liftOver	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrUnknown:0A>G								None (None upstream) : None (None downstream)																								0.0																																					p.L84P												.	.	0			c.T251C	X						.																																			148576921	SO:0001628	intergenic_variant	4110	exon5																															Unknown.37:g.0A>G		Somatic		Capture	Illumina HiSeq	Phase_I	148576921	NM_001011544		Missense_Mutation	SNP		37																																																																																				0	0								
ASB9	140462	broad.mit.edu	37	X	15272944	15272944	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:15272944G>A	ENST00000380488.4	-	3	470	c.197C>T	c.(196-198)aCg>aTg	p.T66M	ASB9_ENST00000380483.3_Missense_Mutation_p.T66M|ASB9_ENST00000546332.1_Missense_Mutation_p.T66M|ASB9_ENST00000473862.1_5'UTR|ASB9_ENST00000380485.3_Missense_Mutation_p.T66M	NM_001031739.2	NP_001026909.1	Q96DX5	ASB9_HUMAN	ankyrin repeat and SOCS box containing 9	66					intracellular signal transduction (GO:0035556)|positive regulation of protein catabolic process (GO:0045732)|protein ubiquitination (GO:0016567)	mitochondrion (GO:0005739)		p.T66M(1)		breast(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(10)	15	Hepatocellular(33;0.183)					ATGATCTGCCGTGATGATGTT	0.512																																					p.T66M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C197T	X						.						121.0	114.0	116.0					X																	15272944		2203	4300	6503	15182865	SO:0001583	missense	140462	exon4			AK000643	CCDS14163.1, CCDS35208.1, CCDS55372.1	Xp22.2	2013-01-10	2011-01-25		ENSG00000102048	ENSG00000102048		"""Ankyrin repeat domain containing"""	17184	protein-coding gene	gene with protein product		300890	"""ankyrin repeat and SOCS box-containing 9"""			12076535	Standard	NM_001031739		Approved	DKFZP564L0862, MGC4954, FLJ20636	uc004cwl.3	Q96DX5	OTTHUMG00000021172	ENST00000380488.4:c.197C>T	X.37:g.15272944G>A	ENSP00000369855:p.Thr66Met	Somatic		Capture	Illumina HiSeq	Phase_I	15182865	NM_001168531	A8K8A5|Q9BVF5|Q9NWS5|Q9Y4T3	Missense_Mutation	SNP	ENST00000380488.4	37	CCDS35208.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.716447	0.48622	.	.	ENSG00000102048	ENST00000380483;ENST00000380485;ENST00000380488;ENST00000546332	T;T;T;T	0.63913	0.55;-0.07;-0.07;-0.07	5.93	5.93	0.95920	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.75133	0.3808	L	0.49640	1.575	0.52099	D	0.999945	P;D;D;D	0.89917	0.867;0.999;0.988;1.0	P;D;P;D	0.78314	0.473;0.988;0.872;0.991	T	0.72740	-0.4202	9	.	.	.	-15.9361	18.0905	0.89474	0.0:0.0:1.0:0.0	.	66;66;66;66	Q7Z4A2;Q9BVF5;Q96DX5;Q96DX5-2	.;.;ASB9_HUMAN;.	M	66	ENSP00000369850:T66M;ENSP00000369852:T66M;ENSP00000369855:T66M;ENSP00000438943:T66M	.	T	-	2	0	ASB9	15182865	1.000000	0.71417	0.820000	0.32676	0.037000	0.13140	7.587000	0.82613	2.494000	0.84150	0.600000	0.82982	ACG		0.512	ASB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055844.1		
ZNF185	7739	broad.mit.edu	37	X	152087589	152087589	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:152087589A>T	ENST00000370268.4	+	7	531	c.494A>T	c.(493-495)gAg>gTg	p.E165V	ZNF185_ENST00000318504.7_Missense_Mutation_p.E165V|ZNF185_ENST00000539731.1_Missense_Mutation_p.E165V|ZNF185_ENST00000324823.6_Missense_Mutation_p.E30V|ZNF185_ENST00000449285.2_Missense_Mutation_p.E165V|ZNF185_ENST00000370270.2_Missense_Mutation_p.E165V|ZNF185_ENST00000535861.1_Missense_Mutation_p.E165V|ZNF185_ENST00000318529.8_Missense_Mutation_p.E30V			O15231	ZN185_HUMAN	zinc finger protein 185 (LIM domain)	165	Poly-Glu.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.E25V(1)|p.E165V(1)		NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(3)	12	Acute lymphoblastic leukemia(192;6.56e-05)					gaggaggaggaggTGGTGCCA	0.582																																					p.E165V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.A494T	X						.						57.0	56.0	56.0					X																	152087589		2038	4148	6186	151838245	SO:0001583	missense	7739	exon7			AK056517	CCDS48184.1, CCDS55528.1, CCDS55529.1, CCDS55530.1, CCDS55531.1, CCDS55532.1, CCDS69832.1	Xq28	2012-08-08			ENSG00000147394	ENSG00000147394		"""Zinc fingers, C2H2-type"""	12976	protein-coding gene	gene with protein product		300381				9268636	Standard	NM_001178106		Approved		uc011myg.2	O15231	OTTHUMG00000024187	ENST00000370268.4:c.494A>T	X.37:g.152087589A>T	ENSP00000359291:p.Glu165Val	Somatic		Capture	Illumina HiSeq	Phase_I	151838245	NM_007150	A4FTV3|A6NME5|B4DLE9|B7Z771|B8K2L9|B8K2M0|B8K2M1|B8K2M2|E9PFR6|F5GXF7|F5GZL4|F8W8V7|H0Y4M8|O00345|Q8N1R8|Q9NSD2	Missense_Mutation	SNP	ENST00000370268.4	37	CCDS48184.1	.	.	.	.	.	.	.	.	.	.	A	14.06	2.422547	0.43020	.	.	ENSG00000147394	ENST00000535861;ENST00000539731;ENST00000449285;ENST00000318504;ENST00000535156;ENST00000324823;ENST00000433245;ENST00000370268;ENST00000318529;ENST00000370270	T;T;T;T;T	0.49432	0.78;0.8;0.8;0.81;0.8	0.436	0.436	0.16549	.	.	.	.	.	T	0.40546	0.1121	N	0.08118	0	0.22693	N	0.998848	D;P;P;P;P;P;P	0.55172	0.97;0.862;0.89;0.89;0.89;0.89;0.89	B;B;P;P;P;P;P	0.61397	0.427;0.188;0.607;0.607;0.888;0.607;0.607	T	0.27673	-1.0067	8	0.59425	D	0.04	.	.	.	.	.	165;165;165;165;165;165;30	O15231-3;B8K2L9;B8K2M0;F5GZL4;F5GXF7;O15231;F8W8V7	.;.;.;.;.;ZN185_HUMAN;.	V	165;165;165;165;30;30;30;165;30;25	ENSP00000440847:E165V;ENSP00000444367:E165V;ENSP00000395228:E165V;ENSP00000312782:E165V;ENSP00000359291:E165V	ENSP00000312782:E165V	E	+	2	0	ZNF185	151838245	0.970000	0.33590	0.833000	0.33012	0.266000	0.26442	1.141000	0.31528	0.360000	0.24265	0.158000	0.16466	GAG		0.582	ZNF185-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000377480.1	NM_007150	
ZNF275	10838	broad.mit.edu	37	X	152612437	152612437	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:152612437A>C	ENST00000421401.3	+	4	471	c.294A>C	c.(292-294)gaA>gaC	p.E98D	ZNF275_ENST00000440091.1_Missense_Mutation_p.E128D|ZNF275_ENST00000370251.3_Missense_Mutation_p.E98D|ZNF275_ENST00000370249.2_Missense_Mutation_p.E45D			Q9NSD4	ZN275_HUMAN	zinc finger protein 275	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E45D(1)		endometrium(5)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	16	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TGCCCATAGAACATCATTTTG	0.547																																					p.E98D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A294C	X						.						83.0	86.0	85.0					X																	152612437		2064	4188	6252	152265631	SO:0001583	missense	10838	exon4			BC041602		Xq28	2013-01-08			ENSG00000063587	ENSG00000063587		"""Zinc fingers, C2H2-type"", ""-"""	13069	protein-coding gene	gene with protein product							Standard	NM_001080485		Approved		uc004fhg.2	Q9NSD4	OTTHUMG00000067450	ENST00000421401.3:c.294A>C	X.37:g.152612437A>C	ENSP00000398977:p.Glu98Asp	Somatic		Capture	Illumina HiSeq	Phase_I	152265631	NM_001080485	A6NE92	Missense_Mutation	SNP	ENST00000421401.3	37		.	.	.	.	.	.	.	.	.	.	A	9.589	1.125736	0.20959	.	.	ENSG00000063587	ENST00000370251;ENST00000421401;ENST00000440091;ENST00000370249	T;T;T;T	0.09255	3.0;3.07;3.07;3.09	4.11	-6.54	0.01860	.	0.000000	0.42294	D	0.000739	T	0.06280	0.0162	N	0.24115	0.695	0.09310	N	1	P;P	0.43392	0.698;0.805	B;B	0.35813	0.211;0.211	T	0.03374	-1.1043	10	0.66056	D	0.02	-25.8	17.5834	0.87974	0.1348:0.0:0.8652:0.0	.	98;98	Q9NSD4;A6NFS0	ZN275_HUMAN;.	D	98;98;128;45	ENSP00000359271:E98D;ENSP00000398977:E98D;ENSP00000411097:E128D;ENSP00000359269:E45D	ENSP00000359269:E45D	E	+	3	2	ZNF275	152265631	0.000000	0.05858	0.001000	0.08648	0.743000	0.42351	-2.383000	0.01063	-2.016000	0.00945	-0.462000	0.05337	GAA		0.547	ZNF275-201	KNOWN	basic	protein_coding	protein_coding		NM_001080485	
TREX2	11219	broad.mit.edu	37	X	152710635	152710635	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:152710635A>G	ENST00000334497.2	-	11	1524	c.383T>C	c.(382-384)cTg>cCg	p.L128P	TREX2_ENST00000393862.2_Missense_Mutation_p.L85P|TREX2_ENST00000370231.2_Missense_Mutation_p.L85P|TREX2_ENST00000402951.1_Missense_Mutation_p.L128P|TREX2_ENST00000414588.1_Missense_Mutation_p.L127P|TREX2_ENST00000338525.2_Missense_Mutation_p.L85P|TREX2_ENST00000330912.2_Missense_Mutation_p.L85P|TREX2_ENST00000370232.1_Missense_Mutation_p.L128P|HAUS7_ENST00000484394.1_5'Flank			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	128					DNA catabolic process, exonucleolytic (GO:0000738)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)	nucleus (GO:0005634)	3'-5'-exodeoxyribonuclease activity (GO:0008296)|exodeoxyribonuclease III activity (GO:0008853)|magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)	p.L128P(1)|p.L85P(1)		endometrium(4)|large_intestine(2)|lung(3)|ovary(2)	11	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GCATCGCGCCAGGCCCTCACT	0.677								Editing and processing nucleases																													p.L85P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T254C	X						.						18.0	18.0	18.0					X																	152710635		2199	4289	6488	152363829	SO:0001583	missense	11219	exon2			AF151107	CCDS35437.1	Xq28	2012-05-08			ENSG00000183479	ENSG00000183479			12270	protein-coding gene	gene with protein product		300370				10391904	Standard	NM_080701		Approved		uc011myp.2	Q9BQ50	OTTHUMG00000159319	ENST00000334497.2:c.383T>C	X.37:g.152710635A>G	ENSP00000334993:p.Leu128Pro	Somatic		Capture	Illumina HiSeq	Phase_I	152363829	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	A	14.31	2.497059	0.44352	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53;1.53;1.53	4.95	4.95	0.65309	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.37715	U	0.001979	T	0.60130	0.2245	M	0.88640	2.97	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67650	-0.5616	10	0.87932	D	0	-9.7299	11.5943	0.50964	1.0:0.0:0.0:0.0	.	127;128	Q06S70;Q9BQ50	.;TREX2_HUMAN	P	85;85;85;128;128;128;127;85	ENSP00000377442:L85P;ENSP00000333441:L85P;ENSP00000345218:L85P;ENSP00000334993:L128P;ENSP00000359252:L128P;ENSP00000386078:L128P;ENSP00000401692:L127P;ENSP00000359251:L85P	ENSP00000333441:L85P	L	-	2	0	TREX2	152363829	1.000000	0.71417	0.653000	0.29593	0.075000	0.17131	4.028000	0.57246	1.637000	0.50538	0.381000	0.24937	CTG		0.677	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701	
PLXNB3	5365	broad.mit.edu	37	X	153034415	153034415	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:153034415G>T	ENST00000361971.5	+	5	1393	c.1279G>T	c.(1279-1281)Ggc>Tgc	p.G427C	PLXNB3_ENST00000538776.1_Missense_Mutation_p.G80C|U52111.14_ENST00000434284.1_RNA|PLXNB3_ENST00000538966.1_Missense_Mutation_p.G450C|PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538282.1_Intron|U52111.14_ENST00000416854.1_RNA	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	427	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell chemotaxis (GO:0060326)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell migration (GO:0030336)|negative regulation of GTPase activity (GO:0034260)|negative regulation of lamellipodium assembly (GO:0010593)|positive chemotaxis (GO:0050918)|positive regulation of endothelial cell proliferation (GO:0001938)|semaphorin-plexin signaling pathway (GO:0071526)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)	p.G427C(1)		central_nervous_system(1)|endometrium(7)|large_intestine(2)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	32	all_hematologic(71;4.25e-06)|all_lung(58;3.83e-05)|Lung NSC(58;5.54e-05)|Acute lymphoblastic leukemia(192;6.56e-05)					CTTTCTCCACGGCTCCCAGGG	0.632																																					p.G450C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1348T	X						.						107.0	97.0	100.0					X																	153034415		2203	4300	6503	152687609	SO:0001583	missense	5365	exon6			AF149019	CCDS14729.1, CCDS55536.1	Xq28	2008-02-05			ENSG00000198753	ENSG00000198753		"""Plexins"""	9105	protein-coding gene	gene with protein product		300214		PLXN6		10520995	Standard	NM_005393		Approved	PLEXR, PLEXB3	uc010nuk.2	Q9ULL4	OTTHUMG00000024217	ENST00000361971.5:c.1279G>T	X.37:g.153034415G>T	ENSP00000355378:p.Gly427Cys	Somatic		Capture	Illumina HiSeq	Phase_I	152687609	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.553078	0.45487	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776	T;T;T	0.10763	2.84;2.84;3.51	5.27	2.29	0.28610	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (3);	0.431762	0.23773	N	0.044710	T	0.23410	0.0566	M	0.65498	2.005	0.25964	N	0.982581	D;D;D;D	0.76494	0.995;0.999;0.997;0.995	P;D;D;D	0.65233	0.756;0.921;0.933;0.925	T	0.05869	-1.0859	10	0.66056	D	0.02	.	6.1721	0.20422	0.3861:0.0:0.6139:0.0	.	80;109;450;427	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	C	450;427;80	ENSP00000442736:G450C;ENSP00000355378:G427C;ENSP00000445569:G80C	ENSP00000355378:G427C	G	+	1	0	PLXNB3	152687609	0.689000	0.27690	0.045000	0.18777	0.273000	0.26683	0.880000	0.28159	0.034000	0.15491	0.513000	0.50165	GGC		0.632	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1		
ATP6AP1	537	broad.mit.edu	37	X	153662699	153662699	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:153662699C>T	ENST00000369762.2	+	7	891	c.830C>T	c.(829-831)gCg>gTg	p.A277V	GDI1_ENST00000447750.2_5'Flank	NM_001183.4	NP_001174.2	Q15904	VAS1_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 1	277					ATP hydrolysis coupled proton transport (GO:0015991)|establishment of organelle localization (GO:0051656)|pH reduction (GO:0045851)|positive regulation of bone resorption (GO:0045780)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoclast development (GO:2001206)|proton transport (GO:0015992)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)|vacuole (GO:0005773)	ATP binding (GO:0005524)|proton-transporting ATP synthase activity, rotational mechanism (GO:0046933)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)	p.A277V(1)		breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(5)	14	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTCTCTGTGGCGTACAAGGAC	0.552																																					p.A277V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C830T	X						.						151.0	130.0	137.0					X																	153662699		2203	4300	6503	153315893	SO:0001583	missense	537	exon7			D16469	CCDS35451.1	Xq28	2010-03-10	2003-08-28	2003-08-29	ENSG00000071553	ENSG00000071553			868	protein-coding gene	gene with protein product		300197	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump), subunit 1"""	ATP6S1, ATP6IP1		8733135, 8281148	Standard	NM_001183		Approved	ORF, XAP-3, VATPS1, 16A, Ac45, XAP3, CF2	uc004flf.1	Q15904	OTTHUMG00000033291	ENST00000369762.2:c.830C>T	X.37:g.153662699C>T	ENSP00000358777:p.Ala277Val	Somatic		Capture	Illumina HiSeq	Phase_I	153315893	NM_001183	A6ZKI4|Q8NBT4|Q9H0C7	Missense_Mutation	SNP	ENST00000369762.2	37	CCDS35451.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525210	0.27299	.	.	ENSG00000071553	ENST00000369762;ENST00000422890;ENST00000445849	.	.	.	5.49	2.54	0.30619	.	0.611092	0.18862	N	0.129101	T	0.28366	0.0701	L	0.37630	1.12	0.09310	N	0.999996	B;B	0.15930	0.006;0.015	B;B	0.17098	0.017;0.017	T	0.18116	-1.0347	9	0.22706	T	0.39	-0.5312	6.5813	0.22596	0.315:0.5962:0.0:0.0888	.	237;277	B3KR70;Q15904	.;VAS1_HUMAN	V	277;207;101	.	ENSP00000358777:A277V	A	+	2	0	ATP6AP1	153315893	0.062000	0.20869	0.091000	0.20842	0.144000	0.21451	0.463000	0.21972	0.490000	0.27771	-0.297000	0.09499	GCG		0.552	ATP6AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081639.4	NM_001183	
