#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
HTRA1	5654	broad.mit.edu	37	10	124248513	124248513	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr10:124248513C>T	ENST00000368984.3	+	2	696	c.568C>T	c.(568-570)Cgc>Tgc	p.R190C		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	190					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R190C(1)		endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				CGAATTGTTTCGCAAGTAAAG	0.448																																					p.R190C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C568T	10						.						99.0	92.0	95.0					10																	124248513		2203	4300	6503	124238503	SO:0001583	missense	5654	exon2			AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"""Serine peptidases / Serine peptidases"""	9476	protein-coding gene	gene with protein product		602194	"""protease, serine, 11 (IGF binding)"""	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.568C>T	10.37:g.124248513C>T	ENSP00000357980:p.Arg190Cys	Somatic		Capture	Illumina HiSeq	Phase_I	124238503	NM_002775	D3DRE4|Q9UNS5	Missense_Mutation	SNP	ENST00000368984.3	37	CCDS7630.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808957	0.90707	.	.	ENSG00000166033	ENST00000368984;ENST00000435263	D	0.88509	-2.39	5.42	5.42	0.78866	Peptidase cysteine/serine, trypsin-like (1);	0.000000	0.85682	D	0.000000	D	0.93259	0.7852	M	0.76002	2.32	0.80722	D	1	D	0.76494	0.999	P	0.58620	0.842	D	0.92818	0.6270	10	0.45353	T	0.12	-7.6266	19.2248	0.93814	0.0:1.0:0.0:0.0	.	190	Q92743	HTRA1_HUMAN	C	190;157	ENSP00000357980:R190C	ENSP00000357980:R190C	R	+	1	0	HTRA1	124238503	1.000000	0.71417	0.964000	0.40570	0.979000	0.70002	4.714000	0.61902	2.532000	0.85374	0.655000	0.94253	CGC		0.448	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775	
ITIH2	3698	broad.mit.edu	37	10	7768964	7768964	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr10:7768964T>G	ENST00000358415.4	+	10	1202	c.1036T>G	c.(1036-1038)Ttc>Gtc	p.F346V	ITIH2_ENST00000379587.4_Missense_Mutation_p.F335V	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	346	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.F346V(1)		NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						AGAAGACCATTTCTCTGTGAT	0.383																																					p.F346V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1036G	10						.						118.0	112.0	114.0					10																	7768964		2203	4300	6503	7808970	SO:0001583	missense	3698	exon10			X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1036T>G	10.37:g.7768964T>G	ENSP00000351190:p.Phe346Val	Somatic		Capture	Illumina HiSeq	Phase_I	7808970	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.227906	0.79576	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.78481	-1.18;-1.18	5.09	5.09	0.68999	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.85716	0.5761	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87339	0.2330	10	0.87932	D	0	-25.6733	14.8729	0.70471	0.0:0.0:0.0:1.0	.	346	P19823	ITIH2_HUMAN	V	346;335	ENSP00000351190:F346V;ENSP00000368906:F335V	ENSP00000351190:F346V	F	+	1	0	ITIH2	7808970	1.000000	0.71417	0.993000	0.49108	0.818000	0.46254	7.596000	0.82721	1.922000	0.55676	0.450000	0.29827	TTC		0.383	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
GLRX3	10539	broad.mit.edu	37	10	131943509	131943509	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr10:131943509G>C	ENST00000368644.1	+	2	149	c.127G>C	c.(127-129)Gct>Cct	p.A43P	GLRX3_ENST00000331244.5_Missense_Mutation_p.A43P	NM_001199868.1	NP_001186797.1	O76003	GLRX3_HUMAN	glutaredoxin 3	43	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|regulation of the force of heart contraction (GO:0002026)	extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	electron carrier activity (GO:0009055)|iron-sulfur cluster binding (GO:0051536)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein disulfide oxidoreductase activity (GO:0015035)	p.A43P(2)		endometrium(1)|large_intestine(5)|lung(7)	13		all_cancers(35;9.59e-07)|all_epithelial(44;1.48e-06)|Lung NSC(174;0.00566)|all_lung(145;0.00949)|Colorectal(57;0.142)|all_neural(114;0.16)|Breast(234;0.173)|Glioma(114;0.222)		OV - Ovarian serous cystadenocarcinoma(35;0.00218)		GGCACCATGGGCTCCACAGTG	0.358																																					p.A43P												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G127C	10						.						93.0	93.0	93.0					10																	131943509		2203	4300	6503	131833499	SO:0001583	missense	10539	exon2			AJ010841	CCDS7661.1	10q26	2009-05-29	2007-08-16	2007-08-16	ENSG00000108010	ENSG00000108010			15987	protein-coding gene	gene with protein product	"""glutaredoxin 4"""	612754	"""thioredoxin-like 2"""	TXNL2		10636891, 11124703	Standard	NM_006541		Approved	PICOT, bA500G10.4, GRX3, GLRX4, GRX4	uc001lkm.2	O76003	OTTHUMG00000019267	ENST00000368644.1:c.127G>C	10.37:g.131943509G>C	ENSP00000357633:p.Ala43Pro	Somatic		Capture	Illumina HiSeq	Phase_I	131833499	NM_001199868	B3KMP7|B3KMQ5|D3DRG2|Q5JV01|Q96CE0|Q9P1B0|Q9P1B1	Missense_Mutation	SNP	ENST00000368644.1	37	CCDS7661.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481132	0.63849	.	.	ENSG00000108010	ENST00000331244;ENST00000368644	T;T	0.03301	3.98;3.98	5.18	4.27	0.50696	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.000000	0.85682	D	0.000000	T	0.24005	0.0581	M	0.92738	3.34	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.15752	-1.0426	10	0.62326	D	0.03	-9.4077	13.9058	0.63834	0.0:0.0:0.8464:0.1536	.	43	O76003	GLRX3_HUMAN	P	43	ENSP00000330836:A43P;ENSP00000357633:A43P	ENSP00000330836:A43P	A	+	1	0	GLRX3	131833499	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	7.525000	0.81892	1.391000	0.46566	-0.309000	0.09137	GCT		0.358	GLRX3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051021.1	NM_006541	
RNH1	6050	broad.mit.edu	37	11	499973	499974	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:499973_499974insC	ENST00000534797.1	-	3	1705_1706	c.298_299insG	c.(298-300)gccfs	p.A100fs	RNH1_ENST00000356187.5_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000397604.3_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000397615.2_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000354420.2_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000533410.1_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000438658.2_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000397614.1_Frame_Shift_Ins_p.A100fs|RNH1_ENST00000533592.1_5'Flank			O60930	RNH1_HUMAN	ribonuclease/angiogenin inhibitor 1	0					mitochondrial DNA replication (GO:0006264)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)|RNA binding (GO:0003723)|RNA-DNA hybrid ribonuclease activity (GO:0004523)	p.A100fs*79(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(49;3.02e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;1.26e-26)|Epithelial(43;1.34e-25)|OV - Ovarian serous cystadenocarcinoma(40;5.31e-20)|BRCA - Breast invasive adenocarcinoma(625;8.01e-05)|Lung(200;0.0378)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CCCGCAGCCGGCCCCCGTCAGG	0.688																																					p.A100fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.299_300insG	11						.																																			489974	SO:0001589	frameshift_variant	6050	exon4				CCDS7697.1	11p15.5	2008-02-05	2005-06-01	2005-06-01	ENSG00000023191	ENSG00000023191			10074	protein-coding gene	gene with protein product		173320	"""ribonuclease/angiogenin inhibitor"""	RNH			Standard	NM_203386		Approved	RAI	uc001lpo.1	P13489	OTTHUMG00000119086	ENST00000534797.1:c.299dupG	11.37:g.499978_499978dupC	ENSP00000433999:p.Ala100fs	Somatic		Capture	Illumina HiSeq	Phase_I	489973	NM_203388	B3KQU4|O60523|O60857|Q57Z93|Q5U0C1|Q6FHD4	Frame_Shift_Ins	INS	ENST00000534797.1	37	CCDS7697.1																																																																																				0.688	RNH1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384301.1	NM_203389	
B3GNT1	11041	broad.mit.edu	37	11	66114134	66114135	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:66114134_66114135insG	ENST00000311181.4	-	1	1028_1029	c.882_883insC	c.(880-885)ccctgcfs	p.C295fs	BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank|RP11-867G23.8_ENST00000531602.1_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	295					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)	p.C295fs*68(1)		breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						GGTGCCTGGCAGGGGGTGCACA	0.614																																					p.C295fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.883_884insC	11						.																																			65870711	SO:0001589	frameshift_variant	11041	exon1			AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"""Beta 3-glycosyltransferases"""	15685	protein-coding gene	gene with protein product	"""N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"""	605517	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"""	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.883dupC	11.37:g.66114139_66114139dupG	ENSP00000309096:p.Cys295fs	Somatic		Capture	Illumina HiSeq	Phase_I	65870710	NM_006876	Q4TTN0	Frame_Shift_Ins	INS	ENST00000311181.4	37	CCDS8136.1																																																																																				0.614	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876	
TTC17	55761	broad.mit.edu	37	11	43400785	43400785	+	Silent	SNP	G	G	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:43400785G>T	ENST00000039989.4	+	2	176	c.162G>T	c.(160-162)gtG>gtT	p.V54V	TTC17_ENST00000299240.6_Silent_p.V54V|RP11-484D2.5_ENST00000530042.1_RNA	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	54					actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)		p.V54V(1)		breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						GCTTGCAGGTGGATTCACCAA	0.358																																					p.V54V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G162T	11						.						150.0	155.0	154.0					11																	43400785		2203	4300	6503	43357361	SO:0001819	synonymous_variant	55761	exon2			AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.162G>T	11.37:g.43400785G>T		Somatic		Capture	Illumina HiSeq	Phase_I	43357361	NM_018259	G3XAB3|Q8NEC0	Silent	SNP	ENST00000039989.4	37	CCDS31466.1																																																																																				0.358	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
NUP160	23279	broad.mit.edu	37	11	47809761	47809761	+	Missense_Mutation	SNP	G	G	A	rs535059681		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:47809761G>A	ENST00000378460.2	-	31	3765	c.3719C>T	c.(3718-3720)aCg>aTg	p.T1240M	NUP160_ENST00000530326.1_Missense_Mutation_p.T1126M	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	1240					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.T1240M(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						AAAGACTGGCGTTAAGGGAAG	0.398																																					p.T1240M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3719T	11						.						56.0	53.0	54.0					11																	47809761		2201	4298	6499	47766337	SO:0001583	missense	23279	exon31			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.3719C>T	11.37:g.47809761G>A	ENSP00000367721:p.Thr1240Met	Somatic		Capture	Illumina HiSeq	Phase_I	47766337	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Missense_Mutation	SNP	ENST00000378460.2	37	CCDS31484.1	.	.	.	.	.	.	.	.	.	.	G	17.96	3.515723	0.64634	.	.	ENSG00000030066	ENST00000378460;ENST00000530326	T;T	0.49432	1.37;0.78	5.78	3.87	0.44632	.	0.159743	0.56097	D	0.000039	T	0.53706	0.1813	L	0.55481	1.735	0.32310	N	0.563912	D	0.71674	0.998	P	0.56216	0.794	T	0.63462	-0.6632	10	0.49607	T	0.09	.	9.5399	0.39246	0.0666:0.0:0.6803:0.253	.	1240	Q12769	NU160_HUMAN	M	1240;1126	ENSP00000367721:T1240M;ENSP00000433590:T1126M	ENSP00000367721:T1240M	T	-	2	0	NUP160	47766337	1.000000	0.71417	0.932000	0.37286	0.963000	0.63663	3.147000	0.50639	0.766000	0.33244	0.549000	0.68633	ACG		0.398	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
OR8K1	390157	broad.mit.edu	37	11	56113952	56113952	+	Silent	SNP	A	A	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:56113952A>C	ENST00000279783.2	+	1	532	c.438A>C	c.(436-438)gtA>gtC	p.V146V		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	146						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V146V(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					CAGAGAAAGTACTTTGGGTGC	0.398										HNSCC(65;0.19)																											p.V146V												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A438C	11						.						199.0	201.0	200.0					11																	56113952		2201	4296	6497	55870528	SO:0001819	synonymous_variant	390157	exon1			AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.438A>C	11.37:g.56113952A>C		Somatic		Capture	Illumina HiSeq	Phase_I	55870528	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																				0.398	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
NUMA1	4926	broad.mit.edu	37	11	71719737	71719737	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:71719737G>C	ENST00000393695.3	-	20	5544	c.5213C>G	c.(5212-5214)aCc>aGc	p.T1738S	NUMA1_ENST00000358965.6_Missense_Mutation_p.T1724S|NUMA1_ENST00000351960.6_Missense_Mutation_p.T602S	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1									p.T1738S(1)		central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TCCTGACCTGGTGATACTGAG	0.502			T	RARA	APL																																p.T1738S			Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5213G	11						.						62.0	60.0	61.0					11																	71719737		2200	4293	6493	71397385	SO:0001583	missense	4926	exon20			Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5213C>G	11.37:g.71719737G>C	ENSP00000377298:p.Thr1738Ser	Somatic		Capture	Illumina HiSeq	Phase_I	71397385	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.71|18.71	3.683049|3.683049	0.68157|0.68157	.|.	.|.	ENSG00000137497|ENSG00000137497	ENST00000541584|ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	.|T;T;T	.|0.24151	.|1.87;2.33;2.33	4.74|4.74	4.74|4.74	0.60224|0.60224	.|.	.|0.359140	.|0.24096	.|N	.|0.041586	T|T	0.21509|0.21509	0.0518|0.0518	N|N	0.19112|0.19112	0.55|0.55	0.31362|0.31362	N|N	0.681277|0.681277	.|P;B;B;P;P	.|0.46859	.|0.51;0.143;0.017;0.51;0.885	.|B;B;B;B;B	.|0.43052	.|0.107;0.117;0.019;0.107;0.406	T|T	0.04930|0.04930	-1.0917|-1.0917	5|10	.|0.41790	.|T	.|0.15	.|.	17.8772|17.8772	0.88828|0.88828	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1744;1208;1724;1738;602	.|Q4LE64;Q59HB8;Q14980-2;Q14980;Q9BTE9	.|.;.;.;NUMA1_HUMAN;.	A|S	569|602;1724;1738;1287;693	.|ENSP00000260051:T602S;ENSP00000351851:T1724S;ENSP00000377298:T1738S	.|ENSP00000260051:T602S	P|T	-|-	1|2	0|0	NUMA1|NUMA1	71397385|71397385	1.000000|1.000000	0.71417|0.71417	0.865000|0.865000	0.33974|0.33974	0.771000|0.771000	0.43674|0.43674	3.894000|3.894000	0.56250|0.56250	2.618000|2.618000	0.88619|0.88619	0.561000|0.561000	0.74099|0.74099	CCA|ACC		0.502	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
TYR	7299	broad.mit.edu	37	11	89018075	89018075	+	Missense_Mutation	SNP	T	T	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr11:89018075T>G	ENST00000263321.5	+	4	1821	c.1319T>G	c.(1318-1320)aTt>aGt	p.I440S		NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	440					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.I440S(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	GATTTCTTTATTTCATCCAAA	0.368																																					p.I440S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1319G	11						.						71.0	72.0	72.0					11																	89018075		2201	4298	6499	88657723	SO:0001583	missense	7299	exon4			M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.1319T>G	11.37:g.89018075T>G	ENSP00000263321:p.Ile440Ser	Somatic		Capture	Illumina HiSeq	Phase_I	88657723	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.377839	0.42105	.	.	ENSG00000077498	ENST00000263321	D	0.98602	-5.02	4.68	4.68	0.58851	Uncharacterised domain, di-copper centre (2);	0.285120	0.33005	N	0.005384	D	0.95277	0.8468	M	0.63843	1.955	0.37593	D	0.920243	P	0.43094	0.799	B	0.33339	0.162	D	0.93963	0.7242	9	.	.	.	.	5.5118	0.16884	0.1529:0.0821:0.0:0.765	.	440	P14679	TYRO_HUMAN	S	440	ENSP00000263321:I440S	.	I	+	2	0	TYR	88657723	0.972000	0.33761	1.000000	0.80357	0.960000	0.62799	2.048000	0.41278	1.760000	0.52011	0.454000	0.30748	ATT		0.368	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
TENC1	23371	broad.mit.edu	37	12	53452902	53452903	+	Frame_Shift_Ins	INS	-	-	C	rs142183380		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr12:53452902_53452903insC	ENST00000314250.6	+	18	1767_1768	c.1477_1478insC	c.(1477-1479)accfs	p.T493fs	TENC1_ENST00000546602.1_Frame_Shift_Ins_p.T493fs|TENC1_ENST00000379902.3_Frame_Shift_Ins_p.T369fs|TENC1_ENST00000549700.1_Frame_Shift_Ins_p.T493fs|TENC1_ENST00000451358.1_Frame_Shift_Ins_p.T493fs|TENC1_ENST00000552570.1_Frame_Shift_Ins_p.T493fs|TENC1_ENST00000314276.3_Frame_Shift_Ins_p.T503fs	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	493	Pro-rich.				cellular homeostasis (GO:0019725)|collagen metabolic process (GO:0032963)|intracellular signal transduction (GO:0035556)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|multicellular organismal homeostasis (GO:0048871)|negative regulation of cell proliferation (GO:0008285)|response to muscle activity (GO:0014850)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.A496fs*31(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(19)|ovary(1)|pancreas(1)|stomach(3)	34						TCCCCGGCAGACCCCCCCGGCA	0.678																																					p.T503fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1507_1508insC	12						.																																			51739170	SO:0001589	frameshift_variant	23371	exon18			AF518729	CCDS8842.1, CCDS8843.1, CCDS8844.1	12q13.13	2013-02-14	2004-03-05			ENSG00000111077		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	19737	protein-coding gene	gene with protein product	"""tensin 2"""	607717	"""tensin like C1 domain-containing phosphatase"""				Standard	NM_015319		Approved	KIAA1075, C1-TEN, TNS2	uc001sbp.3	Q63HR2	OTTHUMG00000169730	ENST00000314250.6:c.1484dupC	12.37:g.53452909_53452909dupC	ENSP00000319684:p.Thr493fs	Somatic		Capture	Illumina HiSeq	Phase_I	51739169	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Frame_Shift_Ins	INS	ENST00000314250.6	37	CCDS8843.1																																																																																				0.678	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754	
TAS2R8	50836	broad.mit.edu	37	12	10959036	10959036	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr12:10959036G>A	ENST00000240615.2	-	1	856	c.544C>T	c.(544-546)Ccc>Tcc	p.P182S		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	182					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)|taste receptor activity (GO:0008527)	p.P182S(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						AGAGTCAAGGGTTCAAAGTAT	0.328																																					p.P182S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C544T	12						.						155.0	138.0	144.0					12																	10959036		2203	4300	6503	10850303	SO:0001583	missense	50836	exon1			AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.544C>T	12.37:g.10959036G>A	ENSP00000240615:p.Pro182Ser	Somatic		Capture	Illumina HiSeq	Phase_I	10850303	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	37	CCDS8632.1	.	.	.	.	.	.	.	.	.	.	G	1.650	-0.514270	0.04200	.	.	ENSG00000121314	ENST00000240615	T	0.35605	1.3	4.92	-1.99	0.07457	GPCR, rhodopsin-like superfamily (1);	1.020170	0.07876	U	0.968679	T	0.18467	0.0443	L	0.28274	0.84	0.09310	N	1	B	0.15141	0.012	B	0.24006	0.05	T	0.31888	-0.9927	10	0.11182	T	0.66	.	0.7738	0.01029	0.1927:0.1602:0.2503:0.3968	.	182	Q9NYW2	TA2R8_HUMAN	S	182	ENSP00000240615:P182S	ENSP00000240615:P182S	P	-	1	0	TAS2R8	10850303	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.238000	0.02919	-0.046000	0.13446	0.557000	0.71058	CCC		0.328	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
FOXM1	2305	broad.mit.edu	37	12	2973489	2973489	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr12:2973489delG	ENST00000359843.3	-	8	1331	c.1263delC	c.(1261-1263)cccfs	p.P421fs	FOXM1_ENST00000537018.1_5'Flank|FOXM1_ENST00000342628.2_Frame_Shift_Del_p.P421fs|FOXM1_ENST00000361953.3_Frame_Shift_Del_p.P406fs	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1	421					cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			CACCCACCTTGGGGGCAATGC	0.542																																					p.P406fs												.	.	0			c.1218delC	12						.						106.0	125.0	119.0					12																	2973489		2202	4300	6502	2843750	SO:0001589	frameshift_variant	2305	exon7			Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1263delC	12.37:g.2973489delG	ENSP00000352901:p.Pro421fs	None		Capture	Illumina HiSeq	Phase_I	2843750	NM_202003	O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Frame_Shift_Del	DEL	ENST00000359843.3	37	CCDS8515.1																																																																																				0.542	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953	
GLI1	2735	broad.mit.edu	37	12	57864215	57864215	+	Frame_Shift_Del	DEL	T	T	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T	T	T	T	T	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr12:57864215delT	ENST00000228682.2	+	12	1783	c.1692delT	c.(1690-1692)cctfs	p.P564fs	GLI1_ENST00000543426.1_Frame_Shift_Del_p.P436fs|GLI1_ENST00000546141.1_Frame_Shift_Del_p.P523fs	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	564					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			TGGCCTCTCCTTTCCCCCCTG	0.642																																					p.P436fs	Pancreas(157;841 1936 10503 41495 50368)											.	.	0			c.1308delT	12						.						59.0	60.0	60.0					12																	57864215		2203	4300	6503	56150482	SO:0001589	frameshift_variant	2735	exon10				CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1692delT	12.37:g.57864215delT	ENSP00000228682:p.Pro564fs	None		Capture	Illumina HiSeq	Phase_I	56150482	NM_001160045	D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Frame_Shift_Del	DEL	ENST00000228682.2	37	CCDS8940.1																																																																																				0.642	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
C12orf29	91298	broad.mit.edu	37	12	88439542	88439542	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr12:88439542A>G	ENST00000356891.3	+	5	808	c.605A>G	c.(604-606)aAt>aGt	p.N202S	C12orf29_ENST00000548757.2_3'UTR	NM_001009894.2	NP_001009894.2	Q8N999	CL029_HUMAN	chromosome 12 open reading frame 29	202					hematopoietic progenitor cell differentiation (GO:0002244)			p.N202S(1)		large_intestine(3)|lung(1)|ovary(1)	5						ACAAATATCAATGGAAACCCA	0.343																																					p.N202S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A605G	12						.						66.0	65.0	65.0					12																	88439542		2203	4299	6502	86963673	SO:0001583	missense	91298	exon5			AL137488	CCDS31866.1	12q21.32	2012-05-30			ENSG00000133641	ENSG00000133641			25322	protein-coding gene	gene with protein product						14702039	Standard	NM_001009894		Approved	DKFZp434N2030	uc001tao.3	Q8N999	OTTHUMG00000169870	ENST00000356891.3:c.605A>G	12.37:g.88439542A>G	ENSP00000349358:p.Asn202Ser	Somatic		Capture	Illumina HiSeq	Phase_I	86963673	NM_001009894	Q569K5|Q6AWA8|Q6PEK5|Q8IYQ5|Q9NT75	Missense_Mutation	SNP	ENST00000356891.3	37	CCDS31866.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.492548	0.84962	.	.	ENSG00000133641	ENST00000356891	T	0.47528	0.84	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.69142	0.3078	M	0.78801	2.425	0.58432	D	0.999999	D	0.71674	0.998	D	0.80764	0.994	T	0.73620	-0.3925	10	0.87932	D	0	-13.8994	14.4213	0.67185	1.0:0.0:0.0:0.0	.	202	Q8N999	CL029_HUMAN	S	202	ENSP00000349358:N202S	ENSP00000349358:N202S	N	+	2	0	C12orf29	86963673	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.385000	0.90163	2.153000	0.67306	0.533000	0.62120	AAT		0.343	C12orf29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406335.1	NM_001009894	
