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	X1000Genome_AA	X1000Genome_AC	X1000Genome_AF	X1000Genome_AFR_AF	X1000Genome_AMR_AF	X1000Genome_AN	X1000Genome_ASN_AF	X1000Genome_AVGPOST	X1000Genome_CIEND	X1000Genome_CIPOS	X1000Genome_END	X1000Genome_ERATE	X1000Genome_EUR_AF	X1000Genome_HOMLEN	X1000Genome_HOMSEQ	X1000Genome_LDAF	X1000Genome_RSQ	X1000Genome_SNPSOURCE	X1000Genome_SVLEN	X1000Genome_SVTYPE	X1000Genome_THETA	X1000Genome_VT	ACHILLES_Lineage_Results_Top_Genes	CGC_Cancer.Germline.Mut	CGC_Cancer.Molecular.Genetics	CGC_Cancer.Somatic.Mut	CGC_Cancer.Syndrome	CGC_Chr	CGC_Chr.Band	CGC_GeneID	CGC_Name	CGC_Other.Germline.Mut	CGC_Tissue.Type	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	COSMIC_overlapping_primary_sites	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	ESP_AA	ESP_AAC	ESP_AA_AC	ESP_AA_AGE	ESP_AA_GTC	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_CA	ESP_CDP	ESP_CG	ESP_CP	ESP_Chromosome	ESP_DBSNP	ESP_DP	ESP_EA_AC	ESP_EA_AGE	ESP_EA_GTC	ESP_EXOME_CHIP	ESP_FG	ESP_GL	ESP_GM	ESP_GS	ESP_GTC	ESP_GTS	ESP_GWAS_PUBMED	ESP_MAF	ESP_PH	ESP_PP	ESP_Position	ESP_TAC	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	HGNC_Accession.Numbers	HGNC_CCDS.IDs	HGNC_Chromosome	HGNC_Date.Modified	HGNC_Date.Name.Changed	HGNC_Date.Symbol.Changed	HGNC_Ensembl.Gene.ID	HGNC_Ensembl.ID.supplied.by.Ensembl.	HGNC_Entrez.Gene.ID	HGNC_Entrez.Gene.ID.supplied.by.NCBI.	HGNC_Enzyme.IDs	HGNC_Gene.family.description	HGNC_HGNC.ID	HGNC_Locus.Group	HGNC_Locus.Type	HGNC_Name.Synonyms	HGNC_OMIM.ID.supplied.by.NCBI.	HGNC_Previous.Names	HGNC_Previous.Symbols	HGNC_Primary.IDs	HGNC_Pubmed.IDs	HGNC_Record.Type	HGNC_RefSeq.IDs	HGNC_RefSeq.supplied.by.NCBI.	HGNC_Secondary.IDs	HGNC_Status	HGNC_Synonyms	HGNC_UCSC.ID.supplied.by.UCSC.	HGNC_UniProt.ID.supplied.by.UniProt.	HGNC_VEGA.IDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	ORegAnno_bin	UniProt_alt_uniprot_accessions	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP.._NR	dbNSFP_GERP.._RS	dbNSFP_GERP.._RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_fold.degenerate	dbNSFP_genename	dbNSFP_hg18_pos.1.coor.	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_id	gene_type	havana_transcript	secondary_variant_classification	strand	transcript_id	variant_classification	variant_type	key	t_ref_count	t_alt_count
ADAMTS18	170692	broad.mit.edu	37	16	77353780	77353780	+	Missense_Mutation	SNP	G	G	A	rs147816593		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr16:77353780G>A	ENST00000282849.5	-	16	2916	c.2498C>T	c.(2497-2499)gCg>gTg	p.A833V		NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	833	Spacer.				proteolysis	proteinaceous extracellular matrix	metalloendopeptidase activity|zinc ion binding			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						GGGCCCTGGCGCGTACAGACG	0.542		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G	VAL/ALA	1,4395	2.1+/-5.4	0,1,2197	61	60	60		2498	5.5	0.2	16	dbSNP_134	60	0,8600		0,0,4300	no	missense	ADAMTS18	NM_199355.2	64	0,1,6497	AA,AG,GG	NA	0.0,0.0227,0.0077	probably-damaging	833/1222	77353780	1,12995	2198	4300	6498	SO:0001583	missense			AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873	170692	170692		ADAM metallopeptidases with thrombospondin type 1 motif	17110	protein-coding gene	gene with protein product		607512	a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18	ADAMTS21	NA	11867212, 17546048	Standard		NM_199355	NA	Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.2498C>T	16.37:g.77353780G>A	ENSP00000282849:p.Ala833Val	NA	Q6P4R5|Q6ZWJ9	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.141924	0.77775	2.27E-4	0.0	ENSG00000140873	ENST00000282849	T	0.56941	0.43	5.54	5.54	0.83059	ADAM-TS Spacer 1 (1);	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	M	0.87038	2.855	0.80722	D	1	D;D	0.89917	0.997;1.0	P;D	0.81914	0.897;0.995	T	0.81191	-0.1045	10	0.87932	D	0	.	18.4764	0.90793	0.0:0.0:1.0:0.0	.	833;833	Q8TE60-2;Q8TE60	.;ATS18_HUMAN	V	833	ENSP00000282849:A833V	ENSP00000282849:A833V	A	-	2	0	ADAMTS18	75911281	1.000000	0.71417	0.242000	0.24170	0.254000	0.26022	9.378000	0.97191	2.618000	0.88619	0.563000	0.77884	GCG	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000269037.1		-	ENST00000282849.5	Missense_Mutation	SNP	16 : 77353780 - 77353780 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	539	31
ADAMTSL4	54507	broad.mit.edu	37	1	150529196	150529196	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:150529196G>A	ENST00000369038.2	+	8	1877	c.1676G>A	c.(1675-1677)cGt>cAt	p.R559H	RP11-54A4.2_ENST00000442435.2_RNA|ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.R559H|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.R582H|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.R559H			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	559					apoptosis|positive regulation of apoptosis		metalloendopeptidase activity|protease binding			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CGATATAACCGTCCTCCCAGG	0.647		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													95	111	106			NA	NA	1		NA											NA				150529196		2203	4300	6503	SO:0001583	missense			BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382	54507	54507			19706	protein-coding gene	gene with protein product		610113	thrombospondin repeat containing 1	TSRC1	NA	12706885	Standard	NM_019032	NM_019032	NA	Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.1676G>A	1.37:g.150529196G>A	ENSP00000358034:p.Arg559His	NA	Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	37	CCDS955.1	.	.	.	.	.	.	.	.	.	.	G	16.85	3.235869	0.58886	.	.	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000407995;ENST00000369039;ENST00000369038	T;T;T;T	0.55413	0.52;0.52;0.52;0.52	4.54	4.54	0.55810	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.65852	0.2731	M	0.85777	2.775	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.995;0.993;0.988	T	0.70992	-0.4721	9	0.72032	D	0.01	.	8.4206	0.32698	0.1047:0.0:0.8953:0.0	.	582;582;559;559	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	H	559;559;97;582;559	ENSP00000358037:R559H;ENSP00000271643:R559H;ENSP00000358035:R582H;ENSP00000358034:R559H	ENSP00000271643:R559H	R	+	2	0	ADAMTSL4	148795820	0.988000	0.35896	0.629000	0.29254	0.140000	0.21249	5.061000	0.64319	2.346000	0.79739	0.462000	0.41574	CGT	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084395.4		+	ENST00000369038.2	Missense_Mutation	SNP	1 : 150529196 - 150529196 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	1038	50
AMPD1	270	broad.mit.edu	37	1	115216697	115216697	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:115216697C>T	ENST00000369538.3	-	13	1941	c.1894G>A	c.(1894-1896)Gtg>Atg	p.V632M	AMPD1_ENST00000520113.2_Missense_Mutation_p.V636M|AMPD1_ENST00000353928.6_Missense_Mutation_p.V603M	NM_001172626.1	NP_001166097.1	P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	603					purine base metabolic process|purine ribonucleoside monophosphate biosynthetic process|purine-containing compound salvage	cytosol	AMP deaminase activity|metal ion binding			NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(17)|ovary(3)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	45	all_epithelial(7;7.83e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;4.64e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	Adenosine monophosphate(DB00131)	TACTGTAGCACGGGACTCTGA	0.353		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													60	63	62			NA	NA	1		NA											NA				115216697		2203	4300	6503	SO:0001583	missense			M60092	CCDS876.1, CCDS876.2, CCDS53349.1	1p13	2010-02-10	2010-02-10		ENSG00000116748	ENSG00000116748	270	270	3.5.4.6		468	protein-coding gene	gene with protein product	AMPD isoform M, skeletal muscle AMPD	102770	adenosine monophosphate deaminase 1 (isoform M)		NA	1400401	Standard		NM_001172626	NA	Approved	MAD, MADA	uc001efe.2	P23109	OTTHUMG00000011892	ENST00000369538.3:c.1894G>A	1.37:g.115216697C>T	ENSP00000358551:p.Val632Met	NA	Q5TF00	37	CCDS53349.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.647876	0.87958	.	.	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95554	-3.74;-3.74;-3.74	5.96	5.96	0.96718	Adenosine/AMP deaminase (1);	0.052104	0.85682	D	0.000000	D	0.97923	0.9317	M	0.82923	2.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.988;0.996	D	0.98016	1.0368	10	0.87932	D	0	-21.0775	20.4008	0.98991	0.0:1.0:0.0:0.0	.	632;603	Q5TF02;P23109	.;AMPD1_HUMAN	M	636;632;603	ENSP00000430075:V636M;ENSP00000358551:V632M;ENSP00000316520:V603M	ENSP00000316520:V603M	V	-	1	0	AMPD1	115018220	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.818000	0.86416	2.826000	0.97356	0.655000	0.94253	GTG	AMPD1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000032861.2		-	ENST00000369538.3	Missense_Mutation	SNP	1 : 115216697 - 115216697 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	187	9
ASH2L	9070	broad.mit.edu	37	8	37964684	37964684	+	Splice_Site	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:37964684C>T	ENST00000343823.6	+	3	710	c.401C>T	c.(400-402)tCa>tTa	p.S134L	ASH2L_ENST00000545394.1_Intron|ASH2L_ENST00000521652.1_Splice_Site_p.S40L|ASH2L_ENST00000428278.2_Splice_Site_p.S40L|ASH2L_ENST00000250635.7_Splice_Site_p.S40L	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	134					hemopoiesis|histone H3-K4 methylation|positive regulation of cell proliferation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription from RNA polymerase II promoter	Set1C/COMPASS complex	metal ion binding|protein binding|transcription regulatory region DNA binding			NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)	19	Colorectal(12;0.000501)	Lung NSC(58;0.0295)|all_lung(54;0.0413)				ATAGATACCTCGTGAGTACTT	0.408		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													193	175	181			NA	NA	8		NA											NA				37964684		2203	4300	6503	SO:0001630	splice_region_variant			AF056717	CCDS6101.1, CCDS47840.1, CCDS59100.1, CCDS64872.1	8p11.2	2013-01-28	2001-11-28		ENSG00000129691	ENSG00000129691	9070	9070		Zinc fingers, PHD-type	744	protein-coding gene	gene with protein product		604782	ash2 (absent, small, or homeotic, Drosophila, homolog)-like	ASH2L1	NA	10393421	Standard	NM_004674	NM_004674	NA	Approved	ASH2L2, ASH2, Bre2	uc003xkt.5	Q9UBL3	OTTHUMG00000164016	ENST00000343823.6:c.401+1C>T	8.37:g.37964684C>T		NA	A8K7C3|D3DSW9|O60659|O60660|Q96B62	37	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705343	0.68615	.	.	ENSG00000129691	ENST00000343823;ENST00000250635;ENST00000517719;ENST00000428278;ENST00000521652	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	4.82	4.82	0.62117	.	0.114028	0.64402	D	0.000014	T	0.16214	0.0390	N	0.19112	0.55	0.80722	D	1	B;B	0.27732	0.187;0.061	B;B	0.21151	0.033;0.005	T	0.05468	-1.0883	10	0.62326	D	0.03	.	17.9105	0.88932	0.0:1.0:0.0:0.0	.	40;134	Q9UBL3-2;Q9UBL3	.;ASH2L_HUMAN	L	134;40;148;40;40	ENSP00000340896:S134L;ENSP00000250635:S40L;ENSP00000428877:S148L;ENSP00000395310:S40L;ENSP00000430259:S40L	ENSP00000250635:S40L	S	+	2	0	ASH2L	38083841	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.090000	0.41682	2.223000	0.72356	0.557000	0.71058	TCA	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000376749.4	Missense_Mutation	+	ENST00000343823.6	Splice_Site	SNP	8 : 37964684 - 37964684 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	555	39
BBS9	27241	broad.mit.edu	37	7	33407475	33407475	+	Splice_Site	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:33407475G>A	ENST00000242067.6	+	17	2310		c.e17+1		BBS9_ENST00000354265.4_Splice_Site|BBS9_ENST00000355070.2_Splice_Site|BBS9_ENST00000396127.2_Splice_Site|BBS9_ENST00000350941.3_Splice_Site	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	NA					fat cell differentiation|response to stimulus|visual perception	BBSome|cilium membrane|microtubule organizing center|nucleus	protein binding		BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			AAAACTTCTCGTAAGTAAAAC	0.373		NA							Bardet-Biedl syndrome					NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0			GRCh37	CS055613	BBS9	S							149	135	139			NA	NA	7		NA											NA				33407475		2203	4300	6503	SO:0001630	splice_region_variant	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507	27241	27241			30000	protein-coding gene	gene with protein product	parathyroid hormone responsive B1 gene	607968			NA	16380913, 10221542	Standard		XM_005249701	NA	Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.1789+1G>A	7.37:g.33407475G>A		NA	P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	37	CCDS43566.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.496770	0.85069	.	.	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132;ENST00000434373	.	.	.	5.48	5.48	0.80851	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9484	0.92630	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BBS9	33374000	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.787000	0.75099	2.572000	0.86782	0.655000	0.94253	.	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000329064.1	Intron	+	ENST00000242067.6	Splice_Site	SNP	7 : 33407475 - 33407475 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	304	18