GDI1	2664	broad.mit.edu	37	X	153670883	153670883	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:153670883C>T	ENST00000447750.2	+	11	1543	c.1208C>T	c.(1207-1209)tCc>tTc	p.S403F	GDI1_ENST00000465640.1_3'UTR|FAM50A_ENST00000393600.3_5'Flank	NM_001493.2	NP_001484.1	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	403					negative regulation of axonogenesis (GO:0050771)|negative regulation of protein targeting to membrane (GO:0090315)|protein transport (GO:0015031)|Rab protein signal transduction (GO:0032482)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|midbody (GO:0030496)|neuron projection (GO:0043005)|protein complex (GO:0043234)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Rab GDP-dissociation inhibitor activity (GO:0005093)	p.S403F(1)		autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	16	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TGTTCCTGCTCCTACGATGCC	0.582																																					p.S403F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1208T	X						.						147.0	117.0	127.0					X																	153670883		2203	4300	6503	153324077	SO:0001583	missense	2664	exon11			X79353	CCDS35452.1	Xq28	2008-08-01			ENSG00000203879	ENSG00000203879			4226	protein-coding gene	gene with protein product	"""mental retardation, X-linked 41"", ""mental retardation, X-linked 48"", ""rab GDP-dissociation inhibitor, alpha"""	300104		MRX48, MRX41, GDIL		7543319, 7849400	Standard	NM_001493		Approved	RABGDIA, XAP-4, OPHN2, FLJ41411	uc004fli.4	P31150	OTTHUMG00000033293	ENST00000447750.2:c.1208C>T	X.37:g.153670883C>T	ENSP00000394071:p.Ser403Phe	Somatic		Capture	Illumina HiSeq	Phase_I	153324077	NM_001493	P50394|Q6FG50|Q7Z2G6|Q7Z2G9|Q7Z2H5|Q7Z2I6	Missense_Mutation	SNP	ENST00000447750.2	37	CCDS35452.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453548	0.84209	.	.	ENSG00000203879	ENST00000447750;ENST00000369741	D	0.81579	-1.51	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	D	0.91918	0.7441	M	0.93550	3.43	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	D	0.93961	0.7240	10	0.87932	D	0	-18.2528	15.1587	0.72764	0.0:1.0:0.0:0.0	.	403	P31150	GDIA_HUMAN	F	403;373	ENSP00000394071:S403F	ENSP00000358756:S373F	S	+	2	0	GDI1	153324077	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.734000	0.84928	2.168000	0.68352	0.600000	0.82982	TCC		0.582	GDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081649.2	NM_001493	
PLXNA3	55558	broad.mit.edu	37	X	153695786	153695786	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:153695786T>C	ENST00000369682.3	+	19	3588	c.3413T>C	c.(3412-3414)gTc>gCc	p.V1138A		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	1138	IPT/TIG 4.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)	p.V1138A(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GTGCTGGACGTCAAACCGGGC	0.672																																					p.V1138A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3413C	X						.						17.0	14.0	15.0					X																	153695786		2192	4274	6466	153348980	SO:0001583	missense	55558	exon19			X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.3413T>C	X.37:g.153695786T>C	ENSP00000358696:p.Val1138Ala	Somatic		Capture	Illumina HiSeq	Phase_I	153348980	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.189399	0.57909	.	.	ENSG00000130827	ENST00000369682	T	0.01015	5.44	5.37	5.37	0.77165	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);	0.248281	0.40640	N	0.001059	T	0.01765	0.0056	L	0.46157	1.445	0.58432	D	0.999994	B	0.26318	0.146	B	0.36766	0.232	T	0.64228	-0.6457	10	0.33141	T	0.24	.	13.5276	0.61603	0.0:0.0:0.0:1.0	.	1138	P51805	PLXA3_HUMAN	A	1138	ENSP00000358696:V1138A	ENSP00000358696:V1138A	V	+	2	0	PLXNA3	153348980	1.000000	0.71417	0.922000	0.36590	0.808000	0.45660	4.082000	0.57635	1.906000	0.55180	0.430000	0.28490	GTC		0.672	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
SLC10A3	8273	broad.mit.edu	37	X	153716752	153716752	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:153716752C>T	ENST00000393587.4	-	3	791	c.528G>A	c.(526-528)acG>acA	p.T176T	UBL4A_ENST00000369660.4_5'Flank|UBL4A_ENST00000477777.1_5'Flank|SLC10A3_ENST00000369649.4_Silent_p.T147T|SLC10A3_ENST00000393586.1_Silent_p.T231T|SLC10A3_ENST00000263512.4_Silent_p.T176T|UBL4A_ENST00000369653.4_5'Flank	NM_001142391.1|NM_001142392.1	NP_001135863.1|NP_001135864.1	P09131	P3_HUMAN	solute carrier family 10, member 3	176					response to retinoic acid (GO:0032526)	integral component of membrane (GO:0016021)	bile acid:sodium symporter activity (GO:0008508)	p.T176T(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGTGGCAGGCGTGTCTTCAG	0.587																																					p.T176T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G528A	X						.						85.0	83.0	83.0					X																	153716752		2203	4300	6503	153369946	SO:0001819	synonymous_variant	8273	exon2			X12458	CCDS14755.1, CCDS48195.1	Xq28	2013-07-18	2013-07-18		ENSG00000126903	ENSG00000126903		"""Solute carriers"""	22979	protein-coding gene	gene with protein product		312090				8733135	Standard	NM_019848		Approved	P3, DXS253E	uc004flq.3	P09131	OTTHUMG00000013369	ENST00000393587.4:c.528G>A	X.37:g.153716752C>T		Somatic		Capture	Illumina HiSeq	Phase_I	153369946	NM_019848	Q5HY79|Q9BSL2	Silent	SNP	ENST00000393587.4	37	CCDS14755.1																																																																																				0.587	SLC10A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037235.3	NM_019848	
GYG2	8908	broad.mit.edu	37	X	2772118	2772118	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:2772118G>A	ENST00000381163.3	+	5	622	c.340G>A	c.(340-342)Ggg>Agg	p.G114R	GYG2-AS1_ENST00000445107.1_RNA|GYG2_ENST00000398806.3_Missense_Mutation_p.G83R|GYG2_ENST00000338623.5_Missense_Mutation_p.G114R|GYG2_ENST00000542787.1_Missense_Mutation_p.G114R|GYG2_ENST00000381161.1_3'UTR	NM_001079855.1|NM_001184702.1|NM_003918.2	NP_001073324.1|NP_001171631.1|NP_003909.2	O15488	GLYG2_HUMAN	glycogenin 2	114					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	glycogenin glucosyltransferase activity (GO:0008466)	p.G114R(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)	13		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				ACCTGAGCTCGGGCTCACCCT	0.507																																					p.G114R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G340A	X						.						140.0	100.0	114.0					X																	2772118		2203	4298	6501	2782118	SO:0001583	missense	8908	exon5			U94361	CCDS14121.1, CCDS48074.1	Xp22.3	2013-02-22			ENSG00000056998	ENSG00000056998	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4700	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	300198				9857012	Standard	NM_001079855		Approved	GN-2	uc004cqs.1	O15488	OTTHUMG00000021079	ENST00000381163.3:c.340G>A	X.37:g.2772118G>A	ENSP00000370555:p.Gly114Arg	Somatic		Capture	Illumina HiSeq	Phase_I	2782118	NM_001184703	B7WNN6|O15485|O15486|O15487|O15489|O15490	Missense_Mutation	SNP	ENST00000381163.3	37	CCDS14121.1	.	.	.	.	.	.	.	.	.	.	G	17.07	3.296075	0.60086	.	.	ENSG00000056998	ENST00000398806;ENST00000381163;ENST00000338623;ENST00000542787;ENST00000520904	T;T;T;T;T	0.62788	0.0;0.0;0.0;0.0;0.0	3.47	3.47	0.39725	.	0.000000	0.64402	D	0.000009	T	0.79724	0.4495	M	0.84156	2.68	0.52501	D	0.999959	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;0.997;1.0;1.0	D	0.84020	0.0353	10	0.87932	D	0	.	14.6672	0.68918	0.0:0.0:1.0:0.0	.	114;74;83;83;114	O15488-4;O15488-3;A8K8Y1;O15488-2;O15488	.;.;.;.;GLYG2_HUMAN	R	83;114;114;114;83	ENSP00000381786:G83R;ENSP00000370555:G114R;ENSP00000341273:G114R;ENSP00000446092:G114R;ENSP00000430764:G83R	ENSP00000341273:G114R	G	+	1	0	GYG2	2782118	1.000000	0.71417	0.107000	0.21349	0.409000	0.31022	5.822000	0.69265	1.520000	0.48965	0.529000	0.55759	GGG		0.507	GYG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055645.1	NM_003918	
ARSD	414	broad.mit.edu	37	X	2843762	2843762	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:2843762G>A	ENST00000381154.1	-	2	164	c.89C>T	c.(88-90)aCg>aTg	p.T30M	ARSD_ENST00000217890.6_5'UTR	NM_001669.3	NP_001660.2	P51689	ARSD_HUMAN	arylsulfatase D	30					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)	p.T30M(1)		large_intestine(3)|lung(3)	6		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGGTTCACACGTCTTCAGAAG	0.443																																					p.T30M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C89T	X						.						107.0	73.0	84.0					X																	2843762		2203	4300	6503	2853762	SO:0001583	missense	414	exon2			X83572	CCDS35196.1	Xp22.3	2013-02-14			ENSG00000006756	ENSG00000006756		"""Arylsulfatase family"""	717	protein-coding gene	gene with protein product		300002				7720070	Standard	NM_001669		Approved		uc004cqy.3	P51689	OTTHUMG00000021077	ENST00000381154.1:c.89C>T	X.37:g.2843762G>A	ENSP00000370546:p.Thr30Met	Somatic		Capture	Illumina HiSeq	Phase_I	2853762	NM_009589	Q9UHJ8	Missense_Mutation	SNP	ENST00000381154.1	37	CCDS35196.1	.	.	.	.	.	.	.	.	.	.	G	4.321	0.058982	0.08339	.	.	ENSG00000006756	ENST00000381154;ENST00000217890	D	0.96491	-4.03	3.08	0.015	0.14102	.	1.752010	0.04104	U	0.313453	D	0.89952	0.6864	N	0.08118	0	0.09310	N	1	D;P;P	0.54047	0.964;0.926;0.837	B;B;B	0.43018	0.405;0.241;0.138	D	0.85458	0.1165	10	0.34782	T	0.22	.	4.7671	0.13137	0.2454:0.18:0.5745:0.0	.	30;30;30	P51689-2;E9PAW5;P51689	.;.;ARSD_HUMAN	M	30	ENSP00000370546:T30M	ENSP00000217890:T30M	T	-	2	0	ARSD	2853762	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.122000	0.10627	-0.050000	0.13356	0.523000	0.50628	ACG		0.443	ARSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055636.1		
MXRA5	25878	broad.mit.edu	37	X	3238722	3238722	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:3238722T>C	ENST00000217939.6	-	5	5158	c.5004A>G	c.(5002-5004)tcA>tcG	p.S1668S		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	1668						extracellular vesicular exosome (GO:0070062)		p.S1668S(2)		NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				TTGTTGTACTTGATAATCTTG	0.438																																					p.S1668S												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.A5004G	X						.						170.0	161.0	164.0					X																	3238722		2203	4300	6503	3248722	SO:0001819	synonymous_variant	25878	exon5			AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.5004A>G	X.37:g.3238722T>C		Somatic		Capture	Illumina HiSeq	Phase_I	3248722	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																				0.438	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
PRKX	5613	broad.mit.edu	37	X	3592724	3592724	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:3592724C>T	ENST00000262848.5	-	2	604	c.250G>A	c.(250-252)Gac>Aac	p.D84N		NM_005044.4	NP_005035.1	P51817	PRKX_HUMAN	protein kinase, X-linked	84	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|endothelial cell migration (GO:0043542)|endothelial cell proliferation (GO:0001935)|epithelial tube morphogenesis (GO:0060562)|kidney morphogenesis (GO:0060993)|myeloid cell differentiation (GO:0030099)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of epithelial cell differentiation involved in kidney development (GO:2000696)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)	p.D84N(1)		kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(2)	12		all_lung(23;0.000396)|Lung NSC(23;0.00123)				CGGATGACGTCGGGAATGCTC	0.557																																					p.D84N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G250A	X						.						261.0	168.0	200.0					X																	3592724		2203	4300	6503	3602724	SO:0001583	missense	5613	exon2				CCDS14125.1	Xp22.3	2008-08-01			ENSG00000183943	ENSG00000183943	2.7.11.1		9441	protein-coding gene	gene with protein product		300083				7633447	Standard	NM_005044		Approved	PKX1	uc010nde.3	P51817	OTTHUMG00000021087	ENST00000262848.5:c.250G>A	X.37:g.3592724C>T	ENSP00000262848:p.Asp84Asn	Somatic		Capture	Illumina HiSeq	Phase_I	3602724	NM_005044		Missense_Mutation	SNP	ENST00000262848.5	37	CCDS14125.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.247090	0.39697	.	.	ENSG00000183943	ENST00000262848	T	0.66099	-0.19	2.62	2.62	0.31277	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	U	0.000000	T	0.60534	0.2276	N	0.12961	0.28	0.80722	D	1	D	0.71674	0.998	D	0.65573	0.936	T	0.65038	-0.6265	10	0.72032	D	0.01	-22.8372	11.6787	0.51444	0.0:1.0:0.0:0.0	.	84	P51817	PRKX_HUMAN	N	84	ENSP00000262848:D84N	ENSP00000262848:D84N	D	-	1	0	PRKX	3602724	0.999000	0.42202	0.925000	0.36789	0.288000	0.27193	4.614000	0.61183	0.928000	0.37168	0.277000	0.19347	GAC		0.557	PRKX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055659.1	NM_005044	
ACE2	59272	broad.mit.edu	37	X	15596418	15596418	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:15596418A>G	ENST00000252519.3	-	9	1193	c.1091T>C	c.(1090-1092)gTg>gCg	p.V364A	ACE2_ENST00000427411.1_Missense_Mutation_p.V364A			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	364					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)	p.V364A(1)		endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	GTCCATTGTCACCTTTGTGCA	0.413																																					p.V364A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1091C	X						.						84.0	69.0	74.0					X																	15596418		2203	4300	6503	15506339	SO:0001583	missense	59272	exon10			AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"""peptidyl-dipeptidase A"""	300335	"""angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"""			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.1091T>C	X.37:g.15596418A>G	ENSP00000252519:p.Val364Ala	Somatic		Capture	Illumina HiSeq	Phase_I	15506339	NM_021804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.013633	0.35511	.	.	ENSG00000130234	ENST00000252519;ENST00000427411	T;T	0.45276	0.9;0.9	5.6	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.65375	0.2685	H	0.94925	3.6	0.31625	N	0.649819	P	0.35700	0.516	P	0.48114	0.567	T	0.73509	-0.3960	10	0.62326	D	0.03	-21.4745	10.8228	0.46614	0.9251:0.0:0.0749:0.0	.	364	Q9BYF1	ACE2_HUMAN	A	364	ENSP00000252519:V364A;ENSP00000389326:V364A	ENSP00000252519:V364A	V	-	2	0	ACE2	15506339	1.000000	0.71417	0.962000	0.40283	0.349000	0.29174	7.510000	0.81708	0.756000	0.33013	-0.342000	0.07992	GTG		0.413	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1		
BEND2	139105	broad.mit.edu	37	X	18222010	18222010	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:18222010G>A	ENST00000380033.4	-	5	650	c.518C>T	c.(517-519)gCg>gTg	p.A173V	BEND2_ENST00000380030.3_Missense_Mutation_p.A173V	NM_153346.4	NP_699177.2	Q8NDZ0	BEND2_HUMAN	BEN domain containing 2	173								p.A173V(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(11)|liver(1)|lung(21)|ovary(3)|prostate(1)	49						CTGCCTTTCCGCTGGTGGTGA	0.468																																					p.A173V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C518T	X						.						123.0	116.0	118.0					X																	18222010		2203	4300	6503	18131931	SO:0001583	missense	139105	exon5			AK128155	CCDS14184.1, CCDS55375.1	Xp22.22	2012-11-22	2008-10-03	2008-10-03	ENSG00000177324	ENSG00000177324		"""BEN domain containing"""	28509	protein-coding gene	gene with protein product			"""chromosome X open reading frame 20"""	CXorf20		12477932	Standard	NM_153346		Approved	MGC33653	uc004cyj.4	Q8NDZ0	OTTHUMG00000021211	ENST00000380033.4:c.518C>T	X.37:g.18222010G>A	ENSP00000369372:p.Ala173Val	Somatic		Capture	Illumina HiSeq	Phase_I	18131931	NM_153346	E9PFY2|Q4V9S2|Q5JXE5	Missense_Mutation	SNP	ENST00000380033.4	37	CCDS14184.1	.	.	.	.	.	.	.	.	.	.	G	3.897	-0.022790	0.07634	.	.	ENSG00000177324	ENST00000380033;ENST00000380030	T;T	0.25250	1.84;1.81	4.31	-8.61	0.00885	.	1.889440	0.03546	N	0.224721	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B	0.24920	0.054;0.114	B;B	0.13407	0.006;0.009	T	0.17379	-1.0371	10	0.02654	T	1	1.5849	6.5568	0.22464	0.1577:0.0:0.4116:0.4307	.	173;173	E9PFY2;Q8NDZ0	.;BEND2_HUMAN	V	173	ENSP00000369372:A173V;ENSP00000369369:A173V	ENSP00000369369:A173V	A	-	2	0	BEND2	18131931	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.634000	0.02020	-3.345000	0.00182	-0.527000	0.04329	GCG		0.468	BEND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055940.1	NM_153346	