STARD13	90627	broad.mit.edu	37	13	33681011	33681011	+	Missense_Mutation	SNP	A	A	C	rs368036706		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr13:33681011A>C	ENST00000336934.5	-	13	3224	c.3108T>G	c.(3106-3108)caT>caG	p.H1036Q	STARD13_ENST00000399365.3_Missense_Mutation_p.H918Q|STARD13_ENST00000255486.4_Missense_Mutation_p.H1028Q	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	1036	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)	p.H1036Q(1)		breast(2)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	40	all_epithelial(80;0.155)	Lung SC(185;0.0367)		all cancers(112;1.31e-05)|Epithelial(112;0.000142)|BRCA - Breast invasive adenocarcinoma(63;0.00936)|OV - Ovarian serous cystadenocarcinoma(117;0.0533)|Lung(94;0.143)|GBM - Glioblastoma multiforme(144;0.143)		GGGCTTCCTCATGCTCCACGG	0.532																																					p.H1036Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3108G	13						.						130.0	121.0	124.0					13																	33681011		2203	4300	6503	32579011	SO:0001583	missense	90627	exon13			AL049801	CCDS9348.1, CCDS9349.1, CCDS9350.1	13q13.1	2013-08-13	2007-08-16		ENSG00000133121	ENSG00000133121		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19164	protein-coding gene	gene with protein product		609866	"""START domain containing 13"", ""long intergenic non-protein coding RNA 464"""	LINC00464		8812419	Standard	NM_178006		Approved	GT650, DLC2, ARHGAP37	uc001uuw.3	Q9Y3M8	OTTHUMG00000016708	ENST00000336934.5:c.3108T>G	13.37:g.33681011A>C	ENSP00000338785:p.His1036Gln	Somatic		Capture	Illumina HiSeq	Phase_I	32579011	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	A	15.18	2.757146	0.49468	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.38560	1.13;1.13;1.13	5.97	-3.03	0.05429	Lipid-binding START (3);START-like domain (1);	0.241097	0.43110	D	0.000604	T	0.63663	0.2530	M	0.88979	2.995	0.80722	D	1	D;P;D	0.56746	0.977;0.954;0.959	D;D;D	0.66847	0.912;0.947;0.919	T	0.70303	-0.4909	10	0.62326	D	0.03	.	14.1453	0.65347	0.7043:0.0:0.2957:0.0	.	1001;1036;1028	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	Q	918;1028;1036	ENSP00000382300:H918Q;ENSP00000255486:H1028Q;ENSP00000338785:H1036Q	ENSP00000255486:H1028Q	H	-	3	2	STARD13	32579011	0.000000	0.05858	0.952000	0.39060	0.228000	0.25075	-1.475000	0.02335	-0.563000	0.06078	-0.132000	0.14878	CAT		0.532	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
SOHLH2	54937	broad.mit.edu	37	13	36748640	36748640	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr13:36748640G>C	ENST00000379881.3	-	8	942	c.854C>G	c.(853-855)tCt>tGt	p.S285C	SOHLH2_ENST00000554962.1_Missense_Mutation_p.S362C|CCDC169-SOHLH2_ENST00000511166.1_Missense_Mutation_p.S362C	NM_017826.2	NP_060296.2	Q9NX45	SOLH2_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 2	285					multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S285C(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;4.63e-08)|Epithelial(112;2.67e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00272)|BRCA - Breast invasive adenocarcinoma(63;0.00685)|GBM - Glioblastoma multiforme(144;0.0273)		GCCTGGGAGAGACAGCTCAAT	0.403																																					p.S285C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C854G	13						.						191.0	190.0	190.0					13																	36748640		2203	4300	6503	35646640	SO:0001583	missense	54937	exon8			AK000456	CCDS9355.1, CCDS61309.1	13q13.3	2013-05-21			ENSG00000120669	ENSG00000120669		"""Basic helix-loop-helix proteins"""	26026	protein-coding gene	gene with protein product	"""spermatogenesis associated 28"""					12477932	Standard	NM_017826		Approved	FLJ20449, TEB1, bHLHe81, SPATA28		Q9NX45	OTTHUMG00000016728	ENST00000379881.3:c.854C>G	13.37:g.36748640G>C	ENSP00000369210:p.Ser285Cys	Somatic		Capture	Illumina HiSeq	Phase_I	35646640	NM_017826	B4DX90|Q5EGC3|Q8TC74|Q96QX4	Missense_Mutation	SNP	ENST00000379881.3	37	CCDS9355.1	.	.	.	.	.	.	.	.	.	.	G	13.50	2.254691	0.39896	.	.	ENSG00000120669;ENSG00000120669;ENSG00000250709	ENST00000379881;ENST00000554962;ENST00000511166	T;T;T	0.32753	1.44;1.44;1.44	5.41	3.31	0.37934	Helix-loop-helix DNA-binding (1);	0.693217	0.13828	N	0.359901	T	0.31420	0.0796	L	0.51422	1.61	0.09310	N	1	D;D	0.58620	0.983;0.983	P;P	0.46975	0.533;0.533	T	0.11275	-1.0594	10	0.52906	T	0.07	-6.1779	7.7456	0.28866	0.2284:0.0:0.7716:0.0	.	362;285	B4DX90;Q9NX45	.;SOLH2_HUMAN	C	285;362;362	ENSP00000369210:S285C;ENSP00000451542:S362C;ENSP00000421868:S362C	ENSP00000421868:S362C	S	-	2	0	CCDC169-SOHLH2;SOHLH2	35646640	0.002000	0.14202	0.004000	0.12327	0.004000	0.04260	0.694000	0.25512	1.267000	0.44247	0.650000	0.86243	TCT		0.403	SOHLH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044477.2	NM_017826	
MZT1	440145	broad.mit.edu	37	13	73301703	73301705	+	In_Frame_Del	DEL	GCC	GCC	-	rs375939926|rs181034097	byFrequency	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	GCC	GCC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr13:73301703_73301705delGCC	ENST00000377818.3	-	1	120_122	c.36_38delGGC	c.(34-39)gcggcc>gcc	p.12_13AA>A	BORA_ENST00000377815.3_5'Flank|BORA_ENST00000390667.5_5'Flank	NM_001071775.2	NP_001065243.1	Q08AG7	MZT1_HUMAN	mitotic spindle organizing protein 1	12	Poly-Ala.				gamma-tubulin complex localization (GO:0033566)	centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)		p.A16delA(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4						cgccgccgcggccgccgccgccg	0.69																																					p.12_13del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.36_38del	13						.																																			72199706	SO:0001651	inframe_deletion	440145	exon1				CCDS31990.1	13q22.1	2013-08-13	2010-07-22	2010-07-22	ENSG00000204899	ENSG00000204899			33830	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1"""	613448	"""chromosome 13 open reading frame 37"""	C13orf37		20360068	Standard	NM_001071775		Approved	LOC440145, FLJ21869, MGC150539, RP11-11C5.2, MOZART1	uc001viu.2	Q08AG7	OTTHUMG00000017069	ENST00000377818.3:c.36_38delGGC	13.37:g.73301712_73301714delGCC	ENSP00000367049:p.Ala16del	Somatic		Capture	Illumina HiSeq	Phase_I	72199704	NM_001071775	Q5W0P5	In_Frame_Del	DEL	ENST00000377818.3	37	CCDS31990.1																																																																																				0.690	MZT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045249.1	NM_001071775	
RIPK3	11035	broad.mit.edu	37	14	24805566	24805566	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr14:24805566delC	ENST00000216274.5	-	10	1590	c.1372delG	c.(1372-1374)gtgfs	p.V458fs	RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000418030.2_5'Flank|ADCY4_ENST00000396747.3_5'Flank|RIPK3_ENST00000554338.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	458					activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|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)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)	p.V458fs*9(1)		NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		CCAACTTGCACCCCAGAGCAG	0.547																																					p.V458fs	Pancreas(58;918 1191 4668 13304 15331)											.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1372delG	14						.						108.0	108.0	108.0					14																	24805566		2203	4300	6503	23875406	SO:0001589	frameshift_variant	11035	exon10			AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.1372delG	14.37:g.24805566delC	ENSP00000216274:p.Val458fs	Somatic		Capture	Illumina HiSeq	Phase_I	23875406	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Frame_Shift_Del	DEL	ENST00000216274.5	37	CCDS9628.1																																																																																				0.547	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
CTAGE5	4253	broad.mit.edu	37	14	39746268	39746268	+	Splice_Site	SNP	C	C	T	rs185291670		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr14:39746268C>T	ENST00000280083.3	+	2	508	c.194C>T	c.(193-195)tCg>tTg	p.S65L	RP11-407N17.3_ENST00000553728.1_Splice_Site_p.S600L|RP11-407N17.3_ENST00000603904.1_Splice_Site_p.S36L|CTAGE5_ENST00000553352.1_Splice_Site_p.S36L|CTAGE5_ENST00000396165.4_Splice_Site_p.S36L|CTAGE5_ENST00000396158.2_Splice_Site_p.S65L|CTAGE5_ENST00000556148.1_Intron|CTAGE5_ENST00000557038.1_5'UTR|CTAGE5_ENST00000341749.3_Splice_Site_p.S53L|CTAGE5_ENST00000341502.5_Splice_Site_p.S65L|CTAGE5_ENST00000348007.3_Splice_Site_p.S65L			O15320	CTGE5_HUMAN	CTAGE family, member 5	65					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.S65L(1)	CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		AGTTTTAGATCGGTAAGTAAC	0.328																																					p.S53L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C158T	14						.						111.0	106.0	108.0					14																	39746268		2203	4300	6503	38816019	SO:0001630	splice_region_variant	4253	exon2			U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.195+1C>T	14.37:g.39746268C>T		Somatic		Capture	Illumina HiSeq	Phase_I	38816019	NM_203354	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.854215	0.51270	.	.	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000554392;ENST00000555716;ENST00000341749;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.56941	0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43;0.43	5.5	4.59	0.56863	.	0.000000	0.30374	N	0.009777	T	0.59266	0.2181	M	0.80508	2.5	0.41628	D	0.989009	P;P;P;P;P;P	0.44627	0.746;0.746;0.839;0.746;0.839;0.746	B;B;B;B;B;B	0.43194	0.275;0.411;0.3;0.411;0.3;0.411	T	0.65080	-0.6255	9	.	.	.	.	15.1789	0.72938	0.0:0.8579:0.1421:0.0	.	53;65;65;65;36;53	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	L	600;53;53;53;53;36;65;65;65;65;36	ENSP00000452252:S600L;ENSP00000451164:S53L;ENSP00000452395:S53L;ENSP00000343897:S53L;ENSP00000379468:S36L;ENSP00000339286:S65L;ENSP00000379462:S65L;ENSP00000280083:S65L;ENSP00000343912:S65L;ENSP00000450449:S36L	.	S	+	2	0	CTAGE5;RP11-407N17.3	38816019	0.866000	0.29940	0.705000	0.30386	0.006000	0.05464	2.856000	0.48341	1.277000	0.44412	0.650000	0.86243	TCG		0.328	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	Missense_Mutation
PKMYT1	9088	broad.mit.edu	37	16	3023157	3023158	+	Frame_Shift_Ins	INS	-	-	G	rs113543932|rs199526537		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr16:3023157_3023158insG	ENST00000262300.8	-	8	1877_1878	c.1369_1370insC	c.(1369-1371)cggfs	p.R457fs	PKMYT1_ENST00000574730.1_Frame_Shift_Ins_p.R388fs|PAQR4_ENST00000293978.8_3'UTR|PKMYT1_ENST00000574385.1_Frame_Shift_Ins_p.R448fs|PKMYT1_ENST00000440027.2_Frame_Shift_Ins_p.G470fs|PKMYT1_ENST00000573944.1_Frame_Shift_Ins_p.R448fs|PAQR4_ENST00000572687.1_3'UTR|PAQR4_ENST00000318782.8_3'UTR|PKMYT1_ENST00000431515.2_Frame_Shift_Ins_p.R457fs|PKMYT1_ENST00000571102.1_5'Flank	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	457	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.R457fs*14(1)		NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GCACCTGCTCCGGGGGGTGGAG	0.658																																					p.R457fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1370_1371insC	16						.																																			2963159	SO:0001589	frameshift_variant	9088	exon8			AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.1370dupC	16.37:g.3023163_3023163dupG	ENSP00000262300:p.Arg457fs	Somatic		Capture	Illumina HiSeq	Phase_I	2963158	NM_004203	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Frame_Shift_Ins	INS	ENST00000262300.8	37	CCDS10486.1																																																																																				0.658	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
C16orf93	90835	broad.mit.edu	37	16	30772548	30772549	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr16:30772548_30772549insG	ENST00000543610.1	-	2	1167_1168	c.206_207insC	c.(205-207)ccgfs	p.P69fs	RNF40_ENST00000324685.6_5'Flank|C16orf93_ENST00000541260.1_Frame_Shift_Ins_p.P69fs|RNF40_ENST00000357890.5_5'Flank|RNF40_ENST00000402121.3_5'Flank|C16orf93_ENST00000545825.1_Frame_Shift_Ins_p.P69fs|RNF40_ENST00000563683.1_5'Flank	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	69										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						GGGGCAGCGGCGGCTGCGGAAA	0.55																																					p.P69fs												.	.	0			c.207_208insC	16						.																																			30680050	SO:0001589	frameshift_variant	90835	exon2			BC042548	CCDS32434.1, CCDS32434.2, CCDS55993.1	16p11.2	2012-10-10			ENSG00000196118	ENSG00000196118			28078	protein-coding gene	gene with protein product							Standard	NM_001195620		Approved	MGC104706	uc002dzm.3	A1A4V9	OTTHUMG00000167926	ENST00000543610.1:c.207dupC	16.37:g.30772550_30772550dupG	ENSP00000437532:p.Pro69fs	None		Capture	Illumina HiSeq	Phase_I	30680049	NM_001014979	A1A4V8|F5GX13|Q569G2	Frame_Shift_Ins	INS	ENST00000543610.1	37	CCDS32434.2																																																																																				0.550	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979	
ADAD2	161931	broad.mit.edu	37	16	84229275	84229276	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr16:84229275_84229276insC	ENST00000315906.5	+	6	1076_1077	c.1024_1025insC	c.(1024-1026)accfs	p.T342fs	RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|RP11-486L19.2_ENST00000565643.1_RNA|ADAD2_ENST00000268624.3_Frame_Shift_Ins_p.T424fs|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	342	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				RNA processing (GO:0006396)		adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)	p.K426fs*6(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(1)	13						CATCAGCAACACCCCCAAGGGC	0.713																																					p.T424fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1270_1271insC	16						.																																			82786777	SO:0001589	frameshift_variant	161931	exon7			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.1029dupC	16.37:g.84229280_84229280dupC	ENSP00000325153:p.Thr342fs	Somatic		Capture	Illumina HiSeq	Phase_I	82786776	NM_139174	B2RCL6|Q8NA94	Frame_Shift_Ins	INS	ENST00000315906.5	37	CCDS45536.1																																																																																				0.713	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174	
FBXL19	54620	broad.mit.edu	37	16	30939832	30939832	+	Silent	SNP	C	C	T	rs376169841		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr16:30939832C>T	ENST00000380310.2	+	6	890	c.732C>T	c.(730-732)gaC>gaT	p.D244D	FBXL19_ENST00000565690.1_Intron|FBXL19_ENST00000338343.4_Silent_p.D224D|FBXL19_ENST00000471231.2_5'UTR|FBXL19_ENST00000562319.1_Silent_p.D224D	NM_001099784.2	NP_001093254.2	Q6PCT2	FXL19_HUMAN	F-box and leucine-rich repeat protein 19	244	Pro-rich.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)	SCF ubiquitin ligase complex (GO:0019005)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.D244D(1)		breast(2)|endometrium(3)|lung(5)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16						TGGGTGGAGACGCCTGCCTCC	0.647																																					p.D244D												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C732T	16						.			0,3828		0,0,1914	25.0	29.0	28.0		732	-4.4	0.9	16		28	1,8241		0,1,4120	no	coding-synonymous	FBXL19	NM_001099784.2		0,1,6034	TT,TC,CC		0.0121,0.0,0.0083		244/695	30939832	1,12069	1914	4121	6035	30847333	SO:0001819	synonymous_variant	54620	exon6			AK127701	CCDS45465.1, CCDS73873.1	16p11.2	2014-02-20			ENSG00000099364	ENSG00000099364		"""F-boxes / Leucine-rich repeats"""	25300	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1C"""	609085					Standard	NM_001099784		Approved	DKFZp434K0410, Fbl19, JHDM1C, CXXC11	uc002eab.2	Q6PCT2	OTTHUMG00000132403	ENST00000380310.2:c.732C>T	16.37:g.30939832C>T		Somatic		Capture	Illumina HiSeq	Phase_I	30847333	NM_001099784	A8MT10|Q8N789|Q9NT14	De_novo_Start_OutOfFrame	SNP	ENST00000380310.2	37	CCDS45465.1																																																																																				0.647	FBXL19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_019085	
DUS2	54920	broad.mit.edu	37	16	68083443	68083443	+	Silent	SNP	A	A	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr16:68083443A>G	ENST00000565263.1	+	4	656	c.162A>G	c.(160-162)agA>agG	p.R54R	DUS2_ENST00000432752.1_Silent_p.R54R|DUS2_ENST00000358896.6_Silent_p.R54R	NM_017803.3	NP_060273.1	Q9NX74	DUS2L_HUMAN	dihydrouridine synthase 2	54					negative regulation of cell death (GO:0060548)|negative regulation of protein kinase activity (GO:0006469)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	double-stranded RNA binding (GO:0003725)|flavin adenine dinucleotide binding (GO:0050660)|protein kinase inhibitor activity (GO:0004860)|tRNA dihydrouridine synthase activity (GO:0017150)	p.R54R(1)									AGTGCAAGAGAGTTGTTAATG	0.502																																					p.R54R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A162G	16						.						153.0	135.0	141.0					16																	68083443		2198	4300	6498	66640944	SO:0001819	synonymous_variant	54920	exon4				CCDS10859.1, CCDS61970.1	16q22.1	2013-07-23	2013-07-23	2013-07-23	ENSG00000167264	ENSG00000167264			26014	protein-coding gene	gene with protein product	"""SMM1 homolog (S. cerevisiae)"""	609707	"""dihydrouridine synthase 2-like (SMM1, S. cerevisiae)"", ""dihydrouridine synthase 2-like, SMM1 homolog (S. cerevisiae)"", ""dihydrouridine synthase 2-like"""	DUS2L		15994936, 22741570	Standard	NM_017803		Approved	FLJ20399, SMM1	uc002evj.4	Q9NX74	OTTHUMG00000137538	ENST00000565263.1:c.162A>G	16.37:g.68083443A>G		Somatic		Capture	Illumina HiSeq	Phase_I	66640944	NM_017803	A8K3G3|Q4H4D9	Silent	SNP	ENST00000565263.1	37	CCDS10859.1																																																																																				0.502	DUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268869.2	NM_017803	
UNC119	9094	broad.mit.edu	37	17	26879494	26879495	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:26879494_26879495insG	ENST00000335765.4	-	1	191_192	c.81_82insC	c.(79-84)cccatafs	p.I28fs	UNC119_ENST00000484980.1_5'Flank|UNC119_ENST00000301032.4_Frame_Shift_Ins_p.I28fs	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	28	Required for midbody localization.				cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)	p.I28fs*47(1)		breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					GGCTGTGGTATGGGGGCCACGC	0.743																																					p.I28fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.82_83insC	17						.																																			23903622	SO:0001589	frameshift_variant	9094	exon1			U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103			12565	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog A (Chlamydomonas)"""	604011	"""unc119 (C.elegans) homolog"""			8576185, 9538874	Standard	NM_005148		Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.82dupC	17.37:g.26879499_26879499dupG	ENSP00000337040:p.Ile28fs	Somatic		Capture	Illumina HiSeq	Phase_I	23903621	NM_054035	A8K8G4|F1T095|O95126	Frame_Shift_Ins	INS	ENST00000335765.4	37	CCDS11233.1																																																																																				0.743	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255842.2		
CAMTA2	23125	broad.mit.edu	37	17	4875657	4875658	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:4875657_4875658insG	ENST00000348066.3	-	16	2800_2801	c.2677_2678insC	c.(2677-2679)ctafs	p.L893fs	CAMTA2_ENST00000358183.4_Frame_Shift_Ins_p.L893fs|CAMTA2_ENST00000381311.5_Frame_Shift_Ins_p.L895fs|RP5-1050D4.2_ENST00000430920.1_RNA|CAMTA2_ENST00000414043.3_Frame_Shift_Ins_p.L916fs|CAMTA2_ENST00000572543.1_Frame_Shift_Ins_p.L898fs|CAMTA2_ENST00000361571.5_Frame_Shift_Ins_p.L892fs	NM_015099.3	NP_055914.2	O94983	CMTA2_HUMAN	calmodulin binding transcription activator 2	893					cardiac muscle hypertrophy in response to stress (GO:0014898)|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)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	31						CATGAGGAGTAGGGGGGCTTCT	0.629																																					p.L916fs												.	.	0			c.2747_2748insC	17						.																																			4816382	SO:0001589	frameshift_variant	23125	exon16			AB020716	CCDS11063.1, CCDS54071.1, CCDS54072.1, CCDS54073.1	17p13.3	2004-09-01			ENSG00000108509	ENSG00000108509			18807	protein-coding gene	gene with protein product		611508				11925432	Standard	NM_015099		Approved	KIAA0909	uc010cku.2	O94983	OTTHUMG00000099417	ENST00000348066.3:c.2678dupC	17.37:g.4875663_4875663dupG	ENSP00000321813:p.Leu893fs	None		Capture	Illumina HiSeq	Phase_I	4816381	NM_001171167	B9EGL0|D3DTL5|E7EWU5|Q7Z6M8|Q8N3V0|Q8NDG4|Q96G17	Frame_Shift_Ins	INS	ENST00000348066.3	37	CCDS11063.1																																																																																				0.629	CAMTA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216876.1	NM_015099	
TOP3A	7156	broad.mit.edu	37	17	18181318	18181318	+	Missense_Mutation	SNP	C	C	T	rs368210504		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:18181318C>T	ENST00000321105.5	-	18	2712	c.2498G>A	c.(2497-2499)cGg>cAg	p.R833Q	TOP3A_ENST00000540524.1_Missense_Mutation_p.R363Q|TOP3A_ENST00000542570.1_Missense_Mutation_p.R738Q	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	833	2 X 27 AA approximate repeats.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)	p.R833Q(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						AAAGAACTGCCGGCCCCGGTT	0.612																																					p.R833Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2498A	17						.	C	GLN/ARG	1,4405		0,1,2202	34.0	39.0	38.0		2498	5.6	1.0	17		38	0,8600		0,0,4300	no	missense	TOP3A	NM_004618.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	833/1002	18181318	1,13005	2203	4300	6503	18122043	SO:0001583	missense	7156	exon18			U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.2498G>A	17.37:g.18181318C>T	ENSP00000321636:p.Arg833Gln	Somatic		Capture	Illumina HiSeq	Phase_I	18122043	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Missense_Mutation	SNP	ENST00000321105.5	37	CCDS11194.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365457	0.61513	2.27E-4	0.0	ENSG00000177302	ENST00000321105;ENST00000540524;ENST00000542570	T;T;T	0.46451	0.87;0.87;0.87	5.55	5.55	0.83447	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	T	0.77301	0.4110	H	0.96430	3.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.84516	0.0625	10	0.72032	D	0.01	-29.8917	19.4999	0.95090	0.0:1.0:0.0:0.0	.	738;833	B4DK80;Q13472	.;TOP3A_HUMAN	Q	833;363;738	ENSP00000321636:R833Q;ENSP00000446425:R363Q;ENSP00000442336:R738Q	ENSP00000321636:R833Q	R	-	2	0	TOP3A	18122043	1.000000	0.71417	0.999000	0.59377	0.795000	0.44927	7.529000	0.81952	2.621000	0.88768	0.549000	0.68633	CGG		0.612	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