BOD1L1	259282	broad.mit.edu	37	4	13615144	13615144	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr4:13615144G>A	ENST00000040738.5	-	5	1451	c.1316C>T	c.(1315-1317)aCg>aTg	p.T439M		NM_148894.2	NP_683692.2	Q8NFC6	BOD1L_HUMAN	biorientation of chromosomes in cell division 1-like 1	439	Lys-rich.						DNA binding				NA						ACCATCTGACGTAATCTCTCC	0.383		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													171	163	166			NA	NA	4		NA											NA				13615144		2203	4300	6503	SO:0001583	missense			AF528529	CCDS3411.2	4p16.1	2012-04-10	2012-04-10	2012-04-10	ENSG00000038219	ENSG00000038219	259282	259282			31792	protein-coding gene	gene with protein product			family with sequence similarity 44, member A, biorientation of chromosomes in cell division 1-like	FAM44A, BOD1L	NA		Standard	NM_148894	XM_005248150	NA	Approved	FLJ33215, KIAA1327	uc003gmz.1	Q8NFC6	OTTHUMG00000090659	ENST00000040738.5:c.1316C>T	4.37:g.13615144G>A	ENSP00000040738:p.Thr439Met	NA	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	G	19.83	3.900621	0.72754	.	.	ENSG00000038219	ENST00000040738	T	0.09073	3.02	5.49	5.49	0.81192	.	0.152011	0.31020	N	0.008416	T	0.24851	0.0603	M	0.66939	2.045	0.30227	N	0.796234	D	0.89917	1.0	D	0.64506	0.926	T	0.01961	-1.1239	10	0.59425	D	0.04	-2.6448	13.9661	0.64209	0.0731:0.0:0.9269:0.0	.	439	Q8NFC6	BOD1L_HUMAN	M	439	ENSP00000040738:T439M	ENSP00000040738:T439M	T	-	2	0	BOD1L	13224242	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	4.944000	0.63561	2.738000	0.93877	0.655000	0.94253	ACG	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000207321.1		-	ENST00000040738.5	Missense_Mutation	SNP	4 : 13615144 - 13615144 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	561	43
BPTF	2186	broad.mit.edu	37	17	65850550	65850550	+	Nonsense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:65850550C>T	ENST00000306378.6	+	2	1168	c.1108C>T	c.(1108-1110)Cag>Tag	p.Q370*	BPTF_ENST00000335221.5_Nonsense_Mutation_p.Q370*|BPTF_ENST00000321892.4_Nonsense_Mutation_p.Q370*|BPTF_ENST00000424123.3_Nonsense_Mutation_p.Q231*	NM_182641.3	NP_872579.2	Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	370					brain development|chromatin remodeling|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|NURF complex	sequence-specific DNA binding|transcription factor binding|zinc ion binding			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TCTAGTCGATCAGTTTCTTAC	0.418		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													187	184	185			NA	NA	17		NA											NA				65850550		2203	4300	6503	SO:0001587	stop_gained			AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634	2186	2186		Zinc fingers, PHD-type	3581	protein-coding gene	gene with protein product		601819	fetal Alzheimer antigen	FALZ	NA	8975731, 10662542, 16728976	Standard	NM_182641, NM_004459	NM_182641	NA	Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000306378.6:c.1108C>T	17.37:g.65850550C>T	ENSP00000307208:p.Gln370*	NA	Q6NX67|Q7Z7D6|Q9UIG2	37	CCDS11673.1	.	.	.	.	.	.	.	.	.	.	C	32	5.169246	0.94768	.	.	ENSG00000171634	ENST00000544491;ENST00000306378;ENST00000335221;ENST00000321892;ENST00000544778	.	.	.	5.62	5.62	0.85841	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.6584	0.95853	0.0:1.0:0.0:0.0	.	.	.	.	X	275;370;370;370;231	.	ENSP00000307208:Q370X	Q	+	1	0	BPTF	63281012	1.000000	0.71417	0.999000	0.59377	0.406000	0.30931	7.818000	0.86416	2.646000	0.89796	0.655000	0.94253	CAG	BPTF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000255334.2		+	ENST00000306378.6	Nonsense_Mutation	SNP	17 : 65850550 - 65850550 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	742	93
CACNA2D2	9254	broad.mit.edu	37	3	50405102	50405102	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr3:50405102G>A	ENST00000266039.3	-	26	2441	c.2268C>T	c.(2266-2268)gaC>gaT	p.D756D	XXcos-LUCA11.4_ENST00000606665.1_RNA|XXcos-LUCA11.5_ENST00000606589.1_Intron|XXcos-LUCA11.4_ENST00000607362.1_RNA|CACNA2D2_ENST00000423994.2_Silent_p.D763D|CACNA2D2_ENST00000479441.1_Silent_p.D763D|XXcos-LUCA11.4_ENST00000607088.1_RNA|XXcos-LUCA11.4_ENST00000607121.1_RNA|XXcos-LUCA11.4_ENST00000606259.1_RNA|CACNA2D2_ENST00000424201.2_Silent_p.D756D|CACNA2D2_ENST00000360963.3_Silent_p.D687D|CACNA2D2_ENST00000435965.1_Silent_p.D763D|CACNA2D2_ENST00000429770.1_Silent_p.D756D|CACNA2D2_ENST00000395083.1_Silent_p.D756D			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	763					energy reserve metabolic process|regulation of insulin secretion	integral to membrane|plasma membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Gabapentin(DB00996)	TGATGCCACCGTCTGTGGCAG	0.642		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G	,,	1,4405	2.1+/-5.4	0,1,2202	79	77	78		2268,2289,2268	-10.8	0.1	3		78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA2D2	NM_001005505.1,NM_001174051.1,NM_006030.2	,,	0,1,6502	AA,AG,GG	NA	0.0,0.0227,0.0077	,,	756/1146,763/1151,756/1144	50405102	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402	9254	9254		Calcium channel subunits	1400	protein-coding gene	gene with protein product	gene 26	607082			NA		Standard	NM_006030	XM_005265581	NA	Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000266039.3:c.2268C>T	3.37:g.50405102G>A		NA	A7MD15|Q9NY48|Q9UEW0|Q9Y268	37																																																																																				CACNA2D2-002	KNOWN	non_canonical_conserved|basic	protein_coding	NA	protein_coding	OTTHUMT00000346454.2		-	ENST00000266039.3	Silent	SNP	3 : 50405102 - 50405102 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	328	29
CADM3	57863	broad.mit.edu	37	1	159163257	159163257	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:159163257C>T	ENST00000368125.4	+	4	584	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	CADM3_ENST00000368124.4_Missense_Mutation_p.R177W	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	143	Ig-like C2-type 1.				adherens junction organization|cell junction assembly|heterophilic cell-cell adhesion|homophilic cell adhesion	cell-cell junction|integral to membrane	protein homodimerization activity			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(20)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55	all_hematologic(112;0.0429)					ATCTTCATTACGGGAAAAAGA	0.532		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													105	108	107			NA	NA	1		NA											NA				159163257		2203	4300	6503	SO:0001583	missense			AY046418	CCDS1182.1, CCDS44251.1	1q21.2-q22	2013-01-29	2007-02-07	2007-02-07	ENSG00000162706	ENSG00000162706	57863	57863		Immunoglobulin superfamily / V-set domain containing, Immunoglobulin superfamily / C2-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing	17601	protein-coding gene	gene with protein product	nectin-like 1	609743	immunoglobulin superfamily, member 4B	IGSF4B	NA	11536053	Standard	NM_021189	NM_021189	NA	Approved	BIgR, FLJ10698, TSLL1, NECL1, SynCAM3, Necl-1	uc001ftk.2	Q8N126	OTTHUMG00000037177	ENST00000368125.4:c.427C>T	1.37:g.159163257C>T	ENSP00000357107:p.Arg143Trp	NA	Q8IZQ9|Q9NVJ5|Q9UJP1	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559293	0.65538	.	.	ENSG00000162706	ENST00000368124;ENST00000368125;ENST00000416746	T;T;T	0.76060	-0.99;-0.99;-0.99	5.13	5.13	0.70059	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.372580	0.26514	N	0.023944	T	0.73418	0.3584	L	0.39245	1.2	0.36569	D	0.872888	P;D;D	0.76494	0.863;0.999;0.998	D;D;P	0.66979	0.913;0.948;0.787	T	0.77275	-0.2648	10	0.66056	D	0.02	.	11.0641	0.47966	0.1847:0.8152:0.0:0.0	.	143;143;177	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	W	177;143;143	ENSP00000357106:R177W;ENSP00000357107:R143W;ENSP00000387802:R143W	ENSP00000357106:R177W	R	+	1	2	CADM3	157429881	0.004000	0.15560	1.000000	0.80357	0.953000	0.61014	-0.061000	0.11693	2.655000	0.90218	0.655000	0.94253	CGG	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000090330.1		+	ENST00000368125.4	Missense_Mutation	SNP	1 : 159163257 - 159163257 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	489	98
CCRN4L	25819	broad.mit.edu	37	4	139966043	139966043	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr4:139966043C>T	ENST00000280614.2	+	3	904	c.711C>T	c.(709-711)gcC>gcT	p.A237A	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	237					rhythmic process|transcription from RNA polymerase II promoter	nucleus	sequence-specific DNA binding transcription factor activity			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					ATGGTTGTGCCTTATTTTTTC	0.463		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Ovarian(144;566 1842 19130 21379 22209)							NA				0													100	90	93			NA	NA	4		NA											NA				139966043		2203	4300	6503	SO:0001819	synonymous_variant			AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014	25819	25819			14254	protein-coding gene	gene with protein product		608468	CCR4-like (carbon catabolite repression 4, S.cerevisiae)		NA	10521507	Standard	NM_012118	NM_012118	NA	Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.711C>T	4.37:g.139966043C>T		NA	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	37	CCDS3743.1																																																																																			CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257231.3		+	ENST00000280614.2	Silent	SNP	4 : 139966043 - 139966043 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	386	29
CDH20	28316	broad.mit.edu	37	18	59195270	59195270	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr18:59195270G>A	ENST00000262717.4	+	7	1486	c.1088G>A	c.(1087-1089)cGt>cAt	p.R363H	CDH20_ENST00000536675.2_Missense_Mutation_p.R363H|CDH20_ENST00000538374.1_Missense_Mutation_p.R363H			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	363	Cadherin 3.				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CTAGAGATGCGTTTTCTGAAC	0.473		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													117	108	111			NA	NA	18		NA											NA				59195270		2203	4300	6503	SO:0001583	missense			AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542	28316	28316		Cadherins / Major cadherins	1760	protein-coding gene	gene with protein product		605807			NA	10995570	Standard	NM_031891	NM_031891	NA	Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1088G>A	18.37:g.59195270G>A	ENSP00000262717:p.Arg363His	NA	Q495S3	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.800571	0.50315	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.38401	1.14;1.14;1.14	5.88	5.01	0.66863	Cadherin (4);Cadherin-like (1);	0.352394	0.34110	N	0.004250	T	0.44307	0.1287	M	0.79805	2.47	0.39023	D	0.959782	B	0.21905	0.062	B	0.22601	0.04	T	0.48127	-0.9062	10	0.54805	T	0.06	.	14.9937	0.71412	0.0683:0.0:0.9317:0.0	.	363	Q9HBT6	CAD20_HUMAN	H	363	ENSP00000444767:R363H;ENSP00000442226:R363H;ENSP00000262717:R363H	ENSP00000262717:R363H	R	+	2	0	CDH20	57346250	0.997000	0.39634	1.000000	0.80357	0.991000	0.79684	1.798000	0.38814	1.492000	0.48499	0.650000	0.86243	CGT	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256141.2		+	ENST00000262717.4	Missense_Mutation	SNP	18 : 59195270 - 59195270 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	389	36
CDKN2A	1029	broad.mit.edu	37	9	21971120	21971120	+	Nonsense_Mutation	SNP	G	G	A	rs121913388		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr9:21971120G>A	ENST00000479692.2	-	2	99	c.85C>T	c.(85-87)Cga>Tga	p.R29*	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000530628.2_Missense_Mutation_p.P94L|CDKN2A_ENST00000578845.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000498628.2_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000446177.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000361570.3_Missense_Mutation_p.P135L|CDKN2A_ENST00000579122.1_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000494262.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000304494.5_Nonsense_Mutation_p.R80*|CDKN2A_ENST00000497750.1_Nonsense_Mutation_p.R29*|CDKN2A_ENST00000579755.1_Missense_Mutation_p.P94L|CDKN2A_ENST00000498124.1_Nonsense_Mutation_p.R80*			P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	80					cell cycle arrest|cell cycle checkpoint|G1 phase of mitotic cell cycle|G1/S transition of mitotic cell cycle|induction of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of cell-matrix adhesion|negative regulation of cyclin-dependent protein kinase activity|negative regulation of NF-kappaB transcription factor activity|positive regulation of macrophage apoptosis|positive regulation of smooth muscle cell apoptosis|Ras protein signal transduction|replicative senescence	cytosol|nucleus	cyclin-dependent protein kinase inhibitor activity|NF-kappaB binding|protein binding|protein kinase binding	p.0?(1315)|p.R80*(100)|p.?(44)|p.P135L(7)|p.L65fs*38(1)|p.T79fs*37(1)|p.0(1)|p.A76fs*64(1)|p.T79fs*65(1)|p.E61_L94del(1)|p.A68fs*3(1)|p.R80fs*34(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		TGCACGGGTCGGGTGAGAGTG	0.726	R80*(HSC4_UPPER_AERODIGESTIVE_TRACT)|R80*(MEWO_SKIN)	17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1474	Whole gene deletion(1316)|Substitution - Nonsense(100)|Unknown(44)|Substitution - Missense(7)|Deletion - Frameshift(6)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(298)|skin(206)|central_nervous_system(168)|lung(150)|urinary_tract(91)|bone(76)|oesophagus(72)|upper_aerodigestive_tract(63)|soft_tissue(60)|pleura(51)|pancreas(37)|ovary(36)|kidney(32)|breast(32)|biliary_tract(16)|thyroid(15)|NS(14)|stomach(14)|large_intestine(7)|autonomic_ganglia(7)|meninges(7)|liver(6)|salivary_gland(4)|thymus(4)|vulva(3)|endometrium(3)|prostate(2)	GRCh37	CM014695	CDKN2A	M	rs121913388						11	14	13			NA	NA	9		NA											NA				21971120		2172	4246	6418	SO:0001587	stop_gained			L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889	1029	1029			1787	protein-coding gene	gene with protein product		600160	cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)	CDKN2, MLM	NA	8152487, 7606716	Standard	NM_000077	NM_058195	NA	Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000479692.2:c.85C>T	9.37:g.21971120G>A	ENSP00000466887:p.Arg29*	NA	D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.328457|7.328457	0.98214|0.98214	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000361570;ENST00000530628|ENST00000304494;ENST00000446177	D;D|.	0.86497|.	-2.13;-2.02|.	5.93|5.93	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.37136|.	N|.	0.002233|.	T|.	0.44561|.	0.1299|.	L|L	0.36672|0.36672	1.1|1.1	0.47511|0.47511	D|D	0.999443|0.999443	D|.	0.59357|.	0.985|.	B|.	0.40602|.	0.334|.	T|.	0.34825|.	-0.9813|.	10|.	0.13108|0.02654	T|T	0.6|1	-2.989|-2.989	8.7197|8.7197	0.34434|0.34434	0.0759:0.0:0.7715:0.1526|0.0759:0.0:0.7715:0.1526	.|.	135|.	Q8N726|.	CD2A2_HUMAN|.	L|X	135;94|80	ENSP00000355153:P135L;ENSP00000432664:P94L|.	ENSP00000355153:P135L|ENSP00000307101:R80X	P|R	-|-	2|1	0|2	CDKN2A|CDKN2A	21961120|21961120	0.995000|0.995000	0.38212|0.38212	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	2.363000|2.363000	0.44178|0.44178	1.464000|1.464000	0.47987|0.47987	0.650000|0.650000	0.86243|0.86243	CCG|CGA	CDKN2A-008	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000051922.3		-	ENST00000479692.2	Nonsense_Mutation	SNP	9 : 21971120 - 21971120 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	155	18