PHKA2	5256	broad.mit.edu	37	X	18936842	18936842	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:18936842G>A	ENST00000379942.4	-	19	2759	c.2094C>T	c.(2092-2094)gaC>gaT	p.D698D		NM_000292.2	NP_000283.1	P46019	KPB2_HUMAN	phosphorylase kinase, alpha 2 (liver)	698					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.D698D(1)		NS(1)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61	Hepatocellular(33;0.183)					CAGAAAGTATGTCCCGCGTGG	0.428																																					p.D698D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2094T	X						.						123.0	106.0	112.0					X																	18936842		2203	4300	6503	18846763	SO:0001819	synonymous_variant	5256	exon19				CCDS14190.1	Xp22.2-p22.1	2009-07-10			ENSG00000044446	ENSG00000044446	2.7.11.19		8926	protein-coding gene	gene with protein product		300798		PHK, PYK		2387090	Standard	NM_000292		Approved		uc004cyv.4	P46019	OTTHUMG00000021222	ENST00000379942.4:c.2094C>T	X.37:g.18936842G>A		Somatic		Capture	Illumina HiSeq	Phase_I	18846763	NM_000292	A8K1T1|Q6LAJ5|Q7Z6W0|Q96CR3|Q9UDA1	Silent	SNP	ENST00000379942.4	37	CCDS14190.1																																																																																				0.428	PHKA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055960.1	NM_000292	
CNKSR2	22866	broad.mit.edu	37	X	21581500	21581500	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:21581500C>A	ENST00000379510.3	+	13	1574	c.1538C>A	c.(1537-1539)cCt>cAt	p.P513H	CNKSR2_ENST00000425654.2_Missense_Mutation_p.P483H|CNKSR2_ENST00000485012.1_3'UTR|AL928874.1_ENST00000579338.1_RNA|CNKSR2_ENST00000543067.1_Missense_Mutation_p.P464H|CNKSR2_ENST00000279451.4_Missense_Mutation_p.P513H	NM_014927.3	NP_055742.2	Q8WXI2	CNKR2_HUMAN	connector enhancer of kinase suppressor of Ras 2	513	DUF1170.				regulation of signal transduction (GO:0009966)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)		p.P513H(1)		breast(3)|endometrium(8)|kidney(2)|large_intestine(15)|lung(28)|prostate(2)|upper_aerodigestive_tract(3)	61						TCATTGCTACCTAGTTTACAA	0.393																																					p.P464H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1391A	X						.						143.0	130.0	135.0					X																	21581500		2203	4300	6503	21491421	SO:0001583	missense	22866	exon12			AB020709	CCDS14198.1, CCDS55387.1, CCDS55388.1, CCDS55389.1	Xp22.12	2013-01-10			ENSG00000149970	ENSG00000149970		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19701	protein-coding gene	gene with protein product		300724					Standard	NM_014927		Approved	KIAA0902, CNK2, KSR2	uc004czx.2	Q8WXI2	OTTHUMG00000021233	ENST00000379510.3:c.1538C>A	X.37:g.21581500C>A	ENSP00000368824:p.Pro513His	Somatic		Capture	Illumina HiSeq	Phase_I	21491421	NM_001168649	B4DGR4|B7ZLJ1|B9EG83|E7ESA4|O94976|Q5JPK4|Q5JPN0|Q8WXI1	Missense_Mutation	SNP	ENST00000379510.3	37	CCDS14198.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.110325	0.77210	.	.	ENSG00000149970	ENST00000425654;ENST00000543067;ENST00000279451;ENST00000379510	T;T;T;T	0.19669	2.36;2.13;2.17;2.43	6.08	6.08	0.98989	Connector enhancer of kinase suppressor of ras 2 (1);	0.000000	0.85682	D	0.000000	T	0.47303	0.1438	M	0.61703	1.905	0.58432	D	0.999999	D;D;D;D	0.89917	0.994;1.0;1.0;1.0	D;D;D;D	0.83275	0.962;0.975;0.996;0.982	T	0.27905	-1.0060	10	0.52906	T	0.07	-1.6635	19.5097	0.95137	0.0:1.0:0.0:0.0	.	483;464;105;513	B7ZLJ1;B4DGR4;B3KPN2;Q8WXI2	.;.;.;CNKR2_HUMAN	H	483;464;513;513	ENSP00000397906:P483H;ENSP00000444633:P464H;ENSP00000279451:P513H;ENSP00000368824:P513H	ENSP00000279451:P513H	P	+	2	0	CNKSR2	21491421	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.214000	0.72200	2.562000	0.86427	0.600000	0.82982	CCT		0.393	CNKSR2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056019.1	NM_014927	
PCYT1B	9468	broad.mit.edu	37	X	24608140	24608140	+	Splice_Site	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:24608140C>A	ENST00000379144.2	-	4	616	c.486G>T	c.(484-486)aaG>aaT	p.K162N	PCYT1B_ENST00000379145.1_Splice_Site_p.K144N|PCYT1B_ENST00000356768.4_Splice_Site_p.K162N	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	162					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)	p.K162N(1)		breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	TGAGAAGTACCTTGTGTTTTT	0.463																																					p.K144N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G432T	X						.						134.0	106.0	116.0					X																	24608140		2203	4300	6503	24518061	SO:0001630	splice_region_variant	9468	exon4			AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"""phosphate cytidylyltransferase 1, choline, beta isoform"""			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.486+1G>T	X.37:g.24608140C>A		Somatic		Capture	Illumina HiSeq	Phase_I	24518061	NM_001163264	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	37	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	C	18.94	3.729418	0.69074	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	D;D;D	0.96830	-4.14;-4.14;-4.14	5.44	5.44	0.79542	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.94231	0.8148	L	0.45137	1.4	0.80722	D	1	B;B;B	0.29232	0.164;0.238;0.238	B;B;B	0.32393	0.053;0.145;0.145	D	0.92216	0.5780	9	.	.	.	-1.7423	18.3331	0.90277	0.0:1.0:0.0:0.0	.	162;144;162	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	N	144;162;162	ENSP00000368440:K144N;ENSP00000368439:K162N;ENSP00000349211:K162N	.	K	-	3	2	PCYT1B	24518061	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.320000	0.79064	2.524000	0.85096	0.600000	0.82982	AAG		0.463	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845	Missense_Mutation
POLA1	5422	broad.mit.edu	37	X	24732754	24732754	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:24732754T>C	ENST00000379059.3	+	5	427	c.412T>C	c.(412-414)Ttc>Ctc	p.F138L	POLA1_ENST00000379068.3_Missense_Mutation_p.F144L	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	138					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.F138L(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	TAAGTCAATGTTCATTGCTTG	0.333																																					p.F138L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T412C	X						.						104.0	92.0	96.0					X																	24732754		2203	4296	6499	24642675	SO:0001583	missense	5422	exon5				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.412T>C	X.37:g.24732754T>C	ENSP00000368349:p.Phe138Leu	Somatic		Capture	Illumina HiSeq	Phase_I	24642675	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	T	15.13	2.742876	0.49151	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.20463	2.07;2.08	5.92	3.48	0.39840	.	0.101254	0.64402	N	0.000001	T	0.22003	0.0530	M	0.67953	2.075	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.03493	-1.1031	10	0.28530	T	0.3	-1.8813	9.8091	0.40812	0.0:0.1405:0.0:0.8595	.	144;138	A6NMQ1;P09884	.;DPOLA_HUMAN	L	144;138	ENSP00000368358:F144L;ENSP00000368349:F138L	ENSP00000368349:F138L	F	+	1	0	POLA1	24642675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.353000	0.66034	0.313000	0.23062	0.486000	0.48141	TTC		0.333	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
POLA1	5422	broad.mit.edu	37	X	24861721	24861721	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:24861721C>A	ENST00000379059.3	+	34	3971	c.3956C>A	c.(3955-3957)cCt>cAt	p.P1319H	POLA1_ENST00000379068.3_Missense_Mutation_p.P1325H	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1319	DNA-binding region. {ECO:0000255}.				cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)	p.P1319H(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	AAGGCTTCACCTCTGACCTTT	0.368																																					p.P1319H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3956A	X						.						150.0	112.0	124.0					X																	24861721		2203	4300	6503	24771642	SO:0001583	missense	5422	exon34				CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.3956C>A	X.37:g.24861721C>A	ENSP00000368349:p.Pro1319His	Somatic		Capture	Illumina HiSeq	Phase_I	24771642	NM_016937	Q86UQ7	Missense_Mutation	SNP	ENST00000379059.3	37	CCDS14214.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430413	0.83776	.	.	ENSG00000101868	ENST00000379068;ENST00000379059	T;T	0.19669	2.13;2.14	5.82	5.82	0.92795	Zinc finger, DNA-directed DNA polymerase, family B, alpha (1);	0.000000	0.85682	D	0.000000	T	0.53190	0.1781	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54357	-0.8306	10	0.19590	T	0.45	-9.5087	18.6676	0.91497	0.0:1.0:0.0:0.0	.	1319	P09884	DPOLA_HUMAN	H	1325;1319	ENSP00000368358:P1325H;ENSP00000368349:P1319H	ENSP00000368349:P1319H	P	+	2	0	POLA1	24771642	1.000000	0.71417	0.994000	0.49952	0.996000	0.88848	6.663000	0.74431	2.459000	0.83118	0.594000	0.82650	CCT		0.368	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
MAGEB6	158809	broad.mit.edu	37	X	26212305	26212305	+	Silent	SNP	T	T	G	rs4997767		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:26212305T>G	ENST00000379034.1	+	2	491	c.342T>G	c.(340-342)tcT>tcG	p.S114S		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	114	Ser-rich.							p.S114S(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						CCACTGGCTCTCCTGATGCAG	0.537													.|||	42	0.0111258	0.0015	0.0072	3775	,	,		13361	0.0169		0.003	False		,,,				2504	0.0153				p.S114S												.	.	2	Substitution - coding silent(2)	large_intestine(1)|prostate(1)	c.T342G	X						.						85.0	77.0	79.0					X																	26212305		2183	4228	6411	26122226	SO:0001819	synonymous_variant	158809	exon2			AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 4"""	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.342T>G	X.37:g.26212305T>G		None		Capture	Illumina HiSeq	Phase_I	26122226	NM_173523	Q6GS19|Q9H219	Silent	SNP	ENST00000379034.1	37	CCDS14217.1																																																																																				0.537	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523	
DMD	1756	broad.mit.edu	37	X	31222121	31222121	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:31222121C>T	ENST00000357033.4	-	67	9970	c.9764G>A	c.(9763-9765)gGg>gAg	p.G3255E	DMD_ENST00000541735.1_Missense_Mutation_p.G795E|DMD_ENST00000474231.1_Missense_Mutation_p.G795E|DMD_ENST00000378707.3_Missense_Mutation_p.G795E|DMD_ENST00000378702.4_Missense_Mutation_p.G187E|DMD_ENST00000359836.1_Missense_Mutation_p.G795E|DMD_ENST00000378680.2_Missense_Mutation_p.G187E|DMD_ENST00000361471.4_Missense_Mutation_p.G187E|DMD_ENST00000378723.3_Missense_Mutation_p.G187E|DMD_ENST00000378677.2_Missense_Mutation_p.G3251E|DMD_ENST00000343523.2_Missense_Mutation_p.G795E	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	3255	Interaction with SYNM. {ECO:0000250}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.G795E(1)|p.G3250E(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				GTTACTGCCCCCAAAGGATGC	0.418																																					p.G187E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G560A	X						.						66.0	57.0	60.0					X																	31222121		2202	4300	6502	31132042	SO:0001583	missense	1756	exon6			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.9764G>A	X.37:g.31222121C>T	ENSP00000354923:p.Gly3255Glu	Somatic		Capture	Illumina HiSeq	Phase_I	31132042	NM_004015	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	29.4|29.4	4.999006|4.999006	0.93227|0.93227	.|.	.|.	ENSG00000198947|ENSG00000198947	ENST00000534884;ENST00000378682;ENST00000378684;ENST00000378723;ENST00000358062;ENST00000378677;ENST00000357033;ENST00000359836;ENST00000343523;ENST00000542849;ENST00000535280;ENST00000378707;ENST00000541735;ENST00000378702;ENST00000474231;ENST00000361471;ENST00000378680;ENST00000378705|ENST00000465285	T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.77750|.	-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12;-1.12|.	5.35|5.35	5.35|5.35	0.76521|0.76521	EF-hand domain, type 2 (1);|.	0.000000|.	0.37530|.	U|.	0.002051|.	D|.	0.87641|.	0.6228|.	H|H	0.95043|0.95043	3.615|3.615	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.97110|.	0.999;0.998;1.0;1.0;1.0;1.0;0.999;0.994;0.994;1.0;1.0;0.997;0.999;0.999;0.998;1.0|.	D|.	0.91303|.	0.5068|.	10|.	0.87932|.	D|.	0|.	.|.	18.1204|18.1204	0.89569|0.89569	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	187;3247;3255;3251;1914;1911;795;795;795;795;795;3132;187;187;187;187|.	B4DSV7;P11532-4;P11532;E9PDN5;E7EQS7;E7EQS6;F8VX32;E7ESB2;E7EQS5;E7EQR9;F5GZY3;F5GZT3;P11532-5;Q8N754;Q6NSJ9;E9PDN1|.	.;.;DMD_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.|.	E|X	3247;1914;1911;187;951;3251;3255;795;795;3255;3132;795;795;187;795;187;187;45|983	ENSP00000367997:G187E;ENSP00000350765:G951E;ENSP00000367948:G3251E;ENSP00000354923:G3255E;ENSP00000352894:G795E;ENSP00000340057:G795E;ENSP00000367979:G795E;ENSP00000444119:G795E;ENSP00000367974:G187E;ENSP00000417123:G795E;ENSP00000354464:G187E;ENSP00000367951:G187E;ENSP00000367977:G45E|.	ENSP00000340057:G795E|.	G|W	-|-	2|3	0|0	DMD|DMD	31132042|31132042	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.651000|7.651000	0.83577|0.83577	2.471000|2.471000	0.83476|0.83476	0.600000|0.600000	0.82982|0.82982	GGG|TGG		0.418	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
FAM47B	170062	broad.mit.edu	37	X	34961104	34961104	+	Silent	SNP	G	G	T	rs79825675	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:34961104G>T	ENST00000329357.5	+	1	192	c.156G>T	c.(154-156)acG>acT	p.T52T		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	52								p.T52T(1)		breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						TATTTGTGACGGAGGGCATGG	0.552																																					p.T52T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G156T	X						.						70.0	60.0	63.0					X																	34961104		2202	4300	6502	34871025	SO:0001819	synonymous_variant	170062	exon1			BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.156G>T	X.37:g.34961104G>T		Somatic		Capture	Illumina HiSeq	Phase_I	34871025	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																				0.552	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
MAGEB16	139604	broad.mit.edu	37	X	35820382	35820382	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:35820382G>A	ENST00000399989.1	+	2	348	c.69G>A	c.(67-69)caG>caA	p.Q23Q	MAGEB16_ENST00000399992.1_Silent_p.Q55Q|MAGEB16_ENST00000399985.1_Silent_p.Q23Q|MAGEB16_ENST00000399987.1_Silent_p.Q23Q|MAGEB16_ENST00000399988.1_Silent_p.Q23Q	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	23								p.Q190Q(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GTGAGACCCAGAGCCTGGAGG	0.562																																					p.Q23Q												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G69A	X						.						44.0	45.0	45.0					X																	35820382		2066	4189	6255	35730303	SO:0001819	synonymous_variant	139604	exon2				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.69G>A	X.37:g.35820382G>A		Somatic		Capture	Illumina HiSeq	Phase_I	35730303	NM_001099921	A8MU30	Silent	SNP	ENST00000399989.1	37	CCDS43927.1																																																																																				0.562	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1		
MED14	9282	broad.mit.edu	37	X	40523639	40523639	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:40523639C>T	ENST00000324817.1	-	25	3486	c.3368G>A	c.(3367-3369)cGc>cAc	p.R1123H		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	1123	Pro-rich.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.R1123H(1)		NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCCAGGCATGCGTGCTGCTGG	0.527																																					p.R1123H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3368A	X						.						156.0	117.0	130.0					X																	40523639		2203	4300	6503	40408583	SO:0001583	missense	9282	exon25			AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.3368G>A	X.37:g.40523639C>T	ENSP00000323720:p.Arg1123His	Somatic		Capture	Illumina HiSeq	Phase_I	40408583	NM_004229	Q4KMR7|Q9UNB3	Missense_Mutation	SNP	ENST00000324817.1	37	CCDS14254.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887776	0.72410	.	.	ENSG00000180182	ENST00000324817;ENST00000433003	.	.	.	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.50582	0.1624	L	0.53249	1.67	0.80722	D	1	P;P	0.47910	0.902;0.902	B;B	0.33521	0.165;0.165	T	0.57694	-0.7767	9	0.42905	T	0.14	.	18.0405	0.89317	0.0:1.0:0.0:0.0	.	1123;1123	A8KAK5;O60244	.;MED14_HUMAN	H	1123;22	.	ENSP00000323720:R1123H	R	-	2	0	MED14	40408583	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	7.487000	0.81328	2.195000	0.70347	0.600000	0.82982	CGC		0.527	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