TP53	7157	broad.mit.edu	37	17	7578212	7578212	+	Nonsense_Mutation	SNP	G	G	A	rs397516436		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:7578212G>A	ENST00000269305.4	-	6	826	c.637C>T	c.(637-639)Cga>Tga	p.R213*	TP53_ENST00000359597.4_Nonsense_Mutation_p.R213*|TP53_ENST00000445888.2_Nonsense_Mutation_p.R213*|TP53_ENST00000420246.2_Nonsense_Mutation_p.R213*|TP53_ENST00000574684.1_Intron|TP53_ENST00000413465.2_Nonsense_Mutation_p.R213*|TP53_ENST00000455263.2_Nonsense_Mutation_p.R213*	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	213	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> L (in sporadic cancers; somatic mutation).|R -> P (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:16959974}.|R -> Q (in LFS; germline mutation and in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R213*(250)|p.R81*(21)|p.R120*(21)|p.0?(8)|p.?(5)|p.R213G(5)|p.R213fs*35(3)|p.R213fs*34(3)|p.D208_V216delDRNTFRHSV(1)|p.R120G(1)|p.D207_R213delDDRNTFR(1)|p.T211_S215delTFRHS(1)|p.R81fs*>11(1)|p.D208fs*1(1)|p.R120fs*35(1)|p.R81G(1)|p.R209_R213delRNTFR(1)|p.R213fs*2(1)|p.T211fs*28(1)|p.R213_S215>X(1)|p.D207_V216del10(1)|p.R213R(1)|p.R213fs*32(1)|p.R209fs*6(1)|p.R213W(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	ACACTATGTCGAAAAGTGTTT	0.532		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R213X	Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53,central_nervous_system,brain,Substitution - Missense,+1 	.	333	Substitution - Nonsense(292)|Deletion - Frameshift(8)|Whole gene deletion(8)|Substitution - Missense(8)|Deletion - In frame(5)|Insertion - Frameshift(5)|Unknown(5)|Complex - deletion inframe(1)|Substitution - coding silent(1)	large_intestine(89)|breast(45)|lung(37)|upper_aerodigestive_tract(30)|central_nervous_system(18)|skin(16)|oesophagus(15)|stomach(14)|ovary(14)|haematopoietic_and_lymphoid_tissue(10)|urinary_tract(9)|biliary_tract(8)|liver(8)|soft_tissue(5)|endometrium(5)|bone(4)|prostate(3)|thyroid(1)|pancreas(1)|autonomic_ganglia(1)	c.C637T	17	GRCh37	CM951226	TP53	M		.						132.0	118.0	123.0					17																	7578212		2203	4300	6503	7518937	SO:0001587	stop_gained	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.637C>T	17.37:g.7578212G>A	ENSP00000269305:p.Arg213*	Somatic		Capture	Illumina HiSeq	Phase_I	7518937	NM_001126114	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Nonsense_Mutation	SNP	ENST00000269305.4	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	37	6.039727	0.97226	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.28	3.25	0.37280	.	0.057335	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.5444	12.7263	0.57173	0.0:0.0:0.701:0.299	.	.	.	.	X	213;213;213;213;213;213;202;120;81;120;81	.	ENSP00000269305:R213X	R	-	1	2	TP53	7518937	0.971000	0.33674	0.123000	0.21794	0.957000	0.61999	1.659000	0.37387	0.702000	0.31825	0.563000	0.77884	CGA		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
KDM6B	23135	broad.mit.edu	37	17	7751561	7751561	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:7751561delC	ENST00000448097.2	+	11	2286	c.1955delC	c.(1954-1956)gccfs	p.A652fs	KDM6B_ENST00000254846.5_Frame_Shift_Del_p.A652fs			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	652	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.Q654fs*46(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CTGAGTAAAGCCCCCCAGCCT	0.701																																					p.A652fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1955delC	17						.						16.0	21.0	20.0					17																	7751561		1969	4017	5986	7692286	SO:0001589	frameshift_variant	23135	exon11			AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.1955delC	17.37:g.7751561delC	ENSP00000412513:p.Ala652fs	Somatic		Capture	Illumina HiSeq	Phase_I	7692286	NM_001080424	C9IZ40|Q96G33	Frame_Shift_Del	DEL	ENST00000448097.2	37																																																																																					0.701	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
PNPO	55163	broad.mit.edu	37	17	46024107	46024107	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr17:46024107C>T	ENST00000225573.4	+	7	850	c.745C>T	c.(745-747)Cgc>Tgc	p.R249C	PNPO_ENST00000544840.1_Missense_Mutation_p.R231C|PNPO_ENST00000534893.1_Missense_Mutation_p.R154C|RP11-6N17.6_ENST00000580372.1_RNA|RP11-6N17.6_ENST00000582142.1_RNA|PNPO_ENST00000434554.2_Missense_Mutation_p.R206C|RP11-6N17.9_ENST00000582262.1_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	249					pyridoxine biosynthetic process (GO:0008615)|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)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)	p.R249C(1)		endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						CATGACCCACCGCGGGGAGGA	0.597											OREG0024505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R249C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C745T	17						.						59.0	63.0	62.0					17																	46024107		2203	4300	6503	43379106	SO:0001583	missense	55163	exon7			AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"""pyridoxine 5'-phosphate oxidase"""			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.745C>T	17.37:g.46024107C>T	ENSP00000225573:p.Arg249Cys	Somatic	936	Capture	Illumina HiSeq	Phase_I	43379106	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Missense_Mutation	SNP	ENST00000225573.4	37	CCDS11522.1	.	.	.	.	.	.	.	.	.	.	C	13.86	2.363537	0.41902	.	.	ENSG00000108439	ENST00000225573;ENST00000434554;ENST00000544840;ENST00000534893	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.22	2.08	0.27032	Pyridoxine 5&apos (1);FMN-binding split barrel-related (1);-phosphate oxidase, dimerisation, C-terminal (1);FMN-binding split barrel (1);	0.858579	0.10613	N	0.654284	T	0.67841	0.2936	L	0.44542	1.39	0.28583	N	0.910058	B;B;B	0.16166	0.014;0.016;0.012	B;B;B	0.14023	0.01;0.007;0.003	T	0.59198	-0.7499	10	0.56958	D	0.05	1.9809	5.435	0.16476	0.2803:0.5628:0.0:0.1569	.	206;231;249	B4E152;B4E1D7;Q9NVS9	.;.;PNPO_HUMAN	C	249;206;231;154	ENSP00000225573:R249C;ENSP00000399960:R206C;ENSP00000446182:R231C;ENSP00000437480:R154C	ENSP00000225573:R249C	R	+	1	0	PNPO	43379106	0.003000	0.15002	0.241000	0.24154	0.978000	0.69477	0.011000	0.13264	0.197000	0.20387	0.561000	0.74099	CGC		0.597	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
TAF4B	6875	broad.mit.edu	37	18	23854705	23854705	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr18:23854705A>C	ENST00000269142.5	+	4	1674	c.676A>C	c.(676-678)Agt>Cgt	p.S226R	TAF4B_ENST00000400466.2_Missense_Mutation_p.S226R|TAF4B_ENST00000578121.1_Missense_Mutation_p.S226R	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	226					gene expression (GO:0010467)|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)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S226R(1)		breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			GAAGCCTTCAAGTTTGGGAGC	0.428																																					p.S226R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A676C	18						.						159.0	151.0	153.0					18																	23854705		1888	4121	6009	22108703	SO:0001583	missense	6875	exon4			Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.676A>C	18.37:g.23854705A>C	ENSP00000269142:p.Ser226Arg	Somatic		Capture	Illumina HiSeq	Phase_I	22108703	NM_005640	Q29YA4|Q29YA5	Missense_Mutation	SNP	ENST00000269142.5	37	CCDS42421.1	.	.	.	.	.	.	.	.	.	.	A	12.22	1.873145	0.33069	.	.	ENSG00000141384	ENST00000418698;ENST00000269142;ENST00000400466	T;T;T	0.26223	1.75;1.79;1.75	5.81	2.28	0.28536	.	0.742198	0.13517	N	0.381964	T	0.15349	0.0370	L	0.40543	1.245	0.30718	N	0.748574	B;P	0.37864	0.412;0.61	B;B	0.32864	0.1;0.154	T	0.10823	-1.0613	10	0.15952	T	0.53	-1.0225	5.956	0.19273	0.6603:0.0:0.3397:0.0	.	226;226	Q92750;A4PBF7	TAF4B_HUMAN;.	R	226	ENSP00000389365:S226R;ENSP00000269142:S226R;ENSP00000383314:S226R	ENSP00000269142:S226R	S	+	1	0	TAF4B	22108703	0.884000	0.30299	1.000000	0.80357	0.776000	0.43924	2.151000	0.42263	1.040000	0.40099	0.533000	0.62120	AGT		0.428	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
DCC	1630	broad.mit.edu	37	18	50589744	50589744	+	Missense_Mutation	SNP	G	G	A	rs573993465		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr18:50589744G>A	ENST00000442544.2	+	6	1671	c.1055G>A	c.(1054-1056)tGt>tAt	p.C352Y	DCC_ENST00000581580.1_Missense_Mutation_p.C7Y|DCC_ENST00000580146.1_3'UTR|DCC_ENST00000412726.1_Missense_Mutation_p.C200Y	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	352	Ig-like C2-type 4.				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.C352Y(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)		GAGTTTGAATGTACAGTCTCT	0.378																																					p.C352Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1055A	18						.						276.0	260.0	265.0					18																	50589744		2203	4300	6503	48843742	SO:0001583	missense	1630	exon6			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.1055G>A	18.37:g.50589744G>A	ENSP00000389140:p.Cys352Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	48843742	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.873215	0.51695	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	D;D	0.92545	-3.06;-3.06	5.95	5.95	0.96441	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.96867	0.8977	M	0.89214	3.015	0.53688	D	0.999973	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97015	0.9739	10	0.87932	D	0	.	19.1527	0.93495	0.0:0.0:1.0:0.0	.	200;200;352	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	Y	352;285;200	ENSP00000389140:C352Y;ENSP00000397322:C200Y	ENSP00000304146:C285Y	C	+	2	0	DCC	48843742	1.000000	0.71417	0.974000	0.42286	0.992000	0.81027	9.063000	0.93927	2.821000	0.97095	0.650000	0.86243	TGT		0.378	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
JAK3	3718	broad.mit.edu	37	19	17954642	17954643	+	Frame_Shift_Ins	INS	-	-	G	rs201067961|rs139738701	byFrequency	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:17954642_17954643insG	ENST00000527670.1	-	2	280_281	c.251_252insC	c.(250-252)ccgfs	p.P84fs	JAK3_ENST00000458235.1_Frame_Shift_Ins_p.P84fs|JAK3_ENST00000526008.1_5'UTR|JAK3_ENST00000534444.1_Frame_Shift_Ins_p.P84fs			P52333	JAK3_HUMAN	Janus kinase 3	84	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				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)			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)	AGATGTGGCTCGGGGGGAACCA	0.594		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""																																p.P84fs			Dom	yes		19	19p13.1	3718	Janus kinase 3		L	.	.	0			c.252_253insC	19						.																																			17815643	SO:0001589	frameshift_variant	3718	exon3			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.252dupC	19.37:g.17954648_17954648dupG	ENSP00000432511:p.Pro84fs	None		Capture	Illumina HiSeq	Phase_I	17815642	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Frame_Shift_Ins	INS	ENST00000527670.1	37	CCDS12366.1																																																																																				0.594	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
AP2A1	160	broad.mit.edu	37	19	50308928	50308929	+	Frame_Shift_Ins	INS	-	-	C	rs539590706		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:50308928_50308929insC	ENST00000359032.5	+	21	2545_2546	c.2545_2546insC	c.(2545-2547)gccfs	p.A849fs	AP2A1_ENST00000354293.5_Frame_Shift_Ins_p.A827fs	NM_014203.2	NP_055018.2	O95782	AP2A1_HUMAN	adaptor-related protein complex 2, alpha 1 subunit	849					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)|Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of hyaluronan biosynthetic process (GO:1900126)|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)	AP-2 adaptor complex (GO:0030122)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein transporter activity (GO:0008565)	p.Q851fs*55(1)		cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)	19		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;0.0023)|GBM - Glioblastoma multiforme(134;0.0157)		GTACGGTGGCGCCCCCCAGGCC	0.663																																					p.A827fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.2479_2480insC	19						.		,	1,3517		0,1,1758					,	-1.2	0.1			23	3,7673		0,3,3835	no	frameshift,frameshift	AP2A1	NM_130787.2,NM_014203.2	,	0,4,5593	A1A1,A1R,RR		0.0391,0.0284,0.0357	,	,		4,11190				55000741	SO:0001589	frameshift_variant	160	exon20			AA993745	CCDS46148.1, CCDS46149.1	19q13.3	2008-05-23				ENSG00000196961			561	protein-coding gene	gene with protein product		601026		CLAPA1, ADTAA		2564002	Standard	NM_014203		Approved		uc002ppn.3	O95782		ENST00000359032.5:c.2551dupC	19.37:g.50308934_50308934dupC	ENSP00000351926:p.Ala849fs	Somatic		Capture	Illumina HiSeq	Phase_I	55000740	NM_130787	Q96CI7|Q96PP6|Q96PP7|Q9H070	Frame_Shift_Ins	INS	ENST00000359032.5	37	CCDS46148.1																																																																																				0.663	AP2A1-008	NOVEL	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465809.1		
NR1H2	7376	broad.mit.edu	37	19	50837601	50837602	+	Intron	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:50837601_50837602insC	ENST00000600978.1	+	2	74				KCNC3_ENST00000391818.2_5'Flank|KCNC3_ENST00000474951.1_5'Flank|NAPSB_ENST00000527780.1_RNA|NR1H2_ENST00000542413.1_Intron			P55055	NR1H2_HUMAN	nuclear receptor subfamily 1, group H, member 2						cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pinocytosis (GO:0048550)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	apolipoprotein A-I receptor binding (GO:0034191)|ATPase binding (GO:0051117)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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 transcription regulatory region DNA binding RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001133)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.V333fs*4(1)		endometrium(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(2)	8		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		ATTAAACCAGACCCCCCCAATG	0.525																																					.												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	.	19						.																																			55529414	SO:0001627	intron_variant	256236	.			U14534	CCDS42593.1, CCDS58673.1	19q13.3	2013-01-16				ENSG00000131408		"""Nuclear hormone receptors"""	7965	protein-coding gene	gene with protein product	"""liver X receptor-beta"""	600380	"""ubiquitously-expressed nuclear receptor"""	UNR		7782080, 7971966	Standard	NM_007121		Approved	NER, NER-I, RIP15, LXR-b	uc010enw.4	P55055		ENST00000600978.1:c.75-3657->C	19.37:g.50837608_50837608dupC		Somatic		Capture	Illumina HiSeq	Phase_I	55529413	.	A8K490|B4DNM6|E7EWA6|Q12970|Q5I0Y1	Frame_Shift_Ins	INS	ENST00000600978.1	37																																																																																					0.525	NR1H2-012	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000464783.1		
ARRDC5	645432	broad.mit.edu	37	19	4891493	4891493	+	Silent	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:4891493G>A	ENST00000381781.2	-	3	593	c.594C>T	c.(592-594)acC>acT	p.T198T	AC027319.1_ENST00000408608.1_RNA	NM_001080523.1	NP_001073992.1	A6NEK1	ARRD5_HUMAN	arrestin domain containing 5	198								p.T198T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0257)		CTGGCGTGAAGGTGTTCCTTT	0.522																																					p.T198T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C594T	19						.						103.0	98.0	100.0					19																	4891493		2063	4225	6288	4842493	SO:0001819	synonymous_variant	645432	exon3				CCDS45929.1	19p13.3	2007-10-05				ENSG00000205784			31407	protein-coding gene	gene with protein product						12886014	Standard	NM_001080523		Approved		uc002mbm.3	A6NEK1		ENST00000381781.2:c.594C>T	19.37:g.4891493G>A		Somatic		Capture	Illumina HiSeq	Phase_I	4842493	NM_001080523		Silent	SNP	ENST00000381781.2	37	CCDS45929.1																																																																																				0.522	ARRDC5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450443.1	XM_292803	
PLEKHA4	57664	broad.mit.edu	37	19	49362727	49362727	+	Splice_Site	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:49362727C>T	ENST00000263265.6	-	7	1246	c.691G>A	c.(691-693)Gac>Aac	p.D231N	PLEKHA4_ENST00000355496.5_Splice_Site_p.D231N|PLEKHA4_ENST00000596713.1_5'UTR	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	231	Pro-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)	p.D231N(1)		NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		CCTACTCACTCGGGGCTCCTC	0.632																																					p.D231N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G691A	19						.						38.0	34.0	35.0					19																	49362727		2202	4300	6502	54054539	SO:0001630	splice_region_variant	57664	exon7			AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.692+1G>A	19.37:g.49362727C>T		Somatic		Capture	Illumina HiSeq	Phase_I	54054539	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.645532	0.67358	.	.	ENSG00000105559	ENST00000263265;ENST00000355496	T;T	0.15487	2.94;2.42	4.7	4.7	0.59300	.	0.500930	0.20417	N	0.092746	T	0.14056	0.0340	N	0.24115	0.695	0.26371	N	0.976889	P;D	0.58620	0.935;0.983	B;P	0.44597	0.364;0.454	T	0.09058	-1.0692	10	0.40728	T	0.16	.	13.3472	0.60580	0.0:1.0:0.0:0.0	.	231;231	Q9H4M7-2;Q9H4M7	.;PKHA4_HUMAN	N	231	ENSP00000263265:D231N;ENSP00000347683:D231N	ENSP00000263265:D231N	D	-	1	0	PLEKHA4	54054539	0.838000	0.29461	0.999000	0.59377	0.208000	0.24298	1.262000	0.32992	2.629000	0.89072	0.462000	0.41574	GAC		0.632	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		Missense_Mutation
KLK7	5650	broad.mit.edu	37	19	51485145	51485145	+	Silent	SNP	G	G	A	rs377619320		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:51485145G>A	ENST00000391807.1	-	3	200	c.99C>T	c.(97-99)ggC>ggT	p.G33G	KLK7_ENST00000595638.1_5'Flank|CTB-147C22.9_ENST00000594512.1_RNA|KLK7_ENST00000336317.4_Intron|KLK7_ENST00000595820.1_Silent_p.G33G|KLK7_ENST00000597707.1_5'UTR	NM_139277.2	NP_644806.1	P49862	KLK7_HUMAN	kallikrein-related peptidase 7	33	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.G33G(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(11)|ovary(2)	19		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00382)|GBM - Glioblastoma multiforme(134;0.00895)		CACATGGGGCGCCATCAATAA	0.607																																					p.G33G												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C99T	19						.		,,	0,4406		0,0,2203	54.0	49.0	50.0		,99,99	-5.8	0.0	19		50	1,8599	817.2+/-406.9	0,1,4299	no	utr-5,coding-synonymous,coding-synonymous	KLK7	NM_001207053.1,NM_005046.3,NM_139277.2	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	,33/254,33/254	51485145	1,13005	2203	4300	6503	56176957	SO:0001819	synonymous_variant	5650	exon3			L33404	CCDS12812.1, CCDS59414.1	19q13.33	2011-09-07	2006-10-27			ENSG00000169035		"""Kallikreins"", ""Serine peptidases / Serine peptidases"""	6368	protein-coding gene	gene with protein product		604438	"""kallikrein 7 (chymotryptic, stratum corneum)"""	PRSS6		8034709, 16800724, 16800723	Standard	NM_005046		Approved	SCCE	uc021uyj.1	P49862		ENST00000391807.1:c.99C>T	19.37:g.51485145G>A		Somatic		Capture	Illumina HiSeq	Phase_I	56176957	NM_005046	A8K0U5|Q8N5N9|Q8NFV7	Silent	SNP	ENST00000391807.1	37	CCDS12812.1																																																																																				0.607	KLK7-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464344.1	NM_005046	
SIGLEC8	27181	broad.mit.edu	37	19	51955663	51955663	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr19:51955663G>T	ENST00000321424.3	-	7	1536	c.1470C>A	c.(1468-1470)caC>caA	p.H490Q	SIGLEC8_ENST00000430817.1_Missense_Mutation_p.H381Q|SIGLEC8_ENST00000340550.5_Missense_Mutation_p.H397Q	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	490					cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)	p.H490Q(1)		NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TGGAGGGGTTGTGATTCCTCA	0.542																																					p.H490Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1470A	19						.						122.0	111.0	115.0					19																	51955663		2203	4300	6503	56647475	SO:0001583	missense	27181	exon7			AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.1470C>A	19.37:g.51955663G>T	ENSP00000321077:p.His490Gln	Somatic		Capture	Illumina HiSeq	Phase_I	56647475	NM_014442	Q7Z728	Missense_Mutation	SNP	ENST00000321424.3	37	CCDS33086.1	.	.	.	.	.	.	.	.	.	.	.	9.308	1.054924	0.19907	.	.	ENSG00000105366	ENST00000430817;ENST00000321424;ENST00000340550	T;T;T	0.61980	1.36;0.06;1.14	1.12	-2.23	0.06930	.	.	.	.	.	T	0.29556	0.0737	N	0.08118	0	0.09310	N	1	B;P;B	0.35821	0.388;0.523;0.388	B;B;B	0.21708	0.016;0.036;0.016	T	0.13442	-1.0509	9	0.87932	D	0	.	2.0579	0.03585	0.2398:0.0:0.3279:0.4323	.	381;397;490	C9JT30;Q9NYZ4-2;Q9NYZ4	.;.;SIGL8_HUMAN	Q	381;490;397	ENSP00000389142:H381Q;ENSP00000321077:H490Q;ENSP00000339448:H397Q	ENSP00000321077:H490Q	H	-	3	2	SIGLEC8	56647475	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.755000	0.04782	-0.830000	0.04262	0.502000	0.49764	CAC		0.542	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
COL8A2	1296	broad.mit.edu	37	1	36563806	36563807	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:36563806_36563807insG	ENST00000397799.1	-	4	1699_1700	c.1475_1476insC	c.(1474-1476)cctfs	p.P492fs	COL8A2_ENST00000303143.4_Frame_Shift_Ins_p.P492fs|COL8A2_ENST00000481785.1_Frame_Shift_Ins_p.P427fs			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	492	Triple-helical region.				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)	p.G493fs*46(1)		NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				TCCCCTCTCCAGGGGGCCCTGG	0.743																																					p.P492fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1476_1477insC	1						.																																			36336394	SO:0001589	frameshift_variant	1296	exon2			M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1476dupC	1.37:g.36563811_36563811dupG	ENSP00000380901:p.Pro492fs	Somatic		Capture	Illumina HiSeq	Phase_I	36336393	NM_005202	Q5JV31|Q8TEJ5	Frame_Shift_Ins	INS	ENST00000397799.1	37	CCDS403.1																																																																																				0.743	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