CXCR4	7852	broad.mit.edu	37	2	136872710	136872710	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:136872710G>A	ENST00000409817.1	-	1	1103	c.800C>T	c.(799-801)tCc>tTc	p.S267F	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000241393.3_Missense_Mutation_p.S263F	NM_001008540.1	NP_001008540.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	263	Involved in dimerization.				activation of MAPK activity|apoptosis|dendritic cell chemotaxis|elevation of cytosolic calcium ion concentration|entry into host cell|inflammatory response|initiation of viral infection|regulation of chemotaxis|response to hypoxia|response to virus	cell leading edge|cell surface|cytoplasmic membrane-bounded vesicle|integral to membrane|plasma membrane	actin binding|C-X-C chemokine receptor activity|coreceptor activity|myosin light chain binding|ubiquitin binding|ubiquitin protein ligase binding			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.155)	Framycetin(DB00452)	GAGGATGAAGGAGTCGATGCT	0.517		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													228	215	219			NA	NA	2		NA											NA				136872710		2203	4300	6503	SO:0001583	missense			AF005058	CCDS33295.1, CCDS46420.1	2q21	2014-09-17	2002-08-22		ENSG00000121966	ENSG00000121966	NA	7852		CD molecules, GPCR / Class A : Chemokine receptors : C-X-C motif	2561	protein-coding gene	gene with protein product		162643	chemokine (C-X-C motif), receptor 4 (fusin)		NA	9599023, 9379028	Standard		NM_001008540	NA	Approved	LESTR, NPY3R, HM89, NPYY3R, D2S201E, fusin, HSY3RR, NPYR, CD184	uc002tuz.3	P61073	OTTHUMG00000153583	ENST00000409817.1:c.800C>T	2.37:g.136872710G>A	ENSP00000386884:p.Ser267Phe	NA	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	37	CCDS33295.1	.	.	.	.	.	.	.	.	.	.	G	15.06	2.722563	0.48728	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.36699	1.24;1.24	6.17	5.29	0.74685	GPCR, rhodopsin-like superfamily (1);	0.137085	0.64402	D	0.000003	T	0.30634	0.0771	L	0.33189	0.99	0.49483	D	0.99979	P;D	0.57257	0.718;0.979	B;B	0.39503	0.237;0.301	T	0.16719	-1.0393	10	0.87932	D	0	.	17.6818	0.88246	0.0:0.1228:0.8772:0.0	.	263;267	P61073;P61073-2	CXCR4_HUMAN;.	F	267;263;133	ENSP00000386884:S267F;ENSP00000241393:S263F	ENSP00000241393:S263F	S	-	2	0	CXCR4	136589180	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.050000	0.57404	1.615000	0.50252	0.655000	0.94253	TCC	CXCR4-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000331734.1		-	ENST00000409817.1	Missense_Mutation	SNP	2 : 136872710 - 136872710 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	380	13
DCT	1638	broad.mit.edu	37	13	95104903	95104903	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr13:95104903C>T	ENST00000377028.5	-	6	1593				DCT_ENST00000446125.1_Missense_Mutation_p.R398H	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	NA					epidermis development|melanin biosynthetic process from tyrosine	cytosol|integral to membrane|melanosome membrane|microsome	copper ion binding|dopachrome isomerase activity|oxidoreductase activity			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	50	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;3.71e-42)|all_epithelial(2;3.76e-31)|all_lung(2;5.16e-14)|Lung NSC(4;1.33e-13)|Breast(118;0.0013)|Hepatocellular(115;0.00886)|Renal(2;0.00988)		COAD - Colon adenocarcinoma(199;7.07e-05)|GBM - Glioblastoma multiforme(99;0.000472)		gtaaagcaaacgattagaaat	0.274		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								C	HIS/ARG,	0,3136		0,0,1568	146	118	126		1193,	1.3	0	13		126	1,7163		0,1,3581	no	missense,intron	DCT	NM_001129889.1,NM_001922.3	29,	0,1,5149	TT,TC,CC	NA	0.014,0.0,0.0097	,	398/553,	95104903	1,10299	1568	3582	5150	SO:0001627	intron_variant			D17547	CCDS9470.1, CCDS45060.1	13q32	2012-09-28	2012-09-28		ENSG00000080166	ENSG00000080166	1638	1638	5.3.3.12		2709	protein-coding gene	gene with protein product	dopachrome delta-isomerase	191275	tyrosine-related protein 2	TYRP2	NA	8306979	Standard		NM_001922	NA	Approved		uc010afh.3	P40126	OTTHUMG00000017206	ENST00000377028.5:c.1179+7441G>A	13.37:g.95104903C>T		NA		37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	C	4.573	0.106534	0.08780	0.0	1.4E-4	ENSG00000080166	ENST00000446125	D	0.99089	-5.41	2.51	1.31	0.21738	.	.	.	.	.	D	0.96324	0.8801	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	D	0.92849	0.6295	8	0.51188	T	0.08	.	5.7352	0.18063	0.7191:0.2809:0.0:0.0	.	398	Q09GT4	.	H	398	ENSP00000392762:R398H	ENSP00000392762:R398H	R	-	2	0	DCT	93902904	0.001000	0.12720	0.034000	0.17996	0.008000	0.06430	0.036000	0.13819	0.396000	0.25283	-0.565000	0.04167	CGT	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000045461.3		-	ENST00000377028.5	Intron	SNP	13 : 95104903 - 95104903 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	122	14
DRG2	1819	broad.mit.edu	37	17	18003681	18003681	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:18003681C>T	ENST00000583355.1	+	3	242				DRG2_ENST00000395726.4_Silent_p.L158L|DRG2_ENST00000225729.3_Silent_p.L158L			P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	NA					signal transduction		GTP binding			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TCCTAGGTCTCTGCTGGAGAA	0.577		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								C		0,4406		0,0,2203	152	140	144		472	5.4	1	17		144	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DRG2	NM_001388.3		0,2,6501	TT,TC,CC	NA	0.0233,0.0,0.0154		158/365	18003681	2,13004	2203	4300	6503	SO:0001627	intron_variant			X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591	1819	1819			3030	protein-coding gene	gene with protein product		602986	developmentally regulated GTP-binding protein 2		NA	9605870, 7929244	Standard	NM_001388	NM_001388	NA	Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000583355.1:c.226-3434C>T	17.37:g.18003681C>T		NA	B2R8G5|Q9BWB2	37																																																																																				DRG2-025	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000447190.1		+	ENST00000583355.1	Intron	SNP	17 : 18003681 - 18003681 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	701	66
FOXA1	3169	broad.mit.edu	37	14	38061592	38061592	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr14:38061592C>T	ENST00000250448.2	-	2	458	c.397G>A	c.(397-399)Gcc>Acc	p.A133T	FOXA1_ENST00000540786.1_Missense_Mutation_p.A100T|FOXA1_ENST00000545425.2_5'UTR	NM_004496.3	NP_004487.2	P55317	FOXA1_HUMAN	forkhead box A1	133					chromatin remodeling|embryo development|epithelial cell maturation involved in prostate gland development|epithelial tube branching involved in lung morphogenesis|epithelial-mesenchymal signaling involved in prostate gland development|glucose homeostasis|lung epithelial cell differentiation|negative regulation of survival gene product expression|neuron fate specification|pattern specification process|positive regulation of estrogen receptor signaling pathway|positive regulation of mitotic cell cycle|positive regulation of neuron differentiation|positive regulation of sequence-specific DNA binding transcription factor activity|prostate gland epithelium morphogenesis|prostate gland stromal morphogenesis|response to estradiol stimulus|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development	transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|transcription regulatory region DNA binding			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(12)	19	Breast(36;0.0954)|Esophageal squamous(585;0.164)|Hepatocellular(127;0.213)		Lung(238;5.41e-07)|LUAD - Lung adenocarcinoma(48;2.48e-05)|Epithelial(34;0.0454)|LUSC - Lung squamous cell carcinoma(13;0.0917)|all cancers(34;0.0925)|BRCA - Breast invasive adenocarcinoma(188;0.239)	GBM - Glioblastoma multiforme(112;0.0222)		GGGTTCATGGCGGCCGCGTAG	0.736		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													13	15	14			NA	NA	14		NA											NA				38061592		2157	4173	6330	SO:0001583	missense			U39840	CCDS9665.1	14q12-q13	2008-04-10		2002-09-20	ENSG00000129514	ENSG00000129514	3169	3169		Forkhead boxes	5021	protein-coding gene	gene with protein product		602294	hepatocyte nuclear factor 3, alpha	HNF3A	NA	9119385, 8652662	Standard		NM_004496	NA	Approved		uc001wuf.4	P55317	OTTHUMG00000140253	ENST00000250448.2:c.397G>A	14.37:g.38061592C>T	ENSP00000250448:p.Ala133Thr	NA	B2R9H6|Q9H2A0	37	CCDS9665.1	.	.	.	.	.	.	.	.	.	.	C	4.498	0.092298	0.08632	.	.	ENSG00000129514	ENST00000250448;ENST00000540786	T;T	0.18502	2.21;2.21	3.99	1.91	0.25777	Fork-head N-terminal (1);	0.667620	0.14434	N	0.319836	T	0.05868	0.0153	N	0.03608	-0.345	0.22954	N	0.998514	B	0.27997	0.197	B	0.23150	0.044	T	0.40308	-0.9570	10	0.10902	T	0.67	.	8.1718	0.31260	0.4693:0.5307:0.0:0.0	.	133	P55317	FOXA1_HUMAN	T	133;100	ENSP00000250448:A133T;ENSP00000440178:A100T	ENSP00000250448:A133T	A	-	1	0	FOXA1	37131343	0.000000	0.05858	0.991000	0.47740	0.985000	0.73830	-0.572000	0.05881	0.869000	0.35703	0.505000	0.49811	GCC	FOXA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276735.1		-	ENST00000250448.2	Missense_Mutation	SNP	14 : 38061592 - 38061592 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	133	8
FOXQ1	94234	broad.mit.edu	37	6	1313384	1313384	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr6:1313384C>T	ENST00000296839.2	+	1	710	c.445C>T	c.(445-447)Ctc>Ttc	p.L149F		NM_033260.3	NP_150285.3	Q9C009	FOXQ1_HUMAN	forkhead box Q1	149					DNA fragmentation involved in apoptotic nuclear change|embryo development|hair follicle morphogenesis|pattern specification process|positive regulation of caspase activity|positive regulation of transcription from RNA polymerase II promoter|regulation of sequence-specific DNA binding transcription factor activity	transcription factor complex	caspase regulator activity|DNA bending activity|double-stranded DNA binding|estrogen receptor binding|promoter binding|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|ubiquitin conjugating enzyme binding			lung(1)|urinary_tract(1)	2	Ovarian(93;0.0733)	Breast(5;0.052)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.0954)|BRCA - Breast invasive adenocarcinoma(62;0.18)		CAACGAGTACCTCATGGGCAA	0.657		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													35	36	36			NA	NA	6		NA											NA				1313384		2196	4290	6486	SO:0001583	missense			AF153341	CCDS4471.1	6p25	2008-02-05			ENSG00000164379	ENSG00000164379	94234	94234		Forkhead boxes	20951	protein-coding gene	gene with protein product		612788			NA	11747606, 12011061	Standard	NM_033260	NM_033260	NA	Approved	HFH1	uc003mtl.4	Q9C009	OTTHUMG00000016160	ENST00000296839.2:c.445C>T	6.37:g.1313384C>T	ENSP00000296839:p.Leu149Phe	NA	Q9NS06	37	CCDS4471.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821825	0.50633	.	.	ENSG00000164379	ENST00000296839	D	0.96011	-3.88	3.87	1.9	0.25705	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.093430	0.44483	N	0.000458	D	0.91415	0.7291	N	0.25426	0.745	0.45822	D	0.998695	D	0.57571	0.98	P	0.59761	0.863	D	0.90412	0.4410	10	0.66056	D	0.02	.	6.7197	0.23323	0.1739:0.7262:0.0:0.1	.	149	Q9C009	FOXQ1_HUMAN	F	149	ENSP00000296839:L149F	ENSP00000296839:L149F	L	+	1	0	FOXQ1	1258384	0.969000	0.33509	0.955000	0.39395	0.340000	0.28889	0.219000	0.17641	0.643000	0.30638	-1.206000	0.01644	CTC	FOXQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000043410.1		+	ENST00000296839.2	Missense_Mutation	SNP	6 : 1313384 - 1313384 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	304	16
GGT1	2678	broad.mit.edu	37	22	25023843	25023843	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr22:25023843G>A	ENST00000400382.1	+	13	1988	c.1233G>A	c.(1231-1233)ccG>ccA	p.P411P	GGT1_ENST00000404920.1_Silent_p.P67P|GGT1_ENST00000401885.1_Silent_p.P67P|GGT1_ENST00000400383.1_Silent_p.P411P|GGT1_ENST00000248923.4_Silent_p.P411P|GGT1_ENST00000400380.1_Silent_p.P411P|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000403838.1_Silent_p.P67P|GGT1_ENST00000404223.1_Silent_p.P67P|GGT1_ENST00000406383.2_Silent_p.P411P|GGT1_ENST00000404532.1_Silent_p.P67P			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	411					glutathione biosynthetic process	integral to membrane	acyltransferase activity|gamma-glutamyltransferase activity|protein binding			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	TCCGCTCCCCGGTCAGCGGGA	0.597		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													42	48	46			NA	NA	22		NA											NA				25023843		2203	4299	6502	SO:0001819	synonymous_variant			M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2678	2678	2.3.2.2	CD molecules, Gamma-glutamyltransferases	4250	protein-coding gene	gene with protein product		612346		GGT	NA	8104871, 18357469	Standard	NM_013430	NM_001288833	NA	Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.1233G>A	22.37:g.25023843G>A		NA	Q08247|Q14404|Q8TBS1|Q9UMK1	37	CCDS42992.1																																																																																			GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000250797.1		+	ENST00000400382.1	Silent	SNP	22 : 25023843 - 25023843 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	417	20