NYX	60506	broad.mit.edu	37	X	41307058	41307058	+	5'UTR	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:41307058delG	ENST00000342595.2	+	0	372				NYX_ENST00000378220.1_Intron	NM_022567.2	NP_072089.1	Q9GZU5	NYX_HUMAN	nyctalopin						response to stimulus (GO:0050896)|visual perception (GO:0007601)	intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(11)|upper_aerodigestive_tract(1)	17						GGGTTCTCATGGGGCCCTCCT	0.582																																					.												.	.	0			.	X						.																																			41192002	SO:0001623	5_prime_UTR_variant	60506	.			AF254868	CCDS14256.1	Xp11.4	2014-01-28			ENSG00000188937	ENSG00000188937			8082	protein-coding gene	gene with protein product		300278		CSNB1, CSNB4		11062471, 11062472	Standard	NM_022567		Approved	CLRP, CSNB1A	uc004dfh.2	Q9GZU5	OTTHUMG00000021370	ENST00000342595.2:c.-85G>-	X.37:g.41307058delG		Somatic		Capture	Illumina HiSeq	Phase_I	41192002	.	D3DWC0|Q2M1S4|Q5H983|Q9H4J0	De_novo_Start_InFrame	DEL	ENST00000342595.2	37	CCDS14256.1																																																																																				0.582	NYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056256.1	NM_022567	
GPR34	2857	broad.mit.edu	37	X	41555896	41555896	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:41555896T>C	ENST00000378142.4	+	3	1294	c.1010T>C	c.(1009-1011)aTa>aCa	p.I337T	CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|GPR34_ENST00000378138.5_Missense_Mutation_p.I337T|CASK_ENST00000378154.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	337					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)	p.I337T(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						ATTCGCAAAATAATGTGCCAA	0.383																																					p.I337T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1010C	X						.						101.0	85.0	90.0					X																	41555896		2203	4300	6503	41440840	SO:0001583	missense	2857	exon3			AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"""GPCR / Class A : Orphans"""	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.1010T>C	X.37:g.41555896T>C	ENSP00000367384:p.Ile337Thr	Somatic		Capture	Illumina HiSeq	Phase_I	41440840	NM_005300	O95853	Missense_Mutation	SNP	ENST00000378142.4	37	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	T	5.037	0.192602	0.09599	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	T;T	0.35048	1.33;1.33	5.73	3.35	0.38373	.	0.543574	0.19456	N	0.113805	T	0.16685	0.0401	N	0.12746	0.255	0.27581	N	0.949592	B	0.12630	0.006	B	0.12156	0.007	T	0.22138	-1.0225	10	0.14252	T	0.57	-20.8665	5.4626	0.16626	0.0:0.4225:0.0:0.5775	.	337	Q9UPC5	GPR34_HUMAN	T	337;337;290	ENSP00000367384:I337T;ENSP00000367378:I337T	ENSP00000367378:I337T	I	+	2	0	GPR34	41440840	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.638000	0.54332	0.785000	0.33685	0.481000	0.45027	ATA		0.383	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300	
SLC9A7	84679	broad.mit.edu	37	X	46521494	46521494	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:46521494C>T	ENST00000328306.4	-	7	1023	c.998G>A	c.(997-999)gGc>gAc	p.G333D		NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	333					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)	p.G333D(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						GGTAAAAGAGCCACTAAATAT	0.463																																					p.G333D	Pancreas(118;454 1696 1930 13865 39976)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G998A	X						.						57.0	46.0	50.0					X																	46521494		2203	4297	6500	46406438	SO:0001583	missense	84679	exon7			AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"""Solute carriers"""	17123	protein-coding gene	gene with protein product		300368	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 7"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 7"""			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.998G>A	X.37:g.46521494C>T	ENSP00000330320:p.Gly333Asp	Somatic		Capture	Illumina HiSeq	Phase_I	46406438	NM_032591	O75827|Q5JXP9	Missense_Mutation	SNP	ENST00000328306.4	37	CCDS14269.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.752709	0.89753	.	.	ENSG00000065923	ENST00000328306	T	0.20463	2.07	5.02	5.02	0.67125	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.60521	0.2275	H	0.95712	3.71	0.80722	D	1	D;D	0.89917	0.966;1.0	D;D	0.75484	0.948;0.986	T	0.74910	-0.3503	10	0.72032	D	0.01	.	17.8283	0.88673	0.0:1.0:0.0:0.0	.	104;333	B3KPP8;Q96T83	.;SL9A7_HUMAN	D	333	ENSP00000330320:G333D	ENSP00000330320:G333D	G	-	2	0	SLC9A7	46406438	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.355000	0.79434	2.229000	0.72834	0.600000	0.82982	GGC		0.463	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591	
SLC9A7	84679	broad.mit.edu	37	X	46529070	46529070	+	Frame_Shift_Del	DEL	A	A	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:46529070delA	ENST00000328306.4	-	5	790	c.765delT	c.(763-765)tttfs	p.F255fs		NM_001257291.1|NM_032591.2	NP_001244220.1|NP_115980.1	Q96T83	SL9A7_HUMAN	solute carrier family 9, subfamily A (NHE7, cation proton antiporter 7), member 7	255					ion transport (GO:0006811)|potassium ion transmembrane transport (GO:0071805)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)	potassium:proton antiporter activity (GO:0015386)|protein homodimerization activity (GO:0042803)|sodium:proton antiporter activity (GO:0015385)	p.F255fs*11(1)		breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)|skin(1)	21						TGATTGCTCCAAAAAAGAGAC	0.348																																					p.F255fs	Pancreas(118;454 1696 1930 13865 39976)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.765delT	X						.						89.0	78.0	82.0					X																	46529070		2203	4300	6503	46414014	SO:0001589	frameshift_variant	84679	exon5			AF298591	CCDS14269.1, CCDS75967.1	Xp11.3	2013-05-22	2012-03-22		ENSG00000065923	ENSG00000065923		"""Solute carriers"""	17123	protein-coding gene	gene with protein product		300368	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 7"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 7"""			11279194	Standard	NM_001257291		Approved	NHE7	uc004dgv.2	Q96T83	OTTHUMG00000021428	ENST00000328306.4:c.765delT	X.37:g.46529070delA	ENSP00000330320:p.Phe255fs	Somatic		Capture	Illumina HiSeq	Phase_I	46414014	NM_032591	O75827|Q5JXP9	Frame_Shift_Del	DEL	ENST00000328306.4	37	CCDS14269.1																																																																																				0.348	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591	
ZNF81	347344	broad.mit.edu	37	X	47774360	47774360	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:47774360T>G	ENST00000376954.1	+	6	683	c.315T>G	c.(313-315)atT>atG	p.I105M	ZNF81_ENST00000338637.7_Missense_Mutation_p.I105M			P51508	ZNF81_HUMAN	zinc finger protein 81	105					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.I105M(2)		breast(1)|large_intestine(1)|lung(1)|skin(1)	4		all_lung(315;0.0973)				AGAGGAGAATTTCTGGGAAAT	0.348																																					p.I105M												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T315G	X						.						25.0	21.0	22.0					X																	47774360		1801	4059	5860	47659304	SO:0001583	missense	347344	exon5			AK126949	CCDS43933.1	Xp11.23	2013-01-08	2006-05-12		ENSG00000197779	ENSG00000197779		"""Zinc fingers, C2H2-type"", ""-"""	13156	protein-coding gene	gene with protein product		314998	"""zinc finger protein 81 (HFZ20)"", ""mental retardation, X-linked 45"""	MRX45		8507979, 15121780	Standard	NM_007137		Approved	HFZ20	uc022bvq.1	P51508	OTTHUMG00000021462	ENST00000376954.1:c.315T>G	X.37:g.47774360T>G	ENSP00000366153:p.Ile105Met	Somatic		Capture	Illumina HiSeq	Phase_I	47659304	NM_007137	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.545864	0.00926	.	.	ENSG00000197779	ENST00000376954;ENST00000338637;ENST00000399918	T;T	0.07327	3.2;3.2	4.04	2.88	0.33553	.	0.725103	0.11920	N	0.516840	T	0.04998	0.0134	N	0.17082	0.46	0.09310	N	1	B	0.33379	0.41	B	0.31751	0.135	T	0.41016	-0.9532	10	0.33940	T	0.23	.	5.3873	0.16224	0.0:0.1278:0.0:0.8722	.	105	P51508	ZNF81_HUMAN	M	105	ENSP00000366153:I105M;ENSP00000341151:I105M	ENSP00000341151:I105M	I	+	3	3	ZNF81	47659304	0.001000	0.12720	0.030000	0.17652	0.036000	0.12997	0.787000	0.26858	0.715000	0.32103	-0.314000	0.08810	ATT		0.348	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137	
ZNF630	57232	broad.mit.edu	37	X	47919226	47919226	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:47919226T>C	ENST00000409324.3	-	5	831	c.605A>G	c.(604-606)aAc>aGc	p.N202S	ZNF630_ENST00000442455.3_Missense_Mutation_p.N188S|ZNF630-AS1_ENST00000436124.1_RNA|ZNF630_ENST00000276054.4_Missense_Mutation_p.N78S	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						CTTAGTGGGGTTCTTTCTTGC	0.383																																					p.N188S												.	.	0			c.A563G	X						.						56.0	48.0	51.0					X																	47919226		2192	4290	6482	47804170	SO:0001583	missense	57232	exon5			AK000580	CCDS35237.2, CCDS75971.1	Xp11.3-p11.1	2013-01-08			ENSG00000221994	ENSG00000221994		"""Zinc fingers, C2H2-type"", ""-"""	28855	protein-coding gene	gene with protein product		300819					Standard	NM_001037735		Approved	BC037316, dJ54B20.2, FLJ20573, MGC138344	uc004div.4	Q2M218	OTTHUMG00000021463	ENST00000409324.3:c.605A>G	X.37:g.47919226T>C	ENSP00000386393:p.Asn202Ser	None		Capture	Illumina HiSeq	Phase_I	47804170	NM_001190255	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	6.593	0.477684	0.12521	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324;ENST00000428686	T;T;T;T	0.07567	3.3;3.18;3.37;5.36	2.65	-1.94	0.07571	.	.	.	.	.	T	0.05502	0.0145	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36744	-0.9735	9	0.66056	D	0.02	.	6.6461	0.22936	0.0:0.3959:0.0:0.6041	.	202	Q2M218	ZN630_HUMAN	S	188;78;202;202	ENSP00000393163:N188S;ENSP00000354683:N78S;ENSP00000386393:N202S;ENSP00000407278:N202S	ENSP00000354683:N78S	N	-	2	0	ZNF630	47804170	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.319000	0.02702	-0.650000	0.05423	-0.443000	0.05667	AAC		0.383	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735	
SSX6	280657	broad.mit.edu	37	X	47976486	47976486	+	RNA	SNP	G	G	A	rs144718875	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:47976486G>A	ENST00000509958.1	+	0	21							Q7RTT6	SSX6_HUMAN	synovial sarcoma, X breakpoint 6 (pseudogene)						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.P141P(1)		large_intestine(6)|lung(4)|skin(2)|stomach(1)	13						AGCTGTGCCCGCCGGGAAAAG	0.512													.|||	3	0.000794702	0.0008	0.0	3775	,	,		14807	0.0		0.0	False		,,,				2504	0.002				.												.	.	1	Substitution - coding silent(1)	large_intestine(1)	.	X						.	C		7,3821		0,5,2,1626,564	117.0	116.0	116.0			0.7	0.0	X	dbSNP_134	116	1,6717		0,1,0,2427,1862	no	intergenic				0,6,2,4053,2426	AA,AG,A,GG,G		0.0149,0.1829,0.0759			47976486	8,10538	2197	4290	6487	47861430			280657	.			BK000686		Xp11.23	2009-09-11	2009-08-26		ENSG00000171483	ENSG00000171483			19652	pseudogene	pseudogene		300541	"""SSX family pseudogene 2"", ""synovial sarcoma, X breakpoint 6"""	SSXP2		12216073	Standard	NR_028366		Approved	psiSSX2	uc011mlv.2	Q7RTT6	OTTHUMG00000021464		X.37:g.47976486G>A		Somatic		Capture	Illumina HiSeq	Phase_I	47861430	.		Silent	SNP	ENST00000509958.1	37																																																																																					0.512	SSX6-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000362117.1	NR_028366	
SSX3	10214	broad.mit.edu	37	X	48211571	48211571	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48211571C>A	ENST00000298396.2	-	5	346	c.294G>T	c.(292-294)caG>caT	p.Q98H	SSX3_ENST00000376893.3_Missense_Mutation_p.Q98H|SSX3_ENST00000376895.1_Missense_Mutation_p.Q10H	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	98					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)	p.Q98H(1)		endometrium(3)|large_intestine(1)|lung(9)	13						CGAAAGTCATCTGAGGACGTT	0.453																																					p.Q98H	Colon(37;227 826 19399 40970 48007)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G294T	X						.						138.0	124.0	129.0					X																	48211571		2203	4300	6503	48096515	SO:0001583	missense	10214	exon5			U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.294G>T	X.37:g.48211571C>A	ENSP00000298396:p.Gln98His	Somatic		Capture	Illumina HiSeq	Phase_I	48096515	NM_021014	O60223|Q5JQZ3|Q9BRW7	Missense_Mutation	SNP	ENST00000298396.2	37	CCDS14291.1	.	.	.	.	.	.	.	.	.	.	c	8.076	0.771275	0.16051	.	.	ENSG00000165584	ENST00000298396;ENST00000376895;ENST00000376893	T;T;T	0.39997	3.02;1.05;2.96	0.95	0.95	0.19572	.	2.570780	0.02156	U	0.058430	T	0.63260	0.2496	M	0.78801	2.425	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.74348	0.983;0.957	T	0.28427	-1.0044	10	0.49607	T	0.09	.	4.9528	0.14023	0.0:1.0:0.0:0.0	.	98;98	Q9BRW7;Q99909	.;SSX3_HUMAN	H	98;10;98	ENSP00000298396:Q98H;ENSP00000366092:Q10H;ENSP00000366090:Q98H	ENSP00000298396:Q98H	Q	-	3	2	SSX3	48096515	0.000000	0.05858	0.001000	0.08648	0.151000	0.21798	-0.084000	0.11268	0.756000	0.33013	0.171000	0.16805	CAG		0.453	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014	
SLC38A5	92745	broad.mit.edu	37	X	48325402	48325402	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48325402G>A	ENST00000376876.3	-	4	1035	c.192C>T	c.(190-192)agC>agT	p.S64S	SLC38A5_ENST00000376875.1_Silent_p.S13S|SLC38A5_ENST00000317669.5_Silent_p.S64S			Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	64					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)	p.S64S(1)		breast(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	19						CCAGGATGCCGCTGCCCATGA	0.612											OREG0019763	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S64S												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C192T	X						.						61.0	50.0	54.0					X																	48325402		2203	4300	6503	48210346	SO:0001819	synonymous_variant	92745	exon5			AF276889	CCDS14293.1	Xp11.23	2013-05-22			ENSG00000017483	ENSG00000017483		"""Solute carriers"""	18070	protein-coding gene	gene with protein product		300649				11243884	Standard	NM_033518		Approved	SN2, JM24	uc010nid.3	Q8WUX1	OTTHUMG00000024117	ENST00000376876.3:c.192C>T	X.37:g.48325402G>A		Somatic	953	Capture	Illumina HiSeq	Phase_I	48210346	NM_033518	B3KT20|B5MDE6|B7WPJ9|Q6PIW9|Q8WYU2|Q96PQ4	Silent	SNP	ENST00000376876.3	37	CCDS14293.1																																																																																				0.612	SLC38A5-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060724.1	NM_033518	