MTOR	2475	broad.mit.edu	37	1	11264654	11264654	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:11264654C>A	ENST00000361445.4	-	26	3984	c.3908G>T	c.(3907-3909)tGc>tTc	p.C1303F		NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1303					cell growth (GO:0016049)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell development (GO:0007281)|growth (GO:0040007)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of macroautophagy (GO:0016242)|negative regulation of NFAT protein import into nucleus (GO:0051534)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of gene expression (GO:0010628)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of carbohydrate utilization (GO:0043610)|regulation of fatty acid beta-oxidation (GO:0031998)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of protein kinase activity (GO:0045859)|regulation of Rac GTPase activity (GO:0032314)|regulation of response to food (GO:0032095)|response to amino acid (GO:0043200)|response to nutrient (GO:0007584)|response to stress (GO:0006950)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|phosphatidylinositol 3-kinase complex (GO:0005942)|PML body (GO:0016605)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	ATP binding (GO:0005524)|drug binding (GO:0008144)|kinase activity (GO:0016301)|phosphoprotein binding (GO:0051219)|protein serine/threonine kinase activity (GO:0004674)|ribosome binding (GO:0043022)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)	p.C1303F(1)		breast(5)|central_nervous_system(7)|endometrium(20)|kidney(34)|large_intestine(21)|lung(43)|ovary(9)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	149					Everolimus(DB01590)|Pimecrolimus(DB00337)|Sirolimus(DB00877)|Temsirolimus(DB06287)	CAGGGCCCAGCAGGAGCGCAG	0.567																																					p.C1303F												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G3908T	1						.						56.0	55.0	56.0					1																	11264654		2203	4300	6503	11187241	SO:0001583	missense	2475	exon26			L34075	CCDS127.1	1p36	2014-09-17	2009-05-29	2009-05-29	ENSG00000198793	ENSG00000198793			3942	protein-coding gene	gene with protein product	"""FK506 binding protein 12-rapamycin associated protein 2"", ""rapamycin target protein"", ""FKBP12-rapamycin complex-associated protein 1"", ""FKBP-rapamycin associated protein"", ""rapamycin associated protein FRAP2"", ""dJ576K7.1 (FK506 binding protein 12-rapamycin associated protein 1)"", ""rapamycin and FKBP12 target 1"", ""mammalian target of rapamycin"""	601231	"""FK506 binding protein 12-rapamycin associated protein 1"""	FRAP, FRAP2, FRAP1		8008069, 8660990	Standard	NM_004958		Approved	RAFT1, RAPT1, FLJ44809	uc001asd.3	P42345	OTTHUMG00000002001	ENST00000361445.4:c.3908G>T	1.37:g.11264654C>A	ENSP00000354558:p.Cys1303Phe	Somatic		Capture	Illumina HiSeq	Phase_I	11187241	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Missense_Mutation	SNP	ENST00000361445.4	37	CCDS127.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.198894	0.79015	.	.	ENSG00000198793	ENST00000361445;ENST00000539766	T	0.70164	-0.46	5.79	5.79	0.91817	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.84835	0.5560	M	0.87547	2.89	0.80722	D	1	D	0.57571	0.98	D	0.69142	0.962	D	0.86481	0.1791	10	0.87932	D	0	-24.7792	20.0407	0.97588	0.0:1.0:0.0:0.0	.	1303	P42345	MTOR_HUMAN	F	1303	ENSP00000354558:C1303F	ENSP00000354558:C1303F	C	-	2	0	MTOR	11187241	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.409000	0.80053	2.746000	0.94184	0.561000	0.74099	TGC		0.567	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958	
GPR61	83873	broad.mit.edu	37	1	110085828	110085828	+	Missense_Mutation	SNP	G	G	A	rs201647649		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:110085828G>A	ENST00000527748.1	+	2	867	c.184G>A	c.(184-186)Gct>Act	p.A62T	RP5-1160K1.8_ENST00000526411.1_RNA	NM_031936.4	NP_114142.3	Q9BZJ8	GPR61_HUMAN	G protein-coupled receptor 61	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)	p.A62T(2)		breast(1)|central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(9)|stomach(1)|urinary_tract(1)	23		all_epithelial(167;2.83e-05)|all_lung(203;0.00016)|Lung NSC(277;0.000318)|Breast(1374;0.244)		Lung(183;0.0426)|Colorectal(144;0.11)|Epithelial(280;0.128)|all cancers(265;0.132)|LUSC - Lung squamous cell carcinoma(189;0.228)		TGGCAATGCCGCTGTGATGGC	0.612																																					p.A62T												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G184A	1						.						159.0	153.0	155.0					1																	110085828		2203	4300	6503	109887351	SO:0001583	missense	83873	exon2			AF317652	CCDS801.1	1p13.3	2012-08-21			ENSG00000156097	ENSG00000156097		"""GPCR / Class A : Orphans"""	13300	protein-coding gene	gene with protein product		606916				11165367, 11690637	Standard	NM_031936		Approved	BALGR	uc001dxy.2	Q9BZJ8	OTTHUMG00000011633	ENST00000527748.1:c.184G>A	1.37:g.110085828G>A	ENSP00000432456:p.Ala62Thr	Somatic		Capture	Illumina HiSeq	Phase_I	109887351	NM_031936	A8K1W2|Q6NWS0|Q8TDV4|Q96PR4	Missense_Mutation	SNP	ENST00000527748.1	37	CCDS801.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806331	0.90623	.	.	ENSG00000156097	ENST00000527748;ENST00000286603	T	0.71934	-0.61	5.33	5.33	0.75918	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.73536	0.3599	L	0.46614	1.455	0.58432	D	0.999999	D	0.67145	0.996	P	0.59288	0.855	T	0.76597	-0.2901	10	0.72032	D	0.01	-12.7317	18.6137	0.91295	0.0:0.0:1.0:0.0	.	62	Q9BZJ8	GPR61_HUMAN	T	62;190	ENSP00000432456:A62T	ENSP00000286603:A190T	A	+	1	0	GPR61	109887351	1.000000	0.71417	0.937000	0.37676	0.939000	0.58152	9.861000	0.99562	2.479000	0.83701	0.561000	0.74099	GCT		0.612	GPR61-005	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385575.1		
GATAD2B	57459	broad.mit.edu	37	1	153784507	153784507	+	Silent	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:153784507C>T	ENST00000368655.4	-	9	1764	c.1521G>A	c.(1519-1521)acG>acA	p.T507T		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	507					ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.T507T(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCTGCCGAAGCGTATGATGTC	0.443																																					p.T507T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1521A	1						.						123.0	117.0	119.0					1																	153784507		2203	4300	6503	152051131	SO:0001819	synonymous_variant	57459	exon9			AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1521G>A	1.37:g.153784507C>T		Somatic		Capture	Illumina HiSeq	Phase_I	152051131	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Silent	SNP	ENST00000368655.4	37	CCDS1054.1																																																																																				0.443	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
CHRNB2	1141	broad.mit.edu	37	1	154544129	154544129	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:154544129C>T	ENST00000368476.3	+	5	1094	c.830C>T	c.(829-831)aCg>aTg	p.T277M		NM_000748.2	NP_000739.1	P17787	ACHB2_HUMAN	cholinergic receptor, nicotinic, beta 2 (neuronal)	277					action potential (GO:0001508)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|central nervous system projection neuron axonogenesis (GO:0021952)|cognition (GO:0050890)|conditioned taste aversion (GO:0001661)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|lateral geniculate nucleus development (GO:0021771)|learning (GO:0007612)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|neurological system process (GO:0050877)|optic nerve morphogenesis (GO:0021631)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|protein heterooligomerization (GO:0051291)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of circadian sleep/wake cycle, REM sleep (GO:0042320)|regulation of dendrite morphogenesis (GO:0048814)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine secretion (GO:0014059)|regulation of synapse assembly (GO:0051963)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|sensory perception of pain (GO:0019233)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|smooth muscle contraction (GO:0006939)|social behavior (GO:0035176)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)|vestibulocochlear nerve development (GO:0021562)|visual learning (GO:0008542)|visual perception (GO:0007601)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)|ligand-gated ion channel activity (GO:0015276)	p.T277M(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|skin(1)|urinary_tract(3)	28	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		LUSC - Lung squamous cell carcinoma(543;0.185)		Dextromethorphan(DB00514)|Galantamine(DB00674)|Nicotine(DB00184)	CTGGCGCTCACGGTCTTCCTG	0.582																																					p.T277M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C830T	1						.						264.0	196.0	219.0					1																	154544129		2203	4300	6503	152810753	SO:0001583	missense	1141	exon5			U62437	CCDS1070.1	1q21.3	2012-02-11	2006-02-01		ENSG00000160716	ENSG00000160716		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1962	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, beta 2 (neuronal)"""	118507	"""cholinergic receptor, nicotinic, beta polypeptide 2 (neuronal)"""			1505988	Standard	NM_000748		Approved		uc001ffg.3	P17787	OTTHUMG00000037262	ENST00000368476.3:c.830C>T	1.37:g.154544129C>T	ENSP00000357461:p.Thr277Met	Somatic		Capture	Illumina HiSeq	Phase_I	152810753	NM_000748	Q9UEH9	Missense_Mutation	SNP	ENST00000368476.3	37	CCDS1070.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230939	0.79688	.	.	ENSG00000160716	ENST00000368476	D	0.93811	-3.29	4.1	4.1	0.47936	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.97626	0.9222	H	0.96365	3.81	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99060	1.0830	10	0.87932	D	0	.	16.1089	0.81244	0.0:1.0:0.0:0.0	.	277	P17787	ACHB2_HUMAN	M	277	ENSP00000357461:T277M	ENSP00000357461:T277M	T	+	2	0	CHRNB2	152810753	1.000000	0.71417	0.995000	0.50966	0.884000	0.51177	7.608000	0.82898	2.095000	0.63458	0.467000	0.42956	ACG		0.582	CHRNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090697.1	NM_000748	
ETV3L	440695	broad.mit.edu	37	1	157062808	157062808	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A	A	A	A	A	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:157062808A>G	ENST00000454449.2	-	5	1003	c.719T>C	c.(718-720)cTg>cCg	p.L240P		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	240	Pro-rich.				cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Hepatocellular(266;0.158)	Prostate(1639;0.184)				GTTGGAGGGCAGAGGGGGCGG	0.667																																					p.L240P												.	.	0			c.T719C	1						.						11.0	13.0	13.0					1																	157062808		2191	4287	6478	155329432	SO:0001583	missense	440695	exon5			AK131392	CCDS30893.1	1q23.1	2013-09-24	2008-09-12		ENSG00000253831	ENSG00000253831			33834	protein-coding gene	gene with protein product			"""ets variant gene 3-like"""				Standard	NM_001004341		Approved	FLJ16478	uc001fqq.2	Q6ZN32	OTTHUMG00000041325	ENST00000454449.2:c.719T>C	1.37:g.157062808A>G	ENSP00000430271:p.Leu240Pro	None		Capture	Illumina HiSeq	Phase_I	155329432	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	.	.	.	.	.	.	.	.	.	.	A	3.513	-0.099360	0.07010	.	.	ENSG00000253831	ENST00000454449	T	0.09445	2.98	4.18	1.36	0.22044	.	19.146100	0.00735	N	0.000970	T	0.02193	0.0068	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.38520	-0.9657	10	0.37606	T	0.19	.	3.6248	0.08109	0.6224:0.2107:0.1669:0.0	.	240	Q6ZN32	ETV3L_HUMAN	P	240	ENSP00000430271:L240P	ENSP00000430271:L240P	L	-	2	0	ETV3L	155329432	0.141000	0.22595	0.000000	0.03702	0.007000	0.05969	1.686000	0.37669	0.067000	0.16545	0.402000	0.26972	CTG		0.667	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341	
TP73-AS1	57212	broad.mit.edu	37	1	3662434	3662434	+	RNA	DEL	G	G	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	G	G	G	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:3662434delG	ENST00000452079.1	-	0	1452				TP73-AS1_ENST00000418088.1_RNA|TP73-AS1_ENST00000423764.1_RNA|TP73-AS1_ENST00000608600.1_RNA|TP73-AS1_ENST00000544565.1_RNA	NR_033711.1		Q9UF72	T73AS_HUMAN	TP73 antisense RNA 1							extracellular region (GO:0005576)											AGCACCCTGTGGGAGGCTTCA	0.607																																					.												.	.	0			.	1						.						35.0	40.0	38.0					1																	3662434		1932	4149	6081	3652294			57212	.					1p36.32	2014-01-20	2014-01-20	2014-01-20	ENSG00000227372	ENSG00000227372		"""Long non-coding RNAs"""	29052	non-coding RNA	RNA, long non-coding	"""p53-dependent apoptosis modulator"""		"""KIAA0495"""	KIAA0495		9455484, 20477830, 23726844	Standard	NR_033708		Approved	PDAM	uc009vlm.3	Q9UF72	OTTHUMG00000003414		1.37:g.3662434delG		None		Capture	Illumina HiSeq	Phase_I	3652294	.		Frame_Shift_Del	DEL	ENST00000452079.1	37																																																																																					0.607	TP73-AS1-003	KNOWN	basic	antisense	antisense	OTTHUMT00000009558.1	NR_033708	
SCP2	6342	broad.mit.edu	37	1	53420454	53420454	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:53420454G>C	ENST00000528311.1	+	4	427	c.131G>C	c.(130-132)aGt>aCt	p.S44T	SCP2_ENST00000407246.2_Missense_Mutation_p.S101T|SCP2_ENST00000371513.5_Missense_Mutation_p.S81T|SCP2_ENST00000371509.4_Missense_Mutation_p.S81T|SCP2_ENST00000371514.3_Missense_Mutation_p.S125T	NM_001193617.1	NP_001180546.1	Q9BX26	SYCP2_HUMAN	sterol carrier protein 2	0					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)	p.S125T(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	15						GAGAAGATGAGTAAGGGAAGC	0.343																																					p.S44T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G131C	1						.						222.0	230.0	227.0					1																	53420454		2203	4300	6503	53193042	SO:0001583	missense	6342	exon4			M75884	CCDS572.1, CCDS30719.1, CCDS41338.1, CCDS44149.1, CCDS44150.1, CCDS53317.1, CCDS53318.1, CCDS53319.1	1p32	2010-08-20			ENSG00000116171	ENSG00000116171			10606	protein-coding gene	gene with protein product		184755				1703300, 1718316	Standard	NM_001007098		Approved		uc001cur.2	P22307	OTTHUMG00000008936	ENST00000528311.1:c.131G>C	1.37:g.53420454G>C	ENSP00000434132:p.Ser44Thr	Somatic		Capture	Illumina HiSeq	Phase_I	53193042	NM_001193617	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000528311.1	37	CCDS53319.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.449|9.449	1.090090|1.090090	0.20390|0.20390	.|.	.|.	ENSG00000116171|ENSG00000116171	ENST00000371514;ENST00000528311;ENST00000371509;ENST00000407246;ENST00000371513|ENST00000529363	D;D;D;D;D|.	0.96011|.	-3.2;-3.2;-3.88;-3.2;-3.88|.	5.67|5.67	-1.07|-1.07	0.09968|0.09968	Thiolase, N-terminal (1);Thiolase-like (1);|.	0.518243|.	0.21749|.	N|.	0.069712|.	T|T	0.20861|0.20861	0.0502|0.0502	N|N	0.25992|0.25992	0.78|0.78	0.23751|0.23751	N|N	0.996949|0.996949	B;B;B;B|.	0.06786|.	0.001;0.001;0.001;0.0|.	B;B;B;B|.	0.09377|.	0.004;0.001;0.004;0.001|.	T|T	0.24657|0.24657	-1.0154|-1.0154	10|5	0.39692|.	T|.	0.17|.	8.0E-4|8.0E-4	2.9676|2.9676	0.05912|0.05912	0.5509:0.2132:0.1323:0.1036|0.5509:0.2132:0.1323:0.1036	.|.	101;81;125;81|.	C9JC79;A6NM69;P22307;Q6NXF4|.	.;.;NLTP_HUMAN;.|.	T|L	125;44;81;101;81|100	ENSP00000360569:S125T;ENSP00000434132:S44T;ENSP00000360564:S81T;ENSP00000384569:S101T;ENSP00000360568:S81T|.	ENSP00000360564:S81T|.	S|V	+|+	2|1	0|0	SCP2|SCP2	53193042|53193042	0.678000|0.678000	0.27586|0.27586	0.005000|0.005000	0.12908|0.12908	0.119000|0.119000	0.20118|0.20118	1.245000|1.245000	0.32790|0.32790	-0.440000|-0.440000	0.07211|0.07211	-1.142000|-1.142000	0.01873|0.01873	AGT|GTA		0.343	SCP2-010	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387558.1	NM_002979	
C1orf52	148423	broad.mit.edu	37	1	85724354	85724354	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:85724354T>C	ENST00000471115.1	-	2	336	c.328A>G	c.(328-330)Acc>Gcc	p.T110A	C1orf52_ENST00000344356.5_Missense_Mutation_p.T110A|C1orf52_ENST00000294661.4_5'UTR	NM_198077.3	NP_932343.1	Q8N6N3	CA052_HUMAN	chromosome 1 open reading frame 52	110							poly(A) RNA binding (GO:0044822)	p.T110A(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)	10				all cancers(265;0.0105)|Epithelial(280;0.0293)		GTGGTGTAGGTCTCAGGAGGT	0.448																																					p.T110A												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A328G	1						.						102.0	95.0	97.0					1																	85724354		2203	4300	6503	85496942	SO:0001583	missense	148423	exon2			BC029538	CCDS703.1	1p22.3	2008-02-05			ENSG00000162642	ENSG00000162642			24871	protein-coding gene	gene with protein product						11891061	Standard	NM_198077		Approved	gm117, FLJ44982	uc001dkv.3	Q8N6N3	OTTHUMG00000009966	ENST00000471115.1:c.328A>G	1.37:g.85724354T>C	ENSP00000419417:p.Thr110Ala	Somatic		Capture	Illumina HiSeq	Phase_I	85496942	NM_198077	B3KX89|Q8TDK5|Q8TDK6	Missense_Mutation	SNP	ENST00000471115.1	37	CCDS703.1	.	.	.	.	.	.	.	.	.	.	T	14.38	2.518584	0.44763	.	.	ENSG00000162642	ENST00000471115;ENST00000344356	.	.	.	5.62	4.45	0.53987	.	0.489996	0.23367	N	0.048959	T	0.15869	0.0382	L	0.29908	0.895	0.28976	N	0.888925	B;B	0.26195	0.144;0.073	B;B	0.26094	0.066;0.018	T	0.08848	-1.0702	9	0.62326	D	0.03	-9.8156	9.4265	0.38583	0.2767:0.0:0.0:0.7233	.	110;110	Q8N6N3-2;Q8N6N3	.;CA052_HUMAN	A	110	.	ENSP00000345092:T110A	T	-	1	0	C1orf52	85496942	0.999000	0.42202	0.999000	0.59377	0.969000	0.65631	1.397000	0.34543	2.141000	0.66446	0.528000	0.53228	ACC		0.448	C1orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027616.2	NM_198077	
CACNA1S	779	broad.mit.edu	37	1	201058586	201058586	+	Missense_Mutation	SNP	C	C	T	rs370661912		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr1:201058586C>T	ENST00000362061.3	-	6	926	c.700G>A	c.(700-702)Gtg>Atg	p.V234M	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V234M	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	234					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.V234M(1)		NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	ACCGTGGCCACGATATCTGGA	0.572													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20808	0.0		0.0	False		,,,				2504	0.0				p.V234M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G700A	1						.	C	MET/VAL	0,4406		0,0,2203	33.0	29.0	30.0		700	3.0	1.0	1		30	2,8598	2.2+/-6.3	0,2,4298	no	missense	CACNA1S	NM_000069.2	21	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	possibly-damaging	234/1874	201058586	2,13004	2203	4300	6503	199325209	SO:0001583	missense	779	exon6			L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.700G>A	1.37:g.201058586C>T	ENSP00000355192:p.Val234Met	Somatic		Capture	Illumina HiSeq	Phase_I	199325209	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	.	.	.	.	.	.	.	.	.	.	C	6.071	0.381408	0.11466	0.0	2.33E-4	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.96300	-3.97;-3.87	4.85	2.95	0.34219	Ion transport (1);	0.421997	0.21365	U	0.075735	D	0.89458	0.6721	N	0.13043	0.29	0.27212	N	0.959883	B	0.18863	0.031	B	0.26969	0.075	T	0.80696	-0.1267	10	0.41790	T	0.15	.	3.1678	0.06541	0.1982:0.5303:0.0:0.2714	.	234	Q13698	CAC1S_HUMAN	M	234	ENSP00000355192:V234M;ENSP00000356307:V234M	ENSP00000355192:V234M	V	-	1	0	CACNA1S	199325209	0.245000	0.23899	0.994000	0.49952	0.103000	0.19146	-0.287000	0.08388	1.181000	0.42912	0.650000	0.86243	GTG		0.572	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
HSPA12B	116835	broad.mit.edu	37	20	3722944	3722944	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr20:3722944G>A	ENST00000254963.2	+	4	300	c.155G>A	c.(154-156)cGa>cAa	p.R52Q	HSPA12B_ENST00000542646.1_Intron	NM_001197327.1|NM_052970.4	NP_001184256.1|NP_443202.3	Q96MM6	HS12B_HUMAN	heat shock 70kD protein 12B	52							ATP binding (GO:0005524)	p.R52Q(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	14						CCCGAGGTCCGAGCCCCCCAG	0.592																																					p.R52Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G155A	20						.						54.0	55.0	55.0					20																	3722944		2203	4300	6503	3670944	SO:0001583	missense	116835	exon4			AK056712	CCDS13061.1	20p13	2011-09-02	2003-04-10	2003-04-10	ENSG00000132622	ENSG00000132622		"""Heat shock proteins / HSP70"""	16193	protein-coding gene	gene with protein product		610702	"""chromosome 20 open reading frame 60"""	C20orf60		12552099	Standard	NM_052970		Approved	dJ1009E24.2	uc002wjd.3	Q96MM6	OTTHUMG00000031755	ENST00000254963.2:c.155G>A	20.37:g.3722944G>A	ENSP00000254963:p.Arg52Gln	Somatic		Capture	Illumina HiSeq	Phase_I	3670944	NM_001197327	D3DVX7|Q2TAK3|Q9BR52	Missense_Mutation	SNP	ENST00000254963.2	37	CCDS13061.1	.	.	.	.	.	.	.	.	.	.	G	15.80	2.940050	0.52972	.	.	ENSG00000132622	ENST00000254963	T	0.03860	3.78	4.58	4.58	0.56647	.	0.060357	0.64402	D	0.000004	T	0.04318	0.0119	L	0.36672	1.1	0.80722	D	1	P;P	0.49696	0.881;0.927	B;B	0.37091	0.114;0.241	T	0.57353	-0.7826	10	0.15952	T	0.53	.	15.283	0.73801	0.0:0.0:1.0:0.0	.	52;52	B7ZLP2;Q96MM6	.;HS12B_HUMAN	Q	52	ENSP00000254963:R52Q	ENSP00000254963:R52Q	R	+	2	0	HSPA12B	3670944	1.000000	0.71417	0.885000	0.34714	0.978000	0.69477	4.726000	0.61986	2.538000	0.85594	0.655000	0.94253	CGA		0.592	HSPA12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077756.2	NM_052970	
RBPJL	11317	broad.mit.edu	37	20	43940928	43940928	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr20:43940928T>A	ENST00000343694.3	+	6	584	c.512T>A	c.(511-513)cTg>cAg	p.L171Q	RBPJL_ENST00000372743.1_Missense_Mutation_p.L171Q|RBPJL_ENST00000372741.3_Missense_Mutation_p.L171Q	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	171					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.L171Q(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)				cggctggtgctgcggctggtg	0.597																																					p.L171Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T512A	20						.						33.0	36.0	35.0					20																	43940928		2203	4300	6503	43374342	SO:0001583	missense	11317	exon6			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.512T>A	20.37:g.43940928T>A	ENSP00000341243:p.Leu171Gln	Somatic		Capture	Illumina HiSeq	Phase_I	43374342	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.432321	0.83776	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	D;D;D	0.86769	-2.17;-2.17;-2.17	3.9	3.9	0.45041	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.000000	0.56097	D	0.000033	D	0.92021	0.7472	M	0.69823	2.125	0.50039	D	0.999845	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92710	0.6182	10	0.87932	D	0	-17.9935	12.3414	0.55095	0.0:0.0:0.0:1.0	.	171;171	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	Q	171	ENSP00000361828:L171Q;ENSP00000361826:L171Q;ENSP00000341243:L171Q	ENSP00000341243:L171Q	L	+	2	0	RBPJL	43374342	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.440000	0.80464	1.742000	0.51746	0.368000	0.22195	CTG		0.597	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
ZNF335	63925	broad.mit.edu	37	20	44588938	44588938	+	Silent	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr20:44588938G>A	ENST00000322927.2	-	14	2029	c.1929C>T	c.(1927-1929)caC>caT	p.H643H	ZNF335_ENST00000426788.1_Silent_p.H488H	NM_022095.3	NP_071378.1	Q9H4Z2	ZN335_HUMAN	zinc finger protein 335	643					brain development (GO:0007420)|brain morphogenesis (GO:0048854)|cerebral cortex neuron differentiation (GO:0021895)|histone H3-K4 trimethylation (GO:0080182)|in utero embryonic development (GO:0001701)|neuron projection morphogenesis (GO:0048812)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of neurogenesis (GO:0050769)|regulation of gene expression, epigenetic (GO:0040029)|regulation of histone H3-K4 methylation (GO:0051569)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription regulatory region DNA binding (GO:0044212)	p.H643H(1)		NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(13)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	51		Myeloproliferative disorder(115;0.0122)				TGTCACTGACGTGGGACAACT	0.532																																					p.H643H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1929T	20						.						120.0	117.0	118.0					20																	44588938		2203	4300	6503	44022345	SO:0001819	synonymous_variant	63925	exon14			AK026157	CCDS13389.1	20q13.12	2011-09-12			ENSG00000198026	ENSG00000198026		"""Zinc fingers, C2H2-type"""	15807	protein-coding gene	gene with protein product	"""NRC-interacting factor 1"""	610827				12215545, 19131338	Standard	NM_022095		Approved	bA465L10.2, NIF-1	uc002xqw.3	Q9H4Z2	OTTHUMG00000032637	ENST00000322927.2:c.1929C>T	20.37:g.44588938G>A		Somatic		Capture	Illumina HiSeq	Phase_I	44022345	NM_022095	B4DLG7|Q548D0|Q9H684	Silent	SNP	ENST00000322927.2	37	CCDS13389.1																																																																																				0.532	ZNF335-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079553.1	NM_022095	