GPR182	11318	broad.mit.edu	37	12	57389416	57389416	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr12:57389416C>T	ENST00000300098.1	+	2	642	c.423C>T	c.(421-423)atC>atT	p.I141I		NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	141						integral to membrane|plasma membrane	G-protein coupled receptor activity			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						ATAGCAGCATCTTCTTCCTGG	0.592		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													170	139	149			NA	NA	12		NA											NA				57389416		2203	4300	6503	SO:0001819	synonymous_variant			Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856	11318	11318		GPCR / Class A : Orphans	13708	protein-coding gene	gene with protein product		605307	adrenomedullin receptor	ADMR	NA	9367907, 9535752	Standard	NM_007264	NM_007264	NA	Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.423C>T	12.37:g.57389416C>T		NA		37	CCDS8927.1																																																																																			GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000411212.1		+	ENST00000300098.1	Silent	SNP	12 : 57389416 - 57389416 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	390	38
GRIN2D	2906	broad.mit.edu	37	19	48919318	48919318	+	Silent	SNP	C	C	T	rs148340456	byFrequency	TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:48919318C>T	ENST00000263269.3	+	7	1729	c.1641C>T	c.(1639-1641)tcC>tcT	p.S547S		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	547						cell junction|outer membrane-bounded periplasmic space|postsynaptic membrane	extracellular-glutamate-gated ion channel activity|protein binding			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	L-Glutamic Acid(DB00142)|Loperamide(DB00836)|Orphenadrine(DB01173)	AGGAGCGCTCCGAGATCGTGG	0.662		NA											c	1	5e-04	NA	NA	2184	NA	1	,	,	NA	3e-04	0.0013	NA	NA	4e-04	0.95	LOWCOV,EXOME	NA	NA	9e-04	SNP								NA				0								C		0,4406		0,0,2203	109	93	98		1641	-7.8	0.6	19	dbSNP_134	98	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GRIN2D	NM_000836.2		0,3,6500	TT,TC,CC	NA	0.0349,0.0,0.0231		547/1337	48919318	3,13003	2203	4300	6503	SO:0001819	synonymous_variant			U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464	2906	2906		Ligand-gated ion channels / Glutamate receptors, ionotropic, Glutamate receptors	4588	protein-coding gene	gene with protein product	N-methyl-d-aspartate receptor subunit 2D	602717		NMDAR2D	NA	9480759, 9418891	Standard		NM_000836	NA	Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1641C>T	19.37:g.48919318C>T		NA		37	CCDS12719.1																																																																																			GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000466121.1		+	ENST00000263269.3	Silent	SNP	19 : 48919318 - 48919318 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	504	30
H6PD	9563	broad.mit.edu	37	1	9324398	9324398	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:9324398C>A	ENST00000377403.2	+	5	2148	c.1846C>A	c.(1846-1848)Ctg>Atg	p.L616M	H6PD_ENST00000602477.1_Missense_Mutation_p.L627M	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	616	6-phosphogluconolactonase.					endoplasmic reticulum lumen	6-phosphogluconolactonase activity|glucose 1-dehydrogenase|glucose-6-phosphate dehydrogenase activity|NADP binding			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)	NADH(DB00157)	CCACACGCACCTGTGGCTGGT	0.682		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													18	20	19			NA	NA	1		NA											NA				9324398		2187	4269	6456	SO:0001583	missense			AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	9563	9563	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	glucose dehyrogenase	GDH	NA	10349511	Standard	NM_004285	NM_001282587	NA	Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.1846C>A	1.37:g.9324398C>A	ENSP00000366620:p.Leu616Met	NA	Q4TT33|Q66I35|Q68DT3	37	CCDS101.1	.	.	.	.	.	.	.	.	.	.	C	16.77	3.213707	0.58452	.	.	ENSG00000049239	ENST00000377403	T	0.49139	0.79	5.4	5.4	0.78164	Glucosamine/galactosamine-6-phosphate isomerase (1);6-phosphogluconolactonase, DevB-type (1);	0.230625	0.37715	N	0.001970	T	0.66703	0.2816	M	0.88570	2.965	0.39055	D	0.960407	D	0.54397	0.966	P	0.58331	0.837	T	0.74262	-0.3722	10	0.72032	D	0.01	-23.0015	8.9799	0.35959	0.0:0.7713:0.1498:0.0789	.	616	O95479	G6PE_HUMAN	M	616	ENSP00000366620:L616M	ENSP00000366620:L616M	L	+	1	2	H6PD	9246985	0.995000	0.38212	1.000000	0.80357	0.975000	0.68041	0.536000	0.23129	2.536000	0.85505	0.561000	0.74099	CTG	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000004928.2		+	ENST00000377403.2	Missense_Mutation	SNP	1 : 9324398 - 9324398 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	196	9
IGSF9	57549	broad.mit.edu	37	1	159900160	159900160	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:159900160C>T	ENST00000368094.1	-	15	2080	c.1883G>A	c.(1882-1884)cGg>cAg	p.R628Q	IGSF9_ENST00000493195.1_5'UTR|IGSF9_ENST00000361509.3_Missense_Mutation_p.R612Q	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	628	Fibronectin type-III 2.					cell junction|integral to membrane|synapse		p.R612L(1)		central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CACCAGACCCCGCGGAGGGGA	0.652		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1	Substitution - Missense(1)	lung(1)											55	63	60			NA	NA	1		NA											NA				159900160		2202	4298	6500	SO:0001583	missense			AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552	57549	57549		Immunoglobulin superfamily / I-set domain containing, Immunoglobulin superfamily / Immunoglobulin-like domain containing, Fibronectin type III domain containing	18132	protein-coding gene	gene with protein product		609738			NA	11991715	Standard	NM_020789	NM_020789	NA	Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1883G>A	1.37:g.159900160C>T	ENSP00000357073:p.Arg628Gln	NA		37	CCDS44254.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.988769	0.53934	.	.	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.53640	0.61;0.61	5.17	5.17	0.71159	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.37012	N	0.002287	T	0.27489	0.0675	L	0.50333	1.59	0.42485	D	0.992879	P	0.41232	0.743	B	0.33750	0.169	T	0.10941	-1.0608	9	.	.	.	-8.1725	16.1513	0.81624	0.0:1.0:0.0:0.0	.	628	Q9P2J2	TUTLA_HUMAN	Q	612;628	ENSP00000355049:R612Q;ENSP00000357073:R628Q	.	R	-	2	0	IGSF9	158166784	0.010000	0.17322	0.694000	0.30210	0.512000	0.34134	1.424000	0.34848	2.396000	0.81511	0.455000	0.32223	CGG	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000059115.1		-	ENST00000368094.1	Missense_Mutation	SNP	1 : 159900160 - 159900160 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	728	152
KIAA1199	0	broad.mit.edu	37	15	81201475	81201475	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:81201475C>T	ENST00000394685.3	+	14	2044	c.1625C>T	c.(1624-1626)aCg>aTg	p.T542M	KIAA1199_ENST00000220244.3_Missense_Mutation_p.T542M|KIAA1199_ENST00000356249.5_Missense_Mutation_p.T542M|RP11-351M8.2_ENST00000560873.1_RNA|RP11-351M8.1_ENST00000560560.1_Intron			Q8WUJ3	K1199_HUMAN		542										breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						TTGGAGGGCACGGAGCTGAAG	0.552		NA											T	0	0	NA	NA	2184	NA	1	,	,	NA	3e-04	NA	NA	NA	0	0.05	EXOME	NA	NA	6e-04	SNP								NA				0													121	89	100			NA	NA	15		NA											NA				81201475		2203	4300	6503	SO:0001583	missense											NA	NA			NA							NA					NA						ENST00000394685.3:c.1625C>T	15.37:g.81201475C>T	ENSP00000378177:p.Thr542Met	NA	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	37	CCDS10315.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	10.26	1.302383	0.23736	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	T;T;T	0.80123	-1.34;-1.34;-1.34	5.09	5.09	0.68999	Pectin lyase fold/virulence factor (1);	0.291065	0.31177	N	0.008117	T	0.60945	0.2308	N	0.03608	-0.345	0.20307	N	0.999913	B	0.02656	0.0	B	0.01281	0.0	T	0.54043	-0.8352	10	0.54805	T	0.06	-9.3098	10.8753	0.46906	0.0:0.0747:0.0:0.9253	.	542	Q8WUJ3	K1199_HUMAN	M	542	ENSP00000220244:T542M;ENSP00000378177:T542M;ENSP00000348583:T542M	ENSP00000220244:T542M	T	+	2	0	KIAA1199	78988530	1.000000	0.71417	0.995000	0.50966	0.215000	0.24574	5.679000	0.68160	0.787000	0.33731	-0.516000	0.04426	ACG	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000291389.1		+	ENST00000394685.3	Missense_Mutation	SNP	15 : 81201475 - 81201475 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	374	21
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr12:25398284C>A	ENST00000311936.3	-	2	226	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V|KRAS_ENST00000256078.4_Missense_Mutation_p.G12V	NM_004985.3	NP_004976.2	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation).|G -> C (in lung carcinoma; somatic mutation).|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation).|G -> R (in lung cancer and bladder cancer; somatic mutation).|G -> S (in lung carcinoma and GASC; somatic mutation).|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation).		activation of MAPKK activity|axon guidance|blood coagulation|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|Ras protein signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)											91	81	85			NA	NA	12		NA											NA				25398284		2203	4300	6503	SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703	3845	3845			6407	protein-coding gene	gene with protein product		190070	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog, v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	KRAS2	NA		Standard	NM_033360	NM_004985	NA	Approved	KRAS1	uc001rgp.1	P01116		ENST00000311936.3:c.35G>T	12.37:g.25398284C>A	ENSP00000308495:p.Gly12Val	NA	A8K8Z5|B0LPF9|P01118|Q96D10	37	CCDS8702.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	KRAS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000412230.1		-	ENST00000311936.3	Missense_Mutation	SNP	12 : 25398284 - 25398284 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	107	15
LCT	3938	broad.mit.edu	37	2	136564940	136564940	+	Nonsense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:136564940G>A	ENST00000264162.2	-	9	3941	c.3931C>T	c.(3931-3933)Cga>Tga	p.R1311*		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1311	4 X approximate repeats.				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity			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)		ACATACCCTCGAAGGTCTATA	0.522		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													103	97	99			NA	NA	2		NA											NA				136564940		2203	4300	6503	SO:0001587	stop_gained			X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3938	3938	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202			NA		Standard	NM_002299	NM_002299	NA	Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.3931C>T	2.37:g.136564940G>A	ENSP00000264162:p.Arg1311*	NA	Q4ZG58	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	G	38	6.963892	0.97967	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	.	.	.	5.87	4.98	0.66077	.	0.165435	0.53938	D	0.000056	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.877	13.1749	0.59621	0.0:0.0:0.5643:0.4357	.	.	.	.	X	1311;743	.	ENSP00000264162:R1311X	R	-	1	2	LCT	136281410	0.998000	0.40836	1.000000	0.80357	0.748000	0.42578	2.030000	0.41108	1.446000	0.47643	0.655000	0.94253	CGA	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000254657.1		-	ENST00000264162.2	Nonsense_Mutation	SNP	2 : 136564940 - 136564940 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	558	39
MUC16	94025	broad.mit.edu	37	19	9071237	9071237	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr19:9071237C>T	ENST00000397910.4	-	3	16412	c.16209G>A	c.(16207-16209)ccG>ccA	p.P5403P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5405	Thr-rich.				cell adhesion	extracellular space|extrinsic to membrane|integral to membrane|plasma membrane	protein binding	p.P5403P(2)|p.P1036P(1)		NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						TGTAAGTGGCCGGTCTCTCAT	0.502		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				3	Substitution - coding silent(3)	lung(3)						C		1,4181		0,1,2090	407	384	392		16209	-4.4	0	19		392	1,8459		0,1,4229	no	coding-synonymous	MUC16	NM_024690.2		0,2,6319	TT,TC,CC	NA	0.0118,0.0239,0.0158		5403/14508	9071237	2,12640	2091	4230	6321	SO:0001819	synonymous_variant			AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143	94025	94025		Mucins	15582	protein-coding gene	gene with protein product		606154			NA	11369781	Standard	NM_024690	XM_006722941	NA	Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.16209G>A	19.37:g.9071237C>T		NA	Q6ZQW5|Q96RK2	37	CCDS54212.1																																																																																			MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000402806.1		-	ENST00000397910.4	Silent	SNP	19 : 9071237 - 9071237 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	1935	102
MYOZ1	58529	broad.mit.edu	37	10	75391860	75391860	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:75391860G>T	ENST00000359322.4	-	6	1092	c.728C>A	c.(727-729)cCc>cAc	p.P243H		NM_021245.3	NP_067068.1	Q9NP98	MYOZ1_HUMAN	myozenin 1	243					myofibril assembly	nucleus|pseudopodium	FATZ binding			central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					GTCAAACTTGGGCATCTGGAA	0.493		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													96	91	92			NA	NA	10		NA											NA				75391860		2203	4300	6503	SO:0001583	missense			AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791	58529	58529			13752	protein-coding gene	gene with protein product	calsarcin-2	605603	myozenin	MYOZ	NA	11171996, 10984498	Standard		NM_021245	NA	Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.728C>A	10.37:g.75391860G>T	ENSP00000352272:p.Pro243His	NA	Q9H1I7	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170256	0.78452	.	.	ENSG00000177791	ENST00000359322	T	0.70631	-0.5	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.86104	0.5853	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87452	0.2402	10	0.87932	D	0	-11.7099	19.6772	0.95941	0.0:0.0:1.0:0.0	.	243	Q9NP98	MYOZ1_HUMAN	H	243	ENSP00000352272:P243H	ENSP00000352272:P243H	P	-	2	0	MYOZ1	75061866	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.558000	0.82253	2.656000	0.90262	0.655000	0.94253	CCC	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048654.1		-	ENST00000359322.4	Missense_Mutation	SNP	10 : 75391860 - 75391860 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	340	13