GATA1	2623	broad.mit.edu	37	X	48652359	48652359	+	Missense_Mutation	SNP	G	G	A	rs141479621	byFrequency	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48652359G>A	ENST00000376670.3	+	6	1141	c.1030G>A	c.(1030-1032)Ggg>Agg	p.G344R	GATA1_ENST00000376665.3_Intron	NM_002049.3	NP_002040.1	P15976	GATA1_HUMAN	GATA binding protein 1 (globin transcription factor 1)	344					basophil differentiation (GO:0030221)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|cellular response to thyroid hormone stimulus (GO:0097067)|dendritic cell differentiation (GO:0097028)|embryonic hemopoiesis (GO:0035162)|eosinophil differentiation (GO:0030222)|eosinophil fate commitment (GO:0035854)|erythrocyte development (GO:0048821)|erythrocyte differentiation (GO:0030218)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|megakaryocyte differentiation (GO:0030219)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of definitive erythrocyte differentiation (GO:0010724)|regulation of glycoprotein biosynthetic process (GO:0010559)|transcription from RNA polymerase II promoter (GO:0006366)|transcriptional activation by promoter-enhancer looping (GO:0071733)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	C2H2 zinc finger domain binding (GO:0070742)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|enhancer sequence-specific DNA binding (GO:0001158)|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 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 regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.G344R(1)		breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(259)|large_intestine(8)|lung(9)|prostate(1)	283						CAGCGGTAGCGGGAATTGTGG	0.627			"""Mis, F"""		megakaryoblastic leukemia of Downs Syndrome																																p.G344R	Pancreas(9;429 505 11287 29617)		Dom	yes		X	Xp11.23	2623	GATA binding protein 1 (globin transcription factor 1)		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1030A	X						.	G	ARG/GLY	4,3828		0,3,1,1629,567	36.0	31.0	33.0		1030	3.6	0.9	X	dbSNP_134	33	0,6724		0,0,0,2428,1868	no	missense	GATA1	NM_002049.3	125	0,3,1,4057,2435	AA,AG,A,GG,G		0.0,0.1044,0.0379	probably-damaging	344/414	48652359	4,10552	2200	4296	6496	48537303	SO:0001583	missense	2623	exon6			X17254	CCDS14305.1	Xp11.23	2014-09-17	2001-11-28		ENSG00000102145	ENSG00000102145		"""GATA zinc finger domain containing"""	4170	protein-coding gene	gene with protein product	"""nuclear factor, erythroid 1"""	305371	"""GATA-binding protein 1 (globin transcription factor 1)"""	GF1		1999341	Standard	NM_002049		Approved	ERYF1, NFE1, GATA-1, NF-E1	uc004dkq.4	P15976	OTTHUMG00000021504	ENST00000376670.3:c.1030G>A	X.37:g.48652359G>A	ENSP00000365858:p.Gly344Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48537303	NM_002049	Q96GB8	Missense_Mutation	SNP	ENST00000376670.3	37	CCDS14305.1	.	.	.	.	.	.	.	.	.	.	g	16.76	3.212230	0.58452	0.001044	0.0	ENSG00000102145	ENST00000376670	D	0.97850	-4.57	4.47	3.56	0.40772	.	0.634660	0.15186	U	0.275824	D	0.96081	0.8723	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92430	0.5953	10	0.16896	T	0.51	-10.3993	9.0886	0.36596	0.0:0.0:0.7835:0.2165	.	344	P15976	GATA1_HUMAN	R	344	ENSP00000365858:G344R	ENSP00000365858:G344R	G	+	1	0	GATA1	48537303	0.991000	0.36638	0.880000	0.34516	0.593000	0.36681	2.316000	0.43761	1.812000	0.52913	0.365000	0.22127	GGG		0.627	GATA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056517.1	NM_002049	
HDAC6	10013	broad.mit.edu	37	X	48663898	48663898	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48663898A>G	ENST00000334136.5	+	5	543	c.365A>G	c.(364-366)gAg>gGg	p.E122G	HDAC6_ENST00000469223.1_3'UTR|HDAC6_ENST00000413163.2_Missense_Mutation_p.E67G|HDAC6_ENST00000376619.2_Missense_Mutation_p.E122G|HDAC6_ENST00000444343.2_Missense_Mutation_p.E136G			Q9UBN7	HDAC6_HUMAN	histone deacetylase 6	122	Histone deacetylase 1.				aggresome assembly (GO:0070842)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to misfolded protein (GO:0071218)|cellular response to topologically incorrect protein (GO:0035967)|histone deacetylation (GO:0016575)|Hsp90 deacetylation (GO:0070846)|intracellular protein transport (GO:0006886)|lysosome localization (GO:0032418)|macroautophagy (GO:0016236)|misfolded or incompletely synthesized protein catabolic process (GO:0006515)|negative regulation of hydrogen peroxide metabolic process (GO:0010727)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of oxidoreductase activity (GO:0051354)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of proteolysis (GO:0045861)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine deacetylation (GO:0034983)|polyubiquitinated misfolded protein transport (GO:0070845)|positive regulation of chaperone-mediated protein complex assembly (GO:0090035)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of hydrogen peroxide-mediated programmed cell death (GO:1901300)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of signal transduction (GO:0009967)|protein complex disassembly (GO:0043241)|protein deacetylation (GO:0006476)|protein polyubiquitination (GO:0000209)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of establishment of protein localization (GO:0070201)|regulation of gene expression, epigenetic (GO:0040029)|regulation of microtubule-based movement (GO:0060632)|regulation of receptor activity (GO:0010469)|response to growth factor (GO:0070848)|response to misfolded protein (GO:0051788)|response to organic substance (GO:0010033)|response to toxic substance (GO:0009636)|transcription, DNA-templated (GO:0006351)|tubulin deacetylation (GO:0090042)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	aggresome (GO:0016235)|axon (GO:0030424)|caveola (GO:0005901)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|dendrite (GO:0030425)|histone deacetylase complex (GO:0000118)|inclusion body (GO:0016234)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)	alpha-tubulin binding (GO:0043014)|beta-catenin binding (GO:0008013)|core promoter binding (GO:0001047)|dynein complex binding (GO:0070840)|enzyme binding (GO:0019899)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|Hsp90 protein binding (GO:0051879)|microtubule binding (GO:0008017)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|polyubiquitin binding (GO:0031593)|tau protein binding (GO:0048156)|tubulin deacetylase activity (GO:0042903)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(5)|large_intestine(8)|lung(9)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	40					Vorinostat(DB02546)	CTGATCCAGGAGGGCCTCCTA	0.617																																					p.E122G	Pancreas(112;205 1675 2305 8976 15959)											.	.	0			c.A365G	X						.						73.0	56.0	61.0					X																	48663898		2203	4300	6503	48548842	SO:0001583	missense	10013	exon5			AF132609	CCDS14306.1	Xp11.23	2014-06-12			ENSG00000094631	ENSG00000094631			14064	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 90"""	300272				10220385, 10048485	Standard	NM_006044		Approved	KIAA0901, JM21, HD6, FLJ16239, PPP1R90	uc004dks.1	Q9UBN7	OTTHUMG00000034496	ENST00000334136.5:c.365A>G	X.37:g.48663898A>G	ENSP00000334061:p.Glu122Gly	None		Capture	Illumina HiSeq	Phase_I	48548842	NM_006044	O94975|Q6NT75|Q7L3E5|Q96CY0	Missense_Mutation	SNP	ENST00000334136.5	37	CCDS14306.1	.	.	.	.	.	.	.	.	.	.	A	10.20	1.286111	0.23478	.	.	ENSG00000094631	ENST00000423941;ENST00000376643;ENST00000444343;ENST00000376610;ENST00000334136;ENST00000376619;ENST00000436813;ENST00000413163;ENST00000441703;ENST00000426196;ENST00000443563;ENST00000440653	T;T;T;T;T;T;T;T;T;T	0.70282	-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47;-0.47	4.16	1.81	0.25067	Histone deacetylase domain (2);	0.543065	0.18174	N	0.149346	T	0.48059	0.1479	L	0.35644	1.08	0.19575	N	0.999966	B;B;B;P	0.41848	0.109;0.001;0.109;0.763	B;B;B;B	0.30943	0.122;0.008;0.122;0.121	T	0.32508	-0.9904	10	0.18710	T	0.47	-8.4086	5.9179	0.19065	0.7587:0.0:0.2413:0.0	.	112;67;122;122	B4DZN1;E7EUZ1;Q9UBN7;Q9BRX7	.;.;HDAC6_HUMAN;.	G	122;122;136;122;122;122;122;67;122;122;122;122	ENSP00000365831:E122G;ENSP00000398566:E136G;ENSP00000365795:E122G;ENSP00000334061:E122G;ENSP00000365804:E122G;ENSP00000398801:E67G;ENSP00000393916:E122G;ENSP00000402189:E122G;ENSP00000402751:E122G;ENSP00000394377:E122G	ENSP00000334061:E122G	E	+	2	0	HDAC6	48548842	1.000000	0.71417	0.927000	0.36925	0.798000	0.45092	1.957000	0.40392	0.561000	0.29186	0.242000	0.17961	GAG		0.617	HDAC6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083394.2	NM_006044	
GRIPAP1	56850	broad.mit.edu	37	X	48839840	48839840	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48839840G>A	ENST00000376441.1	-	16	1319	c.1285C>T	c.(1285-1287)Cgg>Tgg	p.R429W	GRIPAP1_ENST00000376425.3_Missense_Mutation_p.R398W|GRIPAP1_ENST00000376444.3_Missense_Mutation_p.R384W|GRIPAP1_ENST00000376423.4_Missense_Mutation_p.R376W|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	429						blood microparticle (GO:0072562)|endosome (GO:0005768)		p.R376W(1)|p.R72W(1)		breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						ATGGCCTTCCGCTTCTCCGCA	0.557																																					p.R429W												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C1285T	X						.						92.0	71.0	78.0					X																	48839840		2203	4300	6503	48724784	SO:0001583	missense	56850	exon16			AB032993	CCDS35248.1	Xp11.23	2008-02-05			ENSG00000068400	ENSG00000068400			18706	protein-coding gene	gene with protein product		300408				10896157	Standard	NM_020137		Approved	GRASP-1, GRASP1, KIAA1167, MPMGp800B12492Q3, DKFZp434P0630	uc004dly.1	Q4V328	OTTHUMG00000033192	ENST00000376441.1:c.1285C>T	X.37:g.48839840G>A	ENSP00000365624:p.Arg429Trp	Somatic		Capture	Illumina HiSeq	Phase_I	48724784	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Missense_Mutation	SNP	ENST00000376441.1	37	CCDS35248.1	.	.	.	.	.	.	.	.	.	.	-	11.91	1.780672	0.31502	.	.	ENSG00000068400	ENST00000376425;ENST00000376444;ENST00000376441;ENST00000537291;ENST00000376423	T;T;T;T	0.26660	1.72;1.72;1.72;1.72	4.29	0.618	0.17624	.	0.158061	0.36778	N	0.002416	T	0.35770	0.0943	L	0.32530	0.975	0.30705	N	0.74989	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.989;0.999;0.973	T	0.33574	-0.9863	10	0.51188	T	0.08	-3.7935	12.4238	0.55534	0.0:0.0:0.5543:0.4457	.	376;319;429	Q4V328-2;Q4V328-3;Q4V328	.;.;GRAP1_HUMAN	W	398;384;429;398;376	ENSP00000365608:R398W;ENSP00000365627:R384W;ENSP00000365624:R429W;ENSP00000365606:R376W	ENSP00000365606:R376W	R	-	1	2	GRIPAP1	48724784	1.000000	0.71417	0.997000	0.53966	0.046000	0.14306	2.486000	0.45259	0.110000	0.17919	-0.521000	0.04368	CGG		0.557	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672	
TFE3	7030	broad.mit.edu	37	X	48889018	48889018	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:48889018A>G	ENST00000315869.7	-	9	1437	c.1178T>C	c.(1177-1179)gTg>gCg	p.V393A	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	393	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.V393A(1)	NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GATATAATCCACAGAGGCCTT	0.607			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""																																p.V393A			Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1178C	X						.						31.0	28.0	29.0					X																	48889018		2201	4296	6497	48775962	SO:0001583	missense	7030	exon9			X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.1178T>C	X.37:g.48889018A>G	ENSP00000314129:p.Val393Ala	Somatic		Capture	Illumina HiSeq	Phase_I	48775962	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	a	21.3	4.123954	0.77436	.	.	ENSG00000068323	ENST00000315869	D	0.98493	-4.96	5.64	5.64	0.86602	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98770	0.9586	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.99808	1.1039	10	0.87932	D	0	-16.1407	13.7333	0.62802	1.0:0.0:0.0:0.0	.	393	P19532	TFE3_HUMAN	A	393	ENSP00000314129:V393A	ENSP00000314129:V393A	V	-	2	0	TFE3	48775962	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.220000	0.95180	1.887000	0.54652	0.376000	0.23039	GTG		0.607	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521	
CACNA1F	778	broad.mit.edu	37	X	49066200	49066200	+	Silent	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:49066200G>T	ENST00000376265.2	-	41	4804	c.4743C>A	c.(4741-4743)ggC>ggA	p.G1581G	CACNA1F_ENST00000323022.5_Silent_p.G1570G|CACNA1F_ENST00000376251.1_Silent_p.G1516G	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1581					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.G1581G(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	CGTAGAATTTGCCCACGGTGA	0.582																																					p.G1581G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C4743A	X						.						66.0	55.0	59.0					X																	49066200		2203	4300	6503	48953144	SO:0001819	synonymous_variant	778	exon41			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.4743C>A	X.37:g.49066200G>T		Somatic		Capture	Illumina HiSeq	Phase_I	48953144	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																				0.582	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
CACNA1F	778	broad.mit.edu	37	X	49076957	49076957	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:49076957C>A	ENST00000376265.2	-	19	2455	c.2394G>T	c.(2392-2394)gaG>gaT	p.E798D	CACNA1F_ENST00000323022.5_Missense_Mutation_p.E787D|CACNA1F_ENST00000480889.1_5'Flank|CACNA1F_ENST00000376251.1_Missense_Mutation_p.E733D	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	798	Poly-Glu.				axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.E798D(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TTGCACCCTCCTCTTCCTCTT	0.602																																					p.E798D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2394T	X						.						111.0	66.0	81.0					X																	49076957		2203	4300	6503	48963901	SO:0001583	missense	778	exon19			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.2394G>T	X.37:g.49076957C>A	ENSP00000365441:p.Glu798Asp	Somatic		Capture	Illumina HiSeq	Phase_I	48963901	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	.	5.332	0.246560	0.10130	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	T;T;T	0.14022	2.54;2.54;2.54	5.15	2.27	0.28462	.	0.939693	0.08690	N	0.908053	T	0.10723	0.0262	L	0.41236	1.265	0.20764	N	0.999857	B;B	0.21606	0.058;0.034	B;B	0.20767	0.031;0.014	T	0.45381	-0.9265	10	0.13470	T	0.59	.	6.3476	0.21357	0.0:0.6441:0.0:0.3559	.	787;798	F5CIQ9;O60840	.;CAC1F_HUMAN	D	733;787;798	ENSP00000365427:E733D;ENSP00000321618:E787D;ENSP00000365441:E798D	ENSP00000321618:E787D	E	-	3	2	CACNA1F	48963901	0.847000	0.29606	0.020000	0.16555	0.030000	0.12068	0.013000	0.13310	0.048000	0.15891	0.436000	0.28706	GAG		0.602	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
CACNA1F	778	broad.mit.edu	37	X	49084577	49084577	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:49084577G>A	ENST00000376265.2	-	8	1100	c.1039C>T	c.(1039-1041)Ctg>Ttg	p.L347L	CACNA1F_ENST00000323022.5_Silent_p.L347L|CACNA1F_ENST00000376251.1_Silent_p.L282L	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	347					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.L347L(1)		autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ACCCAGGGCAGTTCATACCCC	0.562																																					p.L347L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1039T	X						.						139.0	86.0	104.0					X																	49084577		2203	4300	6503	48971521	SO:0001819	synonymous_variant	778	exon8			AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.1039C>T	X.37:g.49084577G>A		Somatic		Capture	Illumina HiSeq	Phase_I	48971521	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																				0.562	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
CCDC22	28952	broad.mit.edu	37	X	49099414	49099414	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:49099414T>C	ENST00000376227.3	+	4	594	c.424T>C	c.(424-426)Tgg>Cgg	p.W142R	CCDC22_ENST00000496651.1_3'UTR	NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	142								p.W142R(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						GGCACTGCCTTGGGTCCCGCC	0.597																																					p.W142R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T424C	X						.						51.0	40.0	44.0					X																	49099414		2202	4297	6499	48986358	SO:0001583	missense	28952	exon4			BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.424T>C	X.37:g.49099414T>C	ENSP00000365401:p.Trp142Arg	Somatic		Capture	Illumina HiSeq	Phase_I	48986358	NM_014008	A8K7G1	Missense_Mutation	SNP	ENST00000376227.3	37	CCDS14322.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.300747	0.60195	.	.	ENSG00000101997	ENST00000376227;ENST00000538876	.	.	.	5.02	5.02	0.67125	.	0.060770	0.64402	D	0.000001	T	0.78291	0.4260	M	0.81802	2.56	0.44702	D	0.997695	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.975	T	0.81013	-0.1125	9	0.72032	D	0.01	-6.1328	11.386	0.49785	0.0:0.0:0.0:1.0	.	142;142	B4DLA4;O60826	.;CCD22_HUMAN	R	142	.	ENSP00000365401:W142R	W	+	1	0	CCDC22	48986358	1.000000	0.71417	1.000000	0.80357	0.401000	0.30781	6.021000	0.70832	1.670000	0.50864	0.378000	0.23410	TGG		0.597	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