CDH26	60437	broad.mit.edu	37	20	58564054	58564054	+	Silent	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr20:58564054G>A	ENST00000244047.5	+	9	1430	c.1119G>A	c.(1117-1119)ccG>ccA	p.P373P	CDH26_ENST00000348616.4_Silent_p.P373P			Q8IXH8	CAD26_HUMAN	cadherin 26	373	Cadherin 3. {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.P373P(4)		breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(11)|lung(14)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	44	all_lung(29;0.00963)		BRCA - Breast invasive adenocarcinoma(7;5.58e-09)			AGCTTCAGCCGCCAAGGAAGG	0.557																																					p.P373P												.	.	4	Substitution - coding silent(4)	large_intestine(2)|breast(2)	c.G1119A	20						.						72.0	82.0	79.0					20																	58564054		2203	4300	6503	57997449	SO:0001819	synonymous_variant	60437	exon9			AF169690, AK055202	CCDS13485.1, CCDS13486.1	20q13.33	2010-01-26	2009-11-20		ENSG00000124215	ENSG00000124215		"""Cadherins / Major cadherins"""	15902	protein-coding gene	gene with protein product			"""cadherin-like 26"""				Standard	NM_177980		Approved	VR20	uc002ybe.3	Q8IXH8	OTTHUMG00000032874	ENST00000244047.5:c.1119G>A	20.37:g.58564054G>A		Somatic		Capture	Illumina HiSeq	Phase_I	57997449	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37																																																																																					0.557	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980	
CHCHD10	400916	broad.mit.edu	37	22	24108440	24108441	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr22:24108440_24108441insG	ENST00000484558.2	-	3	851_852	c.283_284insC	c.(283-285)cagfs	p.Q95fs	CHCHD10_ENST00000520222.1_Frame_Shift_Ins_p.S22fs|CHCHD10_ENST00000401675.3_Frame_Shift_Ins_p.Q102fs			Q8WYQ3	CHC10_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 10	95	CHCH.				ATP biosynthetic process (GO:0006754)|negative regulation of ATP citrate synthase activity (GO:2000984)|oxidative phosphorylation (GO:0006119)	mitochondrion (GO:0005739)		p.Q95fs*24(1)		large_intestine(2)|lung(1)	3						CTGCAGGGGCTGGGGGGCAGCG	0.653																																					p.Q95fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.284_285insC	22						.																																			22438441	SO:0001589	frameshift_variant	400916	exon3			AB050774	CCDS13815.1	22q11.23	2011-03-28	2008-06-13	2008-06-13	ENSG00000250479	ENSG00000250479		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	15559	protein-coding gene	gene with protein product		615903	"""chromosome 22 open reading frame 16"""	C22orf16			Standard	XM_006724241		Approved	N27C7-4	uc002zxw.3	Q8WYQ3	OTTHUMG00000150736	ENST00000484558.2:c.284dupC	22.37:g.24108446_24108446dupG	ENSP00000418428:p.Gln95fs	Somatic		Capture	Illumina HiSeq	Phase_I	22438440	NM_213720	A8K0J5	Frame_Shift_Ins	INS	ENST00000484558.2	37	CCDS13815.1																																																																																				0.653	CHCHD10-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000319870.2	NM_213720	
SF3A1	10291	broad.mit.edu	37	22	30741064	30741064	+	Missense_Mutation	SNP	G	G	A	rs370505540		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr22:30741064G>A	ENST00000215793.8	-	4	663	c.509C>T	c.(508-510)aCg>aTg	p.T170M	SF3A1_ENST00000439242.1_Intron	NM_005877.4	NP_005868.1	Q15459	SF3A1_HUMAN	splicing factor 3a, subunit 1, 120kDa	170					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U2-type spliceosomal complex (GO:0005684)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.T170M(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|urinary_tract(1)	29						AAACTGAGCCGTCAGCTTCAC	0.542																																					p.T170M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C509T	22						.	G	,MET/THR	0,4406		0,0,2203	125.0	117.0	120.0		,509	5.4	1.0	22		120	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	SF3A1	NM_001005409.1,NM_005877.4	,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,probably-damaging	,170/794	30741064	1,13005	2203	4300	6503	29071064	SO:0001583	missense	10291	exon4			X85237	CCDS13875.1	22q12.2	2014-09-17	2002-08-29		ENSG00000099995	ENSG00000099995			10765	protein-coding gene	gene with protein product		605595	"""splicing factor 3a, subunit 1, 120kD"""			7489498	Standard	NM_005877		Approved	SF3a120, SAP114, PRPF21, Prp21	uc003ahl.3	Q15459	OTTHUMG00000151005	ENST00000215793.8:c.509C>T	22.37:g.30741064G>A	ENSP00000215793:p.Thr170Met	Somatic		Capture	Illumina HiSeq	Phase_I	29071064	NM_005877	E9PAW1	Missense_Mutation	SNP	ENST00000215793.8	37	CCDS13875.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.942449	0.73672	0.0	1.16E-4	ENSG00000099995	ENST00000215793;ENST00000536049	T	0.59638	0.25	5.4	5.4	0.78164	SWAP/Surp (3);	0.000000	0.85682	D	0.000000	D	0.83547	0.5278	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.87606	0.2500	10	0.87932	D	0	-14.7959	19.3554	0.94410	0.0:0.0:1.0:0.0	.	170	Q15459	SF3A1_HUMAN	M	170;67	ENSP00000215793:T170M	ENSP00000215793:T170M	T	-	2	0	SF3A1	29071064	1.000000	0.71417	0.973000	0.42090	0.968000	0.65278	9.557000	0.98129	2.809000	0.96659	0.655000	0.94253	ACG		0.542	SF3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320916.2	NM_005877	
SLC9A4	389015	broad.mit.edu	37	2	103095684	103095684	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:103095684T>C	ENST00000295269.4	+	2	1100	c.643T>C	c.(643-645)Ttt>Ctt	p.F215L		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	215					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.F215L(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						GCTAGCCGTGTTTGAGGAAGC	0.607																																					p.F215L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T643C	2						.						48.0	38.0	41.0					2																	103095684		2203	4300	6503	102462116	SO:0001583	missense	389015	exon2				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.643T>C	2.37:g.103095684T>C	ENSP00000295269:p.Phe215Leu	Somatic		Capture	Illumina HiSeq	Phase_I	102462116	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	.	.	.	.	.	.	.	.	.	.	T	16.10	3.027904	0.54790	.	.	ENSG00000180251	ENST00000295269	T	0.08634	3.07	5.26	5.26	0.73747	Cation/H+ exchanger (1);	0.000000	0.85682	D	0.000000	T	0.24431	0.0592	M	0.72353	2.195	0.80722	D	1	P	0.50710	0.938	P	0.57324	0.818	T	0.00684	-1.1611	10	0.87932	D	0	.	15.1886	0.73025	0.0:0.0:0.0:1.0	.	215	Q6AI14	SL9A4_HUMAN	L	215	ENSP00000295269:F215L	ENSP00000295269:F215L	F	+	1	0	SLC9A4	102462116	1.000000	0.71417	0.989000	0.46669	0.298000	0.27526	7.982000	0.88131	1.978000	0.57642	0.533000	0.62120	TTT		0.607	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
RANBP2	5903	broad.mit.edu	37	2	109382689	109382689	+	Silent	SNP	T	T	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:109382689T>C	ENST00000283195.6	+	20	5820	c.5694T>C	c.(5692-5694)ttT>ttC	p.F1898F		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	1898					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)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)	p.F1898F(2)	RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						CTGATGGATTTAAATTTGGCA	0.378																																					p.F1898F												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.T5694C	2						.						69.0	83.0	78.0					2																	109382689		2150	4266	6416	108749121	SO:0001819	synonymous_variant	5903	exon20			D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.5694T>C	2.37:g.109382689T>C		Somatic		Capture	Illumina HiSeq	Phase_I	108749121	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Silent	SNP	ENST00000283195.6	37	CCDS2079.1																																																																																				0.378	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
LCT	3938	broad.mit.edu	37	2	136575430	136575430	+	Silent	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:136575430G>A	ENST00000264162.2	-	6	1198	c.1188C>T	c.(1186-1188)aaC>aaT	p.N396N	AC011893.3_ENST00000437007.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	396	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)	p.N396N(1)		breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTCCTTCCACGTTAAAGGCTC	0.622																																					p.N396N												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1188T	2						.						62.0	69.0	67.0					2																	136575430		2203	4299	6502	136291900	SO:0001819	synonymous_variant	3938	exon6			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.1188C>T	2.37:g.136575430G>A		Somatic		Capture	Illumina HiSeq	Phase_I	136291900	NM_002299	Q4ZG58	Silent	SNP	ENST00000264162.2	37	CCDS2178.1																																																																																				0.622	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299	
RAPGEF4	11069	broad.mit.edu	37	2	173891948	173891948	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:173891948G>A	ENST00000397081.3	+	25	2662	c.2519G>A	c.(2518-2520)cGt>cAt	p.R840H	RAPGEF4_ENST00000535187.1_Missense_Mutation_p.R620H|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.R687H|RAPGEF4_ENST00000397087.3_Missense_Mutation_p.R696H|RAPGEF4_ENST00000538974.1_Missense_Mutation_p.R669H|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.R687H|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.R840H|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.R839H	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	840	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.R840H(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			CTCAGCAAGCGTGTTCAGCTA	0.348																																					p.R840H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2519A	2						.						65.0	63.0	64.0					2																	173891948		1807	4072	5879	173600194	SO:0001583	missense	11069	exon25			U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"""cAMP-regulated guanine nucleotide exchange factor II"", "" exchange protein directly activated by cAMP 2"""	606058	"""RAP guanine-nucleotide-exchange factor (GEF) 4"""			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.2519G>A	2.37:g.173891948G>A	ENSP00000380271:p.Arg840His	Somatic		Capture	Illumina HiSeq	Phase_I	173600194	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	37	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	G	32	5.135129	0.94517	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000535187;ENST00000397085	T;T;T;T;T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53;-0.53	5.65	5.65	0.86999	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	D	0.90844	0.7124	H	0.98048	4.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.93797	0.7097	10	0.87932	D	0	.	19.7321	0.96186	0.0:0.0:1.0:0.0	.	696;840	Q8WZA2-3;Q8WZA2	.;RPGF4_HUMAN	H	839;840;840;696;669;687;687;620;71	ENSP00000264111:R839H;ENSP00000380271:R840H;ENSP00000387104:R840H;ENSP00000380276:R696H;ENSP00000440135:R669H;ENSP00000440250:R687H;ENSP00000437384:R687H;ENSP00000438011:R620H;ENSP00000380274:R71H	ENSP00000264111:R839H	R	+	2	0	RAPGEF4	173600194	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.668000	0.90789	0.655000	0.94253	CGT		0.348	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023	
NDUFAF7	55471	broad.mit.edu	37	2	37463254	37463254	+	Missense_Mutation	SNP	C	C	T	rs151093411		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:37463254C>T	ENST00000002125.4	+	3	272	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	NDUFAF7_ENST00000483999.1_Intron|NDUFAF7_ENST00000336237.6_Intron	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	78					methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)	p.R78S(1)|p.R78C(1)									TTATGTGTACCGTGACATGCT	0.299																																					p.R78C												.	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.C232T	2						.	C	,CYS/ARG	1,4403	2.1+/-5.4	0,1,2201	102.0	110.0	108.0		,232	4.5	0.7	2	dbSNP_134	108	0,8592		0,0,4296	no	intron,missense	C2orf56	NM_001083946.1,NM_144736.4	,180	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	,probably-damaging	,78/442	37463254	1,12995	2202	4296	6498	37316758	SO:0001583	missense	55471	exon3				CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.232C>T	2.37:g.37463254C>T	ENSP00000002125:p.Arg78Cys	Somatic		Capture	Illumina HiSeq	Phase_I	37316758	NM_144736	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	C	16.13	3.036867	0.54896	2.27E-4	0.0	ENSG00000003509	ENST00000002125;ENST00000416653;ENST00000439218;ENST00000432075	T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15	5.36	4.49	0.54785	.	0.624606	0.17209	N	0.182807	T	0.75398	0.3844	M	0.79343	2.45	0.21652	N	0.9996	D;B	0.56968	0.978;0.28	B;B	0.36504	0.226;0.016	T	0.71034	-0.4709	10	0.66056	D	0.02	-1.3714	13.9148	0.63890	0.0:0.9259:0.0:0.0741	.	78;78	B4DQY3;Q7L592	.;MIDA_HUMAN	C	78;36;36;36	ENSP00000002125:R78C;ENSP00000410181:R36C;ENSP00000394436:R36C;ENSP00000402959:R36C	ENSP00000002125:R78C	R	+	1	0	C2orf56	37316758	0.080000	0.21391	0.666000	0.29783	0.893000	0.52053	3.785000	0.55424	1.264000	0.44198	0.462000	0.41574	CGT		0.299	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
ADD2	119	broad.mit.edu	37	2	70919535	70919535	+	Splice_Site	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:70919535C>T	ENST00000264436.4	-	7	1149	c.705G>A	c.(703-705)gcG>gcA	p.A235A	AC007395.3_ENST00000457851.1_RNA|ADD2_ENST00000407644.2_Splice_Site_p.A235A|ADD2_ENST00000355733.3_Splice_Site_p.A235A|ADD2_ENST00000430656.1_Splice_Site_p.A251A|ADD2_ENST00000413157.2_Splice_Site_p.A235A	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	235					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)	p.A235A(2)		autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						GTCCACTCACCGCTGCTGTGG	0.567																																					p.A235A												.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.G705A	2						.						48.0	46.0	47.0					2																	70919535		2203	4300	6503	70773043	SO:0001630	splice_region_variant	119	exon7			X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.705+1G>A	2.37:g.70919535C>T		Somatic		Capture	Illumina HiSeq	Phase_I	70773043	NM_001185054	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Silent	SNP	ENST00000264436.4	37	CCDS1906.1																																																																																				0.567	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	Silent
MAP2	4133	broad.mit.edu	37	2	210559979	210559979	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr2:210559979G>T	ENST00000360351.4	+	7	3591	c.3085G>T	c.(3085-3087)Gaa>Taa	p.E1029*	MAP2_ENST00000361559.4_Intron|MAP2_ENST00000447185.1_Nonsense_Mutation_p.E1025*|MAP2_ENST00000392194.1_Intron|MAP2_ENST00000199940.6_Intron	NM_002374.3	NP_002365.3	P11137	MTAP2_HUMAN	microtubule-associated protein 2	1029					axonogenesis (GO:0007409)|cellular response to organic substance (GO:0071310)|central nervous system neuron development (GO:0021954)|dendrite morphogenesis (GO:0048813)|microtubule bundle formation (GO:0001578)|neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|neuronal cell body (GO:0043025)|nuclear periphery (GO:0034399)	dystroglycan binding (GO:0002162)|structural molecule activity (GO:0005198)	p.E1029*(1)		breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(36)|liver(2)|lung(42)|ovary(11)|pancreas(2)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	124		Hepatocellular(293;0.137)|Lung NSC(271;0.163)|Renal(323;0.202)		UCEC - Uterine corpus endometrioid carcinoma (47;6.64e-05)|Epithelial(149;3.12e-100)|all cancers(144;6.88e-91)|Lung(261;0.0624)|LUSC - Lung squamous cell carcinoma(261;0.0662)|STAD - Stomach adenocarcinoma(1183;0.18)	Docetaxel(DB01248)|Estramustine(DB01196)|Paclitaxel(DB01229)	AGCTGAGGTAGAACCATCCAA	0.438																																					p.E1029X	Pancreas(27;423 979 28787 29963)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G3085T	2						.						105.0	104.0	104.0					2																	210559979		2203	4300	6503	210268224	SO:0001587	stop_gained	4133	exon7				CCDS2384.1, CCDS2385.1, CCDS33369.1	2q34-q35	2008-05-27			ENSG00000078018	ENSG00000078018		"""A-kinase anchor proteins"""	6839	protein-coding gene	gene with protein product		157130				3103857, 7479905	Standard	XM_005246554		Approved	MAP2A, MAP2B, MAP2C	uc002vde.1	P11137	OTTHUMG00000132962	ENST00000360351.4:c.3085G>T	2.37:g.210559979G>T	ENSP00000353508:p.Glu1029*	Somatic		Capture	Illumina HiSeq	Phase_I	210268224	NM_002374	Q17S04|Q8IUX2|Q99975|Q99976	Nonsense_Mutation	SNP	ENST00000360351.4	37	CCDS2384.1	.	.	.	.	.	.	.	.	.	.	G	38	6.828218	0.97869	.	.	ENSG00000078018	ENST00000360351;ENST00000447185	.	.	.	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-20.9701	20.6242	0.99512	0.0:0.0:1.0:0.0	.	.	.	.	X	1029;1025	.	ENSP00000353508:E1029X	E	+	1	0	MAP2	210268224	1.000000	0.71417	0.597000	0.28824	0.557000	0.35523	4.356000	0.59430	2.886000	0.99085	0.644000	0.83932	GAA		0.438	MAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256521.2	NM_001039538	
PARP3	10039	broad.mit.edu	37	3	51978589	51978590	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:51978589_51978590insC	ENST00000417220.2	+	5	984_985	c.496_497insC	c.(496-498)gtgfs	p.V166fs	PARP3_ENST00000398755.3_Frame_Shift_Ins_p.V173fs|PARP3_ENST00000431474.1_Frame_Shift_Ins_p.V166fs|RRP9_ENST00000232888.6_5'Flank			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	166					DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|positive regulation of DNA ligation (GO:0051106)|protein ADP-ribosylation (GO:0006471)|protein localization to site of double-strand break (GO:1990166)|regulation of mitotic spindle organization (GO:0060236)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	catalytic activity (GO:0003824)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.V173fs*13(1)		ovary(1)	1				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000541)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GGAAGCTGTGGTGAAGGTGAGA	0.609																																					p.V166fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.496_497insC	3						.																																			51953630	SO:0001589	frameshift_variant	10039	exon4			AF083068	CCDS43097.1, CCDS46839.1	3p22.2-p21.1	2010-07-14	2004-08-20	2004-08-26	ENSG00000041880	ENSG00000041880	2.4.2.30	"""Poly (ADP-ribose) polymerases"""	273	protein-coding gene	gene with protein product	"""poly(ADP-ribose) synthetase-3"", ""NAD+ ADP-ribosyltransferase 3"", ""poly(ADP-ribose) polymerase 3"""	607726	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 3"""	ADPRTL3		10329013	Standard	NM_001003931		Approved	ADPRT3, IRT1, hPARP-3, pADPRT-3	uc003dbz.3	Q9Y6F1	OTTHUMG00000156931	Exception_encountered	3.37:g.51978589_51978590insC	ENSP00000395951:p.Val166fs	Somatic		Capture	Illumina HiSeq	Phase_I	51953629	NM_005485	Q8NER9|Q96CG2|Q9UG81	Frame_Shift_Ins	INS	ENST00000417220.2	37	CCDS43097.1																																																																																				0.609	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4	
CNTN6	27255	broad.mit.edu	37	3	1424750	1424750	+	Missense_Mutation	SNP	G	G	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:1424750G>C	ENST00000446702.2	+	18	2918	c.2291G>C	c.(2290-2292)aGa>aCa	p.R764T	CNTN6_ENST00000539053.1_Missense_Mutation_p.R692T|CNTN6_ENST00000350110.2_Missense_Mutation_p.R764T			Q9UQ52	CNTN6_HUMAN	contactin 6	764	Fibronectin type-III 2. {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.R764T(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)		TTTGTCTACAGAAATGAAAGC	0.458																																					p.R764T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2291C	3						.						163.0	149.0	154.0					3																	1424750		2203	4300	6503	1399750	SO:0001583	missense	27255	exon18			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.2291G>C	3.37:g.1424750G>C	ENSP00000407822:p.Arg764Thr	Somatic		Capture	Illumina HiSeq	Phase_I	1399750	NM_014461	Q2KHM2	Missense_Mutation	SNP	ENST00000446702.2	37	CCDS2557.1	.	.	.	.	.	.	.	.	.	.	G	19.80	3.895132	0.72639	.	.	ENSG00000134115	ENST00000446702;ENST00000539053;ENST00000350110	T;T;T	0.48201	0.82;0.82;0.82	6.08	5.2	0.72013	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.096661	0.43416	D	0.000563	T	0.70527	0.3234	M	0.85710	2.77	0.36576	D	0.87329	D	0.63880	0.993	D	0.72338	0.977	T	0.77197	-0.2676	10	0.32370	T	0.25	.	15.2732	0.73723	0.067:0.0:0.933:0.0	.	764	Q9UQ52	CNTN6_HUMAN	T	764;692;764	ENSP00000407822:R764T;ENSP00000442791:R692T;ENSP00000341882:R764T	ENSP00000341882:R764T	R	+	2	0	CNTN6	1399750	1.000000	0.71417	0.963000	0.40424	0.761000	0.43186	2.414000	0.44627	1.575000	0.49775	0.655000	0.94253	AGA		0.458	CNTN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239235.2	NM_014461	
BTD	686	broad.mit.edu	37	3	15686976	15686976	+	Missense_Mutation	SNP	G	G	A	rs397514429		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:15686976G>A	ENST00000303498.5	+	4	1722	c.1613G>A	c.(1612-1614)cGc>cAc	p.R538H	BTD_ENST00000437172.1_Missense_Mutation_p.R540H|BTD_ENST00000383778.4_Missense_Mutation_p.R518H|BTD_ENST00000449107.1_Missense_Mutation_p.R540H	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	538			R -> C (in BTD deficiency). {ECO:0000269|PubMed:9099842, ECO:0000269|PubMed:9654207}.		biotin metabolic process (GO:0006768)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	biotin carboxylase activity (GO:0004075)|biotinidase activity (GO:0047708)	p.R538H(1)		breast(2)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)	18						CTCTATGGGCGCTTGTATGAG	0.567																																					p.R538H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1613A	3						.						42.0	46.0	45.0					3																	15686976		2178	4254	6432	15661980	SO:0001583	missense	686	exon4			AF018631	CCDS2628.1, CCDS63563.1, CCDS63564.1, CCDS63565.1	3p25	2007-03-26			ENSG00000169814	ENSG00000169814	3.5.1.12		1122	protein-coding gene	gene with protein product		609019				8001986	Standard	NM_001281723		Approved		uc003cah.3	P43251	OTTHUMG00000129861	ENST00000303498.5:c.1613G>A	3.37:g.15686976G>A	ENSP00000306477:p.Arg538His	Somatic		Capture	Illumina HiSeq	Phase_I	15661980	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Missense_Mutation	SNP	ENST00000303498.5	37	CCDS2628.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.594952	0.86953	.	.	ENSG00000169814	ENST00000449107;ENST00000303498;ENST00000437172;ENST00000383778	D;D;D;D	0.95724	-3.79;-3.79;-3.79;-3.79	5.58	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.97704	0.9247	M	0.86268	2.805	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.98364	1.0550	10	0.87932	D	0	-13.6968	14.2862	0.66247	0.0712:0.0:0.9288:0.0	.	540;540;538	A6NHF2;B4DLJ9;P43251	.;.;BTD_HUMAN	H	540;538;540;518	ENSP00000388212:R540H;ENSP00000306477:R538H;ENSP00000400995:R540H;ENSP00000373288:R518H	ENSP00000306477:R538H	R	+	2	0	BTD	15661980	1.000000	0.71417	0.985000	0.45067	0.972000	0.66771	7.349000	0.79376	1.376000	0.46267	0.561000	0.74099	CGC		0.567	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060	
HEG1	57493	broad.mit.edu	37	3	124748257	124748257	+	Missense_Mutation	SNP	T	T	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:124748257T>A	ENST00000311127.4	-	2	459	c.392A>T	c.(391-393)gAg>gTg	p.E131V		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	131					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.E131V(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TGAAAAGTCCTCTTGATTCTG	0.483																																					p.E131V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A392T	3						.						120.0	112.0	114.0					3																	124748257		1904	4130	6034	126230947	SO:0001583	missense	57493	exon2			AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.392A>T	3.37:g.124748257T>A	ENSP00000311502:p.Glu131Val	Somatic		Capture	Illumina HiSeq	Phase_I	126230947	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	T	0.011	-1.739625	0.00681	.	.	ENSG00000173706	ENST00000311127	T	0.38722	1.12	5.52	-3.53	0.04667	.	.	.	.	.	T	0.13415	0.0325	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.06405	0.002;0.001	T	0.30592	-0.9973	9	0.02654	T	1	.	1.4619	0.02398	0.1978:0.0998:0.3045:0.3978	.	131;131	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	V	131	ENSP00000311502:E131V	ENSP00000311502:E131V	E	-	2	0	HEG1	126230947	0.006000	0.16342	0.004000	0.12327	0.122000	0.20287	-0.289000	0.08365	-0.312000	0.08741	0.460000	0.39030	GAG		0.483	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