MYOZ1	58529	broad.mit.edu	37	10	75391861	75391861	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:75391861G>T	ENST00000359322.4	-	6	1091	c.727C>A	c.(727-729)Ccc>Acc	p.P243T		NM_021245.3	NP_067068.1	Q9NP98	MYOZ1_HUMAN	myozenin 1	243					myofibril assembly	nucleus|pseudopodium	FATZ binding			central_nervous_system(1)|large_intestine(5)|lung(2)|ovary(2)|skin(2)	12	Prostate(51;0.0112)					TCAAACTTGGGCATCTGGAAG	0.488		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													96	91	93			NA	NA	10		NA											NA				75391861		2203	4300	6503	SO:0001583	missense			AF240633	CCDS7330.1	10q22.1	2008-07-03	2002-01-10	2002-01-11	ENSG00000177791	ENSG00000177791	58529	58529			13752	protein-coding gene	gene with protein product	calsarcin-2	605603	myozenin	MYOZ	NA	11171996, 10984498	Standard		NM_021245	NA	Approved	FATZ, CS-2	uc001jur.4	Q9NP98	OTTHUMG00000018466	ENST00000359322.4:c.727C>A	10.37:g.75391861G>T	ENSP00000352272:p.Pro243Thr	NA	Q9H1I7	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.136416	0.77662	.	.	ENSG00000177791	ENST00000359322	T	0.70164	-0.46	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.84065	0.5390	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.85787	0.1365	10	0.87932	D	0	-11.7099	19.6772	0.95941	0.0:0.0:1.0:0.0	.	243	Q9NP98	MYOZ1_HUMAN	T	243	ENSP00000352272:P243T	ENSP00000352272:P243T	P	-	1	0	MYOZ1	75061867	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.563000	0.82314	2.656000	0.90262	0.655000	0.94253	CCC	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048654.1		-	ENST00000359322.4	Missense_Mutation	SNP	10 : 75391861 - 75391861 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	335	13
NCAM2	4685	broad.mit.edu	37	21	22656721	22656721	+	Splice_Site	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr21:22656721G>A	ENST00000400546.1	+	3	586		c.e3+1		NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000535285.1_Splice_Site|NCAM2_ENST00000486367.1_Splice_Site	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	NA					neuron cell-cell adhesion	integral to membrane|plasma membrane		p.?(1)		breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GAAATTTACCGTAAGTAATGT	0.294		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1	Unknown(1)	ovary(1)											41	39	40			NA	NA	21		NA											NA				22656721		1821	4076	5897	SO:0001630	splice_region_variant				CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654	4685	4685		Immunoglobulin superfamily / I-set domain containing, Fibronectin type III domain containing	7657	protein-coding gene	gene with protein product		602040			NA	9226371	Standard	NM_004540	NM_004540	NA	Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.337+1G>A	21.37:g.22656721G>A		NA	A8MQ06|Q7Z7F2	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	19.70	3.876114	0.72180	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.134	0.89612	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NCAM2	21578592	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.804000	0.91921	2.632000	0.89209	0.591000	0.81541	.	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000170915.1	Intron	+	ENST00000400546.1	Splice_Site	SNP	21 : 22656721 - 22656721 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	142	7
NF1	4763	broad.mit.edu	37	17	29576089	29576089	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:29576089C>T	ENST00000358273.4	+	30	4445	c.4062C>T	c.(4060-4062)tcC>tcT	p.S1354S	NF1_ENST00000356175.3_Silent_p.S1354S	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1354	Poly-Ser.|Ras-GAP.				actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		TCAGTTCCTCCTCAGAATTCC	0.398		NA	D, Mis, N, F, S, O		neurofibroma, glioma	neurofibroma, glioma			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	12	Whole gene deletion(8)|Unknown(4)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)											167	151	157			NA	NA	17		NA											NA				29576089		2203	4300	6503	SO:0001819	synonymous_variant	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712	4763	4763			7765	protein-coding gene	gene with protein product	neurofibromatosis, von Recklinghausen disease, Watson disease	613113			NA	1715669	Standard	NM_000267	NM_000267	NA	Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4062C>T	17.37:g.29576089C>T		NA	O00662|Q14284|Q14930|Q9UMK3	37	CCDS42292.1																																																																																			NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000256351.2		+	ENST00000358273.4	Silent	SNP	17 : 29576089 - 29576089 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	577	18
NPAS3	64067	broad.mit.edu	37	14	34270009	34270009	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr14:34270009G>A	ENST00000346562.2	+	11	2474	c.2400G>A	c.(2398-2400)gcG>gcA	p.A800A	NPAS3_ENST00000548645.1_Silent_p.A802A|NPAS3_ENST00000357798.5_Silent_p.A819A|NPAS3_ENST00000551492.1_Silent_p.A837A|NPAS3_ENST00000356141.4_Silent_p.A832A	NM_001164749.1|NM_001165893.1|NM_022123.2|NM_173159.2	NP_001158221.1|NP_001159365.1|NP_071406.1|NP_775182.1	Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	832					regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|signal transducer activity			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		TCCGCTACGCGCCCGCCGAGG	0.687		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													27	21	23			NA	NA	14		NA											NA				34270009		2192	4298	6490	SO:0001819	synonymous_variant			AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322	64067	64067		Basic helix-loop-helix proteins	19311	protein-coding gene	gene with protein product		609430			NA		Standard		NM_022123	NA	Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000346562.2:c.2400G>A	14.37:g.34270009G>A		NA	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	37	CCDS9645.1																																																																																			NPAS3-001	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000276644.1		+	ENST00000346562.2	Silent	SNP	14 : 34270009 - 34270009 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	59	8
OR10Q1	219960	broad.mit.edu	37	11	57995470	57995470	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr11:57995470A>G	ENST00000316770.2	-	1	920	c.878T>C	c.(877-879)tTg>tCg	p.L293S		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	293					sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				GCTGTAAAGCAAAGGGTTGAG	0.547		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													144	135	138			NA	NA	11		NA											NA				57995470		2201	4295	6496	SO:0001583	missense			AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475	219960	219960		GPCR / Class A : Olfactory receptors	15134	protein-coding gene	gene with protein product					NA		Standard	NM_001004471	NM_001004471	NA	Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.878T>C	11.37:g.57995470A>G	ENSP00000314324:p.Leu293Ser	NA	Q6IFG4	37	CCDS31547.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.778355	0.49786	.	.	ENSG00000180475	ENST00000316770	T	0.46451	0.87	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34362	N	0.004034	T	0.62913	0.2467	M	0.79926	2.475	0.32070	N	0.594593	D	0.65815	0.995	P	0.61800	0.894	T	0.74481	-0.3651	10	0.87932	D	0	.	13.8047	0.63223	1.0:0.0:0.0:0.0	.	293	Q8NGQ4	O10Q1_HUMAN	S	293	ENSP00000314324:L293S	ENSP00000314324:L293S	L	-	2	0	OR10Q1	57752046	0.712000	0.27916	0.775000	0.31657	0.195000	0.23768	5.574000	0.67424	2.132000	0.65825	0.528000	0.53228	TTG	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000394706.1		-	ENST00000316770.2	Missense_Mutation	SNP	11 : 57995470 - 57995470 G PAAD-TCGA-IB-7889-Tumor-SM-2NW89	799	54
PAPPA2	60676	broad.mit.edu	37	1	176709307	176709307	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:176709307G>A	ENST00000367662.3	+	14	5290	c.4126G>A	c.(4126-4128)Gag>Aag	p.E1376K		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1376					cell differentiation|proteolysis|regulation of cell growth	extracellular region|intracellular|membrane	metalloendopeptidase activity|zinc ion binding			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CTCAGAGGACGAGGGGCAGAA	0.483		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													83	80	81			NA	NA	1		NA											NA				176709307		1979	4162	6141	SO:0001583	missense			BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183	60676	60676			14615	protein-coding gene	gene with protein product			placenta-specific 3	PLAC3	NA	11018262, 11264294	Standard		NM_021936	NA	Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.4126G>A	1.37:g.176709307G>A	ENSP00000356634:p.Glu1376Lys	NA	Q96PH7|Q96PH8|Q9H4C9	37	CCDS41438.1	.	.	.	.	.	.	.	.	.	.	G	9.393	1.075892	0.20227	.	.	ENSG00000116183	ENST00000367662	T	0.01745	4.66	5.3	-2.21	0.06973	.	0.849038	0.10709	N	0.643103	T	0.01976	0.0062	L	0.49256	1.55	0.24431	N	0.994576	B	0.18461	0.028	B	0.13407	0.009	T	0.39941	-0.9589	10	0.54805	T	0.06	-0.3589	4.9535	0.14027	0.3507:0.2614:0.3879:0.0	.	1376	Q9BXP8	PAPP2_HUMAN	K	1376	ENSP00000356634:E1376K	ENSP00000356634:E1376K	E	+	1	0	PAPPA2	174975930	0.973000	0.33851	0.000000	0.03702	0.021000	0.10359	1.361000	0.34136	-0.798000	0.04444	-0.345000	0.07892	GAG	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000084763.1		+	ENST00000367662.3	Missense_Mutation	SNP	1 : 176709307 - 176709307 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	336	31
PKN3	29941	broad.mit.edu	37	9	131477728	131477728	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr9:131477728C>T	ENST00000291906.4	+	15	2190	c.1797C>T	c.(1795-1797)gaC>gaT	p.D599D	PKN3_ENST00000485301.1_Intron	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	599	Protein kinase.				signal transduction	Golgi apparatus|nucleus|perinuclear region of cytoplasm	ATP binding|protein binding|protein kinase C activity	p.D599D(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						TCAGCCGGGACGAGATAGAGA	0.612		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				1	Substitution - coding silent(1)	large_intestine(1)											45	45	45			NA	NA	9		NA											NA				131477728		2203	4300	6503	SO:0001819	synonymous_variant			AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447	29941	29941			17999	protein-coding gene	gene with protein product		610714			NA	10441506	Standard	NM_013355	NM_013355	NA	Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.1797C>T	9.37:g.131477728C>T		NA	Q9UM03	37	CCDS6908.1																																																																																			PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000054487.1		+	ENST00000291906.4	Silent	SNP	9 : 131477728 - 131477728 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	304	15
PLA2G4E	123745	broad.mit.edu	37	15	42276761	42276761	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:42276761G>A	ENST00000399518.3	-	19	2745	c.2259C>T	c.(2257-2259)taC>taT	p.Y753Y	PLA2G4E_ENST00000413860.2_Silent_p.Y724Y|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	741	PLA2c.			C -> Y (in Ref. 1; BAC87034).	phospholipid catabolic process	cytosol|lysosomal membrane	metal ion binding|phospholipase A2 activity			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		CTGGCAGCTCGTATTTGGGGA	0.522		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								G		1,3853		0,1,1926	91	88	89		2259	-6.5	0	15		89	0,8308		0,0,4154	no	coding-synonymous	PLA2G4E	NM_001206670.1		0,1,6080	AA,AG,GG	NA	0.0,0.0259,0.0082		753/869	42276761	1,12161	1927	4154	6081	SO:0001819	synonymous_variant				CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	123745	123745	3.1.1.4		24791	protein-coding gene	gene with protein product					NA	15866882	Standard	NM_198442	NM_001206670	NA	Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.2259C>T	15.37:g.42276761G>A		NA	Q6ZSC0	37	CCDS55962.1																																																																																			PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000252738.2		-	ENST00000399518.3	Silent	SNP	15 : 42276761 - 42276761 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	241	11
PRKAR1B	5575	broad.mit.edu	37	7	720280	720280	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:720280C>T	ENST00000406797.1	-	3	435	c.261G>A	c.(259-261)ccG>ccA	p.P87P	PRKAR1B_ENST00000360274.4_Silent_p.P87P|PRKAR1B_ENST00000403562.1_Silent_p.P87P|PRKAR1B_ENST00000537384.1_Silent_p.P87P|PRKAR1B_ENST00000544935.1_Silent_p.P87P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	87	Dimerization and phosphorylation.				activation of phospholipase C activity|activation of protein kinase A activity|blood coagulation|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|protein phosphorylation|regulation of insulin secretion|transmembrane transport|water transport	cAMP-dependent protein kinase complex|cytosol	cAMP binding|cAMP-dependent protein kinase regulator activity			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCACAGGGTTCGGGGGGGTGG	0.622		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													54	53	54			NA	NA	7		NA											NA				720280		2203	4300	6503	SO:0001819	synonymous_variant			M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	5575	5575	2.7.11.1		9390	protein-coding gene	gene with protein product		176911			NA	1358799, 3479018	Standard		NM_002735	NA	Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.261G>A	7.37:g.720280C>T		NA	Q8N422	37	CCDS34579.1																																																																																			PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000322525.1		-	ENST00000406797.1	Silent	SNP	7 : 720280 - 720280 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	555	59