CCDC22	28952	broad.mit.edu	37	X	49099792	49099792	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:49099792C>A	ENST00000376227.3	+	6	748	c.578C>A	c.(577-579)cCt>cAt	p.P193H	CCDC22_ENST00000496651.1_3'UTR	NM_014008.3	NP_054727.1	O60826	CCD22_HUMAN	coiled-coil domain containing 22	193								p.P193H(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	18						CTTCCAGTCCCTACCCAGGTG	0.667																																					p.P193H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C578A	X						.						33.0	23.0	27.0					X																	49099792		2200	4299	6499	48986736	SO:0001583	missense	28952	exon6			BC000972	CCDS14322.1	Xp11.23	2008-02-05	2005-07-24	2005-07-24	ENSG00000101997	ENSG00000101997			28909	protein-coding gene	gene with protein product		300859	"""chromosome X open reading frame 37"""	CXorf37		12477932	Standard	NM_014008		Approved	JM1	uc004dnd.2	O60826	OTTHUMG00000024141	ENST00000376227.3:c.578C>A	X.37:g.49099792C>A	ENSP00000365401:p.Pro193His	Somatic		Capture	Illumina HiSeq	Phase_I	48986736	NM_014008	A8K7G1	Missense_Mutation	SNP	ENST00000376227.3	37	CCDS14322.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.277309	0.40294	.	.	ENSG00000101997	ENST00000376227;ENST00000538876	.	.	.	4.87	4.87	0.63330	.	0.111788	0.64402	D	0.000014	T	0.65439	0.2691	M	0.75615	2.305	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.961	T	0.58364	-0.7649	9	0.30078	T	0.28	-10.4079	12.5541	0.56244	0.0:1.0:0.0:0.0	.	193;193	B4DLA4;O60826	.;CCD22_HUMAN	H	193	.	ENSP00000365401:P193H	P	+	2	0	CCDC22	48986736	0.478000	0.25917	0.029000	0.17559	0.341000	0.28922	4.519000	0.60517	2.015000	0.59207	0.464000	0.42555	CCT		0.667	CCDC22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060822.1	NM_014008	
SHROOM4	57477	broad.mit.edu	37	X	50378664	50378664	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:50378664C>T	ENST00000289292.7	-	4	692	c.409G>A	c.(409-411)Gtg>Atg	p.V137M	SHROOM4_ENST00000376020.2_Missense_Mutation_p.V137M|SHROOM4_ENST00000460112.3_Missense_Mutation_p.V21M			Q9ULL8	SHRM4_HUMAN	shroom family member 4	137					actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)	p.V137M(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					TGCACACACACGTCACTGTAA	0.567																																					p.V137M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G409A	X						.						52.0	39.0	44.0					X																	50378664		2203	4300	6503	50395404	SO:0001583	missense	57477	exon4			AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.409G>A	X.37:g.50378664C>T	ENSP00000289292:p.Val137Met	Somatic		Capture	Illumina HiSeq	Phase_I	50395404	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	C	12.41	1.929457	0.34096	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.15372	2.86;2.86;2.43	5.8	4.92	0.64577	.	0.222612	0.38548	N	0.001648	T	0.25827	0.0629	L	0.40543	1.245	0.32518	N	0.536687	D	0.71674	0.998	P	0.57324	0.818	T	0.16512	-1.0400	10	0.54805	T	0.06	.	11.4887	0.50369	0.0:0.5927:0.4073:0.0	.	137	Q9ULL8	SHRM4_HUMAN	M	137;137;21	ENSP00000289292:V137M;ENSP00000365188:V137M;ENSP00000421450:V21M	ENSP00000289292:V137M	V	-	1	0	SHROOM4	50395404	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.552000	0.45828	2.448000	0.82819	0.600000	0.82982	GTG		0.567	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
MAGED1	9500	broad.mit.edu	37	X	51637828	51637828	+	Intron	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:51637828C>A	ENST00000375722.1	+	3	297				MAGED1_ENST00000375772.3_Intron|MAGED1_ENST00000326587.7_Intron|MAGED1_ENST00000494718.1_Intron|MAGED1_ENST00000375695.2_Missense_Mutation_p.L51I			Q9Y5V3	MAGD1_HUMAN	melanoma antigen family D, 1						apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|circadian regulation of gene expression (GO:0032922)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of circadian rhythm (GO:0042752)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	transcription coactivator activity (GO:0003713)	p.L51I(1)		breast(1)|endometrium(4)|large_intestine(10)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	32	Ovarian(276;0.236)					TTATTCTCAACTCCGCGATCC	0.637										Multiple Myeloma(10;0.10)																											p.L51I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C151A	X						.						76.0	64.0	68.0					X																	51637828		2203	4300	6503	51654568	SO:0001627	intron_variant	9500	exon3			AF124440	CCDS14337.1, CCDS35279.1	Xp11.23	2008-08-01			ENSG00000179222	ENSG00000179222			6813	protein-coding gene	gene with protein product		300224				10409427	Standard	NM_006986		Approved	NRAGE, DLXIN-1	uc004dpn.3	Q9Y5V3	OTTHUMG00000021540	ENST00000375722.1:c.46-321C>A	X.37:g.51637828C>A		Somatic		Capture	Illumina HiSeq	Phase_I	51654568	NM_001005333	Q5VSH6|Q8IZ84|Q8WY92|Q9H352|Q9HBT4|Q9UF36	Missense_Mutation	SNP	ENST00000375722.1	37	CCDS14337.1	.	.	.	.	.	.	.	.	.	.	C	2.142	-0.396555	0.04899	.	.	ENSG00000179222	ENST00000375695	T	0.03553	3.89	2.13	0.136	0.14780	.	.	.	.	.	T	0.01800	0.0057	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49370	-0.8947	8	0.12430	T	0.62	.	2.5792	0.04814	0.2799:0.5389:0.0:0.1812	.	51	Q9Y5V3-2	.	I	51	ENSP00000364847:L51I	ENSP00000364847:L51I	L	+	1	0	MAGED1	51654568	0.003000	0.15002	0.008000	0.14137	0.203000	0.24098	0.309000	0.19332	-0.056000	0.13221	0.425000	0.28330	CTC		0.637	MAGED1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056593.1	NM_001005332	
XAGE5	170627	broad.mit.edu	37	X	52842196	52842196	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:52842196A>G	ENST00000375501.1	+	2	105	c.105A>G	c.(103-105)gaA>gaG	p.E35E	XAGE5_ENST00000425386.1_Silent_p.E35E|XAGE5_ENST00000351072.1_Silent_p.E35E|XAGE5_ENST00000375503.3_Silent_p.E35E			Q8WWM1	XAGE5_HUMAN	X antigen family, member 5	35								p.E35E(1)		endometrium(1)|large_intestine(1)|lung(5)|ovary(1)	8						AACAAGAAGAACCACCAACTG	0.493																																					p.E35E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A105G	X						.						101.0	75.0	84.0					X																	52842196		2203	4300	6503	52858921	SO:0001819	synonymous_variant	170627	exon3			BC069129	CCDS14346.1	Xp11.23	2010-10-19		2005-01-27	ENSG00000171405	ENSG00000171405			30930	protein-coding gene	gene with protein product	"""cancer/testis antigen family 12, member 5"""		"""G antigen, family D, 5"""	GAGED5		12477932	Standard	NM_130775		Approved	XAGE-5, CT12.5	uc004drd.1	Q8WWM1	OTTHUMG00000021589	ENST00000375501.1:c.105A>G	X.37:g.52842196A>G		Somatic		Capture	Illumina HiSeq	Phase_I	52858921	NM_130775	Q5JS81	Silent	SNP	ENST00000375501.1	37	CCDS14346.1																																																																																				0.493	XAGE5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056689.1	NM_130775	
KDM5C	8242	broad.mit.edu	37	X	53230752	53230752	+	Nonsense_Mutation	SNP	G	G	A	rs370032584		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:53230752G>A	ENST00000375401.3	-	14	2573	c.2041C>T	c.(2041-2043)Cga>Tga	p.R681*	KDM5C_ENST00000375379.3_Nonsense_Mutation_p.R681*|KDM5C_ENST00000404049.3_Nonsense_Mutation_p.R680*|KDM5C_ENST00000375383.3_Nonsense_Mutation_p.R640*|KDM5C_ENST00000452825.3_Nonsense_Mutation_p.R614*|KDM5C_ENST00000465402.1_5'UTR	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	681					histone H3-K4 demethylation (GO:0034720)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-K4 specific) (GO:0032453)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|zinc ion binding (GO:0008270)	p.R681*(2)		autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(30)|large_intestine(9)|lung(17)|oesophagus(1)|ovary(6)|prostate(1)|salivary_gland(1)|skin(1)|upper_aerodigestive_tract(2)	82						AGGGCCTTTCGTAGACGCCGC	0.562			"""N, F, S"""		clear cell renal carcinoma																																p.R681X			Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	.	2	Substitution - Nonsense(2)	large_intestine(1)|kidney(1)	c.C2041T	X						.						86.0	82.0	83.0					X																	53230752		2203	4300	6503	53247477	SO:0001587	stop_gained	8242	exon14			Z29650	CCDS14351.1, CCDS55417.1, CCDS65269.1	Xp11.22-p11.21	2014-01-31	2009-04-06	2009-04-06	ENSG00000126012	ENSG00000126012		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	11114	protein-coding gene	gene with protein product		314690	"""Jumonji, AT rich interactive domain 1C (RBP2-like)"", ""Smcy homolog, X-linked (mouse)"", ""jumonji, AT rich interactive domain 1C"", ""mental retardation, X-linked 13"""	SMCX, JARID1C, MRX13		7951230, 8162017, 19826449	Standard	NM_004187		Approved	DXS1272E, XE169	uc004drz.3	P41229	OTTHUMG00000021606	ENST00000375401.3:c.2041C>T	X.37:g.53230752G>A	ENSP00000364550:p.Arg681*	Somatic		Capture	Illumina HiSeq	Phase_I	53247477	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Nonsense_Mutation	SNP	ENST00000375401.3	37	CCDS14351.1	.	.	.	.	.	.	.	.	.	.	G	45	11.613684	0.99582	.	.	ENSG00000126012	ENST00000452825;ENST00000375401;ENST00000404049;ENST00000375379;ENST00000375383	.	.	.	5.43	5.43	0.79202	.	0.059417	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.565	15.5376	0.76016	0.0:0.0:1.0:0.0	.	.	.	.	X	614;681;680;681;640	.	ENSP00000364528:R681X	R	-	1	2	KDM5C	53247477	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	3.048000	0.49862	2.263000	0.75096	0.600000	0.82982	CGA		0.562	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187	
IQSEC2	23096	broad.mit.edu	37	X	53271078	53271078	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:53271078G>T	ENST00000375368.5	-	9	3073	c.2873C>A	c.(2872-2874)cCt>cAt	p.P958H	IQSEC2_ENST00000396435.3_Missense_Mutation_p.P968H|IQSEC2_ENST00000375365.2_Missense_Mutation_p.P763H			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	958	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)	p.P965H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(4)|skin(1)	29						TCGACGGTGAGGGAGAGACAG	0.567																																					p.P968H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2903A	X						.						85.0	47.0	60.0					X																	53271078		2203	4300	6503	53287803	SO:0001583	missense	23096	exon10			AB011094	CCDS35298.1, CCDS48130.1	Xp11.23	2014-01-31			ENSG00000124313	ENSG00000124313			29059	protein-coding gene	gene with protein product		300522	"""mental retardation, X-linked 1 (non-dysmorphic)"""	MRX1		9628581, 20473311	Standard	NM_001243197		Approved	KIAA0522	uc004dsd.3	Q5JU85	OTTHUMG00000021608	ENST00000375368.5:c.2873C>A	X.37:g.53271078G>T	ENSP00000364517:p.Pro958His	Somatic		Capture	Illumina HiSeq	Phase_I	53287803	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Missense_Mutation	SNP	ENST00000375368.5	37		.	.	.	.	.	.	.	.	.	.	g	24.9	4.583009	0.86748	.	.	ENSG00000124313	ENST00000396435;ENST00000375368;ENST00000375365	T;T;T	0.67865	-0.29;-0.29;-0.29	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.82715	0.5097	M	0.80616	2.505	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.85514	0.1199	10	0.87932	D	0	.	16.6882	0.85315	0.0:0.0:1.0:0.0	.	968;763	Q5JU85-2;Q5JU85-3	.;.	H	968;958;763	ENSP00000379712:P968H;ENSP00000364517:P958H;ENSP00000364514:P763H	ENSP00000364514:P763H	P	-	2	0	IQSEC2	53287803	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.804000	0.99143	2.287000	0.76781	0.589000	0.80489	CCT		0.567	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
HUWE1	10075	broad.mit.edu	37	X	53573424	53573424	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:53573424G>A	ENST00000342160.3	-	69	11345	c.10888C>T	c.(10888-10890)Ctg>Ttg	p.L3630L	HUWE1_ENST00000262854.6_Silent_p.L3630L|HUWE1_ENST00000474288.1_5'UTR			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	3630					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.L3520L(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GTATAACCCAGATGGCGGGCT	0.488																																					p.L3630L												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C10888T	X						.						51.0	47.0	48.0					X																	53573424		2203	4300	6503	53590149	SO:0001819	synonymous_variant	10075	exon70			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.10888C>T	X.37:g.53573424G>A		Somatic		Capture	Illumina HiSeq	Phase_I	53590149	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	9.849	1.193095	0.21954	.	.	ENSG00000086758	ENST00000427052;ENST00000426907	.	.	.	5.57	3.8	0.43715	.	.	.	.	.	T	0.57946	0.2088	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51553	-0.8691	4	.	.	.	.	8.068	0.30672	0.2607:0.0:0.7393:0.0	.	.	.	.	F	2663;467	.	.	S	-	2	0	HUWE1	53590149	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.405000	0.52630	0.539000	0.28788	0.600000	0.82982	TCT		0.488	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
HUWE1	10075	broad.mit.edu	37	X	53581673	53581673	+	Silent	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:53581673C>T	ENST00000342160.3	-	60	8872	c.8415G>A	c.(8413-8415)gaG>gaA	p.E2805E	MIRLET7F2_ENST00000385277.1_RNA|MIR98_ENST00000606724.1_RNA|HUWE1_ENST00000262854.6_Silent_p.E2805E			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2805					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.E2683E(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ATTCCTCTGGCTCTACAGGCA	0.522																																					p.E2805E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G8415A	X						.						95.0	81.0	85.0					X																	53581673		2203	4300	6503	53598398	SO:0001819	synonymous_variant	10075	exon61			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8415G>A	X.37:g.53581673C>T		Somatic		Capture	Illumina HiSeq	Phase_I	53598398	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	C	8.999	0.979684	0.18812	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.84	3.16	0.36331	.	.	.	.	.	T	0.54240	0.1846	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43572	-0.9383	4	.	.	.	.	5.8214	0.18530	0.0:0.627:0.1363:0.2367	.	.	.	.	T	1839	.	.	A	-	1	0	HUWE1	53598398	0.750000	0.28316	0.992000	0.48379	0.997000	0.91878	-0.355000	0.07671	0.248000	0.21435	0.600000	0.82982	GCC		0.522	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
HUWE1	10075	broad.mit.edu	37	X	53644317	53644317	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:53644317G>A	ENST00000342160.3	-	19	2220	c.1763C>T	c.(1762-1764)gCa>gTa	p.A588V	HUWE1_ENST00000262854.6_Missense_Mutation_p.A588V|HUWE1_ENST00000218328.8_Missense_Mutation_p.A588V			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	588					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)	p.A588V(1)		NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						GATAAGCAGTGCATGCAGCAT	0.403																																					p.A588V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1763T	X						.						77.0	53.0	61.0					X																	53644317		2203	4300	6503	53661042	SO:0001583	missense	10075	exon20			AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.1763C>T	X.37:g.53644317G>A	ENSP00000340648:p.Ala588Val	Somatic		Capture	Illumina HiSeq	Phase_I	53661042	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	G	31	5.077096	0.94000	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328	T;T;T	0.58506	0.33;0.33;0.33	5.63	5.63	0.86233	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-type fold (1);	0.064498	0.64402	D	0.000012	T	0.77665	0.4164	M	0.82823	2.61	0.58432	D	0.999999	D	0.76494	0.999	D	0.72625	0.978	T	0.81243	-0.1021	10	0.87932	D	0	.	15.5128	0.75798	0.0:0.0:1.0:0.0	.	588	Q7Z6Z7	HUWE1_HUMAN	V	588	ENSP00000340648:A588V;ENSP00000262854:A588V;ENSP00000218328:A588V	ENSP00000218328:A588V	A	-	2	0	HUWE1	53661042	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.374000	0.97172	2.372000	0.80975	0.594000	0.82650	GCA		0.403	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