PTH1R	5745	broad.mit.edu	37	3	46940315	46940315	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:46940315delC	ENST00000313049.5	+	7	1005	c.802delC	c.(802-804)cccfs	p.P271fs	PTH1R_ENST00000430002.2_Frame_Shift_Del_p.P271fs|PTH1R_ENST00000418619.1_Frame_Shift_Del_p.P271fs|PTH1R_ENST00000449590.1_Frame_Shift_Del_p.P271fs			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor	271					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|bone mineralization (GO:0030282)|bone resorption (GO:0045453)|cell maturation (GO:0048469)|chondrocyte differentiation (GO:0002062)|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 cell proliferation (GO:0008285)|osteoblast development (GO:0002076)|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 inositol phosphate biosynthetic process (GO:0060732)|skeletal system development (GO:0001501)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	parathyroid hormone receptor activity (GO:0004991)|peptide hormone binding (GO:0017046)|protein self-association (GO:0043621)	p.P269fs*17(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(5)|skin(2)|stomach(1)|urinary_tract(2)	19					Preotact(DB05829)|Teriparatide(DB06285)	CGCCCAGGCGCCCCCGCCGCC	0.746																																					p.P268fs												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.802delC	3						.						8.0	8.0	8.0					3																	46940315		2170	4248	6418	46915319	SO:0001589	frameshift_variant	5745	exon8				CCDS2747.1	3p22-p21.1	2012-08-10	2008-11-18	2008-11-18	ENSG00000160801	ENSG00000160801		"""GPCR / Class B : Parathyroid hormone receptors"""	9608	protein-coding gene	gene with protein product		168468	"""parathyroid hormone receptor 1"""	PTHR, PTHR1		8020952	Standard	NM_001184744		Approved		uc021wxg.1	Q03431	OTTHUMG00000133515	ENST00000313049.5:c.802delC	3.37:g.46940315delC	ENSP00000321999:p.Pro271fs	Somatic		Capture	Illumina HiSeq	Phase_I	46915319	NM_001184744	Q2M1U3	Frame_Shift_Del	DEL	ENST00000313049.5	37	CCDS2747.1																																																																																				0.746	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	
GBE1	2632	broad.mit.edu	37	3	81548277	81548277	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:81548277C>T	ENST00000429644.2	-	15	2679	c.2036G>A	c.(2035-2037)cGt>cAt	p.R679H	GBE1_ENST00000489715.1_Missense_Mutation_p.R638H	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	679					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.R679H(1)		breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		AGAATAGGGACGCCCATTATG	0.348									Glycogen Storage Disease, type IV																												p.R679H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2036A	3						.						81.0	74.0	76.0					3																	81548277		1813	4083	5896	81630967	SO:0001583	missense	2632	exon15	Familial Cancer Database	Andersen Disease, Brancher deficiency		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.2036G>A	3.37:g.81548277C>T	ENSP00000410833:p.Arg679His	Somatic		Capture	Illumina HiSeq	Phase_I	81630967	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740382	0.69304	.	.	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715;ENST00000536832	T;T	0.78924	-1.22;-1.22	5.35	4.46	0.54185	Alpha-amylase, C-terminal all beta (1);Glycosyl hydrolase, family 13, all-beta (1);	0.126798	0.53938	D	0.000042	T	0.78898	0.4356	M	0.75150	2.29	0.40075	D	0.976068	P	0.36660	0.564	B	0.39617	0.305	T	0.81163	-0.1058	10	0.72032	D	0.01	-9.4423	13.2872	0.60249	0.1589:0.8411:0.0:0.0	.	679	Q04446	GLGB_HUMAN	H	679;730;638;442	ENSP00000410833:R679H;ENSP00000419638:R638H	ENSP00000264326:R730H	R	-	2	0	GBE1	81630967	1.000000	0.71417	0.039000	0.18376	0.958000	0.62258	3.155000	0.50700	1.215000	0.43411	0.650000	0.86243	CGT		0.348	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
PLD1	5337	broad.mit.edu	37	3	171455389	171455389	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr3:171455389G>A	ENST00000351298.4	-	3	347	c.221C>T	c.(220-222)aCg>aTg	p.T74M	PLD1_ENST00000342215.6_Missense_Mutation_p.T74M|PLD1_ENST00000356327.5_Missense_Mutation_p.T74M|PLD1_ENST00000340989.4_Missense_Mutation_p.T74M	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	74					chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|Ras protein signal transduction (GO:0007265)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)	p.T74M(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|lung(27)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	63	all_cancers(22;4.53e-19)|Ovarian(172;0.00197)|Breast(254;0.186)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)		Choline(DB00122)	GGAGAGATACGTCTGTATATT	0.358																																					p.T74M	NSCLC(149;2174 3517 34058)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C221T	3						.						106.0	104.0	105.0					3																	171455389		2203	4300	6503	172938083	SO:0001583	missense	5337	exon3			U38545	CCDS3216.1, CCDS46957.1	3q26	2013-01-10	2006-02-17		ENSG00000075651	ENSG00000075651	3.1.4.4	"""Pleckstrin homology (PH) domain containing"""	9067	protein-coding gene	gene with protein product	"""choline phosphatase 1"""	602382				9858822, 8530346	Standard	NM_002662		Approved		uc003fhs.3	Q13393	OTTHUMG00000156947	ENST00000351298.4:c.221C>T	3.37:g.171455389G>A	ENSP00000342793:p.Thr74Met	Somatic		Capture	Illumina HiSeq	Phase_I	172938083	NM_001130081		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813057	0.50527	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989;ENST00000418087	T;T;T;T;T	0.44881	3.39;3.39;1.49;3.26;0.91	5.42	2.62	0.31277	.	0.278522	0.36703	N	0.002446	T	0.31796	0.0808	L	0.36672	1.1	0.28574	N	0.910472	P;P	0.41624	0.757;0.753	B;B	0.39339	0.186;0.297	T	0.16129	-1.0413	10	0.46703	T	0.11	-8.7706	10.7529	0.46219	0.2117:0.0:0.7883:0.0	.	97;74	Q59EA4;Q13393	.;PLD1_HUMAN	M	74	ENSP00000348681:T74M;ENSP00000342793:T74M;ENSP00000339936:T74M;ENSP00000340326:T74M;ENSP00000400639:T74M	ENSP00000340326:T74M	T	-	2	0	PLD1	172938083	0.970000	0.33590	0.998000	0.56505	0.987000	0.75469	1.728000	0.38105	0.755000	0.32990	-0.126000	0.14955	ACG		0.358	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662	
FAT4	79633	broad.mit.edu	37	4	126371042	126371042	+	Missense_Mutation	SNP	T	T	A	rs374905704		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr4:126371042T>A	ENST00000394329.3	+	9	8884	c.8871T>A	c.(8869-8871)gaT>gaA	p.D2957E	FAT4_ENST00000335110.5_Missense_Mutation_p.D1255E	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2957	Cadherin 28. {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.D2957E(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						CATCTTCAGATCGAGGTAAAC	0.333																																					p.D2957E												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.T8871A	4						.						68.0	70.0	70.0					4																	126371042		2203	4299	6502	126590492	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.8871T>A	4.37:g.126371042T>A	ENSP00000377862:p.Asp2957Glu	Somatic		Capture	Illumina HiSeq	Phase_I	126590492	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	19.01	3.744205	0.69418	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.67865	-0.29;-0.29	5.34	-4.98	0.03019	Cadherin (4);Cadherin-like (1);	0.000000	0.34986	U	0.003528	T	0.80237	0.4586	M	0.86097	2.795	0.54753	D	0.999989	D;D;D	0.76494	0.996;0.998;0.999	D;D;D	0.85130	0.99;0.997;0.995	T	0.82589	-0.0382	10	0.66056	D	0.02	.	16.5359	0.84373	0.0:0.7818:0.0:0.2182	.	1255;2957;2957	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	E	2957;1255	ENSP00000377862:D2957E;ENSP00000335169:D1255E	ENSP00000335169:D1255E	D	+	3	2	FAT4	126590492	0.990000	0.36364	0.913000	0.36048	0.947000	0.59692	0.491000	0.22419	-0.835000	0.04234	0.533000	0.62120	GAT		0.333	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
UCHL1	7345	broad.mit.edu	37	4	41263916	41263916	+	Silent	SNP	C	C	T	rs142811772		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr4:41263916C>T	ENST00000284440.4	+	6	579	c.435C>T	c.(433-435)gcC>gcT	p.A145A	UCHL1_ENST00000508768.1_Intron|UCHL1_ENST00000512788.1_Silent_p.A145A|UCHL1_ENST00000504818.1_3'UTR|UCHL1_ENST00000503431.1_Silent_p.A145A	NM_004181.4	NP_004172.2	P09936	UCHL1_HUMAN	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	145					adult walking behavior (GO:0007628)|axon target recognition (GO:0007412)|axon transport of mitochondrion (GO:0019896)|cell death (GO:0008219)|cell proliferation (GO:0008283)|eating behavior (GO:0042755)|muscle fiber development (GO:0048747)|negative regulation of MAP kinase activity (GO:0043407)|neuromuscular process (GO:0050905)|protein deubiquitination (GO:0016579)|response to ischemia (GO:0002931)|sensory perception of pain (GO:0019233)|ubiquitin-dependent protein catabolic process (GO:0006511)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	alpha-2A adrenergic receptor binding (GO:0031694)|cysteine-type endopeptidase activity (GO:0004197)|ligase activity (GO:0016874)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.A145A(1)		central_nervous_system(1)|endometrium(2)|large_intestine(3)|skin(2)	8						CCCATGATGCCGTGGCACAGG	0.453													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17264	0.0		0.0	False		,,,				2504	0.0				p.A145A												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C435T	4						.	C		1,4405		0,1,2202	65.0	67.0	67.0		435	-10.3	0.1	4	dbSNP_134	67	0,8600		0,0,4300	no	coding-synonymous	UCHL1	NM_004181.4		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		145/224	41263916	1,13005	2203	4300	6503	40958673	SO:0001819	synonymous_variant	7345	exon6			BC000332	CCDS3462.1	4p13	2011-07-21			ENSG00000154277	ENSG00000154277	3.4.19.12	"""Parkinson disease"""	12513	protein-coding gene	gene with protein product		191342		PARK5		1840236	Standard	NM_004181		Approved	PGP9.5, Uch-L1	uc003gvo.3	P09936	OTTHUMG00000099377	ENST00000284440.4:c.435C>T	4.37:g.41263916C>T		Somatic		Capture	Illumina HiSeq	Phase_I	40958673	NM_004181	Q4W5K6|Q71UM0	Silent	SNP	ENST00000284440.4	37	CCDS3462.1																																																																																				0.453	UCHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216827.1	NM_004181	
FRAS1	80144	broad.mit.edu	37	4	79434613	79434613	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr4:79434613C>T	ENST00000264895.6	+	65	10521	c.10081C>T	c.(10081-10083)Cac>Tac	p.H3361Y		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	3357					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)	p.H3361Y(1)		breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CATGCCGTTGCACAACTTACA	0.473																																					p.H3361Y												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C10081T	4						.						178.0	173.0	175.0					4																	79434613		2034	4187	6221	79653637	SO:0001583	missense	80144	exon65			AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.10081C>T	4.37:g.79434613C>T	ENSP00000264895:p.His3361Tyr	Somatic		Capture	Illumina HiSeq	Phase_I	79653637	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000264895.6	37	CCDS54771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.7|28.7	4.941865|4.941865	0.92526|0.92526	.|.	.|.	ENSG00000138759|ENSG00000138759	ENST00000512123|ENST00000264895	.|T	.|0.13089	.|2.62	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.38506|0.38506	0.1043|0.1043	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.87578	.|0.998	T|T	0.04413|0.04413	-1.0953|-1.0953	5|10	.|0.72032	.|D	.|0.01	.|.	19.8365|19.8365	0.96659|0.96659	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|3361	.|E9PHH6	.|.	V|Y	1589|3361	.|ENSP00000264895:H3361Y	.|ENSP00000264895:H3361Y	A|H	+|+	2|1	0|0	FRAS1|FRAS1	79653637|79653637	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.910000|0.910000	0.53928|0.53928	7.673000|7.673000	0.83973|0.83973	2.694000|2.694000	0.91930|0.91930	0.467000|0.467000	0.42956|0.42956	GCA|CAC		0.473	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FAT1	2195	broad.mit.edu	37	4	187518843	187518843	+	Nonsense_Mutation	SNP	C	C	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr4:187518843C>A	ENST00000441802.2	-	24	12570	c.12361G>T	c.(12361-12363)Gga>Tga	p.G4121*	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4121	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.G4121*(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						TACCTTTCTCCCCTAAAACCC	0.418										HNSCC(5;0.00058)																											p.G4121X	Colon(197;1040 2055 4143 4984 49344)											.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G12361T	4						.						61.0	55.0	57.0					4																	187518843		1899	4124	6023	187755837	SO:0001587	stop_gained	2195	exon24			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.12361G>T	4.37:g.187518843C>A	ENSP00000406229:p.Gly4121*	Somatic		Capture	Illumina HiSeq	Phase_I	187755837	NM_005245		Nonsense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	55	23.368290	0.99954	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000507105	.	.	.	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.7706	0.96363	0.0:1.0:0.0:0.0	.	.	.	.	X	4121;4123;53	.	ENSP00000260147:G4123X	G	-	1	0	FAT1	187755837	1.000000	0.71417	1.000000	0.80357	0.819000	0.46315	7.487000	0.81328	2.697000	0.92050	0.655000	0.94253	GGA		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TCOF1	6949	broad.mit.edu	37	5	149754934	149754935	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr5:149754934_149754935insC	ENST00000504761.2	+	11	1521_1522	c.1521_1522insC	c.(1522-1524)cctfs	p.P508fs	TCOF1_ENST00000394269.3_Frame_Shift_Ins_p.P508fs|TCOF1_ENST00000439160.2_Frame_Shift_Ins_p.P508fs|TCOF1_ENST00000513346.1_Frame_Shift_Ins_p.P508fs|TCOF1_ENST00000377797.3_Frame_Shift_Ins_p.P508fs|TCOF1_ENST00000451292.1_Frame_Shift_Ins_p.P508fs|TCOF1_ENST00000445265.2_Frame_Shift_Ins_p.P431fs|TCOF1_ENST00000323668.7_Frame_Shift_Ins_p.P431fs			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	508					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCCAGGTGAAACCTGCCTCTAC	0.634																																					p.K507fs												.	.	0			c.1521_1522insC	5						.																																			149735128	SO:0001589	frameshift_variant	6949	exon11				CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.1523dupC	5.37:g.149754936_149754936dupC	ENSP00000421655:p.Pro508fs	None		Capture	Illumina HiSeq	Phase_I	149735127	NM_001135244	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Frame_Shift_Ins	INS	ENST00000504761.2	37	CCDS54936.1																																																																																				0.634	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
OTP	23440	broad.mit.edu	37	5	76926220	76926221	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr5:76926220_76926221insG	ENST00000306422.3	-	3	1984_1985	c.846_847insC	c.(844-849)cccggcfs	p.G283fs		NM_032109.2	NP_115485.1	Q5XKR4	OTP_HUMAN	orthopedia homeobox	283					forebrain neuron differentiation (GO:0021879)|hypothalamus cell differentiation (GO:0021979)|neurohypophysis development (GO:0021985)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)	p.G283fs*>44(1)		endometrium(1)|kidney(1)|large_intestine(5)|lung(5)|pancreas(1)	13		all_lung(232;0.00051)|Lung NSC(167;0.000601)|Ovarian(174;0.0105)|Prostate(461;0.214)		OV - Ovarian serous cystadenocarcinoma(54;9.04e-51)|Epithelial(54;1.62e-45)|all cancers(79;4.4e-41)		TTGCTGGGGCCGGGGAGGGAGG	0.733																																					p.G283fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.847_848insC	5						.																																			76961977	SO:0001589	frameshift_variant	23440	exon3				CCDS4039.1	5q14.1	2011-06-20	2007-02-15		ENSG00000171540	ENSG00000171540		"""Homeoboxes / PRD class"""	8518	protein-coding gene	gene with protein product		604529	"""orthopedia homolog (Drosophila)"""			10458915	Standard	NM_032109		Approved		uc003kfg.3	Q5XKR4	OTTHUMG00000102171	ENST00000306422.3:c.847dupC	5.37:g.76926224_76926224dupG	ENSP00000302814:p.Gly283fs	Somatic		Capture	Illumina HiSeq	Phase_I	76961976	NM_032109		Frame_Shift_Ins	INS	ENST00000306422.3	37	CCDS4039.1																																																																																				0.733	OTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220016.2		
APC	324	broad.mit.edu	37	5	112128191	112128191	+	Nonsense_Mutation	SNP	C	C	T	rs397515734		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr5:112128191C>T	ENST00000457016.1	+	7	1074	c.694C>T	c.(694-696)Cga>Tga	p.R232*	APC_ENST00000508376.2_Nonsense_Mutation_p.R232*|APC_ENST00000257430.4_Nonsense_Mutation_p.R232*			P25054	APC_HUMAN	adenomatous polyposis coli	232	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.R232*(13)		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)		ACTTCGTATACGACAGCTTTT	0.308		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.R232X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,large_intestine,NS,Substitution - Nonsense,0 	.	13	Substitution - Nonsense(13)	large_intestine(13)	c.C694T	5	GRCh37	CM920029	APC	M		.						82.0	79.0	80.0					5																	112128191		2202	4300	6502	112156090	SO:0001587	stop_gained	324	exon8	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.694C>T	5.37:g.112128191C>T	ENSP00000413133:p.Arg232*	Somatic		Capture	Illumina HiSeq	Phase_I	112156090	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	40	8.033640	0.98621	.	.	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.19	4.32	0.51571	.	0.206644	0.42682	D	0.000664	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.475	13.9715	0.64242	0.2757:0.7243:0.0:0.0	.	.	.	.	X	232	.	ENSP00000257430:R232X	R	+	1	2	APC	112156090	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	1.535000	0.36061	1.304000	0.44892	-0.158000	0.13435	CGA		0.308	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
PCDHGB7	56099	broad.mit.edu	37	5	140799302	140799302	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr5:140799302G>A	ENST00000398594.2	+	1	1876	c.1876G>A	c.(1876-1878)Gtg>Atg	p.V626M	PCDHGA11_ENST00000518882.1_5'Flank|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7	626	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.V626M(1)		central_nervous_system(2)|endometrium(9)|kidney(6)|large_intestine(13)|lung(15)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(3)	56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACAGGCGAGGTGCGCATGGT	0.662																																					p.V626M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1876A	5						.						53.0	59.0	57.0					5																	140799302		2189	4287	6476	140779486	SO:0001583	missense	56099	exon1			AF152523	CCDS47293.1, CCDS75344.1	5q31	2010-01-26			ENSG00000254122	ENSG00000254122		"""Cadherins / Protocadherins : Clustered"""	8714	other	protocadherin	"""cadherin ME6"""	606304				10380929	Standard	NM_032101		Approved	ME6, PCDH-GAMMA-B7		Q9Y5F8	OTTHUMG00000164054	ENST00000398594.2:c.1876G>A	5.37:g.140799302G>A	ENSP00000381594:p.Val626Met	Somatic		Capture	Illumina HiSeq	Phase_I	140779486	NM_032101	Q9UN63	Missense_Mutation	SNP	ENST00000398594.2	37	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	g	12.02	1.812630	0.32053	.	.	ENSG00000254122	ENST00000398594	T	0.55930	0.49	5.57	3.76	0.43208	Cadherin (4);Cadherin-like (1);	0.295993	0.17762	U	0.162873	T	0.73560	0.3602	M	0.90483	3.12	0.23180	N	0.998162	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.974	T	0.64058	-0.6496	10	0.87932	D	0	.	8.3842	0.32491	0.2645:0.0:0.7355:0.0	.	626;626	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	M	626	ENSP00000381594:V626M	ENSP00000381594:V626M	V	+	1	0	PCDHGB7	140779486	1.000000	0.71417	1.000000	0.80357	0.321000	0.28281	0.930000	0.28858	2.619000	0.88677	0.491000	0.48974	GTG		0.662	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	NM_018927	
GRK6	2870	broad.mit.edu	37	5	176863219	176863221	+	In_Frame_Del	DEL	GAA	GAA	-	rs76969408		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	GAA	GAA					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr5:176863219_176863221delGAA	ENST00000355472.5	+	12	1371_1373	c.1203_1205delGAA	c.(1201-1206)gtgaag>gtg	p.K402del	GRK6_ENST00000355958.5_In_Frame_Del_p.K402del|PRR7-AS1_ENST00000425316.3_RNA|GRK6_ENST00000393576.3_In_Frame_Del_p.K368del|GRK6_ENST00000507633.1_In_Frame_Del_p.K402del|GRK6_ENST00000528793.1_In_Frame_Del_p.K402del	NM_001004106.2|NM_002082.3	NP_001004106.1|NP_002073.2	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6	402	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)	p.K402delK(1)		breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(5)|stomach(1)	25	all_cancers(89;1.15e-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)			AGCGGCTGGTGAAGGAGGTCCCC	0.645																																					p.401_402del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1203_1205del	5						.																																			176795827	SO:0001651	inframe_deletion	2870	exon12				CCDS34303.1, CCDS43406.1, CCDS47348.1	5q35	2011-01-14	2004-02-04	2004-02-06	ENSG00000198055	ENSG00000198055			4545	protein-coding gene	gene with protein product		600869		GPRK6		8415712	Standard	NM_002082		Approved		uc021yiu.1	P43250	OTTHUMG00000163401	ENST00000355472.5:c.1203_1205delGAA	5.37:g.176863219_176863221delGAA	ENSP00000347655:p.Lys402del	Somatic		Capture	Illumina HiSeq	Phase_I	176795825	NM_001004105	O60541|Q13652	In_Frame_Del	DEL	ENST00000355472.5	37	CCDS34303.1																																																																																				0.645	GRK6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373204.1	NM_002082	
HIVEP1	3096	broad.mit.edu	37	6	12164596	12164597	+	Frame_Shift_Ins	INS	-	-	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:12164596_12164597insT	ENST00000379388.2	+	9	8391_8392	c.8059_8060insT	c.(8059-8061)gttfs	p.V2687fs	HIVEP1_ENST00000541134.1_Frame_Shift_Ins_p.V552fs	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2687					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(11)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	90	Breast(50;0.0639)|Ovarian(93;0.0816)	all_hematologic(90;0.117)				AGACAGACAGGTTCCCAGGCCC	0.574																																					p.V2687fs												.	.	0			c.8059_8060insT	6						.																																			12272583	SO:0001589	frameshift_variant	3096	exon9			J05011	CCDS43426.1	6p24-p22.3	2012-10-05	2001-11-28		ENSG00000095951	ENSG00000095951		"""Zinc fingers, C2H2-type"""	4920	protein-coding gene	gene with protein product		194540	"""human immunodeficiency virus type I enhancer-binding protein 1"", ""zinc finger protein 40"""	ZNF40		2037300	Standard	XR_241895		Approved	CIRIP, MBP-1, CRYBP1, PRDII-BF1, ZAS1, Schnurri-1, ZNF40A	uc003nac.3	P15822	OTTHUMG00000014265	ENST00000379388.2:c.8061dupT	6.37:g.12164598_12164598dupT	ENSP00000368698:p.Val2687fs	None		Capture	Illumina HiSeq	Phase_I	12272582	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Frame_Shift_Ins	INS	ENST00000379388.2	37	CCDS43426.1																																																																																				0.574	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114	