PRKG1	5592	broad.mit.edu	37	10	53564378	53564378	+	Missense_Mutation	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr10:53564378G>A	ENST00000373980.4	+	4	1043	c.626G>A	c.(625-627)cGa>cAa	p.R209Q	PRKG1_ENST00000401604.2_Missense_Mutation_p.R194Q|PRKG1_ENST00000373985.1_Missense_Mutation_p.R182Q	NM_006258.3	NP_006249.1	Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	194					actin cytoskeleton organization|platelet activation|signal transduction	cytosol	ATP binding|cGMP binding|cGMP-dependent protein kinase activity			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		GCCATTGATCGACAATGTTTT	0.338		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													116	108	111			NA	NA	10		NA											NA				53564378		2203	4300	6503	SO:0001583	missense				CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	5592	5592	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B	NA	2792381, 1544322	Standard		NM_001098512	NA	Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000373980.4:c.626G>A	10.37:g.53564378G>A	ENSP00000363092:p.Arg209Gln	NA	E2PU10|P14619|Q5JSJ6|Q6P5T7	37	CCDS7244.1	.	.	.	.	.	.	.	.	.	.	G	34	5.387931	0.95988	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000373976	D;D;D;D	0.97378	-4.36;-4.36;-2.08;-2.08	5.42	5.42	0.78866	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.000000	0.64402	D	0.000003	D	0.98516	0.9505	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.99327	1.0908	10	0.72032	D	0.01	-5.7115	17.0633	0.86553	0.0:0.0:1.0:0.0	.	209;194	Q13976-2;Q13976	.;KGP1_HUMAN	Q	194;182;209;67	ENSP00000384200:R194Q;ENSP00000363097:R182Q;ENSP00000363092:R209Q;ENSP00000363087:R67Q	ENSP00000363087:R67Q	R	+	2	0	PRKG1	53234384	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	9.386000	0.97228	2.698000	0.92095	0.591000	0.81541	CGA	PRKG1-002	KNOWN	basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000048103.1		+	ENST00000373980.4	Missense_Mutation	SNP	10 : 53564378 - 53564378 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	354	35
QTRTD1	79691	broad.mit.edu	37	3	113804663	113804663	+	Missense_Mutation	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr3:113804663A>G	ENST00000493014.1	+	6	910	c.842A>G	c.(841-843)tAc>tGc	p.Y281C	QTRTD1_ENST00000479882.1_Missense_Mutation_p.Y264C|QTRTD1_ENST00000281273.4_Missense_Mutation_p.Y387C|QTRTD1_ENST00000485050.1_Missense_Mutation_p.Y399C	NM_001256836.1	NP_001243765.1	Q9H974	QTRD1_HUMAN	queuine tRNA-ribosyltransferase domain containing 1	387					queuosine biosynthetic process	mitochondrion	metal ion binding|queuine tRNA-ribosyltransferase activity			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|skin(2)	10						TTTGAACACTACTTTGGGTTT	0.463		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													185	155	165			NA	NA	3		NA											NA				113804663		2203	4300	6503	SO:0001583	missense			AK023022	CCDS33828.1, CCDS58846.1, CCDS58845.1, CCDS58844.1	3q13.31	2010-11-16			ENSG00000151576	ENSG00000151576	79691	79691			25771	protein-coding gene	gene with protein product					NA	12477932	Standard	NM_024638	NM_024638	NA	Approved	FLJ12960	uc003eaz.4	Q9H974	OTTHUMG00000159336	ENST00000493014.1:c.842A>G	3.37:g.113804663A>G	ENSP00000419169:p.Tyr281Cys	NA	A6NGE9|Q6IA59	37	CCDS58845.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.524255	0.85600	.	.	ENSG00000151576	ENST00000485050;ENST00000281273;ENST00000479882;ENST00000493014	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.85004	0.5598	M	0.89785	3.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.87953	0.2725	9	0.87932	D	0	-16.4311	15.2149	0.73258	1.0:0.0:0.0:0.0	.	281;387	B7Z472;Q9H974	.;QTRD1_HUMAN	C	399;387;264;281	.	ENSP00000281273:Y387C	Y	+	2	0	QTRTD1	115287353	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.273000	0.89887	2.333000	0.79357	0.533000	0.62120	TAC	QTRTD1-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000354711.1		+	ENST00000493014.1	Missense_Mutation	SNP	3 : 113804663 - 113804663 G PAAD-TCGA-IB-7889-Tumor-SM-2NW89	667	31
RGS22	26166	broad.mit.edu	37	8	101076206	101076206	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:101076206A>T	ENST00000523287.1	-	6	836	c.247T>A	c.(247-249)Ttg>Atg	p.L83M	RGS22_ENST00000360863.6_Missense_Mutation_p.L264M|RGS22_ENST00000523437.1_Missense_Mutation_p.L252M			Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	264					negative regulation of signal transduction	cytoplasm|plasma membrane	GTPase activator activity|signal transducer activity		RGS22/SYCP1(2)	breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(33)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	68			Epithelial(11;6.71e-08)|all cancers(13;4.19e-06)|OV - Ovarian serous cystadenocarcinoma(57;0.000469)|STAD - Stomach adenocarcinoma(118;0.169)			TCAGAAATCAATTTGTTGGTT	0.343		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													123	128	126			NA	NA	8		NA											NA				101076206		1809	4071	5880	SO:0001583	missense			AY009106	CCDS43758.1, CCDS69521.1, CCDS75775.1	8q22.2	2014-01-21	2007-08-14		ENSG00000132554	ENSG00000132554	26166	26166		Regulators of G-protein signaling	24499	protein-coding gene	gene with protein product		615650	regulator of G-protein signalling 22		NA		Standard	NM_015668	XM_005250856	NA	Approved	DKFZP434I092, PRTD-NY2, CT145	uc003yjb.1	Q8NE09	OTTHUMG00000164802	ENST00000523287.1:c.247T>A	8.37:g.101076206A>T	ENSP00000429382:p.Leu83Met	NA	Q569L2|Q86Y71|Q9UFN6	37		.	.	.	.	.	.	.	.	.	.	A	14.54	2.564891	0.45694	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437	T;T;T	0.32988	1.45;1.44;1.43	5.45	0.102	0.14522	.	2.260420	0.01579	N	0.020975	T	0.30386	0.0763	L	0.60455	1.87	0.09310	N	1	P;P;B	0.37864	0.61;0.61;0.065	B;B;B	0.39185	0.293;0.293;0.037	T	0.09509	-1.0671	10	0.39692	T	0.17	.	1.6829	0.02835	0.4861:0.1481:0.0809:0.2849	.	252;264;83	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	M	264;252;83;252	ENSP00000354109:L264M;ENSP00000429382:L83M;ENSP00000428212:L252M	ENSP00000354109:L264M	L	-	1	2	RGS22	101145382	0.000000	0.05858	0.000000	0.03702	0.337000	0.28794	-0.768000	0.04715	-0.138000	0.11434	0.528000	0.53228	TTG	RGS22-004	PUTATIVE	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000380366.1		-	ENST00000523287.1	Missense_Mutation	SNP	8 : 101076206 - 101076206 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	1111	62
RIT1	6016	broad.mit.edu	37	1	155880296	155880296	+	Splice_Site	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr1:155880296G>T	ENST00000368323.3	-	3	312	c.108C>A	c.(106-108)gcC>gcA	p.A36A	RIT1_ENST00000368322.3_Splice_Site_p.A53A|RIT1_ENST00000539040.1_5'UTR	NM_006912.5	NP_008843.1	Q92963	RIT1_HUMAN	Ras-like without CAAX 1	36					nerve growth factor receptor signaling pathway|small GTPase mediated signal transduction	intracellular|plasma membrane	calmodulin binding|GTP binding|GTPase activity			breast(1)|kidney(1)|large_intestine(3)|lung(12)|skin(1)|urinary_tract(1)	19	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)		OV - Ovarian serous cystadenocarcinoma(3;1.79e-05)			GCATGGTCATGGCTTCAAAAG	0.393		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													127	121	123			NA	NA	1		NA											NA				155880296		2203	4300	6503	SO:0001630	splice_region_variant			AF084462	CCDS1123.1, CCDS58037.1, CCDS58036.1	1q21.2	2014-05-09	2002-09-11	2002-09-13	ENSG00000143622	ENSG00000143622	6016	6016			10023	protein-coding gene	gene with protein product	Ric-like, expressed in many tissues, GTP-binding protein Roc1	609591	Ric (Drosophila)-like, expressed in many tissues	RIT	NA	8824319, 8918462	Standard	NM_006912	NM_006912	NA	Approved	RIBB, ROC1, MGC125864, MGC125865	uc031pqc.1	Q92963	OTTHUMG00000014104	ENST00000368323.3:c.107-1C>A	1.37:g.155880296G>T		NA	O00646|O00720	37	CCDS1123.1																																																																																			RIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000039593.1	Silent	-	ENST00000368323.3	Splice_Site	SNP	1 : 155880296 - 155880296 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	384	58
RNF144A	9781	broad.mit.edu	37	2	7160800	7160800	+	Silent	SNP	C	C	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr2:7160800C>G	ENST00000320892.6	+	6	940	c.498C>G	c.(496-498)ccC>ccG	p.P166P	RNF144A_ENST00000467276.1_3'UTR	NM_014746.3	NP_055561.2	P50876	R144A_HUMAN	ring finger protein 144A	166						Golgi apparatus|integral to membrane	ligase activity|zinc ion binding			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|prostate(1)	25	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)	all_cancers(51;0.226)		OV - Ovarian serous cystadenocarcinoma(76;0.195)		CCTTCCTCCCCGGGGAGACCA	0.587		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													66	70	68			NA	NA	2		NA											NA				7160800		2203	4300	6503	SO:0001819	synonymous_variant			D79983	CCDS1657.1	2p25.2	2008-02-05	2007-08-20	2007-08-20	ENSG00000151692	ENSG00000151692	9781	9781		RING-type (C3HC4) zinc fingers	20457	protein-coding gene	gene with protein product			ring finger protein 144	RNF144	NA	8724849, 10431818	Standard	NM_014746	NM_014746	NA	Approved	UBCE7IP4, KIAA0161	uc002qys.3	P50876	OTTHUMG00000090353	ENST00000320892.6:c.498C>G	2.37:g.7160800C>G		NA	D6W4Y6|Q585H5	37	CCDS1657.1	.	.	.	.	.	.	.	.	.	.	C	7.556	0.663657	0.14710	.	.	ENSG00000151692	ENST00000432850	T	0.30182	1.54	5.42	-5.68	0.02436	.	0.000000	0.85682	D	0.000000	T	0.16938	0.0407	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17868	-1.0355	7	0.20046	T	0.44	.	2.4736	0.04570	0.3811:0.1371:0.0718:0.41	.	.	.	.	R	162	ENSP00000411616:P162R	ENSP00000411616:P162R	P	+	2	0	RNF144A	7078251	0.025000	0.19082	0.602000	0.28890	0.849000	0.48306	-0.908000	0.04063	-1.362000	0.02166	-0.254000	0.11334	CCG	RNF144A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000206725.2		+	ENST00000320892.6	Silent	SNP	2 : 7160800 - 7160800 G PAAD-TCGA-IB-7889-Tumor-SM-2NW89	638	72
SECISBP2L	9728	broad.mit.edu	37	15	49288724	49288724	+	Missense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:49288724C>A	ENST00000559471.1	-	17	2726	c.2463G>T	c.(2461-2463)atG>atT	p.M821I	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.M776I	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	821										breast(1)|endometrium(5)|kidney(8)|large_intestine(12)|lung(11)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	46						TTGCTGCAACCATATCTTTAT	0.408		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													241	226	231			NA	NA	15		NA											NA				49288724		2197	4295	6492	SO:0001583	missense			BC033001	CCDS32234.1, CCDS53942.1	15q21.1	2014-02-12				ENSG00000138593	9728	9728			28997	protein-coding gene	gene with protein product		615756			NA		Standard	NM_014701	NM_001193489	NA	Approved	KIAA0256	uc001zxe.2	Q93073		ENST00000559471.1:c.2463G>T	15.37:g.49288724C>A	ENSP00000453854:p.Met821Ile	NA	Q8N767	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.747448	0.89663	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	D	0.91843	-2.92	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.90109	0.6910	L	0.29908	0.895	0.58432	D	0.999997	D;P	0.54207	0.965;0.94	B;P	0.47402	0.344;0.546	D	0.91643	0.5328	10	0.72032	D	0.01	.	18.3573	0.90362	0.0:1.0:0.0:0.0	.	821;776	Q93073;Q93073-2	SBP2L_HUMAN;.	I	776;821	ENSP00000261847:M776I	ENSP00000261847:M776I	M	-	3	0	SECISBP2L	47076016	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.300000	0.78841	2.569000	0.86673	0.650000	0.86243	ATG	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000417277.1		-	ENST00000559471.1	Missense_Mutation	SNP	15 : 49288724 - 49288724 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	1204	56
SLC28A1	9154	broad.mit.edu	37	15	85461805	85461805	+	Silent	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:85461805C>T	ENST00000286749.3	+	9	936	c.846C>T	c.(844-846)caC>caT	p.H282H	SLC28A1_ENST00000394573.1_Silent_p.H282H|SLC28A1_ENST00000538177.1_Silent_p.H282H|SLC28A1_ENST00000537703.1_Silent_p.H204H|SLC28A1_ENST00000537624.1_Silent_p.H282H|SLC28A1_ENST00000537216.1_Silent_p.H282H			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	282					nucleobase, nucleoside and nucleotide metabolic process	integral to plasma membrane|membrane fraction	nucleoside binding			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)			TTCTCTACCACGTGGGCCTCA	0.562		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													252	224	233			NA	NA	15		NA											NA				85461805		2203	4299	6502	SO:0001819	synonymous_variant			U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222	9154	9154		Solute carriers	11001	protein-coding gene	gene with protein product		606207	solute carrier family 28 (sodium-coupled nucleoside transporter), member 1		NA	9124315	Standard		NM_004213	NA	Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.846C>T	15.37:g.85461805C>T		NA	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	37	CCDS10334.1																																																																																			SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000308998.2		+	ENST00000286749.3	Silent	SNP	15 : 85461805 - 85461805 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	965	46