FGD1	2245	broad.mit.edu	37	X	54491902	54491902	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:54491902C>T	ENST00000375135.3	-	8	2351	c.1618G>A	c.(1618-1620)Gac>Aac	p.D540N		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	540	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.D540N(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TCCTTGCTGTCCGGGGAGCCA	0.572																																					p.D540N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1618A	X						.						44.0	41.0	42.0					X																	54491902		2203	4300	6503	54508627	SO:0001583	missense	2245	exon8			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3663	protein-coding gene	gene with protein product		300546	"""faciogenital dysplasia (Aarskog-Scott syndrome)"""	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.1618G>A	X.37:g.54491902C>T	ENSP00000364277:p.Asp540Asn	Somatic		Capture	Illumina HiSeq	Phase_I	54508627	NM_004463	Q5H999|Q8N4D9	Missense_Mutation	SNP	ENST00000375135.3	37	CCDS14359.1	.	.	.	.	.	.	.	.	.	.	C	31	5.095538	0.94197	.	.	ENSG00000102302	ENST00000375135	T	0.73897	-0.79	5.43	5.43	0.79202	Dbl homology (DH) domain (5);	0.000000	0.56097	D	0.000035	D	0.90769	0.7102	H	0.96015	3.755	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.93702	0.7016	10	0.87932	D	0	-17.7046	17.0001	0.86378	0.0:1.0:0.0:0.0	.	298;540	B4DS99;P98174	.;FGD1_HUMAN	N	540	ENSP00000364277:D540N	ENSP00000364277:D540N	D	-	1	0	FGD1	54508627	1.000000	0.71417	0.960000	0.40013	0.981000	0.71138	7.691000	0.84191	2.277000	0.76020	0.523000	0.50628	GAC		0.572	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463	
FGD1	2245	broad.mit.edu	37	X	54496799	54496799	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:54496799G>A	ENST00000375135.3	-	4	1484	c.751C>T	c.(751-753)Cca>Tca	p.P251S		NM_004463.2	NP_004454.2	P98174	FGD1_HUMAN	FYVE, RhoGEF and PH domain containing 1	251	Pro-rich.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)	p.P251S(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGCACTGGTGGCTGCGAGGTT	0.682																																					p.P251S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C751T	X						.						28.0	32.0	31.0					X																	54496799		2201	4297	6498	54513524	SO:0001583	missense	2245	exon4			U11690	CCDS14359.1	Xp11.21	2013-01-10	2008-08-01		ENSG00000102302	ENSG00000102302		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	3663	protein-coding gene	gene with protein product		300546	"""faciogenital dysplasia (Aarskog-Scott syndrome)"""	FGDY			Standard	NM_004463		Approved	ZFYVE3	uc004dtg.3	P98174	OTTHUMG00000021627	ENST00000375135.3:c.751C>T	X.37:g.54496799G>A	ENSP00000364277:p.Pro251Ser	Somatic		Capture	Illumina HiSeq	Phase_I	54513524	NM_004463	Q5H999|Q8N4D9	Missense_Mutation	SNP	ENST00000375135.3	37	CCDS14359.1	.	.	.	.	.	.	.	.	.	.	G	4.539	0.100082	0.08731	.	.	ENSG00000102302	ENST00000375135	T	0.79033	-1.23	5.16	4.24	0.50183	.	0.424641	0.20358	N	0.093912	T	0.49626	0.1568	N	0.03608	-0.345	0.24296	N	0.995148	B;B	0.33694	0.421;0.281	B;B	0.25291	0.059;0.041	T	0.35574	-0.9783	10	0.08599	T	0.76	-4.8284	12.8317	0.57750	0.0:0.0:0.8362:0.1638	.	9;251	B4DS99;P98174	.;FGD1_HUMAN	S	251	ENSP00000364277:P251S	ENSP00000364277:P251S	P	-	1	0	FGD1	54513524	0.970000	0.33590	0.616000	0.29078	0.066000	0.16364	0.923000	0.28757	2.327000	0.79052	0.436000	0.28706	CCA		0.682	FGD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056801.1	NM_004463	
MTMR8	55613	broad.mit.edu	37	X	63569908	63569908	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:63569908C>T	ENST00000374852.3	-	5	578	c.511G>A	c.(511-513)Gtt>Att	p.V171I	MTMR8_ENST00000453546.1_Missense_Mutation_p.V171I	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	171	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)|p.V171I(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						CCCAAGGTAACAGATTTAGGA	0.348																																					p.V171I												.	.	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|large_intestine(1)	c.G511A	X						.						119.0	100.0	106.0					X																	63569908		2203	4300	6503	63486633	SO:0001583	missense	55613	exon5			AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.511G>A	X.37:g.63569908C>T	ENSP00000363985:p.Val171Ile	Somatic		Capture	Illumina HiSeq	Phase_I	63486633	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	5.310	0.242564	0.10077	.	.	ENSG00000102043	ENST00000453546;ENST00000374852	D;D	0.91945	-2.94;-2.94	2.96	1.11	0.20524	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.132111	0.28241	U	0.016065	D	0.85265	0.5657	N	0.16307	0.4	0.22171	N	0.999315	B;P	0.46987	0.057;0.888	B;P	0.49192	0.008;0.602	T	0.77138	-0.2698	10	0.23891	T	0.37	.	7.1492	0.25601	0.0:0.7523:0.0:0.2477	.	171;171	B4DQL0;Q96EF0	.;MTMR8_HUMAN	I	171	ENSP00000394003:V171I;ENSP00000363985:V171I	ENSP00000363985:V171I	V	-	1	0	MTMR8	63486633	0.999000	0.42202	0.810000	0.32431	0.982000	0.71751	3.435000	0.52849	0.031000	0.15407	0.513000	0.50165	GTT		0.348	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677	
OTUD6A	139562	broad.mit.edu	37	X	69283015	69283015	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:69283015C>T	ENST00000338352.2	+	1	675	c.641C>T	c.(640-642)aCg>aTg	p.T214M		NM_207320.1	NP_997203.1	Q7L8S5	OTU6A_HUMAN	OTU deubiquitinase 6A	214	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|Variable-loop. {ECO:0000250}.				protein K11-linked deubiquitination (GO:0035871)|protein K27-linked deubiquitination (GO:1990167)|protein K29-linked deubiquitination (GO:0035523)|protein K33-linked deubiquitination (GO:1990168)		ubiquitin-specific protease activity (GO:0004843)	p.T214M(1)		autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(3)|urinary_tract(1)	23						GTGCGCACCACGGCATGGGGA	0.627																																					p.T214M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C641T	X						.						70.0	63.0	66.0					X																	69283015		2203	4300	6503	69199740	SO:0001583	missense	139562	exon1			AK098697	CCDS14395.1	Xq13.1	2014-02-24	2014-02-24			ENSG00000189401		"""OTU domain containing"""	32312	protein-coding gene	gene with protein product		300714	"""OTU domain containing 6A"""			23827681	Standard	NM_207320		Approved	FLJ25831, HSHIN6, DUBA2	uc004dxu.1	Q7L8S5		ENST00000338352.2:c.641C>T	X.37:g.69283015C>T	ENSP00000339389:p.Thr214Met	Somatic		Capture	Illumina HiSeq	Phase_I	69199740	NM_207320	B2RPB7	Missense_Mutation	SNP	ENST00000338352.2	37	CCDS14395.1	.	.	.	.	.	.	.	.	.	.	C	14.16	2.453075	0.43531	.	.	ENSG00000189401	ENST00000338352	T	0.30714	1.52	4.42	-1.96	0.07525	Ovarian tumour, otubain (2);	0.234395	0.42821	D	0.000641	T	0.16557	0.0398	N	0.16368	0.405	0.09310	N	1	P	0.43542	0.81	B	0.43916	0.436	T	0.16600	-1.0397	10	0.87932	D	0	.	4.0208	0.09665	0.2333:0.3334:0.3533:0.0799	.	214	Q7L8S5	OTU6A_HUMAN	M	214	ENSP00000339389:T214M	ENSP00000339389:T214M	T	+	2	0	OTUD6A	69199740	0.005000	0.15991	0.000000	0.03702	0.000000	0.00434	2.110000	0.41873	-0.595000	0.05828	-1.059000	0.02297	ACG		0.627	OTUD6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358763.1	NM_207320	
AWAT1	158833	broad.mit.edu	37	X	69456955	69456955	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:69456955G>A	ENST00000374521.3	+	4	358	c.317G>A	c.(316-318)gGc>gAc	p.G106D	AWAT1_ENST00000480702.1_3'UTR	NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	106					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)	p.G186D(1)		breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						CACCCCCATGGCCTCCTGACC	0.567																																					p.G106D												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G317A	X						.						78.0	50.0	59.0					X																	69456955		2203	4300	6503	69373680	SO:0001583	missense	158833	exon4			BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"""diacylglycerol O-acyltransferase 2-like 3"""	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.317G>A	X.37:g.69456955G>A	ENSP00000363645:p.Gly106Asp	Somatic		Capture	Illumina HiSeq	Phase_I	69373680	NM_001013579	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353190	0.82132	.	.	ENSG00000204195	ENST00000374521	T	0.19806	2.12	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000001	T	0.60881	0.2303	H	0.96861	3.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76143	-0.3067	10	0.87932	D	0	-11.9873	15.1083	0.72336	0.0:0.0:1.0:0.0	.	106	Q58HT5	AWAT1_HUMAN	D	106	ENSP00000363645:G106D	ENSP00000363645:G106D	G	+	2	0	AWAT1	69373680	1.000000	0.71417	0.746000	0.31095	0.914000	0.54420	8.999000	0.93557	2.118000	0.64928	0.405000	0.27470	GGC		0.567	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579	
P2RY4	5030	broad.mit.edu	37	X	69479031	69479031	+	Silent	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:69479031G>A	ENST00000374519.2	-	1	623	c.444C>T	c.(442-444)cgC>cgT	p.R148R		NM_002565.3	NP_002556.1	P51582	P2RY4_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 4	148					phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|transepithelial chloride transport (GO:0030321)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|uridine nucleotide receptor activity (GO:0015065)|UTP-activated nucleotide receptor activity (GO:0045030)	p.R148R(1)		cervix(2)|endometrium(2)|large_intestine(8)|lung(6)	18						CGAGGCGAGGGCGGCCCCAGC	0.602																																					p.R148R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C444T	X						.						55.0	50.0	52.0					X																	69479031		2203	4300	6503	69395756	SO:0001819	synonymous_variant	5030	exon1			X91852	CCDS14398.1	Xq13	2012-08-08			ENSG00000186912	ENSG00000186912		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8542	protein-coding gene	gene with protein product		300038				8537336	Standard	NM_002565		Approved	NRU, P2Y4, UNR, P2P	uc004dxz.1	P51582	OTTHUMG00000021769	ENST00000374519.2:c.444C>T	X.37:g.69479031G>A		Somatic		Capture	Illumina HiSeq	Phase_I	69395756	NM_002565	Q4VBB7|Q4VBB8|Q502W2|Q5JT22	Silent	SNP	ENST00000374519.2	37	CCDS14398.1																																																																																				0.602	P2RY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057058.2	NM_002565	
OGT	8473	broad.mit.edu	37	X	70782825	70782825	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	-	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:70782825delT	ENST00000373719.3	+	16	2323	c.2106delT	c.(2104-2106)actfs	p.T702fs	OGT_ENST00000373701.3_Frame_Shift_Del_p.T692fs	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	702					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)	p.F694fs*12(1)|p.F704fs*12(1)		breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					TGCCCCACACTTTTTTTATTG	0.398																																					p.T692fs												.	.	2	Deletion - Frameshift(2)	large_intestine(2)	c.2076delT	X						.						123.0	111.0	115.0					X																	70782825		2203	4300	6503	70699550	SO:0001589	frameshift_variant	8473	exon16			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.2106delT	X.37:g.70782825delT	ENSP00000362824:p.Thr702fs	Somatic		Capture	Illumina HiSeq	Phase_I	70699550	NM_181673	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Frame_Shift_Del	DEL	ENST00000373719.3	37	CCDS14414.1																																																																																				0.398	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
ACRC	93953	broad.mit.edu	37	X	70824220	70824220	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:70824220G>A	ENST00000373695.1	+	7	1630	c.1093G>A	c.(1093-1095)Gat>Aat	p.D365N	ACRC_ENST00000373696.3_Missense_Mutation_p.D365N			Q96QF7	ACRC_HUMAN	acidic repeat containing	365						nucleus (GO:0005634)		p.D365N(1)		autonomic_ganglia(1)|breast(1)|endometrium(15)|kidney(4)|large_intestine(4)|lung(20)|ovary(5)|prostate(1)|skin(2)|stomach(1)	54	Renal(35;0.156)					CTCCCAGCATGATTCATCTGA	0.483																																					p.D365N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1093A	X						.						70.0	56.0	60.0					X																	70824220		2203	4300	6503	70740945	SO:0001583	missense	93953	exon8			AJ311392	CCDS35326.1	Xq13.1	2010-08-05			ENSG00000147174	ENSG00000147174			15805	protein-coding gene	gene with protein product		300369					Standard	NM_052957		Approved		uc004eae.2	Q96QF7	OTTHUMG00000033327	ENST00000373695.1:c.1093G>A	X.37:g.70824220G>A	ENSP00000362799:p.Asp365Asn	Somatic		Capture	Illumina HiSeq	Phase_I	70740945	NM_052957	B9EG62	Missense_Mutation	SNP	ENST00000373695.1	37	CCDS35326.1	.	.	.	.	.	.	.	.	.	.	G	8.567	0.879215	0.17395	.	.	ENSG00000147174	ENST00000373696;ENST00000373695	T;T	0.32515	1.45;1.45	3.17	0.778	0.18543	.	.	.	.	.	T	0.15392	0.0371	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.08055	0.003	T	0.21552	-1.0242	9	0.41790	T	0.15	.	4.4513	0.11621	0.6807:0.0:0.3193:0.0	.	365	Q96QF7	ACRC_HUMAN	N	365	ENSP00000362800:D365N;ENSP00000362799:D365N	ENSP00000362799:D365N	D	+	1	0	ACRC	70740945	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.279000	0.08479	0.066000	0.16515	-0.370000	0.07254	GAT		0.483	ACRC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081856.1		
RGAG4	340526	broad.mit.edu	37	X	71350438	71350438	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:71350438G>T	ENST00000545866.1	-	1	1320	c.953C>A	c.(952-954)cCg>cAg	p.P318Q	NHSL2_ENST00000540800.1_Intron|RGAG4_ENST00000609883.1_Missense_Mutation_p.P318Q	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	318								p.P391Q(1)		cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					TCCAGGGAGCGGGATAGGCTT	0.473																																					p.P318Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C953A	X						.						108.0	101.0	103.0					X																	71350438		1924	4129	6053	71267163	SO:0001583	missense	340526	exon1			AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.953C>A	X.37:g.71350438G>T	ENSP00000441366:p.Pro318Gln	Somatic		Capture	Illumina HiSeq	Phase_I	71267163	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.351247	0.24512	.	.	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.11604	2.76;2.76	4.13	1.25	0.21368	.	.	.	.	.	T	0.03477	0.0100	N	0.08118	0	0.09310	N	1	P	0.42357	0.777	B	0.32864	0.154	T	0.32877	-0.9890	8	.	.	.	0.2252	2.2068	0.03937	0.1134:0.1894:0.4989:0.1984	.	318	Q5HYW3	RGAG4_HUMAN	Q	318	ENSP00000441366:P318Q;ENSP00000418667:P318Q	.	P	-	2	0	RGAG4	71267163	0.000000	0.05858	0.000000	0.03702	0.947000	0.59692	0.262000	0.18460	0.118000	0.18165	0.600000	0.82982	CCG		0.473	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
RLIM	51132	broad.mit.edu	37	X	73812150	73812150	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:73812150G>A	ENST00000332687.6	-	4	1218	c.1000C>T	c.(1000-1002)Cgg>Tgg	p.R334W	RLIM_ENST00000349225.2_Missense_Mutation_p.R334W	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	334					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.R334W(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TCTCTCTGCCGATATTCTCCA	0.473																																					p.R334W	Esophageal Squamous(169;1899 1923 14997 18818 32118)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1000T	X						.						78.0	67.0	71.0					X																	73812150		2203	4300	6503	73728875	SO:0001583	missense	51132	exon5			AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"""RING-type (C3HC4) zinc fingers"""	13429	protein-coding gene	gene with protein product	"""ring zinc finger protein NY-REN-43antigen"", ""LIM domain interacting ring finger protein"""	300379	"""ring finger protein 12"""	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1000C>T	X.37:g.73812150G>A	ENSP00000328059:p.Arg334Trp	Somatic		Capture	Illumina HiSeq	Phase_I	73728875	NM_183353	B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	G	11.98	1.800345	0.31869	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.12039	2.72;2.72	5.73	3.71	0.42584	.	0.000000	0.85682	D	0.000000	T	0.37100	0.0991	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.31024	-0.9958	10	0.87932	D	0	-0.9988	14.2778	0.66191	0.0:0.0:0.6274:0.3726	.	334	Q9NVW2	RNF12_HUMAN	W	334	ENSP00000328059:R334W;ENSP00000253571:R334W	ENSP00000328059:R334W	R	-	1	2	RLIM	73728875	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.598000	0.54038	1.121000	0.41925	0.600000	0.82982	CGG		0.473	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120	