AKIRIN2	55122	broad.mit.edu	37	6	88411394	88411395	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:88411394_88411395insC	ENST00000257787.5	-	1	532_533	c.8_9insG	c.(7-9)tgcfs	p.C3fs	AKIRIN2_ENST00000420494.2_5'Flank	NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	3					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)	p.C3fs*88(1)		large_intestine(4)	4						GAGTGGCTCCGCACGCCATGGC	0.688																																					p.C3fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.9_10insG	6						.																																			88468114	SO:0001589	frameshift_variant	55122	exon1			BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"""chromosome 6 open reading frame 166"""	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.9dupG	6.37:g.88411395_88411395dupC	ENSP00000257787:p.Cys3fs	Somatic		Capture	Illumina HiSeq	Phase_I	88468113	NM_018064	Q9BQB1	Frame_Shift_Ins	INS	ENST00000257787.5	37	CCDS5013.1																																																																																				0.688	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064	
UBR2	23304	broad.mit.edu	37	6	42626564	42626565	+	Splice_Site	INS	-	-	A	rs35416750|rs543409747|rs35713624|rs398001323	byFrequency	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	A	-	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:42626564_42626565insA	ENST00000372899.1	+	29	3500		c.e29+2		UBR2_ENST00000372883.3_Splice_Site|UBR2_ENST00000372901.1_Splice_Site	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2						cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			TGATCATAGGTaaaaaaaaaaa	0.347																																					.												.	.	0			.	6						.																																			42734543	SO:0001630	splice_region_variant	23304	.			BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.3242+2->A	6.37:g.42626575_42626575dupA		Germline		Capture	Illumina HiSeq	Phase_I	42734542	.	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Splice_Site	INS	ENST00000372899.1	37	CCDS4870.1																																																																																				0.347	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	Intron
OR12D3	81797	broad.mit.edu	37	6	29342715	29342715	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:29342715G>A	ENST00000396806.3	-	1	353	c.350C>T	c.(349-351)gCc>gTc	p.A117V	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	117						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A117V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)	23						ACGGTCAAAGGCCATGATAGC	0.507																																					p.A117V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C350T	6						.						55.0	57.0	56.0					6																	29342715		1510	2709	4219	29450694	SO:0001583	missense	81797	exon1				CCDS4658.1	6p22.1	2013-09-24			ENSG00000112462	ENSG00000112462		"""GPCR / Class A : Olfactory receptors"""	13963	protein-coding gene	gene with protein product							Standard	NM_030959		Approved	hs6M1-27	uc003nme.3	Q9UGF7	OTTHUMG00000031051	ENST00000396806.3:c.350C>T	6.37:g.29342715G>A	ENSP00000380023:p.Ala117Val	Somatic		Capture	Illumina HiSeq	Phase_I	29450694	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.983953	0.53827	.	.	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.13420	2.59	4.18	1.2	0.21068	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.28101	0.0693	M	0.92317	3.295	0.31054	N	0.714931	D	0.67145	0.996	P	0.59825	0.864	T	0.34428	-0.9829	9	0.66056	D	0.02	-8.8896	14.3836	0.66929	0.0:0.4258:0.5742:0.0	.	117	Q9UGF7	O12D3_HUMAN	V	117	ENSP00000380023:A117V	ENSP00000366348:A117V	A	-	2	0	OR12D3	29450694	1.000000	0.71417	0.805000	0.32314	0.149000	0.21700	4.864000	0.62990	0.030000	0.15379	0.195000	0.17529	GCC		0.507	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3		
TRERF1	55809	broad.mit.edu	37	6	42231259	42231259	+	Silent	SNP	C	C	T	rs376132204		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:42231259C>T	ENST00000372922.4	-	8	2245	c.1683G>A	c.(1681-1683)ccG>ccA	p.P561P	TRERF1_ENST00000340840.2_Intron|TRERF1_ENST00000372917.4_Intron|TRERF1_ENST00000354325.2_Intron|TRERF1_ENST00000541110.1_Silent_p.P561P	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	561	Interacts with CREBBP.|Pro-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P561P(1)		breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			gaggcggaggcggcagtggtg	0.637																																					p.P561P												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G1683A	6						.	C		2,4404	4.2+/-10.8	0,2,2201	40.0	38.0	39.0		1683	-1.7	1.0	6		39	0,8598		0,0,4299	no	coding-synonymous	TRERF1	NM_033502.2		0,2,6500	TT,TC,CC		0.0,0.0454,0.0154		561/1201	42231259	2,13002	2203	4299	6502	42339237	SO:0001819	synonymous_variant	55809	exon8			AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1683G>A	6.37:g.42231259C>T		Somatic		Capture	Illumina HiSeq	Phase_I	42339237	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																				0.637	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
FHL5	9457	broad.mit.edu	37	6	97063532	97063532	+	Missense_Mutation	SNP	A	A	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:97063532A>G	ENST00000326771.2	+	7	1119	c.739A>G	c.(739-741)Agc>Ggc	p.S247G	FHL5_ENST00000541107.1_Missense_Mutation_p.S247G	NM_020482.4	NP_065228.4	Q5TD97	FHL5_HUMAN	four and a half LIM domains 5	247	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.S247G(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|urinary_tract(1)	27		all_cancers(76;1.57e-07)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00266)|Colorectal(196;0.0341)|Lung NSC(302;0.204)		BRCA - Breast invasive adenocarcinoma(108;0.0948)		CCAGTGGCATAGCGAATGCTT	0.443																																					p.S247G												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A739G	6						.						111.0	109.0	110.0					6																	97063532		2203	4300	6503	97170253	SO:0001583	missense	9457	exon6			AF278541	CCDS5035.1	6q16.1-q16.3	2008-02-05			ENSG00000112214	ENSG00000112214			17371	protein-coding gene	gene with protein product		605126					Standard	NM_020482		Approved	FLJ33049, ACT, dJ393D12.2	uc003pot.2	Q5TD97	OTTHUMG00000015239	ENST00000326771.2:c.739A>G	6.37:g.97063532A>G	ENSP00000326022:p.Ser247Gly	Somatic		Capture	Illumina HiSeq	Phase_I	97170253	NM_001170807	B2RBD1|E1P526|Q5TD98|Q8WW21|Q9NQU2	Missense_Mutation	SNP	ENST00000326771.2	37	CCDS5035.1	.	.	.	.	.	.	.	.	.	.	A	14.29	2.492216	0.44352	.	.	ENSG00000112214	ENST00000541107;ENST00000326771	D;D	0.87650	-2.28;-2.28	5.66	5.66	0.87406	Zinc finger, LIM-type (5);	0.000000	0.47093	D	0.000241	T	0.76263	0.3963	L	0.61036	1.89	0.43417	D	0.995569	B	0.17038	0.02	B	0.21151	0.033	T	0.72613	-0.4240	10	0.21540	T	0.41	.	10.5738	0.45214	0.9193:0.0:0.0807:0.0	.	247	Q5TD97	FHL5_HUMAN	G	247	ENSP00000442357:S247G;ENSP00000326022:S247G	ENSP00000326022:S247G	S	+	1	0	FHL5	97170253	1.000000	0.71417	0.979000	0.43373	0.978000	0.69477	5.024000	0.64090	2.146000	0.66826	0.533000	0.62120	AGC		0.443	FHL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041559.1	NM_020482	
ZBTB24	9841	broad.mit.edu	37	6	109803200	109803200	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	C	C	C	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:109803200delC	ENST00000230122.3	-	2	197	c.30delG	c.(28-30)gggfs	p.G10fs		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	10	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				hematopoietic progenitor cell differentiation (GO:0002244)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		CAACAAGCTGCCCAGAAGGCT	0.443																																					p.G10fs												.	.	0			c.30delG	6						.						46.0	49.0	48.0					6																	109803200		2187	4291	6478	109909893	SO:0001589	frameshift_variant	9841	exon2			AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	21143	protein-coding gene	gene with protein product	"""POZ (BTB) and AT hook containing zinc finger 2"""	614064	"""zinc finger protein 450"""	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.30delG	6.37:g.109803200delC	ENSP00000230122:p.Gly10fs	None		Capture	Illumina HiSeq	Phase_I	109909893	NM_001164313	Q17RC6|Q5TED5|Q8N455	Frame_Shift_Del	DEL	ENST00000230122.3	37	CCDS34509.1																																																																																				0.443	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	
TTBK1	84630	broad.mit.edu	37	6	43230851	43230853	+	In_Frame_Del	DEL	GCG	GCG	-	rs370081551		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	GCG	GCG					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr6:43230851_43230853delGCG	ENST00000259750.4	+	13	1832_1834	c.1749_1751delGCG	c.(1747-1752)gagcgg>gag	p.R586del	TTBK1_ENST00000304139.5_In_Frame_Del_p.R535del	NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	586					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R586delR(1)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			AGGGCGAAGAGCGGCGGCGGCTG	0.734																																					p.583_584del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.1749_1751del	6						.																																			43338831	SO:0001651	inframe_deletion	84630	exon13			AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.1749_1751delGCG	6.37:g.43230857_43230859delGCG	ENSP00000259750:p.Arg586del	Somatic		Capture	Illumina HiSeq	Phase_I	43338829	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	In_Frame_Del	DEL	ENST00000259750.4	37	CCDS34455.1																																																																																				0.734	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
GJC3	349149	broad.mit.edu	37	7	99527186	99527187	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr7:99527186_99527187insG	ENST00000312891.2	-	1	56_57	c.57_58insC	c.(55-60)cccgtgfs	p.V20fs	RP4-604G5.1_ENST00000456499.1_RNA	NM_181538.2	NP_853516.1	Q8NFK1	CXG3_HUMAN	gap junction protein, gamma 3, 30.2kDa	20					cell communication (GO:0007154)|myelination (GO:0042552)|sensory perception of sound (GO:0007605)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)|myelin sheath (GO:0043209)		p.V20fs*27(1)		breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)	9	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					AGGCGCCCCACGGGGGTGGAGC	0.619																																					p.V20fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.58_59insC	7						.																																			99365123	SO:0001589	frameshift_variant	349149	exon1			AF503615	CCDS34697.1	7q22.1	2008-09-04	2007-11-06	2007-11-06	ENSG00000176402	ENSG00000176402		"""Ion channels / Gap junction proteins (connexins)"""	17495	protein-coding gene	gene with protein product	"""connexin 30.2"""	611925	"""gap junction protein, epsilon 1, 29kDa"""	GJE1			Standard	NM_181538		Approved	CX30.2	uc011kjd.2	Q8NFK1	OTTHUMG00000156649	ENST00000312891.2:c.58dupC	7.37:g.99527191_99527191dupG	ENSP00000325775:p.Val20fs	Somatic		Capture	Illumina HiSeq	Phase_I	99365122	NM_181538	A4D296|Q86XI9	Frame_Shift_Ins	INS	ENST00000312891.2	37	CCDS34697.1																																																																																				0.619	GJC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345052.1	NM_181538	
PPP1R35	221908	broad.mit.edu	37	7	100033281	100033282	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr7:100033281_100033282insG	ENST00000292330.2	-	3	750_751	c.560_561insC	c.(559-561)ccgfs	p.P187fs	RP11-758P17.3_ENST00000475250.1_RNA|PPP1R35_ENST00000476185.1_Intron|RP11-758P17.2_ENST00000492523.1_RNA	NM_145030.2	NP_659467.1	Q8TAP8	PPR35_HUMAN	protein phosphatase 1, regulatory subunit 35	187					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GAGCCTGTGGCGGCAGGAGAGC	0.639																																					p.P187fs												.	.	0			c.561_562insC	7						.																																			99871218	SO:0001589	frameshift_variant	221908	exon3			BC026269	CCDS5694.1	7q22.1	2012-04-17	2011-10-11	2011-10-11	ENSG00000160813	ENSG00000160813		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	28320	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 47"""	C7orf47		12477932	Standard	NM_145030		Approved	MGC22793	uc003uuy.1	Q8TAP8	OTTHUMG00000159540	ENST00000292330.2:c.561dupC	7.37:g.100033283_100033283dupG	ENSP00000292330:p.Pro187fs	None		Capture	Illumina HiSeq	Phase_I	99871217	NM_145030	A4D2C5	Frame_Shift_Ins	INS	ENST00000292330.2	37	CCDS5694.1																																																																																				0.639	PPP1R35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356095.2	NM_145030	
MUC17	140453	broad.mit.edu	37	7	100677461	100677461	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr7:100677461G>A	ENST00000306151.4	+	3	2828	c.2764G>A	c.(2764-2766)Gga>Aga	p.G922R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	922	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)	p.G922R(1)		NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCTGGGGAAGGAAGCACTCC	0.517																																					p.G922R												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2764A	7						.						372.0	329.0	343.0					7																	100677461		2203	4300	6503	100464181	SO:0001583	missense	140453	exon3			AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2764G>A	7.37:g.100677461G>A	ENSP00000302716:p.Gly922Arg	Somatic		Capture	Illumina HiSeq	Phase_I	100464181	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.293	-0.978740	0.02197	.	.	ENSG00000169876	ENST00000306151	T	0.03607	3.87	0.932	-1.86	0.07760	.	.	.	.	.	T	0.02688	0.0081	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46816	-0.9164	9	0.21540	T	0.41	.	5.9245	0.19101	0.435:0.0:0.565:0.0	.	922	Q685J3	MUC17_HUMAN	R	922	ENSP00000302716:G922R	ENSP00000302716:G922R	G	+	1	0	MUC17	100464181	0.001000	0.12720	0.000000	0.03702	0.028000	0.11728	0.122000	0.15687	-1.476000	0.01874	-1.368000	0.01194	GGA		0.517	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CARD11	84433	broad.mit.edu	37	7	2976744	2976744	+	Missense_Mutation	SNP	C	C	T	rs577877958		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr7:2976744C>T	ENST00000396946.4	-	9	1671	c.1268G>A	c.(1267-1269)cGg>cAg	p.R423Q		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	423					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)	p.R416Q(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GGCCTCCCGCCGCACCATCTC	0.607			Mis		DLBCL								C|||	1	0.000199681	0.0	0.0	5008	,	,		20627	0.0		0.0	False		,,,				2504	0.001				p.R423Q			Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G1268A	7						.						146.0	117.0	127.0					7																	2976744		2203	4300	6503	2943270	SO:0001583	missense	84433	exon9			AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1268G>A	7.37:g.2976744C>T	ENSP00000380150:p.Arg423Gln	Somatic		Capture	Illumina HiSeq	Phase_I	2943270	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	36	5.697925	0.96802	.	.	ENSG00000198286	ENST00000396946	T	0.33654	1.4	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.27278	0.0669	N	0.16307	0.4	0.58432	D	0.999999	P	0.51933	0.949	B	0.43809	0.432	T	0.03112	-1.1071	10	0.20519	T	0.43	-34.3605	17.7576	0.88453	0.0:1.0:0.0:0.0	.	423	Q9BXL7	CAR11_HUMAN	Q	423	ENSP00000380150:R423Q	ENSP00000380150:R423Q	R	-	2	0	CARD11	2943270	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.869000	0.69613	2.447000	0.82792	0.561000	0.74099	CGG		0.607	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
SYPL1	6856	broad.mit.edu	37	7	105738197	105738197	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr7:105738197G>A	ENST00000011473.2	-	4	441	c.395C>T	c.(394-396)gCc>gTc	p.A132V	SYPL1_ENST00000455385.2_Missense_Mutation_p.A114V|SYPL1_ENST00000470347.1_Missense_Mutation_p.A114V	NM_006754.3	NP_006745.1	Q16563	SYPL1_HUMAN	synaptophysin-like 1	132	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|integral component of synaptic vesicle membrane (GO:0030285)|secretory granule (GO:0030141)	transporter activity (GO:0005215)	p.A132V(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	7						AAGCAGAAGGGCAGCAATGCA	0.353																																					p.A114V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C341T	7						.						125.0	108.0	114.0					7																	105738197		2203	4300	6503	105525433	SO:0001583	missense	6856	exon3				CCDS5736.1, CCDS47685.1	7q22.2	2005-05-24	2005-05-24	2005-05-24	ENSG00000008282	ENSG00000008282			11507	protein-coding gene	gene with protein product			"""synaptophysin-like protein"""	SYPL			Standard	NM_006754		Approved		uc003vdp.4	Q16563	OTTHUMG00000157587	ENST00000011473.2:c.395C>T	7.37:g.105738197G>A	ENSP00000011473:p.Ala132Val	Somatic		Capture	Illumina HiSeq	Phase_I	105525433	NM_182715	A4D0R2|Q96AR8	Missense_Mutation	SNP	ENST00000011473.2	37	CCDS5736.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.167696|5.167696	0.94768|0.94768	.|.	.|.	ENSG00000008282|ENSG00000008282	ENST00000455385;ENST00000011473;ENST00000470347|ENST00000464029	T;T;T|.	0.26810|.	1.71;1.71;1.71|.	5.63|5.63	5.63|5.63	0.86233|0.86233	Marvel (1);MARVEL-like domain (1);|.	0.048121|.	0.85682|.	D|.	0.000000|.	D|D	0.82903|0.82903	0.5138|0.5138	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	P|.	0.61800|.	0.894|.	D|D	0.83724|0.83724	0.0194|0.0194	10|5	0.52906|.	T|.	0.07|.	-6.6292|-6.6292	18.8146|18.8146	0.92072|0.92072	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	132|.	Q16563|.	SYPL1_HUMAN|.	V|S	114;132;114|38	ENSP00000388336:A114V;ENSP00000011473:A132V;ENSP00000419070:A114V|.	ENSP00000011473:A132V|.	A|P	-|-	2|1	0|0	SYPL1|SYPL1	105525433|105525433	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.069000|8.069000	0.89491|0.89491	2.814000|2.814000	0.96858|0.96858	0.655000|0.655000	0.94253|0.94253	GCC|CCC		0.353	SYPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349221.1		
VPS13B	157680	broad.mit.edu	37	8	100871586	100871587	+	Missense_Mutation	DNP	GC	GC	TA			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	GC	GC					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr8:100871586_100871587GC>TA	ENST00000358544.2	+	57	11108_11109	c.10997_10998GC>TA	c.(10996-10998)aGC>aTA	p.S3666I	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.S3641I	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3666					protein transport (GO:0015031)			p.S3641>?(1)|p.S3666>?(1)		NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			CTGGTGAGAAGCATCGGGAACG	0.594																																					.	Colon(161;2205 2542 7338 31318)											.	.	2	Complex(2)	large_intestine(2)	c.10922_10923TA	8						.																																			100940763	SO:0001583	missense	157680	exon57			AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	Exception_encountered	8.37:g.100871586_100871587delinsTA	ENSP00000351346:p.Ser3666Ile	Somatic		Capture	Illumina HiSeq	Phase_I	100940762	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	DNP	ENST00000358544.2	37	CCDS6280.1																																																																																				0.594	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
COL14A1	7373	broad.mit.edu	37	8	121357725	121357725	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr8:121357725C>T	ENST00000297848.3	+	45	5270	c.5000C>T	c.(4999-5001)gCc>gTc	p.A1667V	COL14A1_ENST00000309791.4_Missense_Mutation_p.A1667V|COL14A1_ENST00000247781.3_Missense_Mutation_p.A1572V	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1									p.A1667V(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)			TCACCTGGAGCCCCTGGTGAA	0.642																																					p.A1667V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5000T	8						.						47.0	48.0	47.0					8																	121357725		2203	4300	6503	121426906	SO:0001583	missense	7373	exon45				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.5000C>T	8.37:g.121357725C>T	ENSP00000297848:p.Ala1667Val	Somatic		Capture	Illumina HiSeq	Phase_I	121426906	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786000	0.70337	.	.	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.93712	-3.27;-3.27;-3.27;-3.27	5.54	5.54	0.83059	.	0.326839	0.36854	N	0.002365	D	0.89160	0.6636	L	0.28649	0.875	0.80722	D	1	B	0.12013	0.005	B	0.15870	0.014	D	0.84292	0.0500	10	0.27785	T	0.31	.	17.3164	0.87225	0.0:1.0:0.0:0.0	.	1667	Q05707	COEA1_HUMAN	V	1667;1667;1572;14	ENSP00000311809:A1667V;ENSP00000297848:A1667V;ENSP00000247781:A1572V;ENSP00000403640:A14V	ENSP00000247781:A1572V	A	+	2	0	COL14A1	121426906	0.947000	0.32204	1.000000	0.80357	0.997000	0.91878	2.998000	0.49465	2.626000	0.88956	0.555000	0.69702	GCC		0.642	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
CEL	1056	broad.mit.edu	37	9	135946602	135946603	+	Frame_Shift_Ins	INS	-	-	C	rs568124543		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:135946602_135946603insC	ENST00000372080.4	+	11	1738_1739	c.1722_1723insC	c.(1723-1725)cccfs	p.P575fs	CEL_ENST00000351304.7_Frame_Shift_Ins_p.P506fs	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	572	17 X 11 AA tandem repeats, glycodomain, O-linked (mucin type).				cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)	p.T577fs*3(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CCACTCCCGTGCCCCCCACGGG	0.762																																					p.V574fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1722_1723insC	9						.																																			134936424	SO:0001589	frameshift_variant	1056	exon11			M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1728dupC	9.37:g.135946608_135946608dupC	ENSP00000361151:p.Pro575fs	Somatic		Capture	Illumina HiSeq	Phase_I	134936423	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Frame_Shift_Ins	INS	ENST00000372080.4	37	CCDS43896.1																																																																																				0.762	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
RABL6	55684	broad.mit.edu	37	9	139722988	139722989	+	Frame_Shift_Ins	INS	-	-	C			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-	-	-	-	-	Unknown	Wildtype	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:139722988_139722989insC	ENST00000311502.7	+	4	592_593	c.356_357insC	c.(355-360)gaccccfs	p.DP119fs	RABL6_ENST00000357466.2_Frame_Shift_Ins_p.DP119fs|MIR4292_ENST00000585012.1_RNA|RABL6_ENST00000371675.3_Frame_Shift_Ins_p.DP4fs|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000432842.2_Frame_Shift_Ins_p.DP81fs|RABL6_ENST00000466096.1_3'UTR|RABL6_ENST00000371671.4_Frame_Shift_Ins_p.DP119fs|RABL6_ENST00000371663.4_Frame_Shift_Ins_p.DP119fs			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	119	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										ATGGAGAACGACCCCCAGGAGG	0.559																																					p.D119fs												.	.	0			c.356_357insC	9						.																																			138842810	SO:0001589	frameshift_variant	55684	exon4			AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.361dupC	9.37:g.139722993_139722993dupC	ENSP00000311134:p.Asp119fs	None		Capture	Illumina HiSeq	Phase_I	138842809	NM_001173988	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Frame_Shift_Ins	INS	ENST00000311502.7	37	CCDS48058.1																																																																																				0.559	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