SLC52A1	55065	broad.mit.edu	37	17	4937373	4937373	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:4937373G>T	ENST00000512825.2	-	3	1822	c.411C>A	c.(409-411)agC>agA	p.S137R	SLC52A1_ENST00000254853.5_Missense_Mutation_p.S137R|SLC52A1_ENST00000424747.1_Missense_Mutation_p.S137R			Q9NWF4	RFT_HUMAN	solute carrier family 52 (riboflavin transporter), member 1	137						integral to plasma membrane	receptor activity|riboflavin transporter activity				NA						GTGGCAGGTGGCTCAGGAAGG	0.592		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													148	145	146			NA	NA	17		NA											NA				4937373		2203	4300	6503	SO:0001583	missense			AY070775	CCDS11066.1	17p13.3	2013-07-17	2013-07-17	2012-02-29	ENSG00000132517	ENSG00000132517	55065	55065		Solute carriers	30225	protein-coding gene	gene with protein product	riboflavin transporter 1	607883	G protein-coupled receptor 172B	GPR172B	NA	12740431, 18632736	Standard	NM_017986	NM_001104577	NA	Approved	FLJ10060, GPCR42, PAR2, hRFT1, RFVT1	uc002gao.4	Q9NWF4	OTTHUMG00000099448	ENST00000512825.2:c.411C>A	17.37:g.4937373G>T	ENSP00000443026:p.Ser137Arg	NA	B5MEV1|B5MEV2|Q6P9E0|Q86UT0	37		.	.	.	.	.	.	.	.	.	.	G	10.67	1.416613	0.25552	.	.	ENSG00000132517	ENST00000254853;ENST00000512825;ENST00000424747	D;D;D	0.89746	-2.56;-2.56;-2.56	1.65	0.59	0.17458	.	0.391568	0.29940	N	0.010814	T	0.82033	0.4949	L	0.47716	1.5	0.31575	N	0.655809	P;B	0.39665	0.682;0.306	B;B	0.38954	0.286;0.117	T	0.77270	-0.2650	10	0.31617	T	0.26	.	7.0735	0.25191	0.0:0.0:0.7302:0.2698	.	137;137	F5H5Y1;Q9NWF4	.;RFT_HUMAN	R	137	ENSP00000254853:S137R;ENSP00000443026:S137R;ENSP00000399979:S137R	ENSP00000254853:S137R	S	-	3	2	GPR172B	4878097	0.991000	0.36638	0.998000	0.56505	0.964000	0.63967	0.606000	0.24194	0.238000	0.21222	-0.310000	0.09108	AGC	SLC52A1-002	NOVEL	basic|exp_conf	protein_coding	NA	protein_coding	OTTHUMT00000438891.1		-	ENST00000512825.2	Missense_Mutation	SNP	17 : 4937373 - 4937373 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	679	56
SMAD4	4089	broad.mit.edu	37	18	48591918	48591918	+	Missense_Mutation	SNP	C	C	T	rs80338963		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr18:48591918C>T	ENST00000588745.1	+	5	793	c.793C>T	c.(793-795)Cgc>Tgc	p.R265C	SMAD4_ENST00000342988.3_Missense_Mutation_p.R361C|SMAD4_ENST00000398417.2_Missense_Mutation_p.R361C			Q13485	SMAD4_HUMAN	SMAD family member 4	361					BMP signaling pathway|negative regulation of cell growth|negative regulation of protein catabolic process|negative regulation of transcription, DNA-dependent|palate development|positive regulation of epithelial to mesenchymal transition|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of SMAD protein import into nucleus|positive regulation of transforming growth factor beta receptor signaling pathway|regulation of transforming growth factor-beta2 production|response to hypoxia|response to transforming growth factor beta stimulus|SMAD protein complex assembly|SMAD protein signal transduction|transforming growth factor beta receptor signaling pathway	activin responsive factor complex|centrosome|cytosol	I-SMAD binding|protein homodimerization activity|R-SMAD binding|transcription regulatory region DNA binding|transforming growth factor beta receptor, common-partner cytoplasmic mediator activity	p.0?(36)|p.R361C(3)|p.R361S(2)|p.?(2)		NS(2)|biliary_tract(19)|breast(9)|central_nervous_system(2)|endometrium(2)|gastrointestinal_tract_(site_indeterminate)(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(142)|liver(2)|lung(27)|oesophagus(4)|ovary(7)|pancreas(180)|prostate(3)|skin(1)|small_intestine(9)|stomach(5)|testis(2)|thyroid(19)|upper_aerodigestive_tract(10)|urinary_tract(2)|vulva(1)	454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)		Colorectal(16;0.0032)|COAD - Colon adenocarcinoma(17;0.0708)|READ - Rectum adenocarcinoma(32;0.155)		TGGAGGAGATCGCTTTTGTTT	0.413		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				43	Whole gene deletion(36)|Substitution - Missense(5)|Unknown(2)	pancreas(26)|large_intestine(4)|lung(3)|breast(3)|stomach(2)|small_intestine(2)|upper_aerodigestive_tract(1)|biliary_tract(1)|oesophagus(1)	GRCh37	CM040450|CM041789|CM981228	SMAD4	M	rs80338963						179	149	159			NA	NA	18		NA											NA				48591918		2203	4300	6503	SO:0001583	missense			U44378	CCDS11950.1	18q21.1	2014-09-17	2006-11-06	2004-05-26	ENSG00000141646	ENSG00000141646	4089	4089		SMADs	6770	protein-coding gene	gene with protein product		600993	MAD, mothers against decapentaplegic homolog 4 (Drosophila), SMAD, mothers against DPP homolog 4 (Drosophila)	MADH4	NA	8553070, 8774881	Standard	NM_005359	NM_005359	NA	Approved	DPC4	uc010xdp.2	Q13485	OTTHUMG00000132696	ENST00000588745.1:c.793C>T	18.37:g.48591918C>T	ENSP00000464901:p.Arg265Cys	NA	A8K405	37	CCDS11950.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.820743	0.90873	.	.	ENSG00000141646	ENST00000342988;ENST00000544926;ENST00000398417	D;D	0.98164	-4.76;-4.76	5.86	5.86	0.93980	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.000000	0.85682	D	0.000000	D	0.99275	0.9747	M	0.94021	3.485	0.80722	A	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99157	1.0860	9	0.87932	D	0	.	18.9646	0.92691	0.0:1.0:0.0:0.0	.	361	Q13485	SMAD4_HUMAN	C	361	ENSP00000341551:R361C;ENSP00000381452:R361C	ENSP00000341551:R361C	R	+	1	0	SMAD4	46845916	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.718000	0.61930	2.771000	0.95319	0.563000	0.77884	CGC	SMAD4-004	NOVEL	not_organism_supported|basic|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000449729.1		+	ENST00000588745.1	Missense_Mutation	SNP	18 : 48591918 - 48591918 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	333	36
SPAM1	6677	broad.mit.edu	37	7	123599604	123599604	+	Silent	SNP	C	C	T	rs146075363		TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:123599604C>T	ENST00000340011.5	+	5	1468	c.1111C>T	c.(1111-1113)Cta>Tta	p.L371L	SPAM1_ENST00000402183.2_Silent_p.L371L|SPAM1_ENST00000460182.1_Silent_p.L371L|SPAM1_ENST00000439500.1_Silent_p.L371L|SPAM1_ENST00000223028.7_Silent_p.L371L	NM_003117.4	NP_003108.2	P38567	HYALP_HUMAN	sperm adhesion molecule 1 (PH-20 hyaluronidase, zona pellucida binding)	371					binding of sperm to zona pellucida|carbohydrate metabolic process|cell adhesion|fusion of sperm to egg plasma membrane	anchored to membrane|plasma membrane	hyalurononglucosaminidase activity			breast(1)|cervix(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(23)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46					Hyaluronidase(DB00070)	CAACGTCACACTAGCAGCCAA	0.378		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								C	,,,,	1,4405	2.1+/-5.4	0,1,2202	106	97	100		1111,1111,1111,1111,1111	2.3	1	7	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPAM1	NM_001174044.1,NM_001174045.1,NM_001174046.1,NM_003117.4,NM_153189.2	,,,,	0,1,6502	TT,TC,CC	NA	0.0,0.0227,0.0077	,,,,	371/510,371/510,371/510,371/512,371/510	123599604	1,13005	2203	4300	6503	SO:0001819	synonymous_variant			L13781	CCDS5790.1, CCDS5791.1	7q31	2008-05-02			ENSG00000106304	ENSG00000106304	NA	6677			11217	protein-coding gene	gene with protein product		600930			NA	8282124, 8575780	Standard		NM_153189	NA	Approved	HYAL5, PH-20, SPAG15	uc003vle.3	P38567	OTTHUMG00000157284	ENST00000340011.5:c.1111C>T	7.37:g.123599604C>T		NA		37	CCDS5790.1																																																																																			SPAM1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000348310.1		+	ENST00000340011.5	Silent	SNP	7 : 123599604 - 123599604 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	389	42
ST8SIA2	8128	broad.mit.edu	37	15	92981637	92981637	+	Silent	SNP	A	A	G			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr15:92981637A>G	ENST00000268164.3	+	4	582	c.345A>G	c.(343-345)ggA>ggG	p.G115G	ST8SIA2_ENST00000539113.1_Silent_p.G94G	NM_006011.3	NP_006002.1	Q92186	SIA8B_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 2	115					axon guidance|N-glycan processing|oligosaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	integral to Golgi membrane	alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity			endometrium(2)|large_intestine(6)|lung(9)|skin(2)|urinary_tract(1)	20	Lung NSC(78;0.0893)|all_lung(78;0.125)		BRCA - Breast invasive adenocarcinoma(143;0.0355)|OV - Ovarian serous cystadenocarcinoma(32;0.203)			TCCTAAAGGGAACCCTGAAGC	0.473		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0								A		0,4396		0,0,2198	153	166	162		345	4.5	1	15		162	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ST8SIA2	NM_006011.3		0,1,6495	GG,GA,AA	NA	0.0116,0.0,0.0077		115/376	92981637	1,12991	2198	4298	6496	SO:0001819	synonymous_variant			U33551	CCDS10372.1	15q26	2013-03-01	2003-01-14	2005-02-07	ENSG00000140557	ENSG00000140557	8128	8128		Sialyltransferases	10870	protein-coding gene	gene with protein product		602546	sialyltransferase 8 (alpha-2, 8-sialytransferase) B	SIAT8B	NA	7559389	Standard	NM_006011	NM_006011	NA	Approved	STX, ST8SIA-II, HsT19690	uc002bra.3	Q92186	OTTHUMG00000149843	ENST00000268164.3:c.345A>G	15.37:g.92981637A>G		NA	Q4VAZ0|Q92470|Q92746	37	CCDS10372.1																																																																																			ST8SIA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000313526.1		+	ENST00000268164.3	Silent	SNP	15 : 92981637 - 92981637 G PAAD-TCGA-IB-7889-Tumor-SM-2NW89	1150	143
SYNPO2	171024	broad.mit.edu	37	4	119948009	119948009	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr4:119948009C>T	ENST00000307142.4	+	3	681	c.485C>T	c.(484-486)cCg>cTg	p.P162L	SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000429713.2_Missense_Mutation_p.P162L|SYNPO2_ENST00000434046.2_Missense_Mutation_p.P162L	NM_133477.2	NP_597734.2	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	162						nucleus|Z disc	14-3-3 protein binding|actin binding|muscle alpha-actinin binding			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GAAACAGGCCCGAGCTACCAA	0.547		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													35	38	37			NA	NA	4		NA											NA				119948009		2203	4300	6503	SO:0001583	missense			AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403	171024	171024			17732	protein-coding gene	gene with protein product					NA	11673475, 17828378	Standard		NM_133477	NA	Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000307142.4:c.485C>T	4.37:g.119948009C>T	ENSP00000306015:p.Pro162Leu	NA	B2RWP6|B2Y8J9|Q9UK89	37	CCDS34054.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.429248	0.00184	.	.	ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046	T;T;T	0.06768	3.26;3.26;3.26	4.56	-5.91	0.02269	.	0.414976	0.17348	N	0.177482	T	0.01489	0.0048	N	0.00237	-1.79	0.09310	N	0.999996	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.47774	-0.9091	10	0.31617	T	0.26	0.9506	8.3027	0.32023	0.1979:0.5711:0.0:0.231	.	162;162;162;162	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.;.;.;SYNP2_HUMAN	L	162	ENSP00000306015:P162L;ENSP00000395143:P162L;ENSP00000390965:P162L	ENSP00000306015:P162L	P	+	2	0	SYNPO2	120167457	0.001000	0.12720	0.000000	0.03702	0.014000	0.08584	0.077000	0.14738	-0.619000	0.05648	-1.181000	0.01715	CCG	SYNPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000364018.1		+	ENST00000307142.4	Missense_Mutation	SNP	4 : 119948009 - 119948009 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	258	38
TEPP	374739	broad.mit.edu	37	16	58010414	58010414	+	Silent	SNP	G	G	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr16:58010414G>A	ENST00000290871.5	+	1	76	c.39G>A	c.(37-39)ctG>ctA	p.L13L	TEPP_ENST00000441824.2_Silent_p.L13L	NM_199046.2	NP_950247.2	Q6URK8	TEPP_HUMAN	testis, prostate and placenta expressed	13						extracellular region				central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)|urinary_tract(1)	8						TTATTCTGCTGCTGTCCATAA	0.517		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													244	182	203			NA	NA	16		NA											NA				58010414		2198	4300	6498	SO:0001819	synonymous_variant			BC104458	CCDS10790.1, CCDS45496.1	16q13	2009-04-20			ENSG00000159648	ENSG00000159648	374739	374739			33745	protein-coding gene	gene with protein product		610264			NA	14652002	Standard	NM_199456	NM_199456	NA	Approved		uc002emv.4	Q6URK8	OTTHUMG00000133463	ENST00000290871.5:c.39G>A	16.37:g.58010414G>A		NA	Q6URK7	37	CCDS10790.1																																																																																			TEPP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000257339.2		+	ENST00000290871.5	Silent	SNP	16 : 58010414 - 58010414 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	511	32
TMX4	56255	broad.mit.edu	37	20	7963022	7963022	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr20:7963022C>T	ENST00000246024.2	-	8	1141	c.926G>A	c.(925-927)cGg>cAg	p.R309Q		NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	309	Glu-rich.				cell redox homeostasis|electron transport chain|transport	integral to membrane				endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						TACTTCCTCCCGGGTCACACC	0.582		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													128	117	121			NA	NA	20		NA											NA				7963022		2203	4300	6503	SO:0001583	missense				CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827	56255	56255		Protein disulfide isomerases	25237	protein-coding gene	gene with protein product	protein disulfide isomerase family A, member 14		thioredoxin domain containing 13	TXNDC13	NA		Standard	NM_021156	NM_021156	NA	Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.926G>A	20.37:g.7963022C>T	ENSP00000246024:p.Arg309Gln	NA	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	37	CCDS13101.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350863	0.24512	.	.	ENSG00000125827	ENST00000246024	T	0.09350	2.99	5.54	-7.71	0.01254	.	2.465280	0.01182	N	0.007100	T	0.02888	0.0086	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35276	-0.9795	10	0.23891	T	0.37	2.3619	0.5542	0.00668	0.2156:0.2763:0.232:0.276	.	309	Q9H1E5	TMX4_HUMAN	Q	309	ENSP00000246024:R309Q	ENSP00000246024:R309Q	R	-	2	0	TMX4	7911022	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.154000	0.03166	-1.638000	0.01529	-0.455000	0.05494	CGG	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000077928.2		-	ENST00000246024.2	Missense_Mutation	SNP	20 : 7963022 - 7963022 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	555	25