ATRX	546	broad.mit.edu	37	X	76937787	76937787	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:76937787C>A	ENST00000373344.5	-	9	3175	c.2961G>T	c.(2959-2961)aaG>aaT	p.K987N	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.K949N	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	987					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.K987N(1)|p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						CTTCAGTTCCCTTTTTGCTCT	0.338			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.K987N			Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	.	.	2	Substitution - Missense(1)|Unknown(1)	large_intestine(1)|bone(1)	c.G2961T	X						.						87.0	95.0	92.0					X																	76937787		2203	4296	6499	76824443	SO:0001583	missense	546	exon9			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.2961G>T	X.37:g.76937787C>A	ENSP00000362441:p.Lys987Asn	Somatic		Capture	Illumina HiSeq	Phase_I	76824443	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	C	0.358	-0.941113	0.02322	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.92595	-3.03;-3.07	5.7	-0.229	0.13094	.	0.520753	0.18599	N	0.136509	D	0.86075	0.5846	L	0.40543	1.245	0.09310	N	0.999999	B;P;B;B	0.35272	0.181;0.493;0.277;0.181	B;B;B;B	0.33620	0.051;0.167;0.109;0.051	T	0.76809	-0.2822	10	0.51188	T	0.08	-2.963	10.4794	0.44684	0.0:0.426:0.0:0.574	.	987;919;949;987	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	N	987;949;914	ENSP00000362441:K987N;ENSP00000378967:K949N	ENSP00000362441:K987N	K	-	3	2	ATRX	76824443	0.000000	0.05858	0.011000	0.14972	0.096000	0.18686	-0.299000	0.08254	-0.033000	0.13736	0.513000	0.50165	AAG		0.338	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
ATP7A	538	broad.mit.edu	37	X	77301887	77301887	+	Silent	SNP	T	T	C			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:77301887T>C	ENST00000341514.6	+	23	4478	c.4323T>C	c.(4321-4323)gaT>gaC	p.D1441D	ATP7A_ENST00000343533.5_Silent_p.D1363D|ATP7A_ENST00000350425.4_Silent_p.D444D	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	1441					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)	p.D1441D(1)		breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TTGGAATAGATGATACCTCAA	0.443																																					p.D1441D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.T4323C	X						.						192.0	182.0	185.0					X																	77301887		2203	4296	6499	77188543	SO:0001819	synonymous_variant	538	exon23			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.4323T>C	X.37:g.77301887T>C		Somatic		Capture	Illumina HiSeq	Phase_I	77188543	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Silent	SNP	ENST00000341514.6	37	CCDS35339.1																																																																																				0.443	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
POU3F4	5456	broad.mit.edu	37	X	82763972	82763972	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:82763972G>A	ENST00000373200.2	+	1	704	c.640G>A	c.(640-642)Gac>Aac	p.D214N	RP3-326L13.3_ENST00000607789.1_lincRNA|RP3-326L13.2_ENST00000607095.1_RNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	214	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cochlea morphogenesis (GO:0090103)|forebrain neuron differentiation (GO:0021879)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|sensory perception of sound (GO:0007605)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	AT DNA binding (GO:0003680)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D214N(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	37						CACGCAGGCCGACGTGGGGTT	0.522																																					p.D214N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G640A	X						.						70.0	56.0	60.0					X																	82763972		2203	4300	6503	82650628	SO:0001583	missense	5456	exon1			X82324	CCDS14450.1	Xq21.1	2011-06-20	2007-07-13		ENSG00000196767	ENSG00000196767		"""Homeoboxes / POU class"""	9217	protein-coding gene	gene with protein product	"""brain-4"""	300039	"""POU domain class 3, transcription factor 4"""	DFN3		7911044, 7581392	Standard	NM_000307		Approved	BRN4, OTF9, DFNX2	uc004eeg.2	P49335	OTTHUMG00000021919	ENST00000373200.2:c.640G>A	X.37:g.82763972G>A	ENSP00000362296:p.Asp214Asn	Somatic		Capture	Illumina HiSeq	Phase_I	82650628	NM_000307	B2RC71|Q5H9G9|Q99410	Missense_Mutation	SNP	ENST00000373200.2	37	CCDS14450.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.607500	0.87157	.	.	ENSG00000196767	ENST00000373200	D	0.86230	-2.09	4.99	4.99	0.66335	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.85682	D	0.000000	D	0.92482	0.7613	M	0.69185	2.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92019	0.5624	10	0.40728	T	0.16	.	17.333	0.87271	0.0:0.0:1.0:0.0	.	214	P49335	PO3F4_HUMAN	N	214	ENSP00000362296:D214N	ENSP00000362296:D214N	D	+	1	0	POU3F4	82650628	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	9.558000	0.98132	2.211000	0.71520	0.525000	0.51046	GAC		0.522	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307	
KLHL4	56062	broad.mit.edu	37	X	86772939	86772939	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:86772939C>A	ENST00000373119.4	+	1	188	c.43C>A	c.(43-45)Cta>Ata	p.L15I	KLHL4_ENST00000373114.4_Missense_Mutation_p.L15I	NM_019117.4	NP_061990.2	Q9C0H6	KLHL4_HUMAN	kelch-like family member 4	15						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.L15I(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(29)|ovary(2)|prostate(1)|skin(1)	67						GAAACAGATCCTAAGGCTACG	0.478																																					p.L15I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C43A	X						.						120.0	109.0	113.0					X																	86772939		2203	4300	6503	86659595	SO:0001583	missense	56062	exon1			AF284765	CCDS14456.1, CCDS14457.1	Xq21.3	2013-01-30	2013-01-30		ENSG00000102271	ENSG00000102271		"""Kelch-like"", ""BTB/POZ domain containing"""	6355	protein-coding gene	gene with protein product		300348	"""kelch (Drosophila)-like 4"", ""kelch-like 4 (Drosophila)"""			11401425	Standard	NM_019117		Approved	KIAA1687, DKELCHL, KHL4	uc004efa.2	Q9C0H6	OTTHUMG00000021946	ENST00000373119.4:c.43C>A	X.37:g.86772939C>A	ENSP00000362211:p.Leu15Ile	Somatic		Capture	Illumina HiSeq	Phase_I	86659595	NM_057162	B2RTW2|Q9Y3J5	Missense_Mutation	SNP	ENST00000373119.4	37	CCDS14457.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508860	0.64410	.	.	ENSG00000102271	ENST00000373119;ENST00000373114	D;D	0.89123	-2.47;-2.45	5.05	2.38	0.29361	.	0.104774	0.37761	N	0.001948	D	0.92711	0.7683	M	0.75264	2.295	0.47698	D	0.999497	D;D	0.76494	0.999;0.999	D;D	0.85130	0.997;0.989	D	0.90969	0.4818	10	0.87932	D	0	.	8.8564	0.35231	0.0:0.7512:0.0:0.2488	.	15;15	Q9C0H6;Q9C0H6-2	KLHL4_HUMAN;.	I	15	ENSP00000362211:L15I;ENSP00000362206:L15I	ENSP00000362206:L15I	L	+	1	2	KLHL4	86659595	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.641000	0.46587	0.184000	0.20083	0.513000	0.50165	CTA		0.478	KLHL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057413.1		
PCDH11X	27328	broad.mit.edu	37	X	91873780	91873780	+	Silent	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:91873780A>G	ENST00000373094.1	+	7	4730	c.3885A>G	c.(3883-3885)ggA>ggG	p.G1295G	PCDH11X_ENST00000406881.1_Silent_p.G1287G|PCDH11X_ENST00000373097.1_Silent_p.G1285G|PCDH11X_ENST00000504220.2_3'UTR|PCDH11X_ENST00000361655.2_Silent_p.G1277G|PCDH11X_ENST00000373088.1_Silent_p.G1258G|PCDH11X_ENST00000298274.8_Silent_p.G1258G	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1295					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.G1295G(1)		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						TTGATCAGGGAGTGCAAGGTA	0.468																																					p.G1295G	NSCLC(38;925 1092 2571 38200 45895)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A3885G	X						.						286.0	249.0	262.0					X																	91873780		2203	4300	6503	91760436	SO:0001819	synonymous_variant	27328	exon7			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.3885A>G	X.37:g.91873780A>G		Somatic		Capture	Illumina HiSeq	Phase_I	91760436	NM_032968	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	37	CCDS14461.1																																																																																				0.468	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
PCDH19	57526	broad.mit.edu	37	X	99662505	99662505	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	-	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:99662505delG	ENST00000373034.4	-	1	2766	c.1091delC	c.(1090-1092)ccgfs	p.P364fs	PCDH19_ENST00000255531.7_Frame_Shift_Del_p.P364fs|PCDH19_ENST00000420881.2_Frame_Shift_Del_p.P364fs	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	364	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P364fs*4(1)		breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						CACGTAGCCCGGGGGGGCGCT	0.607																																					p.P364fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1091delC	X						.						43.0	47.0	46.0					X																	99662505		2188	4265	6453	99549161	SO:0001589	frameshift_variant	57526	exon1			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.1091delC	X.37:g.99662505delG	ENSP00000362125:p.Pro364fs	Somatic		Capture	Illumina HiSeq	Phase_I	99549161	NM_001105243	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Frame_Shift_Del	DEL	ENST00000373034.4	37	CCDS55462.1																																																																																				0.607	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2	NM_020766	
NOX1	27035	broad.mit.edu	37	X	100105207	100105207	+	Nonsense_Mutation	SNP	G	G	A	rs369560908		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:100105207G>A	ENST00000372966.3	-	9	1271	c.1066C>T	c.(1066-1068)Cga>Tga	p.R356*	NOX1_ENST00000372964.1_Intron|NOX1_ENST00000217885.5_Nonsense_Mutation_p.R356*|NOX1_ENST00000372960.4_Nonsense_Mutation_p.R319*	NM_007052.4|NM_013955.2	NP_008983.2|NP_039249.1	Q9Y5S8	NOX1_HUMAN	NADPH oxidase 1	356	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				angiogenesis (GO:0001525)|cell migration (GO:0016477)|cellular response to hyperoxia (GO:0071455)|cellular stress response to acidic pH (GO:1990451)|extracellular matrix organization (GO:0030198)|hydrogen peroxide metabolic process (GO:0042743)|inflammatory response (GO:0006954)|intracellular pH elevation (GO:0051454)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|oxygen metabolic process (GO:0072592)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of JNK cascade (GO:0046330)|positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902177)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation vascular endothelial growth factor production (GO:0010575)|proton transport (GO:0015992)|regulation of blood pressure (GO:0008217)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|respiratory burst (GO:0045730)|signal transduction (GO:0007165)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	cell junction (GO:0030054)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|invadopodium membrane (GO:0071438)|NADPH oxidase complex (GO:0043020)	metal ion binding (GO:0046872)|NADP binding (GO:0050661)|Rac GTPase binding (GO:0048365)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated proton channel activity (GO:0030171)	p.R356*(1)		cervix(1)|lung(3)|ovary(1)|skin(2)	7						CCTGCTGCTCGGATATGAATG	0.463													G|||	3	0.000794702	0.0	0.0	3775	,	,		14741	0.0		0.0	False		,,,				2504	0.0031				p.R356X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1066T	X						.	G	stop/ARG,stop/ARG	0,3835		0,0,1632,571	71.0	71.0	71.0		1066,1066	-0.3	0.3	X		71	1,6727		0,1,2427,1872	no	stop-gained,stop-gained	NOX1	NM_007052.4,NM_013955.2	,	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	,	356/565,356/516	100105207	1,10562	2203	4300	6503	99991863	SO:0001587	stop_gained	27035	exon9			AF127763	CCDS14474.1, CCDS14475.1, CCDS65298.1	Xq22	2008-08-01			ENSG00000007952	ENSG00000007952			7889	protein-coding gene	gene with protein product	"""mitogenic oxidase (pyridine nucleotide-dependent superoxide-generating)"", ""NADPH oxidase homolog-1"", ""NADPH oxidase 1 variant NOH-1L"""	300225				10485709, 10615049	Standard	NM_007052		Approved	NOH1, NOH-1, MOX1, GP91-2	uc004egj.3	Q9Y5S8	OTTHUMG00000022007	ENST00000372966.3:c.1066C>T	X.37:g.100105207G>A	ENSP00000362057:p.Arg356*	Somatic		Capture	Illumina HiSeq	Phase_I	99991863	NM_007052	A8K836|O95691|Q2PP02	Nonsense_Mutation	SNP	ENST00000372966.3	37	CCDS14474.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.633178|4.633178	0.87660|0.87660	0.0|0.0	1.49E-4|1.49E-4	ENSG00000007952|ENSG00000007952	ENST00000427768|ENST00000372966;ENST00000217885;ENST00000372960;ENST00000372957	.|.	.|.	.|.	3.87|3.87	-0.288|-0.288	0.12855|0.12855	.|.	.|0.167856	.|0.40302	.|N	.|0.001129	T|.	0.13329|.	0.0323|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.36866|.	-0.9730|.	3|.	.|0.02654	.|T	.|1	3.7734|3.7734	4.623|4.623	0.12465|0.12465	0.1783:0.0:0.5225:0.2992|0.1783:0.0:0.5225:0.2992	.|.	.|.	.|.	.|.	L|X	40|356;356;319;45	.|.	.|ENSP00000217885:R356X	P|R	-|-	2|1	0|2	NOX1|NOX1	99991863|99991863	1.000000|1.000000	0.71417|0.71417	0.317000|0.317000	0.25265|0.25265	0.979000|0.979000	0.70002|0.70002	3.703000|3.703000	0.54808|0.54808	-0.459000|-0.459000	0.07013|0.07013	0.422000|0.422000	0.28245|0.28245	CCG|CGA		0.463	NOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057495.1	NM_007052	
USP26	83844	broad.mit.edu	37	X	132161205	132161205	+	Frame_Shift_Del	DEL	A	A	-	rs61758857		TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	-	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:132161205delA	ENST00000511190.1	-	6	1513	c.1044delT	c.(1042-1044)tttfs	p.F348fs	USP26_ENST00000370832.1_Frame_Shift_Del_p.F348fs|USP26_ENST00000406273.1_Frame_Shift_Del_p.F348fs	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	348	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)	p.F348fs*7(1)		breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					AGGTATCTTTAAAAAAAAGTA	0.388																																					p.F348fs	NSCLC(104;342 1621 36940 47097 52632)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1044delT	X	GRCh37	CM077651	USP26	M	rs61758857	.						35.0	37.0	36.0					X																	132161205		2198	4295	6493	131988871	SO:0001589	frameshift_variant	83844	exon1			AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1044delT	X.37:g.132161205delA	ENSP00000423390:p.Phe348fs	Somatic		Capture	Illumina HiSeq	Phase_I	131988871	NM_031907	B9WRT6|Q5H9H4	Frame_Shift_Del	DEL	ENST00000511190.1	37	CCDS14635.1																																																																																				0.388	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
F8	2157	broad.mit.edu	37	X	154221252	154221252	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	Illumina			Illumina GAIIx	TCGA-AA-3947-01A-01W-0995-10	TCGA-AA-3947-10A-01W-0995-10	g.chrX:154221252A>G	ENST00000360256.4	-	4	760	c.560T>C	c.(559-561)tTg>tCg	p.L187S		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	187	F5/8 type A 1.|Plastocyanin-like 1.				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.L187S(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)	GCCTGAATTCAAGTCTTTTAC	0.433																																					p.L187S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T560C	X	GRCh37	CM053264	F8	M		.						180.0	154.0	163.0					X																	154221252		2203	4300	6503	153874446	SO:0001583	missense	2157	exon4			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.560T>C	X.37:g.154221252A>G	ENSP00000353393:p.Leu187Ser	Somatic		Capture	Illumina HiSeq	Phase_I	153874446	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	A	14.12	2.440205	0.43326	.	.	ENSG00000185010	ENST00000360256;ENST00000423959	D;D	0.99089	-5.41;-5.41	4.74	4.74	0.60224	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.813404	0.11080	N	0.601961	D	0.98554	0.9517	L	0.39020	1.185	0.25597	N	0.986639	P;D	0.71674	0.901;0.998	P;D	0.70935	0.761;0.971	D	0.94904	0.8059	10	0.72032	D	0.01	-0.0024	9.8977	0.41329	1.0:0.0:0.0:0.0	.	152;187	B1B0G8;P00451	.;FA8_HUMAN	S	187;152	ENSP00000353393:L187S;ENSP00000409446:L152S	ENSP00000353393:L187S	L	-	2	0	F8	153874446	0.988000	0.35896	0.920000	0.36463	0.217000	0.24651	3.130000	0.50508	1.672000	0.50884	0.425000	0.28330	TTG		0.433	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