ENTPD8	377841	broad.mit.edu	37	9	140327669	140327670	+	IGR	INS	-	-	G			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	-	-					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:140327669_140327670insG	ENST00000472938.1	-	0	1749				NOXA1_ENST00000341349.2_Frame_Shift_Ins_p.MG288fs|NOXA1_ENST00000392815.2_Frame_Shift_Ins_p.MG232fs			Q5MY95	ENTP8_HUMAN	ectonucleoside triphosphate diphosphohydrolase 8						nucleoside diphosphate biosynthetic process (GO:0009133)|nucleoside monophosphate biosynthetic process (GO:0009124)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)	p.P291fs*7(1)		biliary_tract(1)|lung(4)|prostate(1)|skin(1)	7	all_cancers(76;0.0926)			OV - Ovarian serous cystadenocarcinoma(145;0.000224)|Epithelial(140;0.000898)		CTGCCGGCAATGGGGGGGCCTG	0.668																																					p.M288fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.863_864insG	9						.			6,4168		0,6,2081						-0.4	0.0			10	15,8177		2,11,4083	no	frameshift	NOXA1	NM_006647.1		2,17,6164	A1A1,A1R,RR		0.1831,0.1437,0.1698				21,12345				139447491	SO:0001628	intergenic_variant	10811	exon10			AY359088	CCDS7043.1, CCDS43913.1	9q34.3	2013-09-20			ENSG00000188833	ENSG00000188833			24860	protein-coding gene	gene with protein product	"""GLSR2492"""					12975309	Standard	NM_198585		Approved	UNQ2492, NTPDase-8	uc004cmw.3	Q5MY95	OTTHUMG00000131831		9.37:g.140327676_140327676dupG		Somatic		Capture	Illumina HiSeq	Phase_I	139447490	NM_006647	A2BG17|Q6UVZ0	Frame_Shift_Ins	INS	ENST00000472938.1	37	CCDS43913.1																																																																																				0.668	ENTPD8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355991.1	NM_198585	
CDK9	1025	broad.mit.edu	37	9	130551554	130551554	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:130551554G>A	ENST00000373264.4	+	7	951	c.851G>A	c.(850-852)cGt>cAt	p.R284H	CDK9_ENST00000373265.2_Missense_Mutation_p.R401H	NM_001261.3	NP_001252.1	P50750	CDK9_HUMAN	cyclin-dependent kinase 9	284	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to cytokine stimulus (GO:0071345)|DNA repair (GO:0006281)|gene expression (GO:0010467)|negative regulation of cell cycle arrest (GO:0071157)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of DNA repair (GO:0006282)|regulation of histone modification (GO:0031056)|replication fork arrest (GO:0043111)|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)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|positive transcription elongation factor complex b (GO:0008024)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|DNA binding (GO:0003677)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|snRNA binding (GO:0017069)|transcription regulatory region DNA binding (GO:0044212)	p.R284H(1)		lung(1)	1						GCCTATGTGCGTGACCCATAC	0.587																																					p.R284H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G851A	9						.						177.0	104.0	129.0					9																	130551554		2203	4300	6503	129591375	SO:0001583	missense	1025	exon7			L25676	CCDS6879.1	9q34.1	2011-11-08	2007-11-21		ENSG00000136807	ENSG00000136807		"""Cyclin-dependent kinases"""	1780	protein-coding gene	gene with protein product		603251	"""cyclin-dependent kinase 9 (CDC2-related kinase)"""	CDC2L4		8170997, 9356449	Standard	NM_001261		Approved	PITALRE, C-2k, TAK	uc004bse.2	P50750	OTTHUMG00000020715	ENST00000373264.4:c.851G>A	9.37:g.130551554G>A	ENSP00000362361:p.Arg284His	Somatic		Capture	Illumina HiSeq	Phase_I	129591375	NM_001261	Q5JU24|Q5JU25|Q5U006|Q96TF1	Missense_Mutation	SNP	ENST00000373264.4	37	CCDS6879.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742313	0.69418	.	.	ENSG00000136807	ENST00000373265;ENST00000373264	T;T	0.43294	0.95;0.95	5.43	4.42	0.53409	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.049288	0.85682	D	0.000000	T	0.28699	0.0711	L	0.29908	0.895	0.43852	D	0.996449	B	0.30851	0.297	B	0.34873	0.191	T	0.18429	-1.0337	10	0.51188	T	0.08	-3.7746	3.9963	0.09559	0.3132:0.0:0.6868:0.0	.	284	P50750	CDK9_HUMAN	H	401;284	ENSP00000362362:R401H;ENSP00000362361:R284H	ENSP00000362361:R284H	R	+	2	0	CDK9	129591375	1.000000	0.71417	0.968000	0.41197	0.801000	0.45260	6.208000	0.72165	2.546000	0.85860	0.591000	0.81541	CGT		0.587	CDK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054235.1		
CIZ1	25792	broad.mit.edu	37	9	130931765	130931765	+	Missense_Mutation	SNP	C	C	T	rs139103399		TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:130931765C>T	ENST00000393608.1	-	13	2267	c.2065G>A	c.(2065-2067)Gtt>Att	p.V689I	CIZ1_ENST00000277465.4_Missense_Mutation_p.V661I|CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Missense_Mutation_p.V715I|CIZ1_ENST00000372938.5_Missense_Mutation_p.V689I|CIZ1_ENST00000357558.5_Missense_Mutation_p.V661I|CIZ1_ENST00000372948.3_Missense_Mutation_p.V633I|CIZ1_ENST00000372954.1_Missense_Mutation_p.V609I|CIZ1_ENST00000541172.1_Missense_Mutation_p.V588I|CIZ1_ENST00000325721.8_Missense_Mutation_p.V660I	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	689					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.V689I(1)		NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						CGGTTGCAAACGGTGCAGAAG	0.562																																					p.V633I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1897A	9						.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	130.0	115.0	120.0		1897,2065,1882,1825,2065	-0.9	0.0	9	dbSNP_134	120	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	29,29,29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign,benign	633/843,689/899,628/838,609/819,689/899	130931765	1,13005	2203	4300	6503	129971586	SO:0001583	missense	25792	exon14			AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.2065G>A	9.37:g.130931765C>T	ENSP00000377232:p.Val689Ile	Somatic		Capture	Illumina HiSeq	Phase_I	129971586	NM_001131015	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Missense_Mutation	SNP	ENST00000393608.1	37	CCDS6894.1	.	.	.	.	.	.	.	.	.	.	C	1.374	-0.585396	0.03827	0.0	1.16E-4	ENSG00000148337	ENST00000372954;ENST00000393608;ENST00000538431;ENST00000357558;ENST00000325721;ENST00000537314;ENST00000541172;ENST00000277465;ENST00000372948;ENST00000372938;ENST00000415526	T;T;T;T;T;T;T;T;T;T	0.34859	1.34;1.5;1.42;1.67;1.5;1.93;1.67;1.36;1.5;2.1	5.34	-0.871	0.10642	Zinc finger, C2H2-like (1);Zinc finger, double-stranded RNA binding (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	1.123250	0.06831	N	0.793944	T	0.18002	0.0432	N	0.05124	-0.11	0.09310	N	1	B;B;B;B;B;B;B	0.14805	0.011;0.01;0.004;0.004;0.006;0.008;0.006	B;B;B;B;B;B;B	0.16289	0.011;0.004;0.003;0.004;0.015;0.003;0.004	T	0.29852	-0.9998	9	.	.	.	1.0E-4	10.2	0.43077	0.0:0.6031:0.0:0.3969	.	715;628;633;609;689;660;661	B7Z3U7;B4E0A3;Q9ULV3-4;Q9ULV3-3;Q9ULV3;Q9ULV3-2;Q5SYW2	.;.;.;.;CIZ1_HUMAN;.;.	I	609;689;715;661;660;628;588;661;633;689;611	ENSP00000362045:V609I;ENSP00000377232:V689I;ENSP00000439244:V715I;ENSP00000350169:V661I;ENSP00000320374:V660I;ENSP00000445057:V588I;ENSP00000277465:V661I;ENSP00000362039:V633I;ENSP00000362029:V689I;ENSP00000398011:V611I	.	V	-	1	0	CIZ1	129971586	0.019000	0.18553	0.000000	0.03702	0.878000	0.50629	0.337000	0.19841	-0.371000	0.08004	-0.448000	0.05591	GTT		0.562	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
DNM1	1759	broad.mit.edu	37	9	130986608	130986608	+	Silent	SNP	C	C	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chr9:130986608C>A	ENST00000372923.3	+	10	1367	c.1275C>A	c.(1273-1275)ctC>ctA	p.L425L	DNM1_ENST00000475805.1_Intron|DNM1_ENST00000341179.7_Silent_p.L425L|DNM1_ENST00000393594.3_Intron|DNM1_ENST00000486160.1_Intron	NM_004408.2	NP_004399.2	Q05193	DYN1_HUMAN	dynamin 1	425					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.L425L(2)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(15)|lung(6)|ovary(2)|urinary_tract(2)	32						AACCGTGTCTCAAGTGTGTGG	0.577																																					p.L425L	GBM(113;146 1575 2722 28670 29921)											.	.	2	Substitution - coding silent(2)	large_intestine(2)	c.C1275A	9						.						127.0	111.0	116.0					9																	130986608		2203	4300	6503	130026429	SO:0001819	synonymous_variant	1759	exon10			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.1275C>A	9.37:g.130986608C>A		Somatic		Capture	Illumina HiSeq	Phase_I	130026429	NM_001005336	A6NLM6|Q5SYX0|Q5SYX2|Q6P3T6|Q86VD2	Silent	SNP	ENST00000372923.3	37	CCDS6895.1																																																																																				0.577	DNM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054367.1	NM_004408	
TENM1	10178	broad.mit.edu	37	X	123657429	123657429	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:123657429C>T	ENST00000371130.3	-	17	2881	c.2818G>A	c.(2818-2820)Gac>Aac	p.D940N	TENM1_ENST00000422452.2_Missense_Mutation_p.D940N	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	940					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.D942N(1)									GGGGATCGGTCGAAGATTAAG	0.423																																					p.D940N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2818A	X						.						89.0	74.0	79.0					X																	123657429		2203	4300	6503	123485110	SO:0001583	missense	10178	exon17			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.2818G>A	X.37:g.123657429C>T	ENSP00000360171:p.Asp940Asn	Somatic		Capture	Illumina HiSeq	Phase_I	123485110	NM_014253	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.212959	0.58452	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.13307	2.6;2.6	5.79	5.79	0.91817	.	0.234538	0.44688	D	0.000424	T	0.10723	0.0262	N	0.22421	0.69	0.42605	D	0.993295	P;B;B	0.36483	0.555;0.357;0.164	B;B;B	0.27500	0.08;0.036;0.032	T	0.08493	-1.0719	10	0.46703	T	0.11	.	19.0488	0.93034	0.0:1.0:0.0:0.0	.	939;940;940	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	N	940	ENSP00000360171:D940N;ENSP00000403954:D940N	ENSP00000360171:D940N	D	-	1	0	ODZ1	123485110	1.000000	0.71417	0.997000	0.53966	0.830000	0.47004	3.714000	0.54889	2.448000	0.82819	0.600000	0.82982	GAC		0.423	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
ARHGAP36	158763	broad.mit.edu	37	X	130217828	130217828	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:130217828C>T	ENST00000276211.5	+	4	785	c.440C>T	c.(439-441)gCg>gTg	p.A147V	ARHGAP36_ENST00000370921.1_Missense_Mutation_p.A11V|ARHGAP36_ENST00000370922.1_Missense_Mutation_p.A135V	NM_144967.3	NP_659404.2	Q6ZRI8	RHG36_HUMAN	Rho GTPase activating protein 36	147					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.A147V(2)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(3)|large_intestine(16)|lung(31)|ovary(4)|prostate(4)|skin(3)|urinary_tract(2)	71						GGTCAGGCTGCGGGCCGTCGT	0.612																																					p.A147V												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C440T	X						.						101.0	98.0	99.0					X																	130217828		2203	4300	6503	130045509	SO:0001583	missense	158763	exon4				CCDS14628.1, CCDS65320.1	Xq26.1	2011-06-29			ENSG00000147256	ENSG00000147256		"""Rho GTPase activating proteins"""	26388	protein-coding gene	gene with protein product							Standard	NM_144967		Approved	FLJ30058	uc004evz.3	Q6ZRI8	OTTHUMG00000022402	ENST00000276211.5:c.440C>T	X.37:g.130217828C>T	ENSP00000276211:p.Ala147Val	Somatic		Capture	Illumina HiSeq	Phase_I	130045509	NM_144967	B7Z234|B7Z439|Q5JRL9|Q5JRM0|Q5JRM1|Q96NU6	Missense_Mutation	SNP	ENST00000276211.5	37	CCDS14628.1	.	.	.	.	.	.	.	.	.	.	C	3.167	-0.170901	0.06421	.	.	ENSG00000147256	ENST00000276211;ENST00000370922;ENST00000423277;ENST00000412432;ENST00000370921	T;T;T;T	0.10668	2.9;2.91;2.91;2.85	4.3	0.475	0.16774	.	3.347820	0.01163	N	0.006684	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	B;B;B	0.17268	0.021;0.021;0.005	B;B;B	0.13407	0.009;0.009;0.003	T	0.30357	-0.9981	10	0.30854	T	0.27	.	0.7601	0.01005	0.1749:0.3706:0.2223:0.2321	.	116;135;147	Q6ZRI8-2;Q6ZRI8-4;Q6ZRI8	.;.;RHG36_HUMAN	V	147;135;99;116;11	ENSP00000276211:A147V;ENSP00000359960:A135V;ENSP00000408515:A116V;ENSP00000359959:A11V	ENSP00000276211:A147V	A	+	2	0	ARHGAP36	130045509	0.000000	0.05858	0.002000	0.10522	0.037000	0.13140	-0.425000	0.07017	-0.052000	0.13311	0.600000	0.82982	GCG		0.612	ARHGAP36-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355073.1	NM_144967	
ATP11C	286410	broad.mit.edu	37	X	138897073	138897073	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	A	A					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:138897073A>T	ENST00000327569.3	-	5	497	c.399T>A	c.(397-399)aaT>aaA	p.N133K	ATP11C_ENST00000361648.2_Missense_Mutation_p.N133K|ATP11C_ENST00000370557.1_Missense_Mutation_p.N130K|ATP11C_ENST00000370543.1_Missense_Mutation_p.N133K|ATP11C_ENST00000359686.2_Missense_Mutation_p.N133K	NM_173694.4	NP_775965	Q8NB49	AT11C_HUMAN	ATPase, class VI, type 11C	133					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.N133K(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)					CTCGCTTTGCATTTTCAATAA	0.294																																					p.N133K												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T399A	X						.						96.0	82.0	87.0					X																	138897073		2202	4297	6499	138724739	SO:0001583	missense	286410	exon5			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.399T>A	X.37:g.138897073A>T	ENSP00000332756:p.Asn133Lys	Somatic		Capture	Illumina HiSeq	Phase_I	138724739	NM_001010986	Q5JT69|Q5JT70|Q5JT71|Q5JT72|Q5JT73|Q6ZND5|Q6ZU50|Q6ZUP7|Q70IJ9|Q70IK0|Q8WX24	Missense_Mutation	SNP	ENST00000327569.3	37	CCDS14668.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.695802	0.30052	.	.	ENSG00000101974	ENST00000370557;ENST00000361648;ENST00000327569;ENST00000370543;ENST00000359686	D;D;D;D;D	0.88896	-2.44;-2.44;-2.44;-2.44;-2.44	4.29	3.02	0.34903	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.240273	0.43110	D	0.000602	T	0.81866	0.4913	L	0.37897	1.145	0.32560	N	0.531245	B;B	0.11235	0.003;0.004	B;B	0.15052	0.007;0.012	T	0.81890	-0.0725	10	0.59425	D	0.04	.	8.2668	0.31819	0.8032:0.1968:0.0:0.0	.	133;133	Q8NB49-3;Q8NB49	.;AT11C_HUMAN	K	130;133;133;133;133	ENSP00000359588:N130K;ENSP00000355165:N133K;ENSP00000332756:N133K;ENSP00000359574:N133K;ENSP00000352715:N133K	ENSP00000332756:N133K	N	-	3	2	ATP11C	138724739	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.159000	0.42339	1.715000	0.51383	0.393000	0.25936	AAT		0.294	ATP11C-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354945.1	NM_173694	
MAGEC1	9947	broad.mit.edu	37	X	140994517	140994517	+	Missense_Mutation	SNP	C	C	A	rs62611966	byFrequency	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:140994517C>A	ENST00000285879.4	+	4	1613	c.1327C>A	c.(1327-1329)Ctc>Atc	p.L443I	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	443								p.L443I(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CCAGTCTCCTCTCCAGATTCC	0.453										HNSCC(15;0.026)																											p.L443I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1327A	X						.						98.0	107.0	104.0					X																	140994517		2200	4292	6492	140822183	SO:0001583	missense	9947	exon4			AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1327C>A	X.37:g.140994517C>A	ENSP00000285879:p.Leu443Ile	Somatic		Capture	Illumina HiSeq	Phase_I	140822183	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	2.630	-0.286646	0.05605	.	.	ENSG00000155495	ENST00000285879	T	0.02258	4.37	0.131	0.131	0.14755	.	.	.	.	.	T	0.01189	0.0039	N	0.08118	0	0.19300	N	0.999978	P	0.51933	0.949	B	0.40101	0.319	T	0.52624	-0.8551	9	0.25751	T	0.34	.	5.9545	0.19265	0.0:0.9994:0.0:6.0E-4	.	443	O60732	MAGC1_HUMAN	I	443	ENSP00000285879:L443I	ENSP00000285879:L443I	L	+	1	0	MAGEC1	140822183	0.000000	0.05858	0.015000	0.15790	0.015000	0.08874	0.065000	0.14466	0.157000	0.19338	0.158000	0.16466	CTC		0.453	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
FAM47A	158724	broad.mit.edu	37	X	34148328	34148328	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:34148328G>A	ENST00000346193.3	-	1	2119	c.2068C>T	c.(2068-2070)Cgt>Tgt	p.R690C		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	690								p.R690C(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						ATCTTCACACGCTGTGCGGTA	0.428																																					p.R690C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2068T	X						.						88.0	85.0	86.0					X																	34148328		2202	4300	6502	34058249	SO:0001583	missense	158724	exon1			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.2068C>T	X.37:g.34148328G>A	ENSP00000345029:p.Arg690Cys	Somatic		Capture	Illumina HiSeq	Phase_I	34058249	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	G	4.064	0.009671	0.07912	.	.	ENSG00000185448	ENST00000346193	T	0.41758	0.99	1.49	-2.98	0.05513	.	.	.	.	.	T	0.21145	0.0509	N	0.14661	0.345	0.09310	N	1	D	0.59767	0.986	B	0.43809	0.432	T	0.09640	-1.0665	9	0.45353	T	0.12	.	2.5543	0.04756	0.3059:0.0:0.4404:0.2537	.	690	Q5JRC9	FA47A_HUMAN	C	690	ENSP00000345029:R690C	ENSP00000345029:R690C	R	-	1	0	FAM47A	34058249	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.012000	0.12699	-1.272000	0.02427	-0.498000	0.04607	CGT		0.428	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
ZMYM3	9203	broad.mit.edu	37	X	70468622	70468622	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:70468622G>A	ENST00000353904.2	-	9	1838	c.1651C>T	c.(1651-1653)Cgc>Tgc	p.R551C	ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373988.1_Missense_Mutation_p.R553C|ZMYM3_ENST00000373998.1_Missense_Mutation_p.R551C|ZMYM3_ENST00000373984.3_Missense_Mutation_p.R553C|ZMYM3_ENST00000314425.5_Missense_Mutation_p.R551C	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	551					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R551C(1)		breast(1)|central_nervous_system(7)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(12)|lung(17)|ovary(1)|prostate(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(35;0.156)					GAGAGGCTGCGGCGGCAGAAG	0.572																																					p.R551C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1651T	X						.						32.0	31.0	32.0					X																	70468622		2200	4300	6500	70385347	SO:0001583	missense	9203	exon9			AB002383	CCDS14409.1, CCDS55443.1, CCDS55444.1	Xq13.1	2013-01-08	2005-12-19	2005-12-19	ENSG00000147130	ENSG00000147130		"""Zinc fingers, MYM type"""	13054	protein-coding gene	gene with protein product		300061	"""zinc finger protein 261"""	ZNF261		10486218	Standard	NM_201599		Approved	ZNF198L2, DXS6673E, KIAA0385, MYM	uc004dzh.2	Q14202	OTTHUMG00000021799	ENST00000353904.2:c.1651C>T	X.37:g.70468622G>A	ENSP00000343909:p.Arg551Cys	Somatic		Capture	Illumina HiSeq	Phase_I	70385347	NM_001171162	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	37	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	g	12.82	2.051266	0.36181	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373984;ENST00000373988	T;T;T;T;T	0.48836	1.38;0.8;1.38;1.38;1.38	5.38	4.46	0.54185	TRASH (1);Zinc finger, MYM-type (1);	0.095822	0.41938	D	0.000797	T	0.58680	0.2139	L	0.42245	1.32	0.30611	N	0.759465	D;D	0.89917	1.0;1.0	D;D	0.74674	0.972;0.984	T	0.61023	-0.7146	10	0.72032	D	0.01	-11.7188	12.3926	0.55366	0.0:0.0:0.7311:0.2689	.	551;551	Q14202-2;Q14202	.;ZMYM3_HUMAN	C	551;551;551;553;553	ENSP00000322845:R551C;ENSP00000363110:R551C;ENSP00000343909:R551C;ENSP00000363096:R553C;ENSP00000363100:R553C	ENSP00000322845:R551C	R	-	1	0	ZMYM3	70385347	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	3.140000	0.50585	2.260000	0.74910	0.183000	0.17082	CGC		0.572	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599	
SYTL4	94121	broad.mit.edu	37	X	99956963	99956963	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C					Unknown	Unknown	Somatic	Phase_I	WXS	none			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:99956963C>T	ENST00000372989.1	-	4	402	c.71G>A	c.(70-72)cGa>cAa	p.R24Q	SYTL4_ENST00000454200.2_Missense_Mutation_p.R24Q|SYTL4_ENST00000276141.6_Missense_Mutation_p.R24Q|SYTL4_ENST00000372981.1_Missense_Mutation_p.R24Q|SYTL4_ENST00000455616.1_Missense_Mutation_p.R24Q|SYTL4_ENST00000263033.5_Missense_Mutation_p.R24Q	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	24	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.R24Q(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CTCTTCATCTCGCTGTAGAAC	0.443																																					p.R24Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G71A	X						.						112.0	105.0	107.0					X																	99956963		2203	4300	6503	99843619	SO:0001583	missense	94121	exon3				CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.71G>A	X.37:g.99956963C>T	ENSP00000362080:p.Arg24Gln	Somatic		Capture	Illumina HiSeq	Phase_I	99843619	NM_001129896	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	ENST00000372989.1	37	CCDS14472.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274074	0.95459	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033;ENST00000372981	D;D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;-1.57	5.21	5.21	0.72293	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.93281	0.7859	M	0.92970	3.365	0.40390	D	0.979534	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.976	D	0.95113	0.8240	9	.	.	.	-10.6929	17.6937	0.88276	0.0:1.0:0.0:0.0	.	24;24	Q96C24-2;Q96C24	.;SYTL4_HUMAN	Q	24	ENSP00000362080:R24Q;ENSP00000390252:R24Q;ENSP00000403556:R24Q;ENSP00000276141:R24Q;ENSP00000263033:R24Q;ENSP00000362072:R24Q	.	R	-	2	0	SYTL4	99843619	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	4.288000	0.59007	2.297000	0.77311	0.600000	0.82982	CGA		0.443	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737	
MAGEA10	4109	broad.mit.edu	37	X	151304073	151304073	+	Missense_Mutation	SNP	C	C	T	rs145553450	byFrequency	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454_PCR_WGA			Illumina GAIIx	TCGA-AA-3980-01A-02W-0995-10	TCGA-AA-3980-10A-01W-0999-10	g.chrX:151304073C>T	ENST00000370323.4	-	4	336	c.20G>A	c.(19-21)cGt>cAt	p.R7H	RP11-1007I13.4_ENST00000509345.2_RNA|MAGEA10_ENST00000244096.3_Missense_Mutation_p.R7H	NM_001251828.1|NM_021048.4	NP_001238757.1|NP_066386	P43363	MAGAA_HUMAN	melanoma antigen family A, 10	7						nucleus (GO:0005634)		p.R7H(1)		endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GCAGCGCTGACGCTTTGGAGC	0.602																																					p.R7H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G20A	X						.	C	HIS/ARG,,HIS/ARG	0,3833		0,0,0,1631,571	86.0	88.0	87.0		20,,20	0.6	0.0	X	dbSNP_134	87	1,6725		0,0,1,2428,1869	no	missense,intron,missense	MAGEA10,MAGEA10-MAGEA5	NM_001011543.1,NM_001204811.1,NM_021048.3	29,,29	0,0,1,4059,2440	TT,TC,T,CC,C		0.0149,0.0,0.0095	probably-damaging,,probably-damaging	7/370,,7/370	151304073	1,10558	2202	4298	6500	151054729	SO:0001583	missense	4109	exon4				CCDS14705.1	Xq28	2009-03-13			ENSG00000124260	ENSG00000124260			6797	protein-coding gene	gene with protein product	"""MAGE-10 antigen"", ""melanoma-associated antigen 10"", ""cancer/testis antigen family 1, member 10"""	300343		MAGE10		8575766	Standard	NM_001011543		Approved	MGC10599, CT1.10	uc004ffl.3	P43363	OTTHUMG00000024180	ENST00000370323.4:c.20G>A	X.37:g.151304073C>T	ENSP00000359347:p.Arg7His	Somatic		Capture	Illumina HiSeq	Phase_I	151054729	NM_021048		Missense_Mutation	SNP	ENST00000370323.4	37	CCDS14705.1	.	.	.	.	.	.	.	.	.	.	C	8.597	0.885841	0.17540	0.0	1.49E-4	ENSG00000124260	ENST00000370323;ENST00000244096;ENST00000444834;ENST00000427322	T;T;T;T	0.04502	3.61;3.61;3.61;3.61	2.54	0.552	0.17230	Melanoma associated antigen, MAGE, N-terminal (1);	4.932270	0.00531	N	0.000218	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B	0.33748	0.423	B	0.26517	0.07	T	0.32161	-0.9917	10	0.56958	D	0.05	.	4.3557	0.11178	0.2587:0.4915:0.2498:0.0	.	7	P43363	MAGAA_HUMAN	H	7	ENSP00000359347:R7H;ENSP00000244096:R7H;ENSP00000406161:R7H;ENSP00000391977:R7H	ENSP00000244096:R7H	R	-	2	0	MAGEA10	151054729	0.000000	0.05858	0.000000	0.03702	0.330000	0.28571	0.488000	0.22371	0.035000	0.15519	0.292000	0.19580	CGT		0.602	MAGEA10-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060916.3	NM_021048	