TP53	7157	broad.mit.edu	37	17	7577046	7577046	+	Nonsense_Mutation	SNP	C	C	A			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr17:7577046C>A	ENST00000420246.2	-	8	1024	c.892G>T	c.(892-894)Gag>Tag	p.E298*	TP53_ENST00000445888.2_Nonsense_Mutation_p.E298*|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.E298*|TP53_ENST00000455263.2_Nonsense_Mutation_p.E298*|TP53_ENST00000269305.4_Nonsense_Mutation_p.E298*	NM_001126114.2|NM_001276696.1	NP_001119586.1|NP_001263625.1	P04637	P53_HUMAN	tumor protein p53	298	Interaction with HIPK1 (By similarity).		E -> A (in a sporadic cancer; somatic mutation).|E -> D (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> Q (in sporadic cancers; somatic mutation).|E -> V (in sporadic cancers; somatic mutation).		activation of caspase activity by cytochrome c|base-excision repair|blood coagulation|cell cycle arrest|cell differentiation|cell proliferation|cellular protein localization|cellular response to drug|cellular response to glucose starvation|cellular response to hypoxia|cellular response to ionizing radiation|cellular response to UV|determination of adult lifespan|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|ER overload response|interspecies interaction between organisms|negative regulation of apoptosis|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of helicase activity|negative regulation of transcription from RNA polymerase II promoter|nucleotide-excision repair|oxidative stress-induced premature senescence|positive regulation of histone deacetylation|positive regulation of neuron apoptosis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of reactive oxygen species metabolic process|positive regulation of thymocyte apoptosis|positive regulation of transcription from RNA polymerase II promoter|protein localization|protein tetramerization|Ras protein signal transduction|regulation of mitochondrial membrane permeability|replicative senescence|response to antibiotic|response to gamma radiation|response to X-ray	cytoplasm|cytosol|endoplasmic reticulum|insoluble fraction|mitochondrion|nuclear chromatin|nuclear matrix|nucleolus|nucleus|PML body|protein complex|replication fork	ATP binding|chaperone binding|chromatin binding|copper ion binding|damaged DNA binding|DNA strand annealing activity|histone acetyltransferase binding|p53 binding|protease binding|protein binding|protein heterodimerization activity|protein kinase binding|protein N-terminus binding|protein phosphatase 2A binding|RNA polymerase II transcription factor binding|sequence-specific DNA binding transcription factor activity|transcription regulatory region DNA binding|transcription repressor activity|ubiquitin protein ligase binding|zinc ion binding	p.E298*(49)|p.0?(8)|p.?(2)|p.E298K(1)|p.L299fs*2(1)|p.L265_K305del41(1)|p.E298fs*53(1)|p.G293fs*1(1)|p.E298Q(1)|p.E298_P301delELPP(1)|p.H296_S303delHHELPPGS(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)		GGGGGCAGCTCGTGGTGAGGC	0.567		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)				NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA		Pancreas(47;798 1329 9957 10801)	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		L, E, M, O	67	Substitution - Nonsense(49)|Whole gene deletion(8)|Deletion - In frame(3)|Unknown(2)|Deletion - Frameshift(2)|Substitution - Missense(2)|Insertion - Frameshift(1)	lung(21)|upper_aerodigestive_tract(13)|breast(6)|bone(5)|haematopoietic_and_lymphoid_tissue(4)|urinary_tract(4)|central_nervous_system(2)|oesophagus(2)|ovary(2)|pancreas(2)|liver(2)|large_intestine(1)|stomach(1)|salivary_gland(1)|skin(1)	GRCh37	CM031387	TP53	M							110	96	101			NA	NA	17		NA											NA				7577046		2203	4300	6503	SO:0001587	stop_gained	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	7157	7157			11998	protein-coding gene	gene with protein product	Li-Fraumeni syndrome	191170			NA	6396087, 3456488, 2047879	Standard	NM_000546	NM_001126115	NA	Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000420246.2:c.892G>T	17.37:g.7577046C>A	ENSP00000391127:p.Glu298*	NA	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	37	CCDS45606.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603544	0.66445	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.26	-4.03	0.04021	.	0.553557	0.18174	N	0.149346	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	-12.8318	5.9489	0.19234	0.0:0.2155:0.4162:0.3682	.	.	.	.	X	298;298;298;298;298;287;166	.	ENSP00000269305:E298X	E	-	1	0	TP53	7517771	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.837000	0.04377	-0.441000	0.07201	-0.218000	0.12543	GAG	TP53-005	KNOWN	NMD_exception|basic|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000367401.1		-	ENST00000420246.2	Nonsense_Mutation	SNP	17 : 7577046 - 7577046 A PAAD-TCGA-IB-7889-Tumor-SM-2NW89	450	42
TRPS1	7227	broad.mit.edu	37	8	116616325	116616325	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:116616325C>T	ENST00000395715.3	-	4	2448	c.1871G>A	c.(1870-1872)cGa>cAa	p.R624Q	TRPS1_ENST00000220888.5_Missense_Mutation_p.R611Q|TRPS1_ENST00000519674.1_Missense_Mutation_p.R611Q|TRPS1_ENST00000520276.1_Missense_Mutation_p.R615Q|TRPS1_ENST00000519076.1_Intron	NM_001282902.1|NM_001282903.1|NM_014112.2	NP_001269831.1|NP_001269832.1|NP_054831.2	Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	611					negative regulation of transcription from RNA polymerase II promoter|NLS-bearing substrate import into nucleus|regulation of chondrocyte differentiation|skeletal system development|transcription from RNA polymerase II promoter	nucleus	protein binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			ATGTTTGACTCGCGAGCTTCC	0.478		NA							Langer-Giedion syndrome					NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													69	70	69			NA	NA	8		NA											NA				116616325		2034	4189	6223	SO:0001583	missense	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447	7227	7227		GATA zinc finger domain containing, Zinc fingers, C2H2-type	12340	protein-coding gene	gene with protein product		604386			NA	8530105, 10615131, 10647898	Standard	NM_014112	NM_001282903	NA	Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000395715.3:c.1871G>A	8.37:g.116616325C>T	ENSP00000379065:p.Arg624Gln	NA	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	37	CCDS6318.2	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729920	0.48833	.	.	ENSG00000104447	ENST00000395715;ENST00000220888;ENST00000520276;ENST00000519674	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.87	5.87	0.94306	.	0.183848	0.49305	D	0.000160	T	0.23886	0.0578	L	0.27053	0.805	0.40856	D	0.983791	D;D;D	0.69078	0.991;0.994;0.997	P;D;D	0.69479	0.563;0.921;0.964	T	0.00717	-1.1596	10	0.72032	D	0.01	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	615;611;624	Q9UHF7-3;Q9UHF7;Q9UHF7-2	.;TRPS1_HUMAN;.	Q	624;611;615;611	ENSP00000379065:R624Q;ENSP00000220888:R611Q;ENSP00000428680:R615Q;ENSP00000429174:R611Q	ENSP00000220888:R611Q	R	-	2	0	TRPS1	116685500	1.000000	0.71417	0.587000	0.28692	0.015000	0.08874	5.682000	0.68182	2.941000	0.99782	0.655000	0.94253	CGA	TRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000286435.3		-	ENST00000395715.3	Missense_Mutation	SNP	8 : 116616325 - 116616325 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	407	63
TSHZ2	128553	broad.mit.edu	37	20	51872260	51872260	+	Missense_Mutation	SNP	C	C	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	C	C	-	-	C	C	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr20:51872260C>T	ENST00000371497.5	+	2	3150	c.2263C>T	c.(2263-2265)Cgc>Tgc	p.R755C	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R752C|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R752C	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	755					multicellular organismal development	nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CGTGTCCAGGCGCTACCTGTT	0.512		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													93	90	91			NA	NA	20		NA											NA				51872260		2203	4300	6503	SO:0001583	missense			AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463	128553	128553		Teashirt zinc fingers, Homeoboxes / ZF class, Zinc fingers, C2H2-type	13010	protein-coding gene	gene with protein product		614118	chromosome 20 open reading frame 17, zinc finger protein 218, teashirt family zinc finger 2	C20orf17, ZNF218	NA	9671742	Standard	NM_173485	NM_173485	NA	Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2263C>T	20.37:g.51872260C>T	ENSP00000360552:p.Arg755Cys	NA	Q4VXM4|Q6N003|Q8N260	37	CCDS33490.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992826	0.35131	.	.	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.50277	0.75;0.75	5.23	5.23	0.72850	.	0.475787	0.23196	N	0.050846	T	0.43144	0.1234	M	0.68317	2.08	0.34997	D	0.755567	P	0.49358	0.923	B	0.34452	0.183	T	0.65709	-0.6102	10	0.87932	D	0	-5.9641	13.7395	0.62838	0.1538:0.8461:0.0:0.0	.	755	Q9NRE2	TSH2_HUMAN	C	755;752;281	ENSP00000360552:R755C;ENSP00000333114:R752C	ENSP00000333114:R752C	R	+	1	0	TSHZ2	51305667	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	3.499000	0.53310	2.438000	0.82558	0.579000	0.79373	CGC	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000080398.6		+	ENST00000371497.5	Missense_Mutation	SNP	20 : 51872260 - 51872260 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	556	36
WHSC1L1	54904	broad.mit.edu	37	8	38187221	38187221	+	Missense_Mutation	SNP	G	G	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	G	G	-	-	G	G	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr8:38187221G>T	ENST00000317025.8	-	6	1773	c.1256C>A	c.(1255-1257)aCc>aAc	p.T419N	WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T419N|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T419N|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T419N	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	419					cell differentiation|cell growth|regulation of transcription, DNA-dependent|transcription, DNA-dependent	chromosome	histone-lysine N-methyltransferase activity|zinc ion binding			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			TGGTCGTCGGGTTTTTTTAAC	0.433		NA	T	NUP98	AML									NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA				Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	0													111	107	108			NA	NA	8		NA											NA				38187221		2203	4300	6503	SO:0001583	missense			AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548	54904	54904			12767	protein-coding gene	gene with protein product		607083			NA	10802047, 23269674	Standard	NM_023034	NM_023034	NA	Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1256C>A	8.37:g.38187221G>T	ENSP00000313983:p.Thr419Asn	NA	D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	37	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	G	8.652	0.898580	0.17686	.	.	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985	D;D;D;T	0.95137	-3.62;-3.62;-3.62;-0.48	5.6	4.65	0.58169	.	0.608282	0.13904	U	0.354722	D	0.82870	0.5131	N	0.02011	-0.69	0.25889	N	0.983491	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.68580	-0.5371	10	0.12103	T	0.63	.	11.164	0.48533	0.0:0.0:0.5948:0.4052	.	419;419;419;419	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	N	419;419;356;419;419	ENSP00000393284:T419N;ENSP00000313983:T419N;ENSP00000434730:T419N;ENSP00000313410:T419N	ENSP00000313410:T419N	T	-	2	0	WHSC1L1	38306378	0.785000	0.28726	0.870000	0.34147	0.989000	0.77384	1.199000	0.32235	2.634000	0.89283	0.650000	0.86243	ACC	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000381924.3		-	ENST00000317025.8	Missense_Mutation	SNP	8 : 38187221 - 38187221 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	502	21
ZNF716	441234	broad.mit.edu	37	7	57528604	57528604	+	Missense_Mutation	SNP	A	A	T			TCGA-IB-7889-01A-11D-2154-08	TCGA-IB-7889-10A-01D-2154-08	A	A	-	-	A	A	Unknown	Untested	Somatic	NA	WXS	none	NA	NA	Illumina HiSeq	01ca4fa5-629f-433d-ab6a-e0a8b2417ddc	273e3c23-c89d-4142-a9c3-59c5ec1224dc	g.chr7:57528604A>T	ENST00000420713.1	+	4	549	c.437A>T	c.(436-438)aAc>aTc	p.N146I		NM_001159279.1	NP_001152751.1			zinc finger protein 716	NA										breast(1)|kidney(1)|lung(20)|ovary(2)	24						AATTATGTTAACCAATGTTTG	0.343		NA												NA	NA	NA	NA	NA	NA	NA			NA	NA	NA	NA	NA	NA	NA		NA	NA	NA									NA				0													212	197	201			NA	NA	7		NA											NA				57528604		692	1591	2283	SO:0001583	missense			AK131575	CCDS55112.1	7p11.1	2013-01-08			ENSG00000182111	ENSG00000182111	441234	441234		Zinc fingers, C2H2-type, -	32458	protein-coding gene	gene with protein product					NA		Standard	NM_001159279	NM_001159279	NA	Approved	FLJ46189	uc011kdi.1	A6NP11	OTTHUMG00000156689	ENST00000420713.1:c.437A>T	7.37:g.57528604A>T	ENSP00000394248:p.Asn146Ile	NA		37	CCDS55112.1	.	.	.	.	.	.	.	.	.	.	A	12.35	1.911336	0.33721	.	.	ENSG00000182111	ENST00000420713;ENST00000418732	T	0.05580	3.42	0.195	0.195	0.15151	.	.	.	.	.	T	0.07999	0.0200	L	0.46819	1.47	0.09310	N	0.999999	D	0.54397	0.966	P	0.48030	0.564	T	0.28618	-1.0038	9	0.59425	D	0.04	.	4.8229	0.13400	0.9998:0.0:2.0E-4:0.0	.	134	A6NP11	ZN716_HUMAN	I	146;134	ENSP00000394248:N146I	ENSP00000387687:N134I	N	+	2	0	ZNF716	57532546	0.050000	0.20438	0.039000	0.18376	0.039000	0.13416	0.000000	0.12993	0.257000	0.21650	0.254000	0.18369	AAC	ZNF716-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NA	protein_coding	OTTHUMT00000345309.1		+	ENST00000420713.1	Missense_Mutation	SNP	7 : 57528604 - 57528604 T PAAD-TCGA-IB-7889-Tumor-SM-2NW89	148	8
